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| ====== Complete AP Biology Study Guide ====== | ====== Complete AP Biology Study Guide ====== | ||
| * Credit: Weshe2005 on reddit, | * Credit: Weshe2005 on reddit, | ||
| - | * If u think u can clean of the formatting please do so. Refer to [[wiki: | + | * If u think u can clean of the formatting please do so. Refer to wiki: |
| - | **Useful Links:** | + | Useful Links: |
| - | Cliff Notes: | + | Cliff Notes: https:// |
| - | **Practice Resources** | + | Practice Resources |
| - | * 2013: [[https:// | + | * 2013: https:// |
| - | * 2012: [[https:// | + | * 2012: https:// |
| - | **Past FRQs: ** | + | Past FRQs: |
| - | * [[https:// | + | * https:// |
| - | * FRQ 2020: [[https:// | + | * FRQ 2020: https:// |
| * FRQ: 2021: https:// | * FRQ: 2021: https:// | ||
| =====Unit 1: Properties Water, Dehydration Synthesis & Hydrolysis; Carbs and Lipids===== | =====Unit 1: Properties Water, Dehydration Synthesis & Hydrolysis; Carbs and Lipids===== | ||
| - | **Topics 1.1-1.4** | + | Topics 1.1-1.4 |
| - | **KEY OVERVIEWS** | + | KEY OVERVIEWS |
| * How properties of water that result from its polarity and hydrogen bonding affect its biological function | * How properties of water that result from its polarity and hydrogen bonding affect its biological function | ||
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| ====Chemistry==== | ====Chemistry==== | ||
| - | **Trace Elements:** required by organisms in minute amounts | + | Trace Elements: required by organisms in minute amounts |
| Essential elements: C, H, O, N (most abundant) | Essential elements: C, H, O, N (most abundant) | ||
| Line 52: | Line 52: | ||
| * Single covalent, double covalent, and triple covalent bonds form when two, four, and six electrons are shared respectively | * Single covalent, double covalent, and triple covalent bonds form when two, four, and six electrons are shared respectively | ||
| - | **Nonpolar Covalent Bonds** | + | Nonpolar Covalent Bonds |
| * When electrons are shared equally → atoms have same/ | * When electrons are shared equally → atoms have same/ | ||
| Line 58: | Line 58: | ||
| * No charge = hydrophobic | * No charge = hydrophobic | ||
| - | **Polar Covalent Bonds** | + | Polar Covalent Bonds |
| * When electron are shared unequally → atoms have diff electronegativity | * When electron are shared unequally → atoms have diff electronegativity | ||
| Line 66: | Line 66: | ||
| * Yes charge = hydrophilic | * Yes charge = hydrophilic | ||
| - | **Hydrogen Bonds** | + | Hydrogen Bonds |
| * Weak bonds between molecules; form when (+) charged hydrogen atom in one covalently bonded molecule is attracted to (-) charged area of another covalently bonded molecule → results from polarity | * Weak bonds between molecules; form when (+) charged hydrogen atom in one covalently bonded molecule is attracted to (-) charged area of another covalently bonded molecule → results from polarity | ||
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| Vocab | Vocab | ||
| - | **Heat of fusion:** energy required to change water from a solid to liquid | + | Heat of fusion: energy required to change water from a solid to liquid |
| - | **Heat of evaporation: | + | Heat of evaporation: |
| - | **Mass Number:** number of protons and neutrons | + | Mass Number: number of protons and neutrons |
| - | **Isotopes:** atoms of same elements with diff mass/number of neutrons | + | Isotopes: atoms of same elements with diff mass/number of neutrons |
| - | **Electronegativity: | + | Electronegativity: |
| * Allows oxygen to form polar and hydrogen bonds | * Allows oxygen to form polar and hydrogen bonds | ||
| - | **Energy:** capacity to do work | + | Energy: capacity to do work |
| - | **Potential energy:** energy that matter has because of location | + | Potential energy: energy that matter has because of location |
| * Electrons have potential energy because of distance from nucleus | * Electrons have potential energy because of distance from nucleus | ||
| - | **Electron Shell:** distance from nucleus where electrons found | + | Electron Shell: distance from nucleus where electrons found |
| * Further = more energy | * Further = more energy | ||
| - | **Valence electrons:** outermost electrons | + | Valence electrons: outermost electrons |
| * Determine chemical behavior | * Determine chemical behavior | ||
| - | **Molecule:** 2 or more atoms held by bonds | + | Molecule: 2 or more atoms held by bonds |
| * Molecule shape determined by position of valence electrons orbitals | * Molecule shape determined by position of valence electrons orbitals | ||
| - | **Compound:** | + | Compound: |
| two or more different elements joined together chemically | two or more different elements joined together chemically | ||
| Line 121: | Line 121: | ||
| * The hydrogen bonds between water molecules result in cohesion, adhesion, and high surface tension, self-regulation, | * The hydrogen bonds between water molecules result in cohesion, adhesion, and high surface tension, self-regulation, | ||
| - | | + | * Cohesion: water molecules attached to each other (bcuz of HB) |
| * Makes water “sticky” | * Makes water “sticky” | ||
| * Ex: water molecules evaporate from leaf by pulling on neighboring water which then draw up molecules behind them | * Ex: water molecules evaporate from leaf by pulling on neighboring water which then draw up molecules behind them | ||
| - | | + | * Adhesion: water molecules attached to OTHER things |
| * Positively charged part attract negatively charged ends of other polar compounds and vice versa | * Positively charged part attract negatively charged ends of other polar compounds and vice versa | ||
| - | * Cohesion + Adhesion allows for **capillary action:** transport of water up roots & against gravity | + | * Cohesion + Adhesion allows for capillary action: transport of water up roots & against gravity |
| * Water pulls each other up and can adhere to narrow tubing during transpiration | * Water pulls each other up and can adhere to narrow tubing during transpiration | ||
| - | | + | * Surface tensions: “Tendency of molecules to be pulled from the surface to the interior of a liquid” |
| * Water has high surface tension bcuz of increased HB forces at surface that resist being stretched/ | * Water has high surface tension bcuz of increased HB forces at surface that resist being stretched/ | ||
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| Versatility as a Solvent | Versatility as a Solvent | ||
| - | | + | * Solvent: dissolving agent Solute: substance dissolved |
| * Water versatile solvent because polar molecules are attracted to other polar molecules and form HB (adhesive) | * Water versatile solvent because polar molecules are attracted to other polar molecules and form HB (adhesive) | ||
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| * Water helps cell transport substances throughout the body (ex. nutrients, antibiotics) | * Water helps cell transport substances throughout the body (ex. nutrients, antibiotics) | ||
| - | | + | * Hydrophilic: |
| Acids and Bases | Acids and Bases | ||
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| * Water is an acid and base | * Water is an acid and base | ||
| - | | + | * Hydrogen Ion: Single proton, highly reactive/ |
| * Acids and bases cause imbalance in H and OH | * Acids and bases cause imbalance in H and OH | ||
| - | | + | * Acids: decrease pH, ione in water to increase H+, less hydronium ion. 0-6 |
| - | | + | * Bases: increase pH decreases H+, more OH; 8-14 |
| * Bases break into OH which can combine with H+ to create water (accept H+) | * Bases break into OH which can combine with H+ to create water (accept H+) | ||
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| * Resist shifts in pH by donating H⁺ to a solution when bases are added, and accepting H⁺ when acids are added | * Resist shifts in pH by donating H⁺ to a solution when bases are added, and accepting H⁺ when acids are added | ||
| - | | + | * pH Scale: measures the concentration of H+ → Formula: pH = -Log[h+] |
| * Change of one pH number represents a tenfold change in hydrogen concentration | * Change of one pH number represents a tenfold change in hydrogen concentration | ||
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| * Carbon is essential for all life → leads to diversity, forms cell structure, and is used to build all macromolecules | * Carbon is essential for all life → leads to diversity, forms cell structure, and is used to build all macromolecules | ||
| - | * Diversity of organisms due to carbon' | + | * Diversity of organisms due to carbon' |
| * Form strong bonds with C, H, O, N | * Form strong bonds with C, H, O, N | ||
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| * Factors that determine an organic molecules’ properties | * Factors that determine an organic molecules’ properties | ||
| - | | + | * Carbon Backbone - central part of organic molecule, bonding sites of atoms that determines their structure (function/ |
| * Rings, linear, branching, single/ | * Rings, linear, branching, single/ | ||
| * Carbon atoms bond to other carbon atoms to form very long carbon chains/ | * Carbon atoms bond to other carbon atoms to form very long carbon chains/ | ||
| - | | + | * Functional Groups branch off carbon backbone & determine chemical properties of an organic compound |
| * In a reaction the backbone is unchanged & only functional groups react | * In a reaction the backbone is unchanged & only functional groups react | ||
| - | **Hydrocarbons** | + | Hydrocarbons |
| * Long chains of covalently bonded carbon and hydrogen | * Long chains of covalently bonded carbon and hydrogen | ||
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| * “Compounds with same formula but diff arrangement of atoms” = structure determines function | * “Compounds with same formula but diff arrangement of atoms” = structure determines function | ||
| - | | + | * Structural: placement of carbons is diff which results in diff bonding functional groups and properties |
| - | | + | * Geometric: functional groups branching of backbone are diff caused by variations around carbon double bond |
| * Cis: functional groups on same side | * Cis: functional groups on same side | ||
| * Trans: functional groups on opp side | * Trans: functional groups on opp side | ||
| < | < | ||
| + | |||
| <img src=" | <img src=" | ||
| + | |||
| </ | </ | ||
| - | | + | * Enantiomers/ |
| Functional Groups Continued | Functional Groups Continued | ||
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| * TRUE for amino acids which always have amino and carboxyl group | * TRUE for amino acids which always have amino and carboxyl group | ||
| - | |**Functional Group**|**Examples**|**Characteristics**| | + | |Functional Group|Examples|Characteristics| |
| |-OH Hydroxyl|Alcohols (ethanol, glycerol)|Polar, | |-OH Hydroxyl|Alcohols (ethanol, glycerol)|Polar, | ||
| |-COOH Carboxyl\ • C double bonded to oxygen, single bond to OH\ |Amino acids, fatty acids|Polar, | |-COOH Carboxyl\ • C double bonded to oxygen, single bond to OH\ |Amino acids, fatty acids|Polar, | ||
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| ====1.3: Introduction to Biological Macromolecules==== | ====1.3: Introduction to Biological Macromolecules==== | ||
| - | **Dehydration Synthesis and Hydrolysis** | + | Dehydration Synthesis and Hydrolysis |
| * Used to cleave and form covalent bonds between monomers | * Used to cleave and form covalent bonds between monomers | ||
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| * Structure and function of polymers depends on the chemical properties and assembly of their monomers | * Structure and function of polymers depends on the chemical properties and assembly of their monomers | ||
| - | | + | * Macromolecule: |
| - | | + | * Polymers: large molecule made up of monomers joined by covalent bonds |
| - | | + | * Monomer: single repeating subunit |
| - | **Nucleic Acids:** | + | Nucleic Acids: |
| - | * Biological information is encoded in **sequences of nucleotide** monomers | + | * Biological information is encoded in sequences of nucleotide monomers |
| * DNA & RNA are polymers of nucleotides; | * DNA & RNA are polymers of nucleotides; | ||
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| Structural Components of Nucleotides | Structural Components of Nucleotides | ||
| - | | + | * Nitrogenous Base: has 2 types; |
| * Purines: Adenine and Guanine with double ring structure | * Purines: Adenine and Guanine with double ring structure | ||
| * Pyrimidines: | * Pyrimidines: | ||
| - | {{Untitled_a1baf95c2be74fad95ea92c3882c2c8f: | + | {{Untitled_a1baf95c2be74fad95ea92c3882c2c8f: |
| - | | + | * Five-carbon sugar: deoxyribose or ribose; nonpolar |
| DNA and RNA synthesis | DNA and RNA synthesis | ||
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| Antiparallel | Antiparallel | ||
| - | | + | * The DNA Molecule has directionality, |
| - | | + | * The two strands run in opposite directions |
| * One strand is arranged 5’ → 3’ end & other is 3’ → 5’ | * One strand is arranged 5’ → 3’ end & other is 3’ → 5’ | ||
| - | | + | * Antiparallel: |
| - | {{Untitled_a1baf95c2be74fad95ea92c3882c2c8f: | + | {{Untitled_a1baf95c2be74fad95ea92c3882c2c8f: |
| - | | + | * Cytosine + Guanine with 3 hydrogen bonds = stronger |
| - | | + | * Adenine + Thymine with 2 hydrogen bonds |
| - | | + | * Purine + Pyrimidine = only uniform diameter suitable for double helix |
| - | **5’ End** | + | 5’ End |
| The phosphate group is bound to the carbon at the 5th position on sugar | The phosphate group is bound to the carbon at the 5th position on sugar | ||
| - | **3’ End** | + | 3’ End |
| Starting from the 5’ end, the positions alternate until it reaches the open -OH attached to 3’ carbon (where phosphate will attach to) | Starting from the 5’ end, the positions alternate until it reaches the open -OH attached to 3’ carbon (where phosphate will attach to) | ||
| - | **DNA vs RNA** | + | DNA vs RNA |
| |DNA has:\ • Double strand \ • Deoxyribose 5-carbon sugar\ ◦ Functional group lacks O2\ • Thymine not Uracil\ • Antiparallel in directionality\ |RNA has:\ • Single strand\ • Ribose 5-carbon sugar\ ◦ Hydroxyl functional group\ • Uracil not Thymine\ | | |DNA has:\ • Double strand \ • Deoxyribose 5-carbon sugar\ ◦ Functional group lacks O2\ • Thymine not Uracil\ • Antiparallel in directionality\ |RNA has:\ • Single strand\ • Ribose 5-carbon sugar\ ◦ Hydroxyl functional group\ • Uracil not Thymine\ | | ||
| - | **DNA and RNA** | + | DNA and RNA |
| - | | + | * DNA and RNA are primary sources and carriers of genetic information. |
| * Have all 3 components of nucleotides joined together w/ dehydration synthesis | * Have all 3 components of nucleotides joined together w/ dehydration synthesis | ||
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| * Bases perpendicular to the sugar-phosphate backbone | * Bases perpendicular to the sugar-phosphate backbone | ||
| - | **Proteins** | + | Proteins |
| Function: | Function: | ||
| - | - **Structural:** ex: keratin in hair, collagen in tissues | + | - Structural: ex: keratin in hair, collagen in tissues |
| - | - **Storage:** ex: casein in milk | + | - Storage: ex: casein in milk |
| - | - **Transport:** ex: membrane of cells and oxygen carrying hemoglobin in red blood cells | + | - Transport: ex: membrane of cells and oxygen carrying hemoglobin in red blood cells |
| - | - **Defensive:** Ex: antibodies that protect against foreign substances | + | - Defensive: Ex: antibodies that protect against foreign substances |
| - | - **Enzymes:** regulate the rate of chemical reactions | + | - Enzymes: regulate the rate of chemical reactions |
| Protein Combination and Separation | Protein Combination and Separation | ||
| - | | + | * Peptide Bond: Covalent bond that holds amino acids together (dehydration synthesis) |
| - | | + | * Polypeptide Chain: Multiple combinations of amino acids bonded together |
| Structure | Structure | ||
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| Always contains amino group (basic), carboxyl (acid), R group, H | Always contains amino group (basic), carboxyl (acid), R group, H | ||
| - | | + | * R Group: |
| * “Random group” → determine chemical properties & differences of amino acids | * “Random group” → determine chemical properties & differences of amino acids | ||
| * R groups determine if they are polar or nonpolar | * R groups determine if they are polar or nonpolar | ||
| - | | + | * The interaction of these R groups determine structure and function of that region |
| * Polar R groups have N, S or O while non-polar have C or H | * Polar R groups have N, S or O while non-polar have C or H | ||
| * Proteins have directionality: | * Proteins have directionality: | ||
| - | * Amino acid are **added onto the carboxyl end** thru dehydration synthesis | + | * Amino acid are added onto the carboxyl end thru dehydration synthesis |
| - | | + | * Dimer: protein with two tertiary structures |
| - | **The 4 Structural Levels of Proteins** | + | The 4 Structural Levels of Proteins |
| PRIMARY STRUCTURE | PRIMARY STRUCTURE | ||
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| SECONDARY STRUCTURE | SECONDARY STRUCTURE | ||
| - | * Local folding of the amino acid chain (polypeptide) into elements such as alpha-helices and beta sheets thru **hydrogen bonding** | + | * Local folding of the amino acid chain (polypeptide) into elements such as alpha-helices and beta sheets thru hydrogen bonding |
| * Misfoldings lead to prions | * Misfoldings lead to prions | ||
| TERTIARY STRUCTURE | TERTIARY STRUCTURE | ||
| - | * The overall | + | * The overall 3D shape of the protein as a result of different interactions between amino acids |
| * Usually makes up structure of globular proteins; minimizes free energy & increases stability | * Usually makes up structure of globular proteins; minimizes free energy & increases stability | ||
| * Components of a tertiary structure: | * Components of a tertiary structure: | ||
| * Hydrogen bonds and ionic bonds between R groups of amino acids | * Hydrogen bonds and ionic bonds between R groups of amino acids | ||
| - | | + | * Disulfide bonds: sulfur atom in amino acid cysteine bonds to sulfur atoms in another cysteine |
| * Helps maintain folds of amino acid chain | * Helps maintain folds of amino acid chain | ||
| * Hydrophobic interactions/ | * Hydrophobic interactions/ | ||
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| Most proteins are made of a single polypeptide chain but some have multiple chains called | Most proteins are made of a single polypeptide chain but some have multiple chains called | ||
| - | **subunits** | + | subunits |
| that allow for 4th structure. | that allow for 4th structure. | ||
| - | < | + | < |
| + | <img src=" | ||
| + | </ | ||
| * Function: main source of energy (for ATP) and cell structure | * Function: main source of energy (for ATP) and cell structure | ||
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| * Contain carbon, hydrogen and oxygen (1:2:1) held by covalent bonds | * Contain carbon, hydrogen and oxygen (1:2:1) held by covalent bonds | ||
| - | | + | * Pentoses: (5-carbon sugars) include ribose and deoxyribose & make up nucleic acids |
| - | | + | * Hexoses: (6-carbon sugars) are in the food that we eat and include glucose, fructose, and galactose (monosaccharides) |
| Simple: Monosaccharides and Disaccharides | Simple: Monosaccharides and Disaccharides | ||
| Line 456: | Line 460: | ||
| * Polymer made of repeating monosaccharide monomers; usually consisting of glucose | * Polymer made of repeating monosaccharide monomers; usually consisting of glucose | ||
| - | | + | * Cellulose: make up plant wall, non digestible (fiber) in humans, long chains of glucose |
| - | | + | * Chitin: fungi cell wall |
| - | | + | * Glycogen: energy storage in liver and and stomach cells (animals) |
| - | | + | * Starch: long term storage carb for plants, quick energy for humans |
| - | **Lipids: Fats, Steriles, Phospholipids** | + | Lipids: Fats, Steriles, Phospholipids |
| * Function: cell membrane (phospho,) insulation, protection, fat is long term and high energy | * Function: cell membrane (phospho,) insulation, protection, fat is long term and high energy | ||
| Line 475: | Line 479: | ||
| * Structure: 3 acid groups from fatty acids (sat or unsat) + one glycerol. | * Structure: 3 acid groups from fatty acids (sat or unsat) + one glycerol. | ||
| - | | + | * Fatty acids: hydrocarbon with carboxyl group → nonpolar |
| * Vary in structure by number of carbons and placement of single/ | * Vary in structure by number of carbons and placement of single/ | ||
| - | | + | * Saturated fatty acid: single bonds between carbons and two H (is saturated with H) |
| * No double bonds/kinks in chain = molecule can compact together = solid/rigid → build up in bloodstream {{Untitled_a1baf95c2be74fad95ea92c3882c2c8f: | * No double bonds/kinks in chain = molecule can compact together = solid/rigid → build up in bloodstream {{Untitled_a1baf95c2be74fad95ea92c3882c2c8f: | ||
| - | | + | * Unsaturated Fatty Acids: Two or more double covalent bonds |
| * Stops carbon from packing together and hydrogen from saturating them which makes fat more flexible/ | * Stops carbon from packing together and hydrogen from saturating them which makes fat more flexible/ | ||
| - | | + | * Monounsaturated Fatty acid: one double bond and each has only one H |
| - | | + | * *differences in saturation determine the structure and function of lipids%%%% |
| - | Steroids: | + | Steroids: are characterized by four linked carbon rings |
| * Ex. cholesterol, | * Ex. cholesterol, | ||
| Line 501: | Line 505: | ||
| * Hydrophobic tail → Nonpolar bcuz made up of carbon and hydrogen atoms | * Hydrophobic tail → Nonpolar bcuz made up of carbon and hydrogen atoms | ||
| - | **The 4 Carbon Compounds** | + | The 4 Carbon Compounds |
| - | |**Name**|Carbohydrates|Protein|Lipids|Nucleic Acids| | + | |Name|Carbohydrates|Protein|Lipids|Nucleic Acids| |
| - | |**Bond (Covalent)**|Glycosidic|Peptide|Ester|Phosphodiester| | + | |Bond (Covalent)|Glycosidic|Peptide|Ester|Phosphodiester| |
| - | |**Monomers**|Monosaccharides|Amino acids|Glycerol & fatty acids|Nucleotides| | + | |Monomers|Monosaccharides|Amino acids|Glycerol & fatty acids|Nucleotides| |
| - | |**Elements**|C, H, O|C, H, O, **N**, *S|C, H, O, *P|C, H, O, **N**, P| | + | |Elements|C, |
| =====Unit 2.2: Organelles and Cell Size===== | =====Unit 2.2: Organelles and Cell Size===== | ||
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| ====Cellular Organelles==== | ====Cellular Organelles==== | ||
| - | | + | * Cell: basic functional unit of all living things bound by a plasma membrane |
| - | | + | * Cytoplasm: contains organelles suspended in a fluid matrix (cytosol) which consists of water and dissolved substances like proteins and nutrients |
| - | | + | * Organelles: Internal membrane bound bodies within the cytoplasm that serve to separate metabolic reactions and compartmentalize the cell |
| * Within organelles, chemical reactions are isolated and can take place without interference/ | * Within organelles, chemical reactions are isolated and can take place without interference/ | ||
| * Cell can be specialized for specific functions depending on number of specific organelles | * Cell can be specialized for specific functions depending on number of specific organelles | ||
| - | < | + | < |
| + | <img src=" | ||
| + | </ | ||
| * Membrane bound organelle that contains the cell’s DNA/ | * Membrane bound organelle that contains the cell’s DNA/ | ||
| - | | + | * Nucleoli/ |
| - | | + | * Nuclear pores: passageways for proteins and RNA molecules on nucleus surface |
| - | **Ribosomes** | + | Ribosomes |
| * Structure: Made of ribosomal RNA (rRNA) and protein | * Structure: Made of ribosomal RNA (rRNA) and protein | ||
| Line 538: | Line 544: | ||
| * Two types of ribosomes: | * Two types of ribosomes: | ||
| - | | + | * Attached to the Rough ER: makes proteins that are going to be exported from cell |
| - | | + | * Free Ribosomes: makes proteins that will be exclusively used by the cell (ex mito) |
| - | **Endoplasmic Reticulum** | + | Endoplasmic Reticulum |
| * Occurs in two forms: rough and smooth | * Occurs in two forms: rough and smooth | ||
| - | * Rough has small ribosomes attached to the ER < | + | * Rough has small ribosomes attached to the ER < |
| + | <img src=" | ||
| + | </ | ||
| * Synthesizes proteins using the attached ribosome | * Synthesizes proteins using the attached ribosome | ||
| * Ex. ER proteins, membranes, ECM, lysosome proteins; makes glycoproteins by attaching polysaccharides | * Ex. ER proteins, membranes, ECM, lysosome proteins; makes glycoproteins by attaching polysaccharides | ||
| - | | + | * The folded nature of the rough ER compartmentalizes the cell → increases efficiency by allowing multiple processes to happen at once and makes space for ribosomes to make proteins |
| * Smooth ER does NOT have ribosomes bound to it | * Smooth ER does NOT have ribosomes bound to it | ||
| * Found in liver cells and detoxifies/ | * Found in liver cells and detoxifies/ | ||
| - | | + | * Synthesizes lipids and steroid hormones |
| * Helps transport proteins from the ribosome to other parts of the cell | * Helps transport proteins from the ribosome to other parts of the cell | ||
| - | **Golgi Complex** | + | Golgi Complex |
| - | < | + | < |
| + | <img src=" | ||
| + | </ | ||
| * and packaging in vesicles for protein trafficking | * and packaging in vesicles for protein trafficking | ||
| * Receives, modifies, ships | * Receives, modifies, ships | ||
| - | * Structure: Folded membrane bound sacs (**cisternae**) | + | * Structure: Folded membrane bound sacs (cisternae) |
| * Also has vesicles attached to it to ship out proteins to membrane, lysosome, or exterior | * Also has vesicles attached to it to ship out proteins to membrane, lysosome, or exterior | ||
| * Two sides to it: | * Two sides to it: | ||
| - | | + | * The cis face: where all the incoming proteins go to be modified |
| - | | + | * The trans face: where all the modified proteins go to be “shipped out” |
| - | **MITOCHONDRIA** | + | MITOCHONDRIA |
| - | < | + | < |
| + | <img src=" | ||
| + | </ | ||
| Physical Attributes of the Mitochondria | Physical Attributes of the Mitochondria | ||
| Line 580: | Line 592: | ||
| * Contains circular mDNA, ATP synthase & own ribosomes | * Contains circular mDNA, ATP synthase & own ribosomes | ||
| - | |**Cristae**|**Intermembrane Space**|**Inner Membrane**|**Matrix**| | + | |Cristae|Intermembrane Space|Inner Membrane|Matrix| |
| |Convolutions of inner membrane increase surface area → better metabolic efficiency (make more ATP)|Space between two membranes where protons accumulate|Site of oxidative phosphorylation \ Contains ETC and complexes \ Separates region of high/low concentration\ |Fluid material that fills space inside inner membrane \ Site of Krebs Cycle and Pyruvate oxidation\ | | |Convolutions of inner membrane increase surface area → better metabolic efficiency (make more ATP)|Space between two membranes where protons accumulate|Site of oxidative phosphorylation \ Contains ETC and complexes \ Separates region of high/low concentration\ |Fluid material that fills space inside inner membrane \ Site of Krebs Cycle and Pyruvate oxidation\ | | ||
| - | **Lysosomes** | + | Lysosomes |
| * Structure: Vesicles from Golgi that contain hydrolytic enzymes (from rough ER) | * Structure: Vesicles from Golgi that contain hydrolytic enzymes (from rough ER) | ||
| Line 591: | Line 603: | ||
| * Low pH is favorable to hydrolytic enzymes → any enzyme that might escape from lysosomes becomes inactive in neutral pH of cytosol | * Low pH is favorable to hydrolytic enzymes → any enzyme that might escape from lysosomes becomes inactive in neutral pH of cytosol | ||
| - | **Vesicles** | + | Vesicles |
| - | | + | * Transport Vesicles: membrane enclosed sacs that move materials between organelles and plasma membrane |
| * Movement dependent on microtubules and motor proteins | * Movement dependent on microtubules and motor proteins | ||
| - | **Vacuole** | + | Vacuole |
| * Fluid-filled, | * Fluid-filled, | ||
| - | | + | * Food vacuoles: stores food and often merge with lysosome whose digestive enzymes break down food |
| - | | + | * Contractile vacuole: collects and pumps excess water, balances H+ & water |
| - | | + | * Central vacuole: occupies most of interior of plant cells |
| * When fully filled exert turgor (pressure) on cell wall which makes cell rigid | * When fully filled exert turgor (pressure) on cell wall which makes cell rigid | ||
| * Has other functions which specializes cell for specific functions | * Has other functions which specializes cell for specific functions | ||
| Line 613: | Line 625: | ||
| - Act as balancers to maintain homeostasis | - Act as balancers to maintain homeostasis | ||
| - | **Centrioles/ | + | Centrioles/ |
| * Act as microtubule organizing centers | * Act as microtubule organizing centers | ||
| * Centrioles organize and pull replicated chromosomes apart used in cell division | * Centrioles organize and pull replicated chromosomes apart used in cell division | ||
| - | | + | * Centrosome: contains 2 centrioles, not in plants |
| * Basal bodies form and organize flagella and cilia | * Basal bodies form and organize flagella and cilia | ||
| - | **Peroxisomes** | + | Peroxisomes |
| * Contain enzymes that break down hydrogen peroxide (make water and oxygen), fatty acids, and amino acids | * Contain enzymes that break down hydrogen peroxide (make water and oxygen), fatty acids, and amino acids | ||
| Line 630: | Line 642: | ||
| * In plants, found near chloroplast and modify by-products of photorespiration | * In plants, found near chloroplast and modify by-products of photorespiration | ||
| - | **Cytoskeleton** | + | Cytoskeleton |
| * Network of protein fibers and internal structure of cytoplasm | * Network of protein fibers and internal structure of cytoplasm | ||
| Line 639: | Line 651: | ||
| Parts of Cytoskeleton | Parts of Cytoskeleton | ||
| - | | + | * Microtubules: |
| * Made of protein tubulin; organized by centrioles | * Made of protein tubulin; organized by centrioles | ||
| * Found in spindle apparatus + cilia and flagella | * Found in spindle apparatus + cilia and flagella | ||
| - | | + | * Microfilaments: |
| * Made of protein actin | * Made of protein actin | ||
| * Found in muscle cells and cells that move by changing shape (ex: phagocytes) | * Found in muscle cells and cells that move by changing shape (ex: phagocytes) | ||
| - | * In plants allow for **cytoplasmic streaming:** movement of cytoplasmic materials in cell | + | * In plants allow for cytoplasmic streaming: movement of cytoplasmic materials in cell |
| - | | + | * Intermediate filaments: support cell shape and fix organelles in place |
| Flagella and Cilia | Flagella and Cilia | ||
| Line 654: | Line 666: | ||
| * Motile appendages that contain microtubules and protrude from the cell membrane | * Motile appendages that contain microtubules and protrude from the cell membrane | ||
| - | | + | * Flagella: long, few, move snakelike |
| - | | + | * Cilia: short, many, move back-and-forth |
| * In sperm, flagella propels them while cilia sweeps away debris | * In sperm, flagella propels them while cilia sweeps away debris | ||
| Line 677: | Line 689: | ||
| * Function: surrounds cell to provide support, structure, attachment, communication, | * Function: surrounds cell to provide support, structure, attachment, communication, | ||
| - | | + | * Membrane Carbs: help with cell-cell recognition → interact w/ other surface molecules so cells can be sorted into tissues |
| * Glycoproteins and glycolipids: | * Glycoproteins and glycolipids: | ||
| Line 684: | Line 696: | ||
| Key Overview | Key Overview | ||
| - | < | + | < |
| + | <img src=" | ||
| + | </ | ||
| * The larger the ratio is, the more efficient the cell is going to be | * The larger the ratio is, the more efficient the cell is going to be | ||
| * Smaller cells typically have a higher surface area-to-volume ratio | * Smaller cells typically have a higher surface area-to-volume ratio | ||
| Line 696: | Line 710: | ||
| ====Membrane Transport==== | ====Membrane Transport==== | ||
| - | **The Phospholipid Bilayer** | + | The Phospholipid Bilayer |
| * Cell membranes are asymmetrical bcuz the two sides of a cell membrane face different environments and carry out different functions | * Cell membranes are asymmetrical bcuz the two sides of a cell membrane face different environments and carry out different functions | ||
| - | * The polar phosphate regions are **oriented towards the aqueous external or internal environments** | + | * The polar phosphate regions are oriented towards the aqueous external or internal environments |
| - | * The nonpolar hydrocarbon fatty acid regions | + | * The nonpolar hydrocarbon fatty acid regions face each other inside the membrane |
| * Proteins may be loosely attached to inner/outer membrane or extend into the membrane | * Proteins may be loosely attached to inner/outer membrane or extend into the membrane | ||
| * Some are transmembrane | * Some are transmembrane | ||
| - | * Phospholipids (and some proteins) are **amphipathic** | + | * Phospholipids (and some proteins) are amphipathic |
| * Have polar (hydrophilic) and nonpolar (hydrophobic) regions | * Have polar (hydrophilic) and nonpolar (hydrophobic) regions | ||
| Line 727: | Line 741: | ||
| * Functional & structural: lipids provide structure but proteins determine function | * Functional & structural: lipids provide structure but proteins determine function | ||
| - | < | + | < |
| + | <img src=" | ||
| + | </ | ||
| + | <img src=" | ||
| + | </ | ||
| * The cell membrane is amphipathic with a hydrophobic interior, so only nonpolar molecules can pass through → selective permeability | * The cell membrane is amphipathic with a hydrophobic interior, so only nonpolar molecules can pass through → selective permeability | ||
| Line 745: | Line 763: | ||
| Plasma Membrane Proteins | Plasma Membrane Proteins | ||
| - | | + | * Channel proteins: have hydrophilic channels like a tunnel for certain molecules |
| - | | + | * Carrier proteins: bind to molecules (ex: glucose) and change shape to shuttle them across, |
| - | | + | * Transport Proteins: use energy (ATP) to transport materials across membrane against gradient |
| - | | + | * Recognition proteins: give each cell unique identification → distinction between self/ |
| * Ex: glycoproteins | * Ex: glycoproteins | ||
| - | | + | * Receptor proteins: binding sites for hormones or other trigger molecules |
| - | | + | * Enzymes: |
| - | | + | * Anchor proteins: attach cells to other cells or provide anchors for internal filaments < |
| + | <img src=" | ||
| + | </ | ||
| Types of Transport Proteins | Types of Transport Proteins | ||
| - | | + | * Integral proteins: amphipathic, |
| - | | + | * Transmembrane proteins: all across membrane |
| - | | + | * Peripheral protein: not in lipid bilayer: bound to membrane surface → hydrophilic |
| Cell Walls (found in plants) | Cell Walls (found in plants) | ||
| Line 776: | Line 796: | ||
| * The selective permeability of membranes allows for the formation of concentration gradients of solutes across the membrane | * The selective permeability of membranes allows for the formation of concentration gradients of solutes across the membrane | ||
| - | | + | * Concentration Gradients: “Difference of concentration between two substances” |
| - | | + | * Diffusion: movement of molecules so they spread out evenly |
| * Steeper concentration gradient or higher temp = faster diffusion | * Steeper concentration gradient or higher temp = faster diffusion | ||
| Passive Transport | Passive Transport | ||
| - | * The net movement from **high concentration to low concentration** without direct input of metabolic energy (Does NOT need ATP) | + | * The net movement from high concentration to low concentration without direct input of metabolic energy (Does NOT need ATP) |
| * Plays a primary role in the import of material and the export of waste | * Plays a primary role in the import of material and the export of waste | ||
| - | * Includes facilitated diffusion & **simple diffusion:** the molecule is hydrophobic | + | * Includes facilitated diffusion & simple diffusion: the molecule is hydrophobic |
| * Net movement of molecules is random/ | * Net movement of molecules is random/ | ||
| Line 796: | Line 816: | ||
| * Carrier & channel proteins can facilitate movement of ions and larger molecules like amino acids or glucose | * Carrier & channel proteins can facilitate movement of ions and larger molecules like amino acids or glucose | ||
| - | | + | * Ion channels (channel): transport ions, many are gated channels which open/close in response to stimuli |
| - | | + | * Aquaporins (channel): Integral membrane proteins that allow for the passage of water into the cell |
| * Very few water molecules can go through the membrane because are polar so need aquaporins that speed up process | * Very few water molecules can go through the membrane because are polar so need aquaporins that speed up process | ||
| Active Transport | Active Transport | ||
| - | * Proteins move molecules from a **region of low concentration to region of high concentration** | + | * Proteins move molecules from a region of low concentration to region of high concentration |
| - | * It moves **AGAINST** the gradient | + | * It moves AGAINST the gradient |
| * It DOES need ATP | * It DOES need ATP | ||
| Line 819: | Line 839: | ||
| * Uses vesicles to move substances across the plasma membrane; in/out of the cell | * Uses vesicles to move substances across the plasma membrane; in/out of the cell | ||
| - | | + | * Endocytosis: |
| * Vesicle then merges with lysosome to break down food | * Vesicle then merges with lysosome to break down food | ||
| - | - **Phagocytosis: | + | - Phagocytosis: |
| * Plasma membrane wraps around solid material and engulfs it → forms phagocytic vesicle → phagocytic cells attack and engulf bacteria this way | * Plasma membrane wraps around solid material and engulfs it → forms phagocytic vesicle → phagocytic cells attack and engulf bacteria this way | ||
| - | - **Pinocytosis: | + | - Pinocytosis: |
| - | - **Receptor-mediated: | + | - Receptor-mediated: |
| * Membrane pits, receptors and ligands fold inwards and vesicle forms | * Membrane pits, receptors and ligands fold inwards and vesicle forms | ||
| Line 836: | Line 856: | ||
| * “Water diffuses out or in of a cell”; when it does so osmotic pressure may build up → cell expands as it volume increases | * “Water diffuses out or in of a cell”; when it does so osmotic pressure may build up → cell expands as it volume increases | ||
| - | | + | * Turgor Pressure: osmotic pressure that develops when water enters cells |
| * Presses cytoplasm against cell → makes plants rigid and controls rate of osmosis | * Presses cytoplasm against cell → makes plants rigid and controls rate of osmosis | ||
| * Higher water potential = less solutes, lose water; Lower water potential = more solutes, gain water | * Higher water potential = less solutes, lose water; Lower water potential = more solutes, gain water | ||
| - | | + | * Plasmolysis: |
| - | | + | * Cell Lysis: water enters the cell, causing it to swell and burst |
| * More common in animal cells and others that lack a cell wall | * More common in animal cells and others that lack a cell wall | ||
| - | | + | * Hypertonic solution: more solutes |
| * Cell in hypertonic solution has higher water potential (more water) → water leaves cell → cell will shrivel and die | * Cell in hypertonic solution has higher water potential (more water) → water leaves cell → cell will shrivel and die | ||
| - | | + | * Isotonic: no net movement, same amount of water goes in and out |
| - | | + | * Hypotonic: less solutes |
| * Cell in hypotonic in solution has lower water potential (more solutes) → water enters cell → cell will swell and burst; plants become turgid | * Cell in hypotonic in solution has lower water potential (more solutes) → water enters cell → cell will swell and burst; plants become turgid | ||
| Line 858: | Line 878: | ||
| Ion Pumps: | Ion Pumps: | ||
| - | < | + | < |
| + | <img src=" | ||
| + | </ | ||
| * Ion channels/ | * Ion channels/ | ||
| - | | + | * Electrochemical gradient: difference in charge across plasma membrane → determines direction of ionic diffusion. Composed of chemical force & electrical (voltage) |
| - | | + | * Chemical: concentration gradient of ions |
| - | | + | * Electrical: effect of membrane potential |
| - | | + | * Membrane potential: resting voltage across membrane that affects the movement of ions |
| - | | + | * Active Potential: rapid rise and fall in voltage/ |
| - | | + | * Electrogenic pump: primary active transporters that hydrolyze ATP and use released energy to transport ions |
| * Generates voltage (potential energy of ions) & results in diff of charge | * Generates voltage (potential energy of ions) & results in diff of charge | ||
| * Ex: Sodium-Potassium Pump | * Ex: Sodium-Potassium Pump | ||
| - | * Plants have proton pump that pumps H+ rather than sodium and potassium and increases potential energy < | + | * Plants have proton pump that pumps H+ rather than sodium and potassium and increases potential energy < |
| + | <img src=" | ||
| + | </ | ||
| Cotransport: | Cotransport: | ||
| Line 884: | Line 908: | ||
| * Keeps cell polarized | * Keeps cell polarized | ||
| - | * Has (-) & (+) side < | + | * Has (-) & (+) side < |
| + | <img src=" | ||
| + | </ | ||
| * Cell has higher concentration of K+ and lower Na+ than extracellular solution | * Cell has higher concentration of K+ and lower Na+ than extracellular solution | ||
| Line 904: | Line 930: | ||
| =====Metabolism===== | =====Metabolism===== | ||
| - | * **Metabolism**the | + | * Metabolismthe |
| - | | + | * Catabolism: reactions break down molecules and release free energy (exergonic) |
| * Cellular respiration | * Cellular respiration | ||
| - | | + | * Anabolism: reactions build up molecules and absorb energy (endergonic) |
| * Synthesis of proteins and amino acids, ATP synthase | * Synthesis of proteins and amino acids, ATP synthase | ||
| Line 913: | Line 939: | ||
| * Higher temp → faster metabolism cuz most enzymes work better | * Higher temp → faster metabolism cuz most enzymes work better | ||
| - | < | + | < |
| + | <img src=" | ||
| + | </ | ||
| - | **Exergonic:** | + | Exergonic: |
| * Net release of free energy, -G, (usually spontaneous) | * Net release of free energy, -G, (usually spontaneous) | ||
| Line 922: | Line 950: | ||
| * Ex: cellular respiration | * Ex: cellular respiration | ||
| - | **Endergonic** | + | Endergonic |
| - | < | + | < |
| + | <img src=" | ||
| + | </ | ||
| * Products have more energy than reactants | * Products have more energy than reactants | ||
| Line 931: | Line 961: | ||
| Laws of Thermodynamics | Laws of Thermodynamics | ||
| - | | + | * Thermodynamics: |
| - | | + | * Closed systems can reach equilibrium→ then system can no longer be used for work (matter and energy cannot be transferred between system and its surroundings) |
| * Universe is smallest closed system cuz amount of energy is constant | * Universe is smallest closed system cuz amount of energy is constant | ||
| - | | + | * Open system: exchange energy and matter with environment |
| * Ex: Organisms and Earth bcuz get energy from sun | * Ex: Organisms and Earth bcuz get energy from sun | ||
| First Law: “Principle of Conservation of Energy” | First Law: “Principle of Conservation of Energy” | ||
| - | | + | * Energy can be transferred and transformed into a different form but it cannot be created or destroyed |
| * Forms include kinetic energy (energy of motion) and potential energy (stored energy) | * Forms include kinetic energy (energy of motion) and potential energy (stored energy) | ||
| Line 949: | Line 979: | ||
| Second Law: | Second Law: | ||
| - | | + | * “Every energy transfer or transformation increases the entropy (disorder) of the universe” |
| * More energy becomes unusable → things become disorganized and more disorderly | * More energy becomes unusable → things become disorganized and more disorderly | ||
| - | * When energy is converted in a reaction, some of it is **“**lost**” →** reactions increase entropy | + | * When energy is converted in a reaction, some of it is “lost” → reactions increase entropy |
| * Means that some energy becomes unusable/ | * Means that some energy becomes unusable/ | ||
| * Large, complicated molecules have more entropy bcuz of more ways can move around | * Large, complicated molecules have more entropy bcuz of more ways can move around | ||
| - | | + | * Cells require constant input of free energy to maintain their high lvl of organization |
| * Maintains opposition of entropy that increases as a result of chemical reactions | * Maintains opposition of entropy that increases as a result of chemical reactions | ||
| * No input → entropy increases, cells deteriorate, | * No input → entropy increases, cells deteriorate, | ||
| Line 968: | Line 998: | ||
| ====Free Energy Change==== | ====Free Energy Change==== | ||
| - | | + | * Free Energy: portion of systems energy that can perform work when temperature and pressure are uniform throughout (not heat) |
| - | * Formula: | + | * Formula: G= HTS |
| * G= Free energy change | * G= Free energy change | ||
| * H = Enthalpy, change in total energy/heat content | * H = Enthalpy, change in total energy/heat content | ||
| * S=Entropy, what's lost as heat | * S=Entropy, what's lost as heat | ||
| - | | + | * Spontaneous processes occur without energy input, - G (quickly or slowly) |
| * Increases entropy, decrease H, and releases energy for work | * Increases entropy, decrease H, and releases energy for work | ||
| - | | + | * Nonspontaneous: |
| * Ex. monomer to polymer | * Ex. monomer to polymer | ||
| Line 991: | Line 1021: | ||
| EQUILIBRIUM | EQUILIBRIUM | ||
| - | | + | * Equilibrium is a state of maximum stability (low energy); forward and reverse actions occur at the same rate so there is no net change→ no net production of reactants or products |
| * A process is spontaneous and can perform work only if it is moving towards equilibrium | * A process is spontaneous and can perform work only if it is moving towards equilibrium | ||
| Line 1006: | Line 1036: | ||
| ====ATP==== | ====ATP==== | ||
| - | * Principle molecule for storing and transferring energy for cell work and activation energy; converted by enzymes < | + | * Principle molecule for storing and transferring energy for cell work and activation energy; converted by enzymes < |
| + | <img src=" | ||
| + | </ | ||
| Structure | Structure | ||
| Line 1019: | Line 1051: | ||
| * All negatively charged groups → VERY unstable/ | * All negatively charged groups → VERY unstable/ | ||
| - | < | + | < |
| + | <img src=" | ||
| + | </ | ||
| - | | + | * Releases free energy (-G) by hydrolyzing the last (terminal) phosphate group |
| * Inorganic phosphate used to add molecule that has phosphate | * Inorganic phosphate used to add molecule that has phosphate | ||
| Line 1032: | Line 1066: | ||
| ATP Function | ATP Function | ||
| - | | + | * Energy coupling use exergonic reaction of ATP hydrolysis to power endergonic reactions in the cell |
| * Energy released is linked by shared/ | * Energy released is linked by shared/ | ||
| - | * < | + | * < |
| + | <img src=" | ||
| + | </ | ||
| + | <img src=" | ||
| + | </ | ||
| * ATP cannot be made by the body, ATP is converted or recycled in the body | * ATP cannot be made by the body, ATP is converted or recycled in the body | ||
| Line 1048: | Line 1086: | ||
| What are Enzymes? | What are Enzymes? | ||
| - | | + | * Enzyme: globular catalytic protein |
| * All enzymes are catalysts, but not all catalysts are enzymes | * All enzymes are catalysts, but not all catalysts are enzymes | ||
| - | | + | * Catalyst: chemical agent that speeds up a reaction without being consumed by the reaction → can be used over and over again |
| * Do not affect the free energy of a reaction! | * Do not affect the free energy of a reaction! | ||
| Line 1058: | Line 1096: | ||
| * Some enzymes are grouped into complexes, membranes, & organelles (mitochondria) → increase the efficiency of metabolic process | * Some enzymes are grouped into complexes, membranes, & organelles (mitochondria) → increase the efficiency of metabolic process | ||
| - | **Activation Energy Barrier** | + | Activation Energy Barrier |
| * Reacting molecules must collide and have enough energy (AE) needed to reach transition state and break bonds of reactants | * Reacting molecules must collide and have enough energy (AE) needed to reach transition state and break bonds of reactants | ||
| Line 1064: | Line 1102: | ||
| * But bad bcuz speeds up all reactions, denatures proteins & kills cells | * But bad bcuz speeds up all reactions, denatures proteins & kills cells | ||
| - | **Transition State:** | + | Transition State: |
| reactive (unstable) condition of the substrate after enough energy has been absorbed to start the reaction | reactive (unstable) condition of the substrate after enough energy has been absorbed to start the reaction | ||
| Line 1072: | Line 1110: | ||
| * Stabilizes transition state and lowers Ea Barrier | * Stabilizes transition state and lowers Ea Barrier | ||
| * Allow chemical reactions to occur at lower temperatures | * Allow chemical reactions to occur at lower temperatures | ||
| - | * Speeds up natural reactions | + | * Speeds up natural reactions ≠ cause them |
| * Reactions can occur without enzymes, but would be slower & a lot more energy | * Reactions can occur without enzymes, but would be slower & a lot more energy | ||
| Substrate Specificity of Enzyme | Substrate Specificity of Enzyme | ||
| - | | + | * Substrate: reactant an enzyme binds/acts on |
| - | | + | * Enzyme-substrate complex: enzyme binds to substrate and then substrate becomes product |
| * Enzymes might have more than one substrate but always only catalyze ONE type of reaction for each → gives enzyme specificity | * Enzymes might have more than one substrate but always only catalyze ONE type of reaction for each → gives enzyme specificity | ||
| Line 1085: | Line 1123: | ||
| * Specificity of an enzyme is bcuz of shape & polarity which results from amino acid sequence so molecules with (-) charge interact with (+) charged side chains in the active site | * Specificity of an enzyme is bcuz of shape & polarity which results from amino acid sequence so molecules with (-) charge interact with (+) charged side chains in the active site | ||
| - | * Enzymes have an **active site** that binds to substrate because of polarity or shape. | + | * Enzymes have an active site that binds to substrate because of polarity or shape. |
| - | **Induced-Fit Model:** describes how enzymes work | + | Induced-Fit Model: describes how enzymes work |
| * Enzyme and substrate not perfect fit → interactions between enzyme’s amino acids and substrate causes enzyme/ | * Enzyme and substrate not perfect fit → interactions between enzyme’s amino acids and substrate causes enzyme/ | ||
| Line 1097: | Line 1135: | ||
| - Substrate held by weak bonds | - Substrate held by weak bonds | ||
| - | - Active site lowers Ea barrier and speeds up reactions by… < | + | - Active site lowers Ea barrier and speeds up reactions by… < |
| + | <img src=" | ||
| + | </ | ||
| * Orienting substrates correctly to collide (physically) | * Orienting substrates correctly to collide (physically) | ||
| Line 1124: | Line 1164: | ||
| * But only until too high temp & then decreases | * But only until too high temp & then decreases | ||
| - | * At extreme environmental conditions, proteins become | + | * At extreme environmental conditions, proteins become denatured and lose function |
| * Lose 3D shape as HB and peptide bonds break down (irreversible) → can’t bind to substrate | * Lose 3D shape as HB and peptide bonds break down (irreversible) → can’t bind to substrate | ||
| * Most enzymes have optimal pH at 7; digestive proteins (ie pepsin) become active only at low pH | * Most enzymes have optimal pH at 7; digestive proteins (ie pepsin) become active only at low pH | ||
| Line 1131: | Line 1171: | ||
| * More substrate = increased activity until a certain point | * More substrate = increased activity until a certain point | ||
| - | **Cofactors**: nonprotein helpers for catalytic activity (ex. Zinc) | + | Cofactors: nonprotein helpers for catalytic activity (ex. Zinc) |
| - | | + | * Coenzyme: organic cofactors that binds to enzymes active site and increases catalytic activity, usually by donating or taking electrons (ex: vitamins) |
| - | | + | * Inorganic Cofactors: often metal ions |
| * Regulate enzyme activity = regulate metabolism/ | * Regulate enzyme activity = regulate metabolism/ | ||
| Line 1144: | Line 1184: | ||
| * Some bind irreversibly while others held by weak ionic or HB | * Some bind irreversibly while others held by weak ionic or HB | ||
| - | | + | * Competitive inhibitor: mimics substrate and binds to active site which blocks substrates |
| * More substrate can overcome inhibition | * More substrate can overcome inhibition | ||
| - | | + | * Noncompetitive inhibitor: binds to diff site on enzyme, irreversible |
| * Changes shape to make active site less effective | * Changes shape to make active site less effective | ||
| * Ex. Toxins, antibiotics, | * Ex. Toxins, antibiotics, | ||
| Line 1157: | Line 1197: | ||
| * Inhibitors - lock enzyme to be inactive | * Inhibitors - lock enzyme to be inactive | ||
| - | | + | * Cooperativity: |
| * Often occurs in enzymes that consist of multiple subunits (4th), each with own active site | * Often occurs in enzymes that consist of multiple subunits (4th), each with own active site | ||
| * Ex: One substrate molecule primes an enzyme to act on additional substrate molecules more readily | * Ex: One substrate molecule primes an enzyme to act on additional substrate molecules more readily | ||
| Line 1163: | Line 1203: | ||
| =====Unit 3: Photosynthesis\ \ ===== | =====Unit 3: Photosynthesis\ \ ===== | ||
| - | **Key Overview** | + | Key Overview |
| * Organisms capture free energy in sunlight to store chemical energy in organic compounds, which can later be released | * Organisms capture free energy in sunlight to store chemical energy in organic compounds, which can later be released | ||
| Line 1169: | Line 1209: | ||
| * Responsible for atmospheric CO2, Oxygen, organic carbon, & ozone layer | * Responsible for atmospheric CO2, Oxygen, organic carbon, & ozone layer | ||
| - | | + | * Carbon Dioxide + Water + Light Energy ⇒ Glucose + Oxygen |
| * Photosynthesis Processes: | * Photosynthesis Processes: | ||
| - | - **Noncyclic photophosphorylation** use water and energy from sunlight to create ATP, NADPH, and oxygen | + | - Noncyclic photophosphorylation use water and energy from sunlight to create ATP, NADPH, and oxygen |
| - | - **Calvin Cycle:** uses Carbon dioxide and energy in ATP and NADPH to make glucose | + | - Calvin Cycle: uses Carbon dioxide and energy in ATP and NADPH to make glucose |
| - | < | + | < |
| + | <img src=" | ||
| + | </ | ||
| * The site of photosynthesis in plants | * The site of photosynthesis in plants | ||
| Line 1184: | Line 1226: | ||
| * Several membrane systems creates compartments | * Several membrane systems creates compartments | ||
| - | | + | * System of compartmentalization increases surface area and allows organelles to finish their tasks faster |
| - | < | + | < |
| + | <img src=" | ||
| + | </ | ||
| - | |**Outer Membrane**|**Inner Membrane**|**Intermembrane Space**|**Thylakoid Membrane**| | + | |Outer Membrane|Inner Membrane|Intermembrane Space|Thylakoid Membrane| |
| |Semipermeable membranes that regulates flow of ions, proteins and molecules|Semipermeable membranes that regulates flow of ions, proteins and molecules|Space between the inner membrane outer membrane|Folded membranes of the thylakoids that are stacked up into “granums”\ Contains ETC and ATP synthase; source of light reaction\ | | |Semipermeable membranes that regulates flow of ions, proteins and molecules|Semipermeable membranes that regulates flow of ions, proteins and molecules|Space between the inner membrane outer membrane|Folded membranes of the thylakoids that are stacked up into “granums”\ Contains ETC and ATP synthase; source of light reaction\ | | ||
| - | |**Thylakoid**|**Stroma**|**Granum**|**Lumen**| | + | |Thylakoid|Stroma|Granum|Lumen| |
| |Absorbs the light in order to be converted into chemical energy\ Phospholipid bilayer\ |A dense solution, the site of the DARK REACTIONS|Entire stack of thylakoids|Inside of thylakoid where H+ accumulate| | |Absorbs the light in order to be converted into chemical energy\ Phospholipid bilayer\ |A dense solution, the site of the DARK REACTIONS|Entire stack of thylakoids|Inside of thylakoid where H+ accumulate| | ||
| - | |**Mesophyll Cells**|**Bundle Sheaths**|**Guard cells**|**Stomata**| | + | |Mesophyll Cells|Bundle Sheaths|Guard cells|Stomata| |
| |Spongy tissue in the leaf that contains lots of photosynthetic cells\ In C4 carry out light reaction\ |Photosynthetic cells tightly packed around leaf vein \ In C4 carry out Calvin Cycle\ |Flank single stomata and control if is open or closed|Needed for gas exchange \ Water & CO2 enters and oxygen exits\ | | |Spongy tissue in the leaf that contains lots of photosynthetic cells\ In C4 carry out light reaction\ |Photosynthetic cells tightly packed around leaf vein \ In C4 carry out Calvin Cycle\ |Flank single stomata and control if is open or closed|Needed for gas exchange \ Water & CO2 enters and oxygen exits\ | | ||
| - | **History of Photosynthesis** | + | History of Photosynthesis |
| - | | + | * Photosynthesis first evolved in prokaryotic organisms |
| - | | + | * Evidence suggests that they were responsible for the production of an oxygenated atmosphere. |
| - | **The Photosynthetic Pigments** | + | The Photosynthetic Pigments |
| * Process begins with light-absorbing pigments | * Process begins with light-absorbing pigments | ||
| - | | + | * Pigments: absorb specific wavelengths of light and convert sun energy. |
| * Differ in maximum absorption; together pigments complement each other to maximize energy absorption | * Differ in maximum absorption; together pigments complement each other to maximize energy absorption | ||
| - | | + | * Chlorophyll a: (green) captures light directly used in light reaction |
| - | | + | * Chlorophyll b: accessory pigments (pass to chlorophyll a) |
| - | | + | * Carotenoids: |
| Wavelengths | Wavelengths | ||
| Line 1241: | Line 1285: | ||
| * Have a collection of proteins and pigment molecules (chlorophyll a and b) embedded in the thylakoid membrane | * Have a collection of proteins and pigment molecules (chlorophyll a and b) embedded in the thylakoid membrane | ||
| - | | + | * Light harvesting complex: pigments bound to proteins |
| * When energy is absorbed, transfer it until reaches chlorophyll a | * When energy is absorbed, transfer it until reaches chlorophyll a | ||
| - | | + | * Reaction center: proteins with special pair of chlorophyll a |
| * Chlorophyll a: have specific max absorb rates & boost/ | * Chlorophyll a: have specific max absorb rates & boost/ | ||
| - | < | + | < |
| + | <img src=" | ||
| + | </ | ||
| - | |**Photosystem 2**\ The first photosystem.\ • Light its absorbed by chlorophyll P680 → energy boosts electrons to primary electron acceptor \ • Chlorophyll a considered strongest oxidizing agent bcuz gets electrons from water\ • Adds more energy to a SECOND PHOTOSYSTEM (p1)\ |**Photosystem 1**\ • Chlorophyll P700 receives electrons from P1 and light energy boosts it up to a PEA\ • These electrons are now transferred directly to proteins in the thylakoid membrane, activating\ | + | |Photosystem 2\ The first photosystem.\ • Light its absorbed by chlorophyll P680 → energy boosts electrons to primary electron acceptor \ • Chlorophyll a considered strongest oxidizing agent bcuz gets electrons from water\ • Adds more energy to a SECOND PHOTOSYSTEM (p1)\ |Photosystem 1\ • Chlorophyll P700 receives electrons from P1 and light energy boosts it up to a PEA\ • These electrons are now transferred directly to proteins in the thylakoid membrane, activating\ NADPH reductase\ ◦ Reduces NADP+ to NADPH\ | |
| Excitation of Chlorophyll by Light | Excitation of Chlorophyll by Light | ||
| Line 1259: | Line 1305: | ||
| Noncyclic Photophosphorylation | Noncyclic Photophosphorylation | ||
| - | - **Splitting of Water:** water is split → donates electrons to ETC, releases protons and oxygen | + | - Splitting of Water: water is split → donates electrons to ETC, releases protons and oxygen |
| * Electrons from water replace lost electrons from PS II, make ATP, & NADPH | * Electrons from water replace lost electrons from PS II, make ATP, & NADPH | ||
| - | - **Photosystem II:** electrons trapped by P680 are energized by light absorbed by light harvesting complex & passed to PEA | + | - Photosystem II: electrons trapped by P680 are energized by light absorbed by light harvesting complex & passed to PEA |
| - | - **Primary Electron Acceptor:** first in chain of electron acceptors | + | - Primary Electron Acceptor: first in chain of electron acceptors |
| - | - **Electron Transport Chain:** proteins in the thylakoid membrane alternate between oxidized and reduced as they pass electrons from one carrier to the next | + | - Electron Transport Chain: proteins in the thylakoid membrane alternate between oxidized and reduced as they pass electrons from one carrier to the next |
| * No proton gradient w/o redox reactions | * No proton gradient w/o redox reactions | ||
| Line 1273: | Line 1319: | ||
| * Flow of electrons: H₂O → NADPH → Calvin cycle | * Flow of electrons: H₂O → NADPH → Calvin cycle | ||
| - | - **Proton Gradient & Phosphorylation: | + | - Proton Gradient & Phosphorylation: |
| - | - **Photosystem I:** P700 absorbs energy and boosts electrons to primary e- acceptor | + | - Photosystem I: P700 absorbs energy and boosts electrons to primary e- acceptor |
| - | - **NADPH:** two e- pass thru short ETC and combine with NADP+ and H+ to form NADPH by NADPH reductase | + | - NADPH: two e- pass thru short ETC and combine with NADP+ and H+ to form NADPH by NADPH reductase |
| - | | + | * NADPH: coenzyme, reducing agent |
| * ATP and NADPH produced and will be used in the Calvin Cycle to convert CO2 into sugar | * ATP and NADPH produced and will be used in the Calvin Cycle to convert CO2 into sugar | ||
| Line 1291: | Line 1337: | ||
| * Occurs simultaneously with noncyclic to make extra ATP | * Occurs simultaneously with noncyclic to make extra ATP | ||
| - | **Noncyclic Phosphorylation Diagram** | + | Noncyclic Phosphorylation Diagram |
| =====Calvin Cycle===== | =====Calvin Cycle===== | ||
| - | {{Untitled_a1baf95c2be74fad95ea92c3882c2c8f: | + | {{Untitled_a1baf95c2be74fad95ea92c3882c2c8f: |
| * Uses energy captured in the light reactions and transferred to ATP and NADPH to convert CO2 into sugar (glucose) | * Uses energy captured in the light reactions and transferred to ATP and NADPH to convert CO2 into sugar (glucose) | ||
| - | * Occurs in the **stroma; cytosol in autotrophic bacteria** | + | * Occurs in the stroma; cytosol in autotrophic bacteria |
| The Process | The Process | ||
| - | - **Carbon fixation: CO2 combines with ribulose to make organic molecule PGA: catalyzed by rubisco (enzyme)** | + | - Carbon fixation: CO2 combines with ribulose to make organic molecule PGA: catalyzed by rubisco (enzyme) |
| * C3 pathway bcuz first product formed contains three carbon atoms | * C3 pathway bcuz first product formed contains three carbon atoms | ||
| - | - **Reduction: PGA gets energy (H+) from ATP and electrons from NADPH to make G3P** | + | - Reduction: PGA gets energy (H+) from ATP and electrons from NADPH to make G3P |
| * CO2 reduced and NADPH oxidized | * CO2 reduced and NADPH oxidized | ||
| - | | + | * G3P: 3 Carbon, used to make other organic compounds like glucose (2 G3P) |
| - | - **Regeneration: | + | - Regeneration: |
| * 3 CO2 enter to make 6 G3P but only one is net gain because rest are rearranged into ribulose | * 3 CO2 enter to make 6 G3P but only one is net gain because rest are rearranged into ribulose | ||
| - | - **Carb Synthesis: remaining 2 G3P are used to make sugar (Ex: glucose)** | + | - Carb Synthesis: remaining 2 G3P are used to make sugar (Ex: glucose) |
| * For one glucose molecule: cycle turns 6 times, 3 times for one G3P | * For one glucose molecule: cycle turns 6 times, 3 times for one G3P | ||
| - | **Chemiosmosis in Chloroplasts** | + | Chemiosmosis in Chloroplasts |
| - | **Photophosphorylation Process** | + | Photophosphorylation Process |
| - | - **H+ accumulate inside thylakoids: H+ are released into the lumen when water is split , H+ are carried from the stroma to lumen by a cytochrome in ETC** | + | - H+ accumulate inside thylakoids: H+ are released into the lumen when water is split , H+ are carried from the stroma to lumen by a cytochrome in ETC |
| - | - **A pH and electrical gradient across the thylakoid membrane is created. Bcuz H+ ions are (+) → represents potential energy** | + | - A pH and electrical gradient across the thylakoid membrane is created. Bcuz H+ ions are (+) → represents potential energy |
| - | **ATP synthase allows protons to move down their gradient (to stroma):** | + | ATP synthase allows protons to move down their gradient (to stroma): |
| the flow of H+ through ATP synthase provides energy for synthase to phosphorylate ADP to ATP | the flow of H+ through ATP synthase provides energy for synthase to phosphorylate ADP to ATP | ||
| - | **Photosynthesis Mechanisms and Alternatives** | + | Photosynthesis Mechanisms and Alternatives |
| PHOTORESPIRATION | PHOTORESPIRATION | ||
| Line 1357: | Line 1403: | ||
| * During day close stomata and CO2 released for calvin cycle | * During day close stomata and CO2 released for calvin cycle | ||
| - | < | + | < |
| + | <img src=" | ||
| + | </ | ||
| * Minimize photorespiration by using PEP Carboxylase (low affinity for O2) to initially fix CO2 | * Minimize photorespiration by using PEP Carboxylase (low affinity for O2) to initially fix CO2 | ||
| Line 1372: | Line 1420: | ||
| Disadvantage: | Disadvantage: | ||
| - | **Transpiration** | + | Transpiration |
| Transpiration and Photosynthesis | Transpiration and Photosynthesis | ||
| Line 1378: | Line 1426: | ||
| * Basically leaf evaporation; | * Basically leaf evaporation; | ||
| - | * Transpiration function → creates | + | * Transpiration function → creates transpirational pull: water and ions sucked up from roots to xylem (bcuz water attracted to each other and HB) which cools the plant and pumps water and minerals to the leaves for photosynthesis |
| * Transpiration rate can be calculated by measuring amount of water taken up by plants stem | * Transpiration rate can be calculated by measuring amount of water taken up by plants stem | ||
| Line 1389: | Line 1437: | ||
| =====Unit 3: Cellular Respiration===== | =====Unit 3: Cellular Respiration===== | ||
| - | **Key Overview** | + | Key Overview |
| * Catabolic: cells obtain energy by breaking down macromolecules to make ATP & power cellular functions | * Catabolic: cells obtain energy by breaking down macromolecules to make ATP & power cellular functions | ||
| - | | + | * Glucose + Oxygen → Energy + Water + Carbon Dioxide |
| * Glucose is oxidized while Oxygen in reduced | * Glucose is oxidized while Oxygen in reduced | ||
| * Processes in mitochondria need oxygen | * Processes in mitochondria need oxygen | ||
| - | * Photosynthesis uses NAD**P**H | + | * Photosynthesis uses NADPH but respiration uses NADH |
| * Lots of ATP made but only ~half are net gain | * Lots of ATP made but only ~half are net gain | ||
| Line 1409: | Line 1457: | ||
| * 2 Pyruvate (stores potential energy) | * 2 Pyruvate (stores potential energy) | ||
| * Pyruvate is acidic | * Pyruvate is acidic | ||
| - | | + | * 2 (net) ATP (from ADP) |
| * NADH (from NAD+) | * NADH (from NAD+) | ||
| * Inorganic phosphate | * Inorganic phosphate | ||
| Line 1424: | Line 1472: | ||
| * Reverse: NADH broken down to form NAD+ | * Reverse: NADH broken down to form NAD+ | ||
| - | | + | * NADH: reducing agent, carries the electrons to the ETC in mitochondria |
| Pyruvate Oxidation | Pyruvate Oxidation | ||
| * Pyruvate is actively transported from the cytosol to the mitochondrial matrix where further oxidation occurs | * Pyruvate is actively transported from the cytosol to the mitochondrial matrix where further oxidation occurs | ||
| - | | + | * Transportation depends on proton-motive force (H+ gradient) |
| - | | + | * Pyruvate loses carbon from acetyl group→ remaining carbon transferred to coenzyme A (CoA) |
| - | | + | * Result: 2 acetyl CoA, 2 NADH & 2 CO2 made |
| - | | + | * Acetyl CoA: coenzyme, high potential energy, will be oxidized in Krebs Cycle |
| ====KREBS CYCLE==== | ====KREBS CYCLE==== | ||
| - | * Occurs in the mitochondrial matrix; cytosol of prokaryotes < | + | * Occurs in the mitochondrial matrix; cytosol of prokaryotes < |
| + | <img src=" | ||
| + | </ | ||
| * Begins when 2-carbon Acetyl CoA combines with 4-carbon OAA (oxaloacetate) to form citrate | * Begins when 2-carbon Acetyl CoA combines with 4-carbon OAA (oxaloacetate) to form citrate | ||
| Line 1445: | Line 1495: | ||
| * Result: | * Result: | ||
| * 2 CO2 molecules produced | * 2 CO2 molecules produced | ||
| - | | + | * 6 NADH created |
| - | | + | * 2 FADH2 created: makes less ATP bcuz transfers electrons at lower energy level |
| * Electrons are transferred to coenzymes NADH and FADH2 that will donate electrons to be oxidized and then reused | * Electrons are transferred to coenzymes NADH and FADH2 that will donate electrons to be oxidized and then reused | ||
| - | | + | * 2 ATP created but most energy transferred to NAD+ and FAD |
| * Is a closed loop bcuz last part of process reforms 1st molecule | * Is a closed loop bcuz last part of process reforms 1st molecule | ||
| Line 1462: | Line 1512: | ||
| * Enzyme transfers phosphate from substrate molecule to ADP | * Enzyme transfers phosphate from substrate molecule to ADP | ||
| - | **OXIDATIVE PHOSPHORYLATION (electron transfer and chemiosmosis)** | + | OXIDATIVE PHOSPHORYLATION (electron transfer and chemiosmosis) |
| * Process of producing ATP from NADH and FADH2 as electrons give up energy used to phosphorylate ADP to ATP | * Process of producing ATP from NADH and FADH2 as electrons give up energy used to phosphorylate ADP to ATP | ||
| Line 1468: | Line 1518: | ||
| * Occurs in the inner mitochondrial membrane of eukaryotes; plasma membrane of prokaryotes | * Occurs in the inner mitochondrial membrane of eukaryotes; plasma membrane of prokaryotes | ||
| - | | + | * Cytochromes: |
| - | **Mitochondria Structure** | + | Mitochondria Structure |
| - | < | + | < |
| + | <img src=" | ||
| + | </ | ||
| ====ELECTRON TRANSPORT CHAIN==== | ====ELECTRON TRANSPORT CHAIN==== | ||
| Line 1478: | Line 1530: | ||
| * inner mitochondrial membrane | * inner mitochondrial membrane | ||
| - | | + | * Redox reactions needed for proton gradient |
| * Heat allows for hibernation; | * Heat allows for hibernation; | ||
| - | | + | * Carriers = proteins that act as primary electron acceptors |
| * Oxygen is ultimate electron acceptor with most affinity→ process needs oxygen | * Oxygen is ultimate electron acceptor with most affinity→ process needs oxygen | ||
| * Oxygen accepts electrons & protons → forms water | * Oxygen accepts electrons & protons → forms water | ||
| - | * NADH donates | + | * NADH donates 2 electrons → oxidized, reverts back to NAD+, and goes back to glycolysis/ |
| - | | + | * If NADH couldn' |
| Chemiosmosis | Chemiosmosis | ||
| Line 1494: | Line 1546: | ||
| * Couples electron transport and energy release to move protons down their energy gradient and through ATP synthase | * Couples electron transport and energy release to move protons down their energy gradient and through ATP synthase | ||
| - | - **Krebs Cycle produces NADH and FADH2 in matrix** | + | - Krebs Cycle produces NADH and FADH2 in matrix |
| - | - **Electrons are removed from NADH and FADH2** | + | - Electrons are removed from NADH and FADH2 |
| * Removed by protein complexes in the inner membrane → electrons move along ETC from one protein complex to another | * Removed by protein complexes in the inner membrane → electrons move along ETC from one protein complex to another | ||
| - | - **H+ ions (protons) are transported from the matrix to intermembrane space** | + | - H+ ions (protons) are transported from the matrix to intermembrane space |
| * Electrons lose energy as they move down their electrochemical gradient thru redox reactions and complexes → complexes capture released energy to pump H+ | * Electrons lose energy as they move down their electrochemical gradient thru redox reactions and complexes → complexes capture released energy to pump H+ | ||
| - | - **A proton gradient (proton motive force) and electrical gradient (voltage) is established across the inner membrane: represents potential energy** | + | - A proton gradient (proton motive force) and electrical gradient (voltage) is established across the inner membrane: represents potential energy |
| * As H+ are transferred, | * As H+ are transferred, | ||
| - | - **ATP synthase allows protons to flow back into the matrix (down gradient)** | + | - ATP synthase allows protons to flow back into the matrix (down gradient) |
| - | * The flow of protons back through ATP synthase by **chemiosmosis** generates energy for synthase to phosphorylate ADP to ATP | + | * The flow of protons back through ATP synthase by chemiosmosis generates energy for synthase to phosphorylate ADP to ATP |
| - | | + | * Oxidative phosphorylation in cellular respiration |
| - | | + | * Photophosphorylation in photosynthesis |
| - | **The Proton Gradient** | + | The Proton Gradient |
| * Proton gradient = pH gradient = electrochemical (voltage) gradient = stored/ | * Proton gradient = pH gradient = electrochemical (voltage) gradient = stored/ | ||
| - | | + | * Proton Motive Force: force exerted on protons by H+ gradient |
| - | **The ATP Synthase enzyme** | + | The ATP Synthase enzyme |
| * Channel protein that translocates the hydrogen ions from high concentration to low concentration | * Channel protein that translocates the hydrogen ions from high concentration to low concentration | ||
| Line 1541: | Line 1593: | ||
| ====Fermentation==== | ====Fermentation==== | ||
| - | * Allows glycolysis to proceed | + | * Allows glycolysis to proceed when there is no oxygen → produces organic molecules, including alcohol and lactic acid, as waste products. |
| * Goal: To replenish NAD+, so glycolysis can make ATP (w/o oxygen) | * Goal: To replenish NAD+, so glycolysis can make ATP (w/o oxygen) | ||
| Line 1550: | Line 1602: | ||
| * Occurs in cytosol NOT in the mitochondria (no oxygen present, no ETC). | * Occurs in cytosol NOT in the mitochondria (no oxygen present, no ETC). | ||
| - | **Alcohol Fermentation** | + | Alcohol Fermentation |
| * Pyruvate loses 2 carbon dioxide molecules and then reduced by NADH | * Pyruvate loses 2 carbon dioxide molecules and then reduced by NADH | ||
| Line 1577: | Line 1629: | ||
| * Proteins: fuel, broken down into amino acids to make enzymes for cell respiration (biosynthesis/ | * Proteins: fuel, broken down into amino acids to make enzymes for cell respiration (biosynthesis/ | ||
| * Eaten proteins are digested to amino acids; body proteins can be hydrolyzed to amino acids | * Eaten proteins are digested to amino acids; body proteins can be hydrolyzed to amino acids | ||
| - | | + | * Deamination: |
| * Remainders of amino acids are converted into substances that act as intermediate step of glycolysis or krebs | * Remainders of amino acids are converted into substances that act as intermediate step of glycolysis or krebs | ||
| * Fats: digested to glycerol (for glycolysis) and and fatty acids (as Acetyl CoA in Krebs Cycle) | * Fats: digested to glycerol (for glycolysis) and and fatty acids (as Acetyl CoA in Krebs Cycle) | ||
| * When fats are broken down they make more ATP than carbs and release CO2 & water | * When fats are broken down they make more ATP than carbs and release CO2 & water | ||
| - | | + | * Beta Oxidation: breaks fatty acid chain into 2-C that directly enters Krebs |
| Regulation of Cellular Respiration | Regulation of Cellular Respiration | ||
| Line 1599: | Line 1651: | ||
| Similarities | Similarities | ||
| - | |**Photosynthesis**\ • Electrons are sent to the ETC for the light-dependent reactions using a carrier\ • Existence of a proton gradient in the thylakoid space that passes through ATP Synthase to make ATP\ • Similar electron carriers\ |**Cellular Respiration**\ • Electrons are sent to the ETC for oxidative phosphorylation using NADH/FADH\ • Existence of a proton gradient in the intermembrane space that passes through ATP Synthase to make ATP\ • Involve redox reactions\ | | + | |Photosynthesis\ • Electrons are sent to the ETC for the light-dependent reactions using a carrier\ • Existence of a proton gradient in the thylakoid space that passes through ATP Synthase to make ATP\ • Similar electron carriers\ |Cellular Respiration\ • Electrons are sent to the ETC for oxidative phosphorylation using NADH/FADH\ • Existence of a proton gradient in the intermembrane space that passes through ATP Synthase to make ATP\ • Involve redox reactions\ | |
| Differences | Differences | ||
| - | |**Photosynthesis**\ • H+ accumulate in lumen → chemiosmosis moves H+ from lumen to stroma\ • Terminal electron acceptor is NADP+\ • Chloroplast \ • Anabolic → energy absorbed used to make ATP & NADPH\ |**Cellular Respiration**\ • H+ accumulate in lumen → chemiosmosis moves H+ from intermembrane space to matrix \ • Terminal electron acceptor is oxygen\ • (mostly) Mitochondria\ • Catabolic → energy released used to make ATP & power cellular work\ | | + | |Photosynthesis\ • H+ accumulate in lumen → chemiosmosis moves H+ from lumen to stroma\ • Terminal electron acceptor is NADP+\ • Chloroplast \ • Anabolic → energy absorbed used to make ATP & NADPH\ |Cellular Respiration\ • H+ accumulate in lumen → chemiosmosis moves H+ from intermembrane space to matrix \ • Terminal electron acceptor is oxygen\ • (mostly) Mitochondria\ • Catabolic → energy released used to make ATP & power cellular work\ | |
| =====Unit 5: Cell Communication===== | =====Unit 5: Cell Communication===== | ||
| - | **Key Overview** | + | Key Overview |
| * Cells communicate by generating, transmitting, | * Cells communicate by generating, transmitting, | ||
| Line 1614: | Line 1666: | ||
| * Cells ALSO communicate through direct contact with other cells | * Cells ALSO communicate through direct contact with other cells | ||
| - | **PARACRINE SIGNALING** | + | PARACRINE SIGNALING |
| * Cells secrete substances that travel short distances and only affect nearby cells affect bcuz substances are easily absorbed by nearby cells or broken down in extracellular fluid | * Cells secrete substances that travel short distances and only affect nearby cells affect bcuz substances are easily absorbed by nearby cells or broken down in extracellular fluid | ||
| Line 1623: | Line 1675: | ||
| * Allows cells to locally coordinate activities with their neighbors | * Allows cells to locally coordinate activities with their neighbors | ||
| - | **Key Overview** | + | Key Overview |
| * Cells communicate by generating, transmitting, | * Cells communicate by generating, transmitting, | ||
| Line 1629: | Line 1681: | ||
| * Cells ALSO communicate through direct contact with other cells | * Cells ALSO communicate through direct contact with other cells | ||
| - | **PARACRINE SIGNALING** | + | PARACRINE SIGNALING |
| * Cells secrete substances that travel short distances and only affect nearby cells affect bcuz substances are easily absorbed by nearby cells or broken down in extracellular fluid | * Cells secrete substances that travel short distances and only affect nearby cells affect bcuz substances are easily absorbed by nearby cells or broken down in extracellular fluid | ||
| Line 1639: | Line 1691: | ||
| * Especially important during development, | * Especially important during development, | ||
| - | * Ex. **Growth Factors:** proteins secreted during early animal development that stimulate nearby cells to divide → cause growth and repair | + | * Ex. Growth Factors: proteins secreted during early animal development that stimulate nearby cells to divide → cause growth and repair |
| - | | + | * Synaptic signaling: nerve cells release neurotransmitters that cross spaces between cells (synapses) to stimulate or inhibit nerve impulse or muscle contraction |
| * Do not enter the cell | * Do not enter the cell | ||
| - | **AUTOCRINE SIGNALING** | + | AUTOCRINE SIGNALING |
| * A cell signals to itself, releasing a ligand that binds to receptors on its own surface | * A cell signals to itself, releasing a ligand that binds to receptors on its own surface | ||
| * Important during development, | * Important during development, | ||
| - | [[https:// | + | https:// |
| + | <img src=" | ||
| + | </ | ||
| * When cells need to transmit signals over long distances, release hormones into the bloodstream to reach distant target cells | * When cells need to transmit signals over long distances, release hormones into the bloodstream to reach distant target cells | ||
| * Blood stream provides mechanism for distributing signals thru multi cell organisms | * Blood stream provides mechanism for distributing signals thru multi cell organisms | ||
| - | | + | * Hormones: long-distance, |
| * Diff hormones have diff size and structure that allow them to recognize specific molecules and intracellular receptors | * Diff hormones have diff size and structure that allow them to recognize specific molecules and intracellular receptors | ||
| * One hormone can lead to many 2ndry messengers and effects cuz can bind to receptors inside many cells | * One hormone can lead to many 2ndry messengers and effects cuz can bind to receptors inside many cells | ||
| - | [[https:// | + | https:// |
| + | <img src=" | ||
| + | </ | ||
| * Between animal cells → allow proteins, carbs, and lipids of the plasma membrane to transmit information | * Between animal cells → allow proteins, carbs, and lipids of the plasma membrane to transmit information | ||
| * Common in early development | * Common in early development | ||
| - | | + | * Cell junctions: protein complexes in plasma membrane connect cells to share info thru integrins |
| * Necessary to maintain tissue integrity; anchor cells to one another | * Necessary to maintain tissue integrity; anchor cells to one another | ||
| - | | + | * Anchoring Junctions: protein attachments between adjacent animal cells |
| - | * Ex: **Desmosome:** proteins that bind to proteins and associated with intermediate filaments that extend into interior of cell and hold cellular structures together | + | * Ex: Desmosome: proteins that bind to proteins and associated with intermediate filaments that extend into interior of cell and hold cellular structures together |
| - | | + | * Tight Junctions: cell membrane pressed against surface proteins → seal that prevents passage of materials between cells |
| * Ex: digestive tract where materials need to pass thru cells | * Ex: digestive tract where materials need to pass thru cells | ||
| - | Communicating Junctions: | + | Communicating Junctions: allow transfer of chemical or electrical signals |
| - | | + | * Gap junctions: tiny, water-filled channels between animal cells that allow diffusion of ions and small molecules for electrical and chemical signaling between two cells |
| * Prevent cytoplasmic protein and nucleic acids from mixing; ex. Heart pumping | * Prevent cytoplasmic protein and nucleic acids from mixing; ex. Heart pumping | ||
| * Basically channel proteins of two cells that are closely aligned | * Basically channel proteins of two cells that are closely aligned | ||
| - | | + | * Plasmodesmata: |
| * Regulates molecule transfer and gene expression | * Regulates molecule transfer and gene expression | ||
| - | | + | * Cell-Cell Recognition: |
| * The transfer of signalling molecules transmits the current state of one cell to its neighbour | * The transfer of signalling molecules transmits the current state of one cell to its neighbour | ||
| - | | + | * Helpful bcuz allows a group of cells to respond to a signal that only one of them may have received. |
| - | * [[Untitled_a1baf95c2be74fad95ea92c3882c2c8f: | + | * Untitled_a1baf95c2be74fad95ea92c3882c2c8f: |
| =====Signal Transduction Pathways===== | =====Signal Transduction Pathways===== | ||
| * Sequence of molecular interactions that transforms an extracellular signal into a specific cellular response; takes place AFTER a signaling molecule (ligand) binds to receptor | * Sequence of molecular interactions that transforms an extracellular signal into a specific cellular response; takes place AFTER a signaling molecule (ligand) binds to receptor | ||
| * Signal → receptor → 2ndry messengers → proteins activated → cellular response | * Signal → receptor → 2ndry messengers → proteins activated → cellular response | ||
| - | | + | * Ligand: signaling molecule that acts as first messenger |
| * Pathway similarities suggest that ancestral signaling molecules evolved in prokaryotes and were modified later in eukaryotes | * Pathway similarities suggest that ancestral signaling molecules evolved in prokaryotes and were modified later in eukaryotes | ||
| * Signals can come from biological sources (ex: pathogens) or physical sources (ex: chemicals, heat or light) | * Signals can come from biological sources (ex: pathogens) or physical sources (ex: chemicals, heat or light) | ||
| ====THE PROCESS - PART 1: RECEPTION==== | ====THE PROCESS - PART 1: RECEPTION==== | ||
| - | | + | * Signaling Molecules: small molecules that bind to larger receptors of specific target cells |
| - | - **Hydrophilic ligands:** cannot cross membrane and bind to membrane receptors | + | - Hydrophilic ligands: cannot cross membrane and bind to membrane receptors |
| * Ex: proteins that are both large and polar | * Ex: proteins that are both large and polar | ||
| - | - **Hydrophobic ligands:** non-polar signaling molecules that can cross membrane and bind to intracellular receptors**** [[https:// | + | - Hydrophobic ligands: non-polar signaling molecules that can cross membrane and bind to intracellular receptors https:// |
| - | | + | <img src=" |
| - | - **Membrane receptors:** transmembrane & amphipathic; | + | </ |
| - | - **Intracellular receptors:** proteins in cytoplasm or nucleus | + | * Receptors: specific proteins that receive ligands and trigger transduction |
| + | - Membrane receptors: transmembrane & amphipathic; | ||
| + | - Intracellular receptors: proteins in cytoplasm or nucleus | ||
| * When a ligand binds to the cell-surface receptor, the inside part of the receptor “changes” | * When a ligand binds to the cell-surface receptor, the inside part of the receptor “changes” | ||
| * Usually means it changes shape, which may make it active as an enzyme or let it bind to other molecules | * Usually means it changes shape, which may make it active as an enzyme or let it bind to other molecules | ||
| - | | + | * G Protein-Coupled Receptors |
| - | | + | * GPCRs: amphipathic, |
| - | | + | * G protein inactive with GDP and activated when GDP is replaced with GTP |
| * Process Summary | * Process Summary | ||
| - | - **GPCR receives signal: specific messenger ligand binds to outward surface of receptor** | + | - GPCR receives signal: specific messenger ligand binds to outward surface of receptor |
| - | - **GPCR activates G protein: ligand binding activates GPCR → GPCR exchanges a GTP for the GDP on a nearby G protein → activates G protein** | + | - GPCR activates G protein: ligand binding activates GPCR → GPCR exchanges a GTP for the GDP on a nearby G protein → activates G protein |
| - | - **G protein binds to and activities [membrane] effector protein:** | + | - G protein binds to and activities [membrane] effector protein: |
| - | - **Effector protein initiates cellular response:** | + | - Effector protein initiates cellular response: |
| * Enzymatic activity: effector protein may be enzyme that catalyzes specific substrate → ex: protein kinase and initiate kinase cascade | * Enzymatic activity: effector protein may be enzyme that catalyzes specific substrate → ex: protein kinase and initiate kinase cascade | ||
| - | * Produce second messenger | + | * Produce second messenger cAMP: |
| * If effector protein is adenylyl cyclase, enzyme makes cAMP | * If effector protein is adenylyl cyclase, enzyme makes cAMP | ||
| * Pathway activates cytoplasmic protein (ex: protein kinase) | * Pathway activates cytoplasmic protein (ex: protein kinase) | ||
| * Response may be stimulatory or inhibitory | * Response may be stimulatory or inhibitory | ||
| - | * Produce second messenger | + | * Produce second messenger IP3 and DAG: |
| - | * Produce second messenger | + | * Produce second messenger CA2+: |
| - | - **GPCR signaling/ | + | - GPCR signaling/ |
| - | | + | * Receptor Tyrosine Kinases (RTKs) |
| - | | + | * Kinases: Enzyme activated through phosphorylation and can activate a protein by catalyzing transfer of terminal phosphate from ATP to amino acid -- tyrosine with this kind |
| * Protein Kinase A: ser/thr kinase activated by elevated cAMP levels | * Protein Kinase A: ser/thr kinase activated by elevated cAMP levels | ||
| * Can receive growth factor → cell division → malfunctions = cancer | * Can receive growth factor → cell division → malfunctions = cancer | ||
| * Process summary | * Process summary | ||
| - | - **RTK receives signal:** ligand binds to its outer surface | + | - RTK receives signal: ligand binds to its outer surface |
| - | - **RTK forms a dimer:** two RTKs associate → form a pair (dimer) | + | - RTK forms a dimer: two RTKs associate → form a pair (dimer) |
| - | - **RTK is activated by autophosphorylation: | + | - RTK is activated by autophosphorylation: |
| - | - **Relay proteins are phosphorylated** **by RTK** | + | - Relay proteins are phosphorylated by RTK |
| - | - **Relay proteins initiate transduction pathway:** activated relay proteins are released → each relay protein can activate cellular response or initiate protein kinase transduction pathway → each cause different response | + | - Relay proteins initiate transduction pathway: activated relay proteins are released → each relay protein can activate cellular response or initiate protein kinase transduction pathway → each cause different response |
| - | - **RTK pathway deactivated by dephosphorylation or receptor protein packaged in vesicle (endocytosis)** | + | - RTK pathway deactivated by dephosphorylation or receptor protein packaged in vesicle (endocytosis) |
| * GPCRs vs RTKs Pathways | * GPCRs vs RTKs Pathways | ||
| - RTK directly responsible for initiating transduction pathway; GPCR indirectly activates transduction pathway via G protein and effector molecule | - RTK directly responsible for initiating transduction pathway; GPCR indirectly activates transduction pathway via G protein and effector molecule | ||
| - RTK can trigger multiple transduction pathway → direct lots of coordinated responses; | - RTK can trigger multiple transduction pathway → direct lots of coordinated responses; | ||
| - | * GPCR triggers single pathway → single response | + | * GPCR triggers single pathway → single response Ligand-Gated Ion Channels |
| - | | + | * Gated Ion receptor: transmembrane channel protein that opens/ |
| - | - **Ligand-gated ion receptor receives signal: ligand binds to outward face** | + | - Ligand-gated ion receptor receives signal: ligand binds to outward face |
| - | - **Receptor channel opens and ions pass through: Ligand binding caused 3D shape of receptor to change → open or close channel → allows a specific ion to pass thru** | + | - Receptor channel opens and ions pass through: Ligand binding caused 3D shape of receptor to change → open or close channel → allows a specific ion to pass thru |
| - | - **Ions initiate chemical response:** | + | - Ions initiate chemical response: |
| - | - **Ligand-gated ion receptor deactivated when ligand detaches or enzymatically degraded: Ligand binding site can be blocked by allosteric ligand or channel blocker** | + | - Ligand-gated ion receptor deactivated when ligand detaches or enzymatically degraded: Ligand binding site can be blocked by allosteric ligand or channel blocker |
| - | * There are also **voltage-gated ion receptors** that open or close in response to voltage differences across the membrane | + | * There are also voltage-gated ion receptors that open or close in response to voltage differences across the membrane |
| * Transmission of nerve impulse along neuron; Na+ enters → cell more + → if strong enough stimulates voltagegated Na+ channel and then a voltagegated K+ channel to open | * Transmission of nerve impulse along neuron; Na+ enters → cell more + → if strong enough stimulates voltagegated Na+ channel and then a voltagegated K+ channel to open | ||
| * Some controlled by electrical signals, some in organelle membrane (ER) | * Some controlled by electrical signals, some in organelle membrane (ER) | ||
| * Ligand can block binding to stop diseases or open channel to allow flow of CA+, NA+, or K+ | * Ligand can block binding to stop diseases or open channel to allow flow of CA+, NA+, or K+ | ||
| * Example: | * Example: | ||
| - | | + | * Acetylcholine: |
| * Does not enter cytoplasm | * Does not enter cytoplasm | ||
| * Acetylcholine binds to ligand-gated receptor molecules → opens gated channel → allows Na+ to enter cell → cells become more positive → change in membrane voltage (active potential) initiates nerve impulse → can stimulate muscle contraction | * Acetylcholine binds to ligand-gated receptor molecules → opens gated channel → allows Na+ to enter cell → cells become more positive → change in membrane voltage (active potential) initiates nerve impulse → can stimulate muscle contraction | ||
| Line 1752: | Line 1810: | ||
| * SECOND MESSENGERS | * SECOND MESSENGERS | ||
| * Small, non-protein molecules that spread through cell via diffusion and relay/ | * Small, non-protein molecules that spread through cell via diffusion and relay/ | ||
| - | * 2nd Messenger: | + | * 2nd Messenger: Cyclic AMP (cAMP) |
| - | * Created using **adenylyl cyclase** by cutting ATP and two phosphates | + | * Created using adenylyl cyclase by cutting ATP and two phosphates |
| * Can activate protein kinase→ Cell response | * Can activate protein kinase→ Cell response | ||
| - | * 2nd messenger: | + | * 2nd messenger: Ca+ |
| * Ca+ levels stimulate cellular response | * Ca+ levels stimulate cellular response | ||
| * Cell regulates concentration by actively transporting into ER and mitochondria | * Cell regulates concentration by actively transporting into ER and mitochondria | ||
| - | | + | * Signaling Cascade |
| * Many signal transduction pathways include protein modification and phosphorylation cascades | * Many signal transduction pathways include protein modification and phosphorylation cascades | ||
| - | | + | * Kinase cascade or phosphorylation cascade: Series of enzymatic reactions where a kinase enzyme phosphorylates molecules which phosphorylates another molecule, etc. |
| * Benefits: amplify so that small signal made bigger, better regulation/ | * Benefits: amplify so that small signal made bigger, better regulation/ | ||
| * Signaling cascades relay signals from receptors to cell targets → amplify incoming signals → result in appropriate cell response | * Signaling cascades relay signals from receptors to cell targets → amplify incoming signals → result in appropriate cell response | ||
| - | | + | * Scaffold Proteins: large relay proteins attached to each other which improve efficiency of signaling cascade by holding participating enzymes in close proximity |
| * Scaffolding also used to keep members of one signaling cascade isolated from members of another cascade | * Scaffolding also used to keep members of one signaling cascade isolated from members of another cascade | ||
| - | * [[https:// | + | * https:// |
| + | <img src=" | ||
| + | </ | ||
| + | <img src=" | ||
| + | </ | ||
| * Cell carries out specific behavior in response to an extracellular signal | * Cell carries out specific behavior in response to an extracellular signal | ||
| * Cell response depends on pathway taken that leads to nuclear or cytoplasmic response | * Cell response depends on pathway taken that leads to nuclear or cytoplasmic response | ||
| * Cellular response can change its behavior | * Cellular response can change its behavior | ||
| * Ex. yeast cells change shape when mating | * Ex. yeast cells change shape when mating | ||
| - | * Release | + | * Release Pheromones: externally released ligands for communication |
| * Muscle contraction, | * Muscle contraction, | ||
| * Gene expression depends on cell type and gender | * Gene expression depends on cell type and gender | ||
| Line 1779: | Line 1841: | ||
| * Ex. steroids: testosterone, | * Ex. steroids: testosterone, | ||
| * Process Summary | * Process Summary | ||
| - | - **Signaling molecule enters the cytoplasm: must be nonpolar** | + | - Signaling molecule enters the cytoplasm: must be nonpolar |
| - | - **Signaling molecule binds to intracellular receptor, activating it: sometimes activation triggers release of inhibitor that prevents receptor from functioning** | + | - Signaling molecule binds to intracellular receptor, activating it: sometimes activation triggers release of inhibitor that prevents receptor from functioning |
| - | - **Receptor-signaling molecule complex acts as a transcription factor: receptor-signal complex binds to DNA → promote or suppress transcription of genes** | + | - Receptor-signaling molecule complex acts as a transcription factor: receptor-signal complex binds to DNA → promote or suppress transcription of genes |
| - | - **Deactivation of pathway can occur when signaling molecules and receptor proteins are enzymatically degraded:** | + | - Deactivation of pathway can occur when signaling molecules and receptor proteins are enzymatically degraded: |
| - | | + | * The environment can elicit a cellular response. |
| * Signal transduction pathways influence how the cell responds to its environment | * Signal transduction pathways influence how the cell responds to its environment | ||
| * Environment is a major factor that influences which genes will be expressed; explains how the same set of genes can produce different kinds of structure of processes | * Environment is a major factor that influences which genes will be expressed; explains how the same set of genes can produce different kinds of structure of processes | ||
| - | | + | * Quorum sensing: bacteria secrete chemical messengers sensed by other bacteria that allow them to regulate specific pathways in response to population density |
| * Result in biofilms | * Result in biofilms | ||
| - | | + | * Benefits of Signal Transduction Pathways |
| - | - **Amplification: | + | - Amplification: |
| * Small amount of ligand results in large response, relay proteins amplify response and activate many enzymes | * Small amount of ligand results in large response, relay proteins amplify response and activate many enzymes | ||
| - | - **Control: signalling pathways give cells more control over accuracy of the response; All components must function properly → smaller chance that transductions might occur in error** | + | - Control: signalling pathways give cells more control over accuracy of the response; All components must function properly → smaller chance that transductions might occur in error |
| - | - **Multiplicity: | + | - Multiplicity: |
| - | | + | * Specificity of Response |
| * Specificity of pathway is bcuz cells have diff activated genes and proteins so can only bind to molecules with complementary structures which causes cells to respond to signals diff. | * Specificity of pathway is bcuz cells have diff activated genes and proteins so can only bind to molecules with complementary structures which causes cells to respond to signals diff. | ||
| * Variety and combination of different genes in cells & different structure of receptor result in different pathways taken | * Variety and combination of different genes in cells & different structure of receptor result in different pathways taken | ||
| Line 1799: | Line 1861: | ||
| * Cell can only respond if has receptor but pathway determines what response is | * Cell can only respond if has receptor but pathway determines what response is | ||
| * Some cells have more complex pathways but still have similar molecules | * Some cells have more complex pathways but still have similar molecules | ||
| - | | + | * Disease |
| * External signals influence how genes express information as transduction pathway distorted | * External signals influence how genes express information as transduction pathway distorted | ||
| * Ex: Bacteria secrete toxin that disrupts GPCR activity → GTP attached to G protein can’t be converted back to GDP → protein not deactivated & GPCR locked in active state → cell keeps making cAMP → water and Cl- continuously transported out of cell | * Ex: Bacteria secrete toxin that disrupts GPCR activity → GTP attached to G protein can’t be converted back to GDP → protein not deactivated & GPCR locked in active state → cell keeps making cAMP → water and Cl- continuously transported out of cell | ||
| - | | + | * General Summary |
| - | | + | * Step 1: Reception: Ligand binds to the receptor protein |
| - | | + | * Step 2: Signal Transduction Pathway: molecules communicating with each other, relaying and amplifying signal |
| - | | + | * Step 3: Cellular Response: Cell’s response to extracellular signals in the cytoplasm or nucleus, resulting in transcription from the DNA that creates desired proteins Examples provided in the video: Signal transduction may result in change in gene expression and cell function, which may alter phenotype or result in apoptosis |
| * Cytokines regulate gene expression to allow for cell replication and division | * Cytokines regulate gene expression to allow for cell replication and division | ||
| * Expression of the SRY gene triggers the male sexual development pathway in animals | * Expression of the SRY gene triggers the male sexual development pathway in animals | ||
| Line 1813: | Line 1875: | ||
| * Cell undergoes programmed cell death where cell components are orderly disposed of | * Cell undergoes programmed cell death where cell components are orderly disposed of | ||
| * Cell shrinks and then lysosomes’ hydrolytic proteins (proteases, amylases [carbs], nucleases, etc.) fragment DNA and organelles that are packaged vesicles digested by white blood cells | * Cell shrinks and then lysosomes’ hydrolytic proteins (proteases, amylases [carbs], nucleases, etc.) fragment DNA and organelles that are packaged vesicles digested by white blood cells | ||
| - | | + | * Caspases: main proteases, enzymes that cut up proteins and carry out apoptosis. |
| * Reasons | * Reasons | ||
| * Allow for the normal development and maintenance of an organism by selectively killing infected, damaged, or finished cells in an orderly way so dying cell doesn' | * Allow for the normal development and maintenance of an organism by selectively killing infected, damaged, or finished cells in an orderly way so dying cell doesn' | ||
| * DNA damage (mutation) in nucleus | * DNA damage (mutation) in nucleus | ||
| - | * Release of **extracellular death signal** that binds to receptor and initiates phosphorylation cascade that activates nucleases (nucleic acids) and proteases (protein) that break down the cell | + | * Release of extracellular death signal that binds to receptor and initiates phosphorylation cascade that activates nucleases (nucleic acids) and proteases (protein) that break down the cell |
| * Protein misfolding in the nucleus (ex. alzheimers) | * Protein misfolding in the nucleus (ex. alzheimers) | ||
| * Mutations cause cancer, so apoptosis helps prevent this | * Mutations cause cancer, so apoptosis helps prevent this | ||
| Line 1825: | Line 1887: | ||
| * A change/ | * A change/ | ||
| * Chemicals that interfere with any component of the signaling pathway may activate or inhibit it: toxins, antibiotics | * Chemicals that interfere with any component of the signaling pathway may activate or inhibit it: toxins, antibiotics | ||
| - | * [[https:// | + | * https:// |
| - | * Organisms use feedback mechanisms to **maintain their internal environments and respond to internal and external environmental changes.** | + | <img src=" |
| + | </ | ||
| + | * Organisms use feedback mechanisms to maintain their internal environments and respond to internal and external environmental changes. | ||
| * Negative feedback mechanisms maintain homeostasis | * Negative feedback mechanisms maintain homeostasis | ||
| * Tend to push to stability after abnormality, | * Tend to push to stability after abnormality, | ||
| Line 1832: | Line 1896: | ||
| * Ex. Temperature regulation, blood glucose & calcium levels, | * Ex. Temperature regulation, blood glucose & calcium levels, | ||
| * Product accumulates, | * Product accumulates, | ||
| - | | + | * Positive Feedback and Homeostasis |
| * Positive feedback mechanisms amplify responses and processes in organisms. | * Positive feedback mechanisms amplify responses and processes in organisms. | ||
| * Move system away from starting state; tend to push organisms to extreme behaviors | * Move system away from starting state; tend to push organisms to extreme behaviors | ||
| * Still act to maintain homeostasis (less common); occur in abnormal situations and increase abnormality so situation becomes normal | * Still act to maintain homeostasis (less common); occur in abnormal situations and increase abnormality so situation becomes normal | ||
| * Ex. pregnancy contractions, | * Ex. pregnancy contractions, | ||
| - | * [[https:// | + | * https:// |
| + | <img src=" | ||
| + | </ | ||
| * Disrupt homeostasis → Diabetes: cells don’t work so when glucose lvl increases, no insulin made to regulate | * Disrupt homeostasis → Diabetes: cells don’t work so when glucose lvl increases, no insulin made to regulate | ||
| - | | + | * Phosphorylation |
| * The addition of a phosphate group to one or more sites on the protein, which alters the activity of the protein | * The addition of a phosphate group to one or more sites on the protein, which alters the activity of the protein | ||
| * Usually exchanges hydroxyl R group with phosphate | * Usually exchanges hydroxyl R group with phosphate | ||
| * Switches proteins on → increases potential energy and ability for chemical work | * Switches proteins on → increases potential energy and ability for chemical work | ||
| * Protein phosphorylation involved with regulation of transcription, | * Protein phosphorylation involved with regulation of transcription, | ||
| - | * The transfer of the phosphate group is catalyzed by the **kinase** enzyme | + | * The transfer of the phosphate group is catalyzed by the kinase enzyme |
| * Cells contain many different kinases that phosphorylate different targets | * Cells contain many different kinases that phosphorylate different targets | ||
| - | | + | * The reverse: after a protein has been “activated”, |
| * Turns of kinase cascades | * Turns of kinase cascades | ||
| =====Unit 4: The Cell Cycle===== | =====Unit 4: The Cell Cycle===== | ||
| - | **4.6: Cell Cycle Key Overview** | + | 4.6: Cell Cycle Key Overview |
| * Eukaryotic cells divide and transmit genetic information via two highly regulated processes: | * Eukaryotic cells divide and transmit genetic information via two highly regulated processes: | ||
| Line 1857: | Line 1923: | ||
| * Eukaryotic cell division consists of: | * Eukaryotic cell division consists of: | ||
| - | | + | * Mitosis: the division of the genetic material in the nucleus |
| * Ensures the transfer of a complete genome from a parent cell to two genetically identical daughter cells | * Ensures the transfer of a complete genome from a parent cell to two genetically identical daughter cells | ||
| - | | + | * Cytokinesis: |
| - | | + | * Genome: all of organisms genetic material (chromosome) which each cell has a copy of |
| * Function: stores and express cells information that directs its structure, function, and growth and development | * Function: stores and express cells information that directs its structure, function, and growth and development | ||
| * DNA packaged into chromosomes which makes replication/ | * DNA packaged into chromosomes which makes replication/ | ||
| - | | + | * Chromatins: unwound complex of DNA and proteins in interphase, during mitosis condense and become a chromosome |
| - | | + | * Sister chromatid: two identical chromatids joined at one centromere → make up 1 mitotic chromosome |
| - | | + | * Kinetochore: |
| * Every diploid organism has homologous chromosomes: | * Every diploid organism has homologous chromosomes: | ||
| * One from mom and one from dad | * One from mom and one from dad | ||
| ====Mitosis Overview==== | ====Mitosis Overview==== | ||
| - | | + | * Cell Cycle: is a highly regulated series of events for the growth and reproduction of eukaryotic cells |
| * Three stages: Interphase, Mitosis, & Cytokinesis | * Three stages: Interphase, Mitosis, & Cytokinesis | ||
| * Smaller cells better because easier to coordinate chromosomes and microtubules with less ATP | * Smaller cells better because easier to coordinate chromosomes and microtubules with less ATP | ||
| * DNA content doubles during Interphase (S phase) and halves during mitosis | * DNA content doubles during Interphase (S phase) and halves during mitosis | ||
| - | * [[https:// | + | * https:// |
| + | <img src=" | ||
| + | </ | ||
| * Majority of cell cycle, split into 3 phases | * Majority of cell cycle, split into 3 phases | ||
| * All have metabolic activity & growth | * All have metabolic activity & growth | ||
| - | | + | * G1 Phase |
| * Metabolic activity and growth; one chromatid | * Metabolic activity and growth; one chromatid | ||
| - | | + | * S Phase |
| * DNA replication; | * DNA replication; | ||
| - | | + | * G2 Phase |
| * Prepares for cell division | * Prepares for cell division | ||
| - | | + | * M phase |
| * Mitosis and cytokinesis | * Mitosis and cytokinesis | ||
| - | | + | * The G0 Cycle |
| - | * If the cell does not receive the go ahead signal, it will exit the cycle, switching to a nondividing state called the **G0 phase**. | + | * If the cell does not receive the go ahead signal, it will exit the cycle, switching to a nondividing state called the G0 phase. |
| * Can re-enter the cell cycle in response to appropriate cues. | * Can re-enter the cell cycle in response to appropriate cues. | ||
| * Nondividing cells may exit the cell cycle or be held at a particular stage in it | * Nondividing cells may exit the cell cycle or be held at a particular stage in it | ||
| - | * How Does Mitosis Produce 2 Identical Daughter Cells [[https:// | + | * How Does Mitosis Produce 2 Identical Daughter Cells https:// |
| + | <img src=" | ||
| + | </ | ||
| * DNA Replication (Interphase) and separation of chromatids (Anaphase) | * DNA Replication (Interphase) and separation of chromatids (Anaphase) | ||
| * Once duplicated, a chromosome consists of two sister chromatids, connected along their entire length | * Once duplicated, a chromosome consists of two sister chromatids, connected along their entire length | ||
| * Before a cell divides, sister chromatids become individual chromosomes → ensure that daughter cells get a complete/ | * Before a cell divides, sister chromatids become individual chromosomes → ensure that daughter cells get a complete/ | ||
| - | * Sister chromatids attached by cohesins and held most tightly by **centromere:** region of repetitive DNA sequences and proteins | + | * Sister chromatids attached by cohesins and held most tightly by centromere: region of repetitive DNA sequences and proteins |
| * Count chromosomes by number of centromeres but chromatids are double | * Count chromosomes by number of centromeres but chromatids are double | ||
| - | | + | * MITOTIC SPINDLE |
| * Consists of mitotic fibers, centrosomes, | * Consists of mitotic fibers, centrosomes, | ||
| * Fibers made up of microtubules and proteins: control chromosome movement | * Fibers made up of microtubules and proteins: control chromosome movement | ||
| * Elongate by adding tubulin | * Elongate by adding tubulin | ||
| - | | + | * Asters: microtubules that hold together two centrioles to make a centrosome |
| * Spindle is complete when asters elongate and touch membrane | * Spindle is complete when asters elongate and touch membrane | ||
| * Two kinds of microtubules: | * Two kinds of microtubules: | ||
| - | | + | * Kinetochore Microtubules: |
| - | | + | * Non-kinetochore microtubules: |
| ====Mitosis: | ====Mitosis: | ||
| * G2 of Interphase The last part of interphase: | * G2 of Interphase The last part of interphase: | ||
| Line 1910: | Line 1980: | ||
| * Each centrosomes contain two centrioles | * Each centrosomes contain two centrioles | ||
| * duplicated chromosomes but not condensed/ | * duplicated chromosomes but not condensed/ | ||
| - | * [[https:// | + | * https:// |
| + | <img src=" | ||
| + | </ | ||
| * Nucleoli gone, nuclear envelope thinning | * Nucleoli gone, nuclear envelope thinning | ||
| * Chromatin fibers condense into tightly coiled and visible chromosomes | * Chromatin fibers condense into tightly coiled and visible chromosomes | ||
| * Mitotic spindle begins to form by adding tubulin units to microtubules | * Mitotic spindle begins to form by adding tubulin units to microtubules | ||
| * Centrosomes move away by lengthening microtubules | * Centrosomes move away by lengthening microtubules | ||
| - | * [[https:// | + | * https:// |
| + | <img src=" | ||
| + | </ | ||
| * Nuclear envelope gone | * Nuclear envelope gone | ||
| * Kinetochores form at centromere of each chromatid | * Kinetochores form at centromere of each chromatid | ||
| * 2 types of microtubules form and go into nuclear area | * 2 types of microtubules form and go into nuclear area | ||
| - | * [[https:// | + | * https:// |
| + | <img src=" | ||
| + | </ | ||
| * Chromosomes line up at metaphase plane (equidistant between spindles two poles) | * Chromosomes line up at metaphase plane (equidistant between spindles two poles) | ||
| - | * [[https:// | + | * https:// |
| + | <img src=" | ||
| + | </ | ||
| * Shortest stage | * Shortest stage | ||
| * Sister chromatids become individual chromosomes when cohesion proteins are cleaved → are reeled to opposite poles as microtubules shorten by uncoupling tubulin units | * Sister chromatids become individual chromosomes when cohesion proteins are cleaved → are reeled to opposite poles as microtubules shorten by uncoupling tubulin units | ||
| - | * [[https:// | + | * https:// |
| + | <img src=" | ||
| + | </ | ||
| * Two daughter nucleoli form from parent fragments and endomembrane system; one at each pole | * Two daughter nucleoli form from parent fragments and endomembrane system; one at each pole | ||
| * chromo decondense & become chromatin, microtubules depolymerize | * chromo decondense & become chromatin, microtubules depolymerize | ||
| * nucleoli & envelope reappears | * nucleoli & envelope reappears | ||
| * cleavage furrow begins to separate the two into sister cells | * cleavage furrow begins to separate the two into sister cells | ||
| - | * [[https:// | + | * https:// |
| - | * Animal cells: carry out cytokinesis by forming a **cleavage furrow:** groove that forms as purse strings are tightened | + | <img src=" |
| + | </ | ||
| + | * Animal cells: carry out cytokinesis by forming a cleavage furrow: groove that forms as purse strings are tightened | ||
| * Actin filaments (microfilaments) form a ring inside plasma membrane between two nuclei → microfilaments shorten → stimulate cell contraction that causes cell to pinch inwards until divides | * Actin filaments (microfilaments) form a ring inside plasma membrane between two nuclei → microfilaments shorten → stimulate cell contraction that causes cell to pinch inwards until divides | ||
| - | * [[https:// | + | * https:// |
| - | * Plants cells: cell wall too rigid so can’t pinch inward, instead vesicles from golgi move to middle and make a **cell plate** which fuses with cell membrane and produces 2 daughter cells | + | <img src=" |
| - | * [[https:// | + | </ |
| + | * Plants cells: cell wall too rigid so can’t pinch inward, instead vesicles from golgi move to middle and make a cell plate which fuses with cell membrane and produces 2 daughter cells | ||
| + | * https:// | ||
| + | <img src=" | ||
| + | </ | ||
| - Asexual Reproduction: | - Asexual Reproduction: | ||
| - Growth and development: | - Growth and development: | ||
| - Tissue repair: replace old cells, injuries to a cell can be repaired by replicating the cell in a healthy form | - Tissue repair: replace old cells, injuries to a cell can be repaired by replicating the cell in a healthy form | ||
| ====Regulations of the Cell Cycle==== | ====Regulations of the Cell Cycle==== | ||
| - | | + | * Internal Regulation of the Cell Cycle |
| // | // | ||
| - | - **Surface-to-volume ratio: when surface area is small compared to volume → cell growth stops or cell division begins** | + | - Surface-to-volume ratio: when surface area is small compared to volume → cell growth stops or cell division begins |
| - | - **Genome-to-volume ratio: ability of genome to function is limited by by finite amount of genetic material** | + | - Genome-to-volume ratio: ability of genome to function is limited by by finite amount of genetic material |
| * Cell grows → volume increases but genome size stays constant → G/V decreases → cell doesn’t have enough material to regulate cellular activities | * Cell grows → volume increases but genome size stays constant → G/V decreases → cell doesn’t have enough material to regulate cellular activities | ||
| * Factors that regulate cell cycle become distorted → can lose control of production of growth enzymes → cells become cancerous | * Factors that regulate cell cycle become distorted → can lose control of production of growth enzymes → cells become cancerous | ||
| - | | + | * Molecular Regulation of Cell Cycle |
| - | - **Interactions between cyclins and cyclin-dependent kinases regulate the cell cycle & control checkpoints** | + | - Interactions between cyclins and cyclin-dependent kinases regulate the cell cycle & control checkpoints |
| - | | + | * Cyclin: proteins whose levels fluctuate in cell cycle (highest at G2) |
| * Function: phosphorylates (& combines) CDKs to regulate the cell cycle | * Function: phosphorylates (& combines) CDKs to regulate the cell cycle | ||
| - | | + | * CDKs: kinase enzyme whose levels remain constant; activated by cyclins thru phosphorylation |
| * Function: prepares for cell division & responsible for advancing cell past cell cycle checkpoints | * Function: prepares for cell division & responsible for advancing cell past cell cycle checkpoints | ||
| - | * CDKs + Cyclins= Cyclin-CDK complexes such as **Maturation Promoting Factor (MPF)** | + | * CDKs + Cyclins= Cyclin-CDK complexes such as Maturation Promoting Factor (MPF) |
| * CDKs increase in lvls with cyclins | * CDKs increase in lvls with cyclins | ||
| - | * [[https:// | + | * https:// |
| + | <img src=" | ||
| + | </ | ||
| * Shows that it peaks at mitosis & drops again at every checkpoint | * Shows that it peaks at mitosis & drops again at every checkpoint | ||
| * Red Line: Cyclin | * Red Line: Cyclin | ||
| * It “cycles”: | * It “cycles”: | ||
| - | | + | * Maturation Promoting Factor |
| * Cyclin-CDK complex that advances cell cycle through G2 checkpoint by phosphorylating and activating proteins involved with chromosome condensation, | * Cyclin-CDK complex that advances cell cycle through G2 checkpoint by phosphorylating and activating proteins involved with chromosome condensation, | ||
| * Is self-regulating because starts process that destroys its own cyclin | * Is self-regulating because starts process that destroys its own cyclin | ||
| - | - **Checkpoints: | + | - Checkpoints: |
| * Each checkpoint has a specific cyclin-cdk that advances the cell past it | * Each checkpoint has a specific cyclin-cdk that advances the cell past it | ||
| - | | + | * G1 checkpoint\ -\ committed step: leads to cell division\ - checks cell size, growth factors, nutrients, and the environment\ - checks DNA, if damaged → repair → if failed triggers apoptosis \ \ %%%%environment: |
| - | | + | * Growth factors: proteins released by certain cells that stimulate other cells to divide |
| - | | + | * Density dependent inhibition: crowded cells stop dividing, stop past one layer |
| * This gives the currently existing cells a better chance to survive | * This gives the currently existing cells a better chance to survive | ||
| - | | + | * Anchorage dependence: cells must be attached to a substrate in order to divide |
| * Ex: flat surface of neighboring cell or dish | * Ex: flat surface of neighboring cell or dish | ||
| * Cancer cells exhibit neither density dependence or anchorage dependence | * Cancer cells exhibit neither density dependence or anchorage dependence | ||
| ====CANCER & Disruptions to the Cell Cycle==== | ====CANCER & Disruptions to the Cell Cycle==== | ||
| - | | + | * Disruptions to cell cycle or inability to carry out apoptosis can lead to cancer |
| - | | + | * Cancer Cells |
| - | | + | * Cancer: unregulated/ |
| * Normal cells become cancer cells by the accumulation of mutations affecting proto-oncogenes and tumor-suppressor genes | * Normal cells become cancer cells by the accumulation of mutations affecting proto-oncogenes and tumor-suppressor genes | ||
| * If gene mutates, protein product (often enzyme) changes which changes its function and causes improper regulation | * If gene mutates, protein product (often enzyme) changes which changes its function and causes improper regulation | ||
| Line 1980: | Line 2068: | ||
| * Do not display anchorage dependence of density-dependence (divide past one layer) | * Do not display anchorage dependence of density-dependence (divide past one layer) | ||
| * Evade signals that trigger apoptosis when something goes wrong | * Evade signals that trigger apoptosis when something goes wrong | ||
| - | | + | * Proto-oncogenes: |
| - | | + | * Oncogenes: dysfunctional, |
| - | | + | * Transformation: |
| * Causes for Oncogenes | * Causes for Oncogenes | ||
| - | - **Gene Translocations: | + | - Gene Translocations: |
| - | * [[Untitled_a1baf95c2be74fad95ea92c3882c2c8f: | + | * Untitled_a1baf95c2be74fad95ea92c3882c2c8f: |
| - | - **Gene Amplification: | + | - Gene Amplification: |
| - | - **Epigenetic: abnormal chromatin condensation → proto-oncogene expressed at the wrong time or amount** | + | - Epigenetic: abnormal chromatin condensation → proto-oncogene expressed at the wrong time or amount |
| - | - **Point Mutations:** | + | - Point Mutations: |
| - In promoter, enhancer/ | - In promoter, enhancer/ | ||
| - Within gene → could code for protein that is more/less to degradation | - Within gene → could code for protein that is more/less to degradation | ||
| Line 1994: | Line 2082: | ||
| * Cannot directly inherit cancer cuz need more than one oncogene but can be predisposed by being passed down a couple | * Cannot directly inherit cancer cuz need more than one oncogene but can be predisposed by being passed down a couple | ||
| * Major difference between the two tumors/ | * Major difference between the two tumors/ | ||
| - | | + | * Benign: ~5 mutations, generate mass, abnormal but NOT cancerous cuz do not spread→ stay at the original site due to specificity of structure |
| - | | + | * Malignant: impairs the function of organ it’s in, cancerous ~7 mutations, |
| - | | + | * Can metastasize: |
| * Release their own growth factors and cause blood vessels to grow towards it so it can nourish and spread | * Release their own growth factors and cause blood vessels to grow towards it so it can nourish and spread | ||
| * Causes for changes in malignant tumours: excessive buildup, altered metabolism, cell surface changes, secrete sig. molecules | * Causes for changes in malignant tumours: excessive buildup, altered metabolism, cell surface changes, secrete sig. molecules | ||
| * Treatments | * Treatments | ||
| * Radiation that harms localized tumours more than normal cells | * Radiation that harms localized tumours more than normal cells | ||
| - | | + | * Chemotherapy: |
| - | | + | * GENES AND CANCER |
| * Each cancer is caused by a different set of mutated genes, so there is no possible cure-all | * Each cancer is caused by a different set of mutated genes, so there is no possible cure-all | ||
| * Genetic Alterations and Cancer | * Genetic Alterations and Cancer | ||
| - | | + | * Tumor-suppressor genes: genes that can inhibit cell division and prevent cancer from developing (growth-inhibiting) |
| * Most mutated → stimulated cell division | * Most mutated → stimulated cell division | ||
| * Protein products repair DNA, control adhesion, and regulate cell signalling pathways that inhibit cell cycle | * Protein products repair DNA, control adhesion, and regulate cell signalling pathways that inhibit cell cycle | ||
| * Defective version of a protein in an inhibitory pathway (p53) fails to act as a tumour-suppressor. | * Defective version of a protein in an inhibitory pathway (p53) fails to act as a tumour-suppressor. | ||
| - | * Interference with Normal Cell Signaling Pathways factor With P53 Transcription Factor: | + | * Interference with Normal Cell Signaling Pathways factor With P53 Transcription Factor: Untitled_a1baf95c2be74fad95ea92c3882c2c8f: |
| * Activated by signal transduction pathway when DNA is damaged from external factors and promotes transcription of cycle-inhibiting proteins | * Activated by signal transduction pathway when DNA is damaged from external factors and promotes transcription of cycle-inhibiting proteins | ||
| - | * Without P53 Transcription Factor: | + | * Without P53 Transcription Factor: https:// |
| + | <img src=" | ||
| + | </ | ||
| * If gene mutates, damaged cells can proliferate and spread, becoming tumor | * If gene mutates, damaged cells can proliferate and spread, becoming tumor | ||
| * Increased cell division | * Increased cell division | ||
| - | | + | * Ras gene: Untitled_a1baf95c2be74fad95ea92c3882c2c8f: |
| * Gene that codes for G protein that relays growth factor message | * Gene that codes for G protein that relays growth factor message | ||
| * When gene is mutated, causes ras protein to be overexpressed and cell cycle overstimulated | * When gene is mutated, causes ras protein to be overexpressed and cell cycle overstimulated | ||
| - | * In **sexual reproduction** two parents produce offspring with a unique combination of genes. | + | * In sexual reproduction two parents produce offspring with a unique combination of genes. |
| * In eu. results in gamete formation | * In eu. results in gamete formation | ||
| * Increases genetic variation bcuz random mutations can be shuffled between organisms | * Increases genetic variation bcuz random mutations can be shuffled between organisms | ||
| - | * **Zygote:** fertilized egg, diploid | + | * Zygote: fertilized egg, diploid |
| * Brief stage and then mitosis of zygote results in all of your body cells | * Brief stage and then mitosis of zygote results in all of your body cells | ||
| - | * **Haploid (n):** cells with half of the number of chromosomes (ex. n=23) | + | * Haploid (n): cells with half of the number of chromosomes (ex. n=23) |
| - | * **Gametes:** haploid sperm and egg created thru meiosis and pass on genes; not made by mitosis cuz if they did number of chromosomes would keep doubling | + | * Gametes: haploid sperm and egg created thru meiosis and pass on genes; not made by mitosis cuz if they did number of chromosomes would keep doubling |
| * Gametes receive one allele per trait | * Gametes receive one allele per trait | ||
| * Number of alleles determines how many different types of gametes | * Number of alleles determines how many different types of gametes | ||
| - | * **Diploid (2n): cells with two sets of chromosomes (2n=46)** | + | * Diploid (2n): cells with two sets of chromosomes (2n=46) |
| - | | + | * Somatic Cells: (normal) body cells, that have 46 chromosomes (23 pairs), half from mom half from dad |
| - | * **Homologous chromosomes(homologs): | + | * Homologous chromosomes(homologs): |
| + | <img src=" | ||
| + | </ | ||
| * One maternal and other paternal | * One maternal and other paternal | ||
| - | * **Allele:** different versions of the same gene controlling a trait caused by mutations→ contribute to overall phenotype | + | * Allele: different versions of the same gene controlling a trait caused by mutations→ contribute to overall phenotype |
| * Organism can only inherit 2 alleles for one trait | * Organism can only inherit 2 alleles for one trait | ||
| - | * **Locus (loci):** exact location of a gene on a chromosome | + | * Locus (loci): exact location of a gene on a chromosome |
| - | * **Tetrad:** Made up of two pairs of sister chromatids that have synapsed | + | * Tetrad: Made up of two pairs of sister chromatids that have synapsed |
| - | * **Karyotype:** picture showing 23 pairs of chromosomes (usually at metaphase) | + | * Karyotype: picture showing 23 pairs of chromosomes (usually at metaphase) |
| - | | + | * Autosomal pairs (22): all of the genes for normal traits |
| - | | + | * Sex chromosomes (23rd): determine sex, XY male and XX female |
| * Organism vs Organism: | * Organism vs Organism: | ||
| * Organisms differ in number of chromosome and whether diploid or haploid is dominant | * Organisms differ in number of chromosome and whether diploid or haploid is dominant | ||
| - | * **Animals** are mainly diploid because their body cells are somatic and not germline | + | * Animals are mainly diploid because their body cells are somatic and not germline |
| - | * **Fungi Life Cycle:** are usually haploid but most form temporary diploid structures for sexual reproduction | + | * Fungi Life Cycle: are usually haploid but most form temporary diploid structures for sexual reproduction |
| * Can’t cut one set of chromosomes in half so they do not have meiosis during haploid | * Can’t cut one set of chromosomes in half so they do not have meiosis during haploid | ||
| - | * **Plant Life Cycle:** both haploid and diploid split equally so there is no dominant stage (multicellular) | + | * Plant Life Cycle: both haploid and diploid split equally so there is no dominant stage (multicellular) |
| - | | + | * Alternation of generations: |
| - | | + | * Sporophyte: multicellular diploid plant Gametophyte: |
| * Gametophyte mitosis directly leads to the formation of gametes | * Gametophyte mitosis directly leads to the formation of gametes | ||
| * ex. A diploid plant (sporophyte) produces, by meiosis, a spore that gives rise to a multicellular gametophyte | * ex. A diploid plant (sporophyte) produces, by meiosis, a spore that gives rise to a multicellular gametophyte | ||
| Line 2051: | Line 2143: | ||
| =====Sexual Life Cycle: | =====Sexual Life Cycle: | ||
| alteration of halving and doubling chromosome count in each generation | alteration of halving and doubling chromosome count in each generation | ||
| - | * In **sexual reproduction** two parents produce offspring with a unique combination of genes. | + | * In sexual reproduction two parents produce offspring with a unique combination of genes. |
| * In eu. results in gamete formation | * In eu. results in gamete formation | ||
| * Increases genetic variation bcuz random mutations can be shuffled between organisms | * Increases genetic variation bcuz random mutations can be shuffled between organisms | ||
| - | * **Zygote:** fertilized egg, diploid | + | * Zygote: fertilized egg, diploid |
| * Brief stage and then mitosis of zygote results in all of your body cells | * Brief stage and then mitosis of zygote results in all of your body cells | ||
| - | * **Haploid (n):** cells with half of the number of chromosomes (ex. n=23) | + | * Haploid (n): cells with half of the number of chromosomes (ex. n=23) |
| - | * **Gametes:** haploid sperm and egg created thru meiosis and pass on genes; not made by mitosis cuz if they did number of chromosomes would keep doubling | + | * Gametes: haploid sperm and egg created thru meiosis and pass on genes; not made by mitosis cuz if they did number of chromosomes would keep doubling |
| * Gametes receive one allele per trait | * Gametes receive one allele per trait | ||
| * Number of alleles determines how many different types of gametes | * Number of alleles determines how many different types of gametes | ||
| - | * **Diploid (2n): cells with two sets of chromosomes (2n=46)** | + | * Diploid (2n): cells with two sets of chromosomes (2n=46) |
| - | | + | * Somatic Cells: (normal) body cells, that have 46 chromosomes (23 pairs), half from mom half from dad |
| - | * **Homologous chromosomes(homologs): | + | * Homologous chromosomes(homologs): |
| + | <img src=" | ||
| + | </ | ||
| * One maternal and other paternal | * One maternal and other paternal | ||
| - | * **Allele:** different versions of the same gene controlling a trait caused by mutations→ contribute to overall phenotype | + | * Allele: different versions of the same gene controlling a trait caused by mutations→ contribute to overall phenotype |
| * Organism can only inherit 2 alleles for one trait | * Organism can only inherit 2 alleles for one trait | ||
| - | * **Locus (loci):** exact location of a gene on a chromosome | + | * Locus (loci): exact location of a gene on a chromosome |
| - | * **Tetrad:** Made up of two pairs of sister chromatids that have synapsed | + | * Tetrad: Made up of two pairs of sister chromatids that have synapsed |
| - | * **Karyotype:** picture showing 23 pairs of chromosomes (usually at metaphase) | + | * Karyotype: picture showing 23 pairs of chromosomes (usually at metaphase) |
| - | | + | * Autosomal pairs (22): all of the genes for normal traits |
| - | | + | * Sex chromosomes (23rd): determine sex, XY male and XX female |
| * Organism vs Organism: | * Organism vs Organism: | ||
| * Organisms differ in number of chromosome and whether diploid or haploid is dominant | * Organisms differ in number of chromosome and whether diploid or haploid is dominant | ||
| - | * **Animals** are mainly diploid because their body cells are somatic and not germline | + | * Animals are mainly diploid because their body cells are somatic and not germline |
| - | * **Fungi Life Cycle:** are usually haploid but most form temporary diploid structures for sexual reproduction | + | * Fungi Life Cycle: are usually haploid but most form temporary diploid structures for sexual reproduction |
| * Can’t cut one set of chromosomes in half so they do not have meiosis during haploid | * Can’t cut one set of chromosomes in half so they do not have meiosis during haploid | ||
| - | * **Plant Life Cycle:** both haploid and diploid split equally so there is no dominant stage (multicellular) | + | * Plant Life Cycle: both haploid and diploid split equally so there is no dominant stage (multicellular) |
| - | | + | * Alternation of generations: |
| - | | + | * Sporophyte: multicellular diploid plant Gametophyte: |
| * Gametophyte mitosis directly leads to the formation of gametes | * Gametophyte mitosis directly leads to the formation of gametes | ||
| * ex. A diploid plant (sporophyte) produces, by meiosis, a spore that gives rise to a multicellular gametophyte | * ex. A diploid plant (sporophyte) produces, by meiosis, a spore that gives rise to a multicellular gametophyte | ||
| ====Meiosis: | ====Meiosis: | ||
| - | [[Untitled_a1baf95c2be74fad95ea92c3882c2c8f: | + | Untitled_a1baf95c2be74fad95ea92c3882c2c8f: |
| - | | + | * Meiosis: specialized cell division that yields 4 nonidentical, |
| * Only occurs specialized (diploid) cells like testes & ovaries in humans to make sperm and egg | * Only occurs specialized (diploid) cells like testes & ovaries in humans to make sperm and egg | ||
| - | * Involves | + | * Involves two rounds of division (meiosis 1 & 2) |
| - | * Purpose is to **produce genetic variation in gametes;** process that ensures each gamete receives both maternal and paternal chromosomes | + | * Purpose is to produce genetic variation in gametes; process that ensures each gamete receives both maternal and paternal chromosomes |
| - | | + | * Meiosis 1 and Meiosis 2: Process Overview |
| * Meiosis 1: focuses on the separation of homologous chromosomes | * Meiosis 1: focuses on the separation of homologous chromosomes | ||
| * Meiosis 2: separate sister chromatids (analogous to mitosis) | * Meiosis 2: separate sister chromatids (analogous to mitosis) | ||
| - | | + | * Meiosis 1: Detailed Process Prophase 1 Metaphase 1 Chromatin begin to condense into chromosomes\ Homologs pair up; there are 2 of these, called\ Tetrads\ • Crossing over occurs\ Homologous chromosomes/ |
| - | | + | * Synapsis: Homologous chromosome pair with each other |
| - | | + | * Allows for crossing over |
| - | | + | * Crossing Over: Chromosome from each parent align in a way so DNA sequences cross over and exchange genetic material → combines maternal and paternal alleles into single chromo (recombinant chromosome) → increased genetic diversity among gametes |
| * When homologs cross over, specific proteins break/ | * When homologs cross over, specific proteins break/ | ||
| * Physical constraints: | * Physical constraints: | ||
| - | | + | * Chiasmata (sing. Chiasma): Point of contact between two nonsister chromatids where crossing over will occur https:// |
| + | <img src=" | ||
| + | </ | ||
| * Holds homologous pairs together due to sister chromatid cohesion | * Holds homologous pairs together due to sister chromatid cohesion | ||
| * Absence leads to aneuploidy | * Absence leads to aneuploidy | ||
| * Chromosomes that look like its parent (1 and 4) parental | * Chromosomes that look like its parent (1 and 4) parental | ||
| * Chromosomes that are crossed over: ( 2 and 3): recombinant | * Chromosomes that are crossed over: ( 2 and 3): recombinant | ||
| - | | + | * Mitosis vs Meiosis |
| * Both have separation of sister chromatids | * Both have separation of sister chromatids | ||
| - | * [[Untitled_a1baf95c2be74fad95ea92c3882c2c8f: | + | * Untitled_a1baf95c2be74fad95ea92c3882c2c8f: |
| + | <img src=" | ||
| + | </ | ||
| * When genes mutate, they take multiple forms with each gene slightly differing in sequence of base DNA (alleles) | * When genes mutate, they take multiple forms with each gene slightly differing in sequence of base DNA (alleles) | ||
| - | | + | * Three mechanisms to contribute to genetic variation |
| - | | + | * Independent assortment of chromosomes |
| * Gametes get random chromosome from parent → many combinations | * Gametes get random chromosome from parent → many combinations | ||
| * The number of combinations possible when chromosomes assort independently into gametes is 2^(n), where n is the haploid number. | * The number of combinations possible when chromosomes assort independently into gametes is 2^(n), where n is the haploid number. | ||
| - | | + | * Crossing over |
| * Creates chromosomes w/ new combination of alleles + mixes up pre-existing genes and mutations | * Creates chromosomes w/ new combination of alleles + mixes up pre-existing genes and mutations | ||
| - | | + | * Random fertilization: |
| - | | + | * Fertilization |
| - | * Occurs when sperm penetrates the membrane of egg → combine maternal and paternal genes in a fertilized egg (zygote) [offspring with both maternal & paternal traits]→ series of **cleavage** divisions (rapid cell division w/o cell growth) forms fetus | + | * Occurs when sperm penetrates the membrane of egg → combine maternal and paternal genes in a fertilized egg (zygote) [offspring with both maternal & paternal traits]→ series of cleavage divisions (rapid cell division w/o cell growth) forms fetus |
| * Process increases genetic variation in populations by creating new combinations of alleles in zygotes | * Process increases genetic variation in populations by creating new combinations of alleles in zygotes | ||
| * Fertilization restores diploid number here & allows process of meiosis to be repeated | * Fertilization restores diploid number here & allows process of meiosis to be repeated | ||
| =====Unit 5: Heredity===== | =====Unit 5: Heredity===== | ||
| - | **Unit 5.3 Mendelian Genetics** | + | Unit 5.3 Mendelian Genetics |
| Vocabulary: | Vocabulary: | ||
| - | | + | * Genotype: the set of alleles carried by an organism |
| - | | + | * Phenotype: an organism’s observable features; expression of alleles |
| - | | + | * Characters: a heritable feature (a gene) which varies. (ie. hair colour) |
| - | | + | * Trait: different form of a character (ex. brown) |
| * Variant traits are called alleles. A gene can have multiple alleles | * Variant traits are called alleles. A gene can have multiple alleles | ||
| - | | + | * Dominant: always expressed |
| - | | + | * Recessive: masked by dominant |
| - | | + | * Hybrid: cross of two “true-breeding”; |
| - | | + | * True breeding: when self-bred, produces offspring with same traits → homozygous |
| - | | + | * Pure Breeding: 100% same organism with no variation, self-bred |
| - | | + | * Wild Type: Normal, type |
| - | | + | * Parental Type: offspring phenotypically same as the parents |
| - | | + | * Recombinant Type: offspring different from the parents (both traits) |
| * Results from crossing over between genes | * Results from crossing over between genes | ||
| * Rare bcuz crossover between genes close together are uncommon | * Rare bcuz crossover between genes close together are uncommon | ||
| - | **Homozygous Dominant:** two dominant alleles | + | Homozygous Dominant: two dominant alleles |
| - | **Homozygous Recessive:** two recessive alleles | + | Homozygous Recessive: two recessive alleles |
| - | **Heterozygous: | + | Heterozygous: |
| one dominant allele, one recessive allele | one dominant allele, one recessive allele | ||
| Line 2158: | Line 2256: | ||
| ====Mendel' | ====Mendel' | ||
| - | | + | * P generation: Parental generation, Mendel crossed a purebred purple with a purebred white plant |
| - | * People used to believe in **blending inheritance: | + | * People used to believe in blending inheritance: |
| * Ex: a tall person mates with short person = medium height baby | * Ex: a tall person mates with short person = medium height baby | ||
| - | | + | * F1 generation: created only purple plants, traits didn’t blend → proved blending inheritance wrong |
| - | | + | * F2 generation: offspring produced by breeding F1 Generation; Mendel bred purple hybrids and created 75% purple and 25% white flowers |
| * Showed that traits do not blend together, can be hidden and come out in a later generation | * Showed that traits do not blend together, can be hidden and come out in a later generation | ||
| - | **Types of Crosses** | + | Types of Crosses |
| - | [[https:// | + | https:// |
| + | <img src=" | ||
| + | </ | ||
| - | - **Dihybrid Cross: investigating** **two** **traits (Ex: stem length** **and** **flower color) [16 squares → use FOIL]** | + | - Dihybrid Cross: investigating two traits (Ex: stem length and flower color) [16 squares → use FOIL] |
| * For dihybrids, the ratio is D/D : D/r : r/D : r/r | * For dihybrids, the ratio is D/D : D/r : r/D : r/r | ||
| - | | + | * Testcross: find out the unknown allele that corresponds with the dominant phenotype of an organism |
| * Cross the dominant organism with a homozygous recessive organism, if any of their offspring are recessive, then the dominant organism is heterozygous (Bb) | * Cross the dominant organism with a homozygous recessive organism, if any of their offspring are recessive, then the dominant organism is heterozygous (Bb) | ||
| Important Ratios | Important Ratios | ||
| - | | + | * 3:1 → Heterozygous x Heterozygous monohybrid cross |
| - | | + | * 1:2:1 genotypic ratio |
| - | | + | * 9:3:3:1 → dihybrid cross in which all alleles undergo independent assortment (unlinked) |
| * Heterozygous x Heterozygous | * Heterozygous x Heterozygous | ||
| - | **4:4:4:4** | + | 4:4:4:4 |
| → Heterozygous x Homozygous dihybrid cross | → Heterozygous x Homozygous dihybrid cross | ||
| - | **Mendel' | + | Mendel' |
| - | **Law of Segregation** | + | Law of Segregation |
| * Describes how alleles are segregated into different gametes and reunited after fertilization | * Describes how alleles are segregated into different gametes and reunited after fertilization | ||
| Line 2201: | Line 2301: | ||
| * Process in meiosis that ensures gametes get both maternal and paternal chromosomes | * Process in meiosis that ensures gametes get both maternal and paternal chromosomes | ||
| - | **Mendel’s Law of Independent Assortment** | + | Mendel’s Law of Independent Assortment |
| * Every character is inherited on its own bcuz alleles of different genes randomly orient during metaphase I and are sorted independent of the other one. | * Every character is inherited on its own bcuz alleles of different genes randomly orient during metaphase I and are sorted independent of the other one. | ||
| Line 2213: | Line 2313: | ||
| ====Rules of Probability==== | ====Rules of Probability==== | ||
| - | [[https:// | + | https:// |
| + | <img src=" | ||
| + | </ | ||
| - | **For harder problems, where there are 2 alleles (AaBb)** | + | For harder problems, where there are 2 alleles (AaBb) |
| * Mutually exclusive (can’t happen at same time) = or | * Mutually exclusive (can’t happen at same time) = or | ||
| - | **Multiplication Rule** | + | Multiplication Rule |
| * Two or more independent events (and) | * Two or more independent events (and) | ||
| Line 2226: | Line 2328: | ||
| * Memorize cross probabilities | * Memorize cross probabilities | ||
| - | | + | * Rr x rr = ½ Rr & ½ rr |
| - | | + | * Rr x RR = ½ Rr & ½ RR (probability of dominant phenotype is 1) |
| - | | + | * Rr x Rr = ¼ RR, ½ Rr & ¼ rr (probability of dominant phenotype is .75) |
| - | | + | * RR x rr = 4/4 Rr (probability of dominant is 1) |
| Finding Number of Unique Gametes Given Genotype | Finding Number of Unique Gametes Given Genotype | ||
| Line 2238: | Line 2340: | ||
| ====Chromosomal Inheritance and Environment Effects on Phenotype==== | ====Chromosomal Inheritance and Environment Effects on Phenotype==== | ||
| - | | + | * Multifactorial characters: many factors, such as genes and environment affect phenotype |
| - | | + | * Pedigree Analysis: Square is male, circle is female, painted in means they have that trait |
| * X-linked dom → father passes to all daughters; X-linked recessive → mother passes to all sons | * X-linked dom → father passes to all daughters; X-linked recessive → mother passes to all sons | ||
| Relationship Among Alleles of a Single Gene | Relationship Among Alleles of a Single Gene | ||
| - | [[Untitled_a1baf95c2be74fad95ea92c3882c2c8f: | + | Untitled_a1baf95c2be74fad95ea92c3882c2c8f: |
| - | - **Incomplete dominance of either allele:** heterozygous phenotype is intermediate between two homozygous | + | - Incomplete dominance of either allele: heterozygous phenotype is intermediate between two homozygous |
| * Dominant allele doesn' | * Dominant allele doesn' | ||
| - | - **Codominance: | + | - Codominance: |
| * People that are MM (L^M, L^M) produce the one molecule that appears on surface of blood cells, NN (L^NL^N) produce the other; and those who are MN (L^M, L^N) produce both | * People that are MM (L^M, L^M) produce the one molecule that appears on surface of blood cells, NN (L^NL^N) produce the other; and those who are MN (L^M, L^N) produce both | ||
| - | - **Pleiotropy:** one gene affects multiple phenotypic characters | + | - Pleiotropy: one gene affects multiple phenotypic characters |
| * Ex: sickle cell disease | * Ex: sickle cell disease | ||
| - | - **Multiple alleles:** some genes have more that two alleles | + | - Multiple alleles: some genes have more that two alleles |
| * Ex: blood group that produces A, B, and O blood types, there are 3 possible alleles → I^A, I^B, or i | * Ex: blood group that produces A, B, and O blood types, there are 3 possible alleles → I^A, I^B, or i | ||
| * Superscripts used because the two alleles, A and B, are codominant; lowercase i is recessive when expressed with others | * Superscripts used because the two alleles, A and B, are codominant; lowercase i is recessive when expressed with others | ||
| Line 2264: | Line 2366: | ||
| Relationships Among Multiple Genes | Relationships Among Multiple Genes | ||
| - | - **Epistasis:** Expression of one gene affects/ | + | - Epistasis: Expression of one gene affects/ |
| * Ex: hair color in labradors where B codes for melanin better (black) than b (brown). Second allele E needed to deposit melanin; ee is dysfunctional so no produced melanin is deposited (yellow) | * Ex: hair color in labradors where B codes for melanin better (black) than b (brown). Second allele E needed to deposit melanin; ee is dysfunctional so no produced melanin is deposited (yellow) | ||
| - | - **Polygenic Inheritance: | + | - Polygenic Inheritance: |
| * Interaction of many genes that affect a single phenotype (Ex: height, very short → very tall) | * Interaction of many genes that affect a single phenotype (Ex: height, very short → very tall) | ||
| - | | + | * Quantitative Characters: Controlled multiple gene which vary/add up along a continuum; affected by polygenic inheritance |
| * E.g. eye color, skin color → three genes produce melanin, skin color determined by how much genes are expressed | * E.g. eye color, skin color → three genes produce melanin, skin color determined by how much genes are expressed | ||
| * Any human character that is polygenic, cannot be predicted (like eye color) | * Any human character that is polygenic, cannot be predicted (like eye color) | ||
| - | **Environmental Impact on Phenotype** | + | Environmental Impact on Phenotype |
| * Environmental factors influence gene expression and can lead to phenotypic plasticity. | * Environmental factors influence gene expression and can lead to phenotypic plasticity. | ||
| - | | + | * Phenotypic plasticity: When the same genotype can result in multiple phenotypes under different environmental conditions |
| * Examples: | * Examples: | ||
| Line 2290: | Line 2392: | ||
| Examples | Examples | ||
| - | - **Nutrition: not enough nutrients can inhibit growth and plants without enough nitrogen may not flower** | + | - Nutrition: not enough nutrients can inhibit growth and plants without enough nitrogen may not flower |
| * May also influence expression of genetic disorders (lactose intolerance) | * May also influence expression of genetic disorders (lactose intolerance) | ||
| * Ex: ppl cannot metabolize specific amino acid → amino acid accumulates → brain cells die → death; minimizing amino acid → safe | * Ex: ppl cannot metabolize specific amino acid → amino acid accumulates → brain cells die → death; minimizing amino acid → safe | ||
| * Organisms w/ mutation so cant syhtnesize amino acid can grow in environment w/ amino acid | * Organisms w/ mutation so cant syhtnesize amino acid can grow in environment w/ amino acid | ||
| - | - **Temperature: | + | - Temperature: |
| - | | + | * Influences sex dertermination in some reptiles |
| * Eggs incubated at lower temperatures become males; those at higher temperatures become females | * Eggs incubated at lower temperatures become males; those at higher temperatures become females | ||
| - | * Influences fur & skin color of animals**,** melanin production (more UV = more melanin) | + | * Influences fur & skin color of animals, melanin production (more UV = more melanin) |
| - | - **Soil pH:** | + | - Soil pH: |
| * Influences flower color; blue in low pH and pink in high pH | * Influences flower color; blue in low pH and pink in high pH | ||
| - | - **Released Chemicals** | + | - Released Chemicals |
| * Chemical signals can affect gene expression and often needed to elicit mating | * Chemical signals can affect gene expression and often needed to elicit mating | ||
| Line 2312: | Line 2414: | ||
| * Ex: yeast cells only mate with yeast cells of opposite mating type; yeast releases signalling molecule (pheromone) → only opposite yeast respond | * Ex: yeast cells only mate with yeast cells of opposite mating type; yeast releases signalling molecule (pheromone) → only opposite yeast respond | ||
| - | **Multifactorial Diseases and Disorders** | + | Multifactorial Diseases and Disorders |
| Behavior of Recessive Alleles | Behavior of Recessive Alleles | ||
| Line 2318: | Line 2420: | ||
| * Recessive allele that causes a genetic disorder (a) codes for no protein or malfunction or misfolding | * Recessive allele that causes a genetic disorder (a) codes for no protein or malfunction or misfolding | ||
| - | | + | * Recessively inherited: must be homozygous recessive |
| - | | + | * Carriers: heterozygous individual with recessive allele and can pass on disease |
| * (Aa) usually have normal phenotype because (A) codes for enough | * (Aa) usually have normal phenotype because (A) codes for enough | ||
| - | | + | * Cystic Fibrosis: caused by a mutated channel gene that causes ppl with two recessive to not have chloride transport |
| * Pleiotropy: affects multiple organs | * Pleiotropy: affects multiple organs | ||
| - | | + | * Sickle Cell Anemia: mutated hemoglobin gene also recessively inherited |
| - | | + | * Tay Sachs Disease: mutated gene codes for a defective lipid breakdown protein in the brain |
| * BUT at the molecular level, is incomplete dominance, bcuz only digest half the amount of enzymes | * BUT at the molecular level, is incomplete dominance, bcuz only digest half the amount of enzymes | ||
| Dominantly Inherited Disorders | Dominantly Inherited Disorders | ||
| - | **Lethal Dominant:** | + | Lethal Dominant: |
| only needs one copy to kill (heteroz) | only needs one copy to kill (heteroz) | ||
| Line 2342: | Line 2444: | ||
| * Evidence: parallels between genes during meiosis and behavior of chromosomes | * Evidence: parallels between genes during meiosis and behavior of chromosomes | ||
| - | | + | * Autosomal Inheritance: |
| * Male and female equally likely to inherit the gene | * Male and female equally likely to inherit the gene | ||
| - | **T. H. Morgan:** | + | T. H. Morgan: |
| * Discovered sex-linkage of genes | * Discovered sex-linkage of genes | ||
| Line 2360: | Line 2462: | ||
| Linked Genes | Linked Genes | ||
| - | | + | * Linked Genes: two genes found on the same autosomal chromosome and usually inherited together (not assorted independently) |
| * Linked genes sometimes crossover to seperate & create new allele combinations → allows natural selection to act on them | * Linked genes sometimes crossover to seperate & create new allele combinations → allows natural selection to act on them | ||
| * Goes against Mendel’s Law of Independent Assortment (every character inherited on its own and ASSUMES EVERY GENE IS FOUND ON A DIFFERENT CHROMOSOME) | * Goes against Mendel’s Law of Independent Assortment (every character inherited on its own and ASSUMES EVERY GENE IS FOUND ON A DIFFERENT CHROMOSOME) | ||
| - | * When OBSERVED amounts do not match the EXPECTED offspring phenotype → genes must be linked | + | * When OBSERVED amounts do not match the EXPECTED offspring phenotype → genes must be linked https:// |
| + | <img src=" | ||
| + | </ | ||
| * Expected: parental & recombinant type are equal | * Expected: parental & recombinant type are equal | ||
| * More than 50% offspring look the same as parent = genes are linked | * More than 50% offspring look the same as parent = genes are linked | ||
| - | [[https:// | + | https:// |
| + | <img src=" | ||
| + | </ | ||
| * “AKA rate of crossing over” and is directly proportional to the distance between the two linked genes | * “AKA rate of crossing over” and is directly proportional to the distance between the two linked genes | ||
| * Genes are farther apart → more likely to cross over | * Genes are farther apart → more likely to cross over | ||
| - | * Genes are closer together → more likely to be inherited | + | * Genes are closer together → more likely to be inherited https:// |
| + | <img src=" | ||
| + | </ | ||
| - | | + | * Percent Recombination: |
| * 50% RF is max, < 25% = genes are close | * 50% RF is max, < 25% = genes are close | ||
| Line 2380: | Line 2488: | ||
| * (high map units = high percent recombination = independent assortment & crossing over more likely) | * (high map units = high percent recombination = independent assortment & crossing over more likely) | ||
| - | **Sex Chromosomes** | + | Sex Chromosomes |
| * X chromosome is bigger and contains more genes than y | * X chromosome is bigger and contains more genes than y | ||
| Line 2387: | Line 2495: | ||
| * Sex is determined by interactions of gene products | * Sex is determined by interactions of gene products | ||
| * Ex. gene WNT4 needed for female gonad, XY egg with extra gene copy can develop female gonad | * Ex. gene WNT4 needed for female gonad, XY egg with extra gene copy can develop female gonad | ||
| - | | + | * SRY Gene: found on Y, makes males male, directs development of male anatomical features |
| * X chromosome contains genes for more than reproduction | * X chromosome contains genes for more than reproduction | ||
| Line 2394: | Line 2502: | ||
| Inheritance of Sex-Linked Genes | Inheritance of Sex-Linked Genes | ||
| - | | + | * Sex-Linked Genes: gene located on either sex chromosomes, |
| * Males and females inherit diff number of X chromosomes which results in pattern of inheritance | * Males and females inherit diff number of X chromosomes which results in pattern of inheritance | ||
| Line 2403: | Line 2511: | ||
| * Ex. any male that gets recessive X-linked allele got it from mom and will express trait bcuz only need one copy of X | * Ex. any male that gets recessive X-linked allele got it from mom and will express trait bcuz only need one copy of X | ||
| - | | + | * X-linked Disorders: caused by absence of gene on X chromosome locus which results in missing protein (Ex: hemophilia) |
| - | **Abnormal Chromosome Number** | + | Abnormal Chromosome Number |
| - | | + | * Nondisjunction: |
| + | <img src=" | ||
| + | </ | ||
| - | - **Meiosis: failure for two homologous chromosomes (maternal and paternal migrate along spindle fibers together) or two chromatids** | + | - Meiosis: failure for two homologous chromosomes (maternal and paternal migrate along spindle fibers together) or two chromatids |
| - | - **Mitosis: Failure of two chromatids to separate** | + | - Mitosis: Failure of two chromatids to separate |
| - | * Happens most often during embryonic development and results in **mosaicism** in which fraction of body cells (descendents) have extra or missing chromosome | + | * Happens most often during embryonic development and results in mosaicism in which fraction of body cells (descendents) have extra or missing chromosome |
| - | - **Polyploidy occurs if all chromosomes undergo meiotic nondisjunction and produce gametes with twice number** | + | - Polyploidy occurs if all chromosomes undergo meiotic nondisjunction and produce gametes with twice number |
| * If polyploid gamete fertilized with similar gametes → polyploid zygote (common in plants) | * If polyploid gamete fertilized with similar gametes → polyploid zygote (common in plants) | ||
| - | | + | * Aneuploidy: genome with extra or missing chromosomes; |
| - | * Can result in **monosomic** zygotes (missing a chromosome) or **trisomic** (extra) | + | * Can result in monosomic zygotes (missing a chromosome) or trisomic (extra) |
| * Mitosis will then spread abnormality; | * Mitosis will then spread abnormality; | ||
| - | **X Inactivation** | + | X Inactivation |
| * During embryonic development of female mammals, one of the 2 X chromosomes does not uncoil into chromatin. | * During embryonic development of female mammals, one of the 2 X chromosomes does not uncoil into chromatin. | ||
| - | * Instead | + | * Instead X-Inactivation occurs and one chromosome remains coiled as a compact body called barr body |
| * Inactivation makes sure that only one type of protein is made | * Inactivation makes sure that only one type of protein is made | ||
| - | | + | * Barr body: inactive X chromosomes (most of genes not expressed or interact [in dom./rec manner] with other chromosome) |
| * Thus only alleles on one active X chromosome are expressed | * Thus only alleles on one active X chromosome are expressed | ||
| Line 2446: | Line 2556: | ||
| * But in (rare) case where all cells with X^N inactivated, | * But in (rare) case where all cells with X^N inactivated, | ||
| - | [[https:// | + | https:// |
| + | <img src=" | ||
| + | </ | ||
| * Calico cats female bcuz heterozygotes inherit two X-linked alleles for hair color → some cells will express red and other black color | * Calico cats female bcuz heterozygotes inherit two X-linked alleles for hair color → some cells will express red and other black color | ||
| Line 2459: | Line 2571: | ||
| * Occurs during gamete formation & results in one allele silenced thru methylation (not expressed in offspring) | * Occurs during gamete formation & results in one allele silenced thru methylation (not expressed in offspring) | ||
| - | * Reversed in gonads during meiosis | + | * Reversed in gonads during meiosis https:// |
| + | <img src=" | ||
| + | </ | ||
| - | **Inheritance of Organelle Genes** | + | Inheritance of Organelle Genes |
| * Inheritance of traits controlled by organelles are inherited only from mother since male gamete (pollen or sperm) delivers negligible cytoplasm | * Inheritance of traits controlled by organelles are inherited only from mother since male gamete (pollen or sperm) delivers negligible cytoplasm | ||
| * Mother has mutation in an organelle (ex: mitochondria) → passed to all kids | * Mother has mutation in an organelle (ex: mitochondria) → passed to all kids | ||
| - | * This **Maternal Inheritance** can trace specific genome from progeny back thru generation | + | * This Maternal Inheritance can trace specific genome from progeny back thru generation |
| - | ** Unit 6: DNA Structure and Replication** | + | Unit 6: DNA Structure and Replication |
| - | **Molecular Biology** | + | Molecular Biology |
| * Chromosomes are a condensed complex of DNA & proteins that contain the genetic information passed from parent to offspring | * Chromosomes are a condensed complex of DNA & proteins that contain the genetic information passed from parent to offspring | ||
| Line 2476: | Line 2590: | ||
| * Structure: chromosome → gene → DNA → nucleosome → histone proteins | * Structure: chromosome → gene → DNA → nucleosome → histone proteins | ||
| - | | + | * Central Dogma: DNA → RNA → proteins/ |
| * Some proteins: form basic cell structure and appearance, enzymes that regulate chemical reactions that direct metabolism for cell development, | * Some proteins: form basic cell structure and appearance, enzymes that regulate chemical reactions that direct metabolism for cell development, | ||
| Line 2482: | Line 2596: | ||
| * Except for asexually reproducing organisms and identical twins, DNA of every individual is different→ results from variation in sequence of nucleotides → generate diff RNA → produce diff proteins which control diff traits | * Except for asexually reproducing organisms and identical twins, DNA of every individual is different→ results from variation in sequence of nucleotides → generate diff RNA → produce diff proteins which control diff traits | ||
| - | |**Nucleic Acid**|**Sugar**|**Nitrogen Bases**|**Function**|**Structure**| | + | |Nucleic Acid|Sugar|Nitrogen Bases|Function|Structure| |
| |DNA|Deoxyribose|Adenine, | |DNA|Deoxyribose|Adenine, | ||
| |RNA \ (involved in protein synthesis\ |Ribose|Adenine, | |RNA \ (involved in protein synthesis\ |Ribose|Adenine, | ||
| Line 2488: | Line 2602: | ||
| |RNA \ (involved in regulating gene expression)\ |Ribose|Adenine, | |RNA \ (involved in regulating gene expression)\ |Ribose|Adenine, | ||
| - | **Prokaryotes Vs. Eukaryotes** | + | Prokaryotes Vs. Eukaryotes |
| Replication Similarities | Replication Similarities | ||
| Line 2496: | Line 2610: | ||
| Differences | Differences | ||
| - | |**Prokaryotes**\ They have circular chromosomes so don’t need telomeres \ Chromosomes have one, unique origin of replication\ |**Eukaryotes**\ They have linear chromosomes with ends called\ | + | |Prokaryotes\ They have circular chromosomes so don’t need telomeres \ Chromosomes have one, unique origin of replication\ |Eukaryotes\ They have linear chromosomes with ends called\ telomeres\ Chromosomes have multiple origins to accommodate much larger size of chromosomes\ | |
| - | **Packing of Eukaryotic DNA:** | + | Packing of Eukaryotic DNA: |
| - | * DNA usually so densely packed that it’s largely inaccessible to the replication machinery | + | * DNA usually so densely packed that it’s largely inaccessible to the replication machinery Untitled_a1baf95c2be74fad95ea92c3882c2c8f: |
| * Acts as a way of regulating gene expression | * Acts as a way of regulating gene expression | ||
| - | | + | * Euchromatin: |
| - | | + | * Heterochromatic: |
| - | [[Untitled_a1baf95c2be74fad95ea92c3882c2c8f: | + | Untitled_a1baf95c2be74fad95ea92c3882c2c8f: |
| * Bind tightly to DNA bcuz histones amino acids are (+) charged and DNA is (-) | * Bind tightly to DNA bcuz histones amino acids are (+) charged and DNA is (-) | ||
| - | **Nucleosomes** | + | Nucleosomes |
| - | **:**tight complexes of DNA double helix in chromatin wrapped around bundle of eight histone molecules | + | :tight complexes of DNA double helix in chromatin wrapped around bundle of eight histone molecules |
| - | **Early Experiments** | + | Early Experiments |
| - | - **Griffith discovered that genetic information can be transferred from dead bacteria to living bacteria.** | + | - Griffith discovered that genetic information can be transferred from dead bacteria to living bacteria. |
| * Griff inserted dead pathogenic bacteria & harmless strain into mouse → mouse died | * Griff inserted dead pathogenic bacteria & harmless strain into mouse → mouse died | ||
| - | * Showed evidence for **transformation: | + | * Showed evidence for transformation: |
| - | - **Avery, MacLeod and McCarty identify DNA as the hereditary information of a cell:** | + | - Avery, MacLeod and McCarty identify DNA as the hereditary information of a cell: |
| * Using same bacteria, removed proteins and polysaccharide from coat of dead, pathogenic bacteria → remaining material was still able to transform bacteria → gave previously harmless bacteria ability to cause disease | * Using same bacteria, removed proteins and polysaccharide from coat of dead, pathogenic bacteria → remaining material was still able to transform bacteria → gave previously harmless bacteria ability to cause disease | ||
| - | - **The Hershey and Chase experiments established that DNA was the genetic material of phages** | + | - The Hershey and Chase experiments established that DNA was the genetic material of phages |
| - | * Knew that **phages** consisted of DNA and proteins | + | * Knew that phages consisted of DNA and proteins |
| * Substituted radioactive sulfur of phage proteins → culture, not bacteria were radioactive → phage proteins did not enter the bacteria | * Substituted radioactive sulfur of phage proteins → culture, not bacteria were radioactive → phage proteins did not enter the bacteria | ||
| * Substituted radioactive phosphorous for phosphorus in bacteria DNA → same procedure → bacteria--not culture-- was radioactive → phage DNA had entered the bacteria | * Substituted radioactive phosphorous for phosphorus in bacteria DNA → same procedure → bacteria--not culture-- was radioactive → phage DNA had entered the bacteria | ||
| - | - **Watson, Crick, Wilkins, and Franklin determined the structure of DNA** | + | - Watson, Crick, Wilkins, and Franklin determined the structure of DNA |
| * Produced X-ray diffraction photograph of DNA → pattern revealed that molecule consisted of two strands wrapped around each other (double helix) | * Produced X-ray diffraction photograph of DNA → pattern revealed that molecule consisted of two strands wrapped around each other (double helix) | ||
| * Proposed that sugar-phosphate material (hydrophilic) formed the outside while nitrogenous bases (hydrophobic) were located inside the molecule | * Proposed that sugar-phosphate material (hydrophilic) formed the outside while nitrogenous bases (hydrophobic) were located inside the molecule | ||
| Line 2534: | Line 2648: | ||
| Notes | Notes | ||
| - | | + | * Gene: DNA sequence that is expressed to form a functional product: either RNA or polypeptide |
| * Molecular viewpoint: traits are the end products of metabolic processes regulated by enzymes | * Molecular viewpoint: traits are the end products of metabolic processes regulated by enzymes | ||
| - | **DNA Replication** | + | DNA Replication |
| * DNA Replication ensures continuity of genetic info | * DNA Replication ensures continuity of genetic info | ||
| Line 2546: | Line 2660: | ||
| * DNA replication occurs in the 5’ - 3’ direction bcuz DNA pol can only attach to 3’ end | * DNA replication occurs in the 5’ - 3’ direction bcuz DNA pol can only attach to 3’ end | ||
| - | **DNA Replication Proteins & Their Functions** | + | DNA Replication Proteins & Their Functions |
| - | |**Helicase**|Unwinds parental double helix at replication forks| | + | |Helicase|Unwinds parental double helix at replication forks| |
| - | |**Single-stranded binding protein**|Binds to, stabilizes, and prevents single-stranded DNA from rejoining until is is used as a template| | + | |Single-stranded binding protein|Binds to, stabilizes, and prevents single-stranded DNA from rejoining until is is used as a template| |
| - | |**Topoisomerase**|Binds ahead of replication forks & relieves overwinding strain by breaking, swiveling, and rejoining DNA strands| | + | |Topoisomerase|Binds ahead of replication forks & relieves overwinding strain by breaking, swiveling, and rejoining DNA strands| |
| - | |**Primase**|Synthesizes an RNA primer at 5’ end of leading strand and at 5’ end of each okazaki fragment| | + | |Primase|Synthesizes an RNA primer at 5’ end of leading strand and at 5’ end of each okazaki fragment| |
| - | |**DNA Ligase**|Joins okazaki fragments w/ covalent bonds; on leading strand joins 3’ end of DNA that replaces primer to rest of leading strand DNA| | + | |DNA Ligase|Joins okazaki fragments w/ covalent bonds; on leading strand joins 3’ end of DNA that replaces primer to rest of leading strand DNA| |
| - | **“Semiconservative”** | + | “Semiconservative” |
| - | * Before duplication, | + | * Before duplication, |
| + | <img src=" | ||
| + | </ | ||
| * This ensures that the DNA replication is identical. | * This ensures that the DNA replication is identical. | ||
| Line 2565: | Line 2681: | ||
| * After two rounds of semi-conservative replication, | * After two rounds of semi-conservative replication, | ||
| - | **The Role of DNA Polymerase** | + | The Role of DNA Polymerase |
| - | **DNA Polymerase I vs. III** | + | DNA Polymerase I vs. III |
| * Both can only add DNA to 3 end | * Both can only add DNA to 3 end | ||
| - | |**Polymerase I**\ Responsible for removing RNA primers on replacing with DNA nucleotides\ |**Polymerase III**\ Uses parental DNA to add DNA nucleotides 3’ end of RNA primers or existing strand\ | | + | |Polymerase I\ Responsible for removing RNA primers on replacing with DNA nucleotides\ |Polymerase III\ Uses parental DNA to add DNA nucleotides 3’ end of RNA primers or existing strand\ | |
| - | **Summary: The Process of DNA Replication** | + | Summary: The Process of DNA Replication |
| - | - **Helicase unwinds the parental double helix at the origin of replication→ forms a Y-shaped replication fork** | + | - Helicase unwinds the parental double helix at the origin of replication→ forms a Y-shaped replication fork |
| - | | + | * Origin of replication: |
| - | - **Single-stranded binding protein attaches to each strand of uncoiled DNA to keep separate** | + | - Single-stranded binding protein attaches to each strand of uncoiled DNA to keep separate |
| - | - **As helicase unwinds the DNA → forces the double helix to twist → group of enzymes topoisomerases break and rejoin the double helix → allow twists to unravel and prevent knots** | + | - As helicase unwinds the DNA → forces the double helix to twist → group of enzymes topoisomerases break and rejoin the double helix → allow twists to unravel and prevent knots |
| - | - **Primase: an enzyme that initiates DNA replication at the origins of replication by placing an initial, short RNA nucleotide strand (RNA primer) using parental DNA as a template** | + | - Primase: an enzyme that initiates DNA replication at the origins of replication by placing an initial, short RNA nucleotide strand (RNA primer) using parental DNA as a template |
| * Primase also slows replication fork | * Primase also slows replication fork | ||
| - | * Need primase and primers bcuz **DNA Polymerase** can only attach to 3’ end of an already existing complementary strand → belongs | + | * Need primase and primers bcuz DNA Polymerase can only attach to 3’ end of an already existing complementary strand → belongs elongation of new DNA at replication fork by assembling new (complementary) strand in the antiparallel 5’ → 3’ direction |
| * Leading strand and every Okazaki fragment on lagging strand must begin with primer | * Leading strand and every Okazaki fragment on lagging strand must begin with primer | ||
| - | - **Since DNA consists of two opposing DNA strands, uncoiled DNA consists of 3’ → 5’ template strand and 5’ → 3’ template strand** | + | - Since DNA consists of two opposing DNA strands, uncoiled DNA consists of 3’ → 5’ template strand and 5’ → 3’ template strand |
| - | - **Leading strand:** For the 3’ → 5’ strand, replication occurs continuously DNA polymerase moves towards the replication fork | + | - Leading strand: For the 3’ → 5’ strand, replication occurs continuously DNA polymerase moves towards the replication fork |
| - | - **Lagging Strand: For the 5’ → 3’ template strand, replication occurs discontinuously as DNA polymerase moves away from the uncoiling replication fork** | + | - Lagging Strand: For the 5’ → 3’ template strand, replication occurs discontinuously as DNA polymerase moves away from the uncoiling replication fork |
| * This is bcuz it can assemble nucleotides only as it moves in 5’ → 3’ direction; takes more time to assemble | * This is bcuz it can assemble nucleotides only as it moves in 5’ → 3’ direction; takes more time to assemble | ||
| - | - [[https:// | + | - https:// |
| + | <img src=" | ||
| + | </ | ||
| * After each complementary segment is assembled & DNA pol III reaches next RNA primer it must return back to the replication fork to begin assembling the next segments | * After each complementary segment is assembled & DNA pol III reaches next RNA primer it must return back to the replication fork to begin assembling the next segments | ||
| - | | + | * Okazaki fragments: Short segments of complementary DNA; have 5' RNA nucleotides & DNA nucleotides 3' |
| - | - **RNA nucleotides of RNA Primer are later replaced with DNA by DNA pol 1** | + | - RNA nucleotides of RNA Primer are later replaced with DNA by DNA pol 1 |
| - | - **DNA ligase joins the sugar-phosphate backbones of Okazaki fragments and closes up gaps thru covalent bonds** | + | - DNA ligase joins the sugar-phosphate backbones of Okazaki fragments and closes up gaps thru covalent bonds |
| - | **Antiparallel Elongation** | + | Antiparallel Elongation |
| * Energy for elongation provided by two additional phosphates that are attached to each nucleotide (total of 3 attached to nitrogen base) | * Energy for elongation provided by two additional phosphates that are attached to each nucleotide (total of 3 attached to nitrogen base) | ||
| * Breaking the bonds that holds extra two provides chemical energy for process | * Breaking the bonds that holds extra two provides chemical energy for process | ||
| - | **Replication of Telomeres** | + | Replication of Telomeres |
| - | | + | * Big problem when replication reaches the end of DNA strand |
| * Eukaryotes can’t complete 5’ end of lagging strand bcuz last primer removed and no 3’ end for DNA pol to add DNA | * Eukaryotes can’t complete 5’ end of lagging strand bcuz last primer removed and no 3’ end for DNA pol to add DNA | ||
| - | | + | * Result: DNA loss → shorter and shorter DNA molecules with uneven ends → can trigger apoptosis |
| - | [[Untitled_a1baf95c2be74fad95ea92c3882c2c8f: | + | Untitled_a1baf95c2be74fad95ea92c3882c2c8f: |
| - | | + | * Telomeres: noncoding, special DNA sequence, 5’-TTAGGG-3 |
| * Telomere Functions: Allows elongation of lagging strand to continue, stops staggered ends, and postpones loss of DNA in replicated chromosomes | * Telomere Functions: Allows elongation of lagging strand to continue, stops staggered ends, and postpones loss of DNA in replicated chromosomes | ||
| Line 2621: | Line 2739: | ||
| * Telomerase activity high in cancer cells and tumors → prolongs life | * Telomerase activity high in cancer cells and tumors → prolongs life | ||
| - | **DNA Proofreading and Repair** | + | DNA Proofreading and Repair |
| * DNA replication error low bcuz of base pairings and DNA polymerase but not perfect so cells have mechanisms to repair errors | * DNA replication error low bcuz of base pairings and DNA polymerase but not perfect so cells have mechanisms to repair errors | ||
| - | * w/o mechanisms → accumulate cancer-causing errors | + | * w/o mechanisms → accumulate cancer-causing errors https:// |
| + | <img src=" | ||
| + | </ | ||
| - | - **Proofreading: | + | - Proofreading: |
| - | - **Mismatch Repair Proteins: other enzymes correct errors in base pairing** | + | - Mismatch Repair Proteins: other enzymes correct errors in base pairing |
| - | - **Excision repair proteins: nucleases identify & cut out damaged DNA → DNA pol 1 replaces → DNA ligase joins** | + | - Excision repair proteins: nucleases identify & cut out damaged DNA → DNA pol 1 replaces → DNA ligase joins |
| Error rate after proofreading is low but not 0 | Error rate after proofreading is low but not 0 | ||
| Line 2645: | Line 2765: | ||
| ---- | ---- | ||
| - | [[Untitled_a1baf95c2be74fad95ea92c3882c2c8f: | + | Untitled_a1baf95c2be74fad95ea92c3882c2c8f: |
| - | [[Untitled_a1baf95c2be74fad95ea92c3882c2c8f: | + | Untitled_a1baf95c2be74fad95ea92c3882c2c8f: |
| - | [[Untitled_a1baf95c2be74fad95ea92c3882c2c8f: | + | Untitled_a1baf95c2be74fad95ea92c3882c2c8f: |
| =====Protein Synthesis===== | =====Protein Synthesis===== | ||
| - | **Overview** | + | Overview |
| * Process that describes how enzymes and other proteins are made from DNA | * Process that describes how enzymes and other proteins are made from DNA | ||
| * Genetic information flows from a sequence of nucleotides in DNA to a sequence of bases in an mRNA molecule to a sequence of amino acids in a protein | * Genetic information flows from a sequence of nucleotides in DNA to a sequence of bases in an mRNA molecule to a sequence of amino acids in a protein | ||
| - | | + | * 3 Steps: Transcription ⇒ mRNA processing ⇒ Translation! |
| - | **Types of RNA molecules** | + | Types of RNA molecules |
| * The sequence of RNA bases + structure of the RNA molecule = RNA function | * The sequence of RNA bases + structure of the RNA molecule = RNA function | ||
| - | |**mRNA**\ Carries info for assembling amino acids into polypeptide chain from DNA to ribosome\ |**tRNA**\ Delivers amino acids from cytosol to a ribosome for their addition to a growing polypeptide chain \ • 3’ end of tRNA covalently attaches to an amino acid \ Other portion, specified by combination of nucleotides is the\ **anticodon** that base pair with mRNA\ Hydrogen bonding between base pairs maintains 3D shape\ |**rRNA**\ Molecules transcribed in the nucleolus and assembled with proteins imported from cytoplasm to form large and small ribosomal subunit\ In cytoplasm, two subunits join to form a ribosome that coordinate activities of mRNA and tRNA\ | | + | |mRNA\ Carries info for assembling amino acids into polypeptide chain from DNA to ribosome\ |tRNA\ Delivers amino acids from cytosol to a ribosome for their addition to a growing polypeptide chain \ • 3’ end of tRNA covalently attaches to an amino acid \ Other portion, specified by combination of nucleotides is the\ anticodon that base pair with mRNA\ Hydrogen bonding between base pairs maintains 3D shape\ |rRNA\ Molecules transcribed in the nucleolus and assembled with proteins imported from cytoplasm to form large and small ribosomal subunit\ In cytoplasm, two subunits join to form a ribosome that coordinate activities of mRNA and tRNA\ | |
| - | **The Genetic Code** | + | The Genetic Code |
| * Identifies amino acid specified by each of possible 64 codons combination | * Identifies amino acid specified by each of possible 64 codons combination | ||
| * Use the mRNA codons not the tRNA anticodons | * Use the mRNA codons not the tRNA anticodons | ||
| - | | + | * Codon: A triplet group of adjacent mRNA nucleotides that codes for one specific amino acid or stop codon |
| * Many amino acids are encoded by more than one codon = redundant | * Many amino acids are encoded by more than one codon = redundant | ||
| * Codon cannot code for more than one amino acid | * Codon cannot code for more than one amino acid | ||
| * Some codons have a dual function: amino acid and start codon | * Some codons have a dual function: amino acid and start codon | ||
| - | | + | * Start Codon: needed to start translation (ex: AUG) |
| - | | + | * Stop Codon: signals end of translation; |
| * 64 ways that 4 nucleotides can be arranged = there are 64 possible codons | * 64 ways that 4 nucleotides can be arranged = there are 64 possible codons | ||
| Line 2681: | Line 2801: | ||
| * Unity/ | * Unity/ | ||
| - | | + | * Aminoacyl tRNA synthetases: |
| ====Transcription==== | ====Transcription==== | ||
| Line 2687: | Line 2807: | ||
| * Transcription is where DNA strands are turned into RNA strands for translation to use. | * Transcription is where DNA strands are turned into RNA strands for translation to use. | ||
| - | - **Initiation:** RNA polymerase recognizes & attaches to a promoter sequence on the DNA and begins to unzip them into two strands | + | - Initiation: RNA polymerase recognizes & attaches to a promoter sequence on the DNA and begins to unzip them into two strands |
| - | | + | * Promoter Sequence: DNA sequence which starts transcription, |
| * Bacteria: RNA pol binds directly to promoter (w/o TF) | * Bacteria: RNA pol binds directly to promoter (w/o TF) | ||
| * Eukaryotes: RNA pol needs transcription factors that guide it and determine where transcription starts and direction | * Eukaryotes: RNA pol needs transcription factors that guide it and determine where transcription starts and direction | ||
| - | - **Elongation:** occurs as RNA polymerase unzips the DNA and assembles RNA nucleotide using one strand of the DNA as a template | + | - Elongation: occurs as RNA polymerase unzips the DNA and assembles RNA nucleotide using one strand of the DNA as a template |
| * Unlike DNA replication: | * Unlike DNA replication: | ||
| * Like DNA replication: | * Like DNA replication: | ||
| - | - **Termination: | + | - Termination: |
| ====mRNA Processing: Enzyme Regulated Modifications of mRNA transcript: | ====mRNA Processing: Enzyme Regulated Modifications of mRNA transcript: | ||
| Line 2702: | Line 2822: | ||
| * In Eukaryotes, mRNA transcript must be processed before can exit the nucleus and be used for translation → Pre-mRNA longer than post mRNA | * In Eukaryotes, mRNA transcript must be processed before can exit the nucleus and be used for translation → Pre-mRNA longer than post mRNA | ||
| - | - **5’ Cap: is added to the 5’ end of mRNA** | + | - 5’ Cap: is added to the 5’ end of mRNA |
| * Guanine nucleotide with 2 additional phosphate groups (forms GTP) | * Guanine nucleotide with 2 additional phosphate groups (forms GTP) | ||
| * Capping provides stability, protection from nucleases, and a point of attachment for small ribosomal subunit | * Capping provides stability, protection from nucleases, and a point of attachment for small ribosomal subunit | ||
| - | - **Poly-A-tail: | + | - Poly-A-tail: |
| * Consists of many adenine nucleotides | * Consists of many adenine nucleotides | ||
| * Provides stability and controls movement of mRNA across the nuclear envelope | * Provides stability and controls movement of mRNA across the nuclear envelope | ||
| - | * At 3’ end of the gene, there is a **poly-A signal sequence** at the last exon of the gene | + | * At 3’ end of the gene, there is a poly-A signal sequence at the last exon of the gene |
| - | * It is transcribed into an RNA sequence that signals where the transcript is cleaved | + | * It is transcribed into an RNA sequence that signals where the transcript is cleaved and the poly-A-tail is added https:// |
| + | <img src=" | ||
| + | </ | ||
| - | - **RNA splicing: removes nucleotide segments from mRNA** | + | - RNA splicing: removes nucleotide segments from mRNA |
| * mRNA (and DNA) contain two kinds of sequences | * mRNA (and DNA) contain two kinds of sequences | ||
| - | | + | * Exons: |
| - | | + | * Introns: |
| * Allow for exon shuffling/ | * Allow for exon shuffling/ | ||
| - | * Uses **spliceosomes: | + | * Uses spliceosomes: |
| - | - **Alternative Splicing: Selective excision of introns and retention of exons → allows diff mRNAs to be generated from same RNA transcript → each code for diff protein product of diff size** | + | - Alternative Splicing: Selective excision of introns and retention of exons → allows diff mRNAs to be generated from same RNA transcript → each code for diff protein product of diff size |
| - | [[Untitled_a1baf95c2be74fad95ea92c3882c2c8f: | + | Untitled_a1baf95c2be74fad95ea92c3882c2c8f: |
| * Often diff exon combinations code for diff subunits (4th) of same protein | * Often diff exon combinations code for diff subunits (4th) of same protein | ||
| Line 2737: | Line 2859: | ||
| * Proteins that will be secreted out of the cell, transported to an organelle (ex: lysosome), or inserted into a membrane are translated into the endoplasmic reticulum | * Proteins that will be secreted out of the cell, transported to an organelle (ex: lysosome), or inserted into a membrane are translated into the endoplasmic reticulum | ||
| - | | + | * Signal peptide: translocate/ |
| Details Prelude | Details Prelude | ||
| Line 2749: | Line 2871: | ||
| * E site (exit): in the third position, tRNA and polypeptide exit ribosome | * E site (exit): in the third position, tRNA and polypeptide exit ribosome | ||
| - | - **Wobble:** rules for base pairing between the third base of a codon and tRNA is flexible | + | - Wobble: rules for base pairing between the third base of a codon and tRNA is flexible https:// |
| + | <img src=" | ||
| + | </ | ||
| * So there are fewer tRNAs than possible amino acid codons | * So there are fewer tRNAs than possible amino acid codons | ||
| Line 2760: | Line 2884: | ||
| Process Steps | Process Steps | ||
| - | - **Initiation: begins when the small ribosomal subunit recognizes & attaches to 5’ cap of mRNA** | + | - Initiation: begins when the small ribosomal subunit recognizes & attaches to 5’ cap of mRNA |
| * A tRNA (with anticodon UAC) carrying the amino acid methionine attaches to mRNA at the start codon AUG | * A tRNA (with anticodon UAC) carrying the amino acid methionine attaches to mRNA at the start codon AUG | ||
| * Large ribosomal subunit attaches to the mRNA with the tRNA → ribosome fully assembled with tRNA occupying the P site | * Large ribosomal subunit attaches to the mRNA with the tRNA → ribosome fully assembled with tRNA occupying the P site | ||
| - | - **Elongation: continues as each tRNA delivers an amino acid one by one according to mRNA sequence** [[Untitled_a1baf95c2be74fad95ea92c3882c2c8f: | + | - Elongation: continues as each tRNA delivers an amino acid one by one according to mRNA sequence Untitled_a1baf95c2be74fad95ea92c3882c2c8f: |
| * A newly arriving tRNA attaches to the first binding site (A site) | * A newly arriving tRNA attaches to the first binding site (A site) | ||
| * rRNA molecule of the large ribosomal subunit catalyzes the formation of a peptide bond between the carboxyl end of the growing polypeptide in the P site and the amino group of the new amino acid in the A site | * rRNA molecule of the large ribosomal subunit catalyzes the formation of a peptide bond between the carboxyl end of the growing polypeptide in the P site and the amino group of the new amino acid in the A site | ||
| Line 2771: | Line 2895: | ||
| * This leaves the A binding site empty → new tRNA can arrive | * This leaves the A binding site empty → new tRNA can arrive | ||
| - | **Termination: | + | Termination: |
| occurs when ribosome encounters stop codon → A site accepts a release factor | occurs when ribosome encounters stop codon → A site accepts a release factor | ||
| - | | + | * Release Factor: protein shaped like a tRNA which binds to stop codon in A site instead of tRNA |
| * GTP hydrolysis dissociates completed polypeptide, | * GTP hydrolysis dissociates completed polypeptide, | ||
| Line 2783: | Line 2907: | ||
| Process Efficiency | Process Efficiency | ||
| - | | + | * Transcription: |
| - | | + | * Translation: |
| * Hydrolysis of GTP increases the accuracy and efficiency | * Hydrolysis of GTP increases the accuracy and efficiency | ||
| - | **Ribozymes** | + | Ribozymes |
| * RNA molecules that function as an enzyme! | * RNA molecules that function as an enzyme! | ||
| Line 2798: | Line 2922: | ||
| - Catalyze formation of peptide bonds and removal of introns | - Catalyze formation of peptide bonds and removal of introns | ||
| - | **Prokaryotes vs. Eukaryotes** | + | Prokaryotes vs. Eukaryotes |
| Transcription | Transcription | ||
| - | |**Prokaryotes**\ Don't need transcription factors \ Have only one type of RNA polymerase\ • RNA pol II does not need TF\ Have poly-a-tail\ but not 5’ cap \ Have operons\ |**Eukaryotes**\ Need transcription factors \ Have 3 types of RNA polymerase\ • RNA pol II needs TF\ Have poly-a-tail\ and 5’cap \ Do not have operons\ | | + | |Prokaryotes\ Don't need transcription factors \ Have only one type of RNA polymerase\ • RNA pol II does not need TF\ Have poly-a-tail\ but not 5’ cap \ Have operons\ |Eukaryotes\ Need transcription factors \ Have 3 types of RNA polymerase\ • RNA pol II needs TF\ Have poly-a-tail\ and 5’cap \ Do not have operons\ | |
| Translation | Translation | ||
| Line 2808: | Line 2932: | ||
| * Both need tRNAs, amino acids, ribosomal subunits, polypeptide factors, and GTP | * Both need tRNAs, amino acids, ribosomal subunits, polypeptide factors, and GTP | ||
| - | |**Prokaryotes**\ Translation occurs at same time as transcription\ |**Eukaryotes**\ Translation is isolated & also on the rough ER\ | | + | |Prokaryotes\ Translation occurs at same time as transcription\ |Eukaryotes\ Translation is isolated & also on the rough ER\ | |
| =====Gene Regulation: Prokaryotic and Eukaryotic===== | =====Gene Regulation: Prokaryotic and Eukaryotic===== | ||
| - | [[Untitled_a1baf95c2be74fad95ea92c3882c2c8f: | + | Untitled_a1baf95c2be74fad95ea92c3882c2c8f: |
| * Cells function differently because they express a unique combination of genes because have they have diff specific transcription factors which activate some genes while suppressing others | * Cells function differently because they express a unique combination of genes because have they have diff specific transcription factors which activate some genes while suppressing others | ||
| Line 2828: | Line 2952: | ||
| * Prokaryotes don’t have RNA splicing or chromatin modification | * Prokaryotes don’t have RNA splicing or chromatin modification | ||
| - | **Operon** | + | Operon |
| * “Unit of DNA that contains functionally related genes that can be coordinately controlled by “on/ | * “Unit of DNA that contains functionally related genes that can be coordinately controlled by “on/ | ||
| * Benefit of Operons: better coordination and control → can regulate cluster of functionally related genes with single on/off switch | * Benefit of Operons: better coordination and control → can regulate cluster of functionally related genes with single on/off switch | ||
| - | - **Promoter: sequence of DNA to which RNA polymerase attaches to begin transcription** | + | - Promoter: sequence of DNA to which RNA polymerase attaches to begin transcription |
| - | - **Operator: DNA site which binds to a regulatory protein that switches operon on/off to either block or promote RNA polymerase and regulate gene expression** | + | - Operator: DNA site which binds to a regulatory protein that switches operon on/off to either block or promote RNA polymerase and regulate gene expression |
| - | - **Structural genes: contains coding DNA→ sequences that code for various related protein subunits that direct production of specific end product** | + | - Structural genes: contains coding DNA→ sequences that code for various related protein subunits that direct production of specific end product |
| - | * Enzyme made like **Tryptophan** can accumulate and inhibit own production by acting as repressor protein and blocking operator | + | * Enzyme made like Tryptophan can accumulate and inhibit own production by acting as repressor protein and blocking operator |
| - | - **Regulatory gene: lies outside operon region → produces a regulatory protein that binds to operator region and controls whether RNA polymerase can begin transcription** | + | - Regulatory gene: lies outside operon region → produces a regulatory protein that binds to operator region and controls whether RNA polymerase can begin transcription |
| - | - **Regulatory proteins are allosteric, can be one of two kinds** | + | - Regulatory proteins are allosteric, can be one of two kinds |
| - | | + | * Repressor protein: blocks attachment of RNA polymerase to promoter region |
| * Stops transcription & translation | * Stops transcription & translation | ||
| - | | + | * Activator protein: promotes attachment of RNA polymerase to promoter region |
| - | | + | * Positive regulation because they must be active in order for transcription to occur |
| - | - **Corepressor: | + | - Corepressor: |
| - | * [[Untitled_a1baf95c2be74fad95ea92c3882c2c8f: | + | * Untitled_a1baf95c2be74fad95ea92c3882c2c8f: |
| - | | + | * Repressible operon: transcription usually on but can be inhibited when repressor binds to it |
| - | | + | * Inducible Operon: transcription usually off but can be turned on when inducer binds to and inactivates repressor protein |
| - | * [[Untitled_a1baf95c2be74fad95ea92c3882c2c8f: | + | * Untitled_a1baf95c2be74fad95ea92c3882c2c8f: |
| - | * Both involve | + | * Both involve negative gene regulation bcuz operons are switched off by active form of repressor protein |
| * In general repressible operons are associated with genes that regulate anabolic pathways while inducible operons are associated with catabolic pathways. | * In general repressible operons are associated with genes that regulate anabolic pathways while inducible operons are associated with catabolic pathways. | ||
| * Positive Gene Regulation | * Positive Gene Regulation | ||
| - | * Gene regulation positive bcuz **activator** regulatory protein directly interacts with operon to increase transcription | + | * Gene regulation positive bcuz activator regulatory protein directly interacts with operon to increase transcription |
| - | * Example: | + | * Example: CAP |
| * CAP is activator protein which becomes active when cAMP binds to it → CAP attaches to promoter → increases RNA pol affinity for lac promoter → increases transcription and directly stimulates gene expression | * CAP is activator protein which becomes active when cAMP binds to it → CAP attaches to promoter → increases RNA pol affinity for lac promoter → increases transcription and directly stimulates gene expression | ||
| * Glucose lvls high → cAMP lvls are down → CAP is inactive | * Glucose lvls high → cAMP lvls are down → CAP is inactive | ||
| * Glucose lvls low → cAMp lvls are high → CAP is activated | * Glucose lvls low → cAMp lvls are high → CAP is activated | ||
| - | | + | * 3 Examples of Gene Regulation |
| - | - **Lac operon: controls breakdown of lactose** | + | - Lac operon: controls breakdown of lactose |
| * No lactose present: In the absence of lactose, the repressor switches off the operon by binding to the operator. | * No lactose present: In the absence of lactose, the repressor switches off the operon by binding to the operator. | ||
| * Lactose Present: When lactose is present, and the bacteria needs to break down to digest it, allolactose (an isomer of lactose) acts as an inducer by binding to the repressor and inactivating it → repressor cannot block the operator, and RNA polymerase can bind to it and begin to transcribe the proteins needed to digest lactose. | * Lactose Present: When lactose is present, and the bacteria needs to break down to digest it, allolactose (an isomer of lactose) acts as an inducer by binding to the repressor and inactivating it → repressor cannot block the operator, and RNA polymerase can bind to it and begin to transcribe the proteins needed to digest lactose. | ||
| - | * Enzymes operon makes are **inducible enzymes** and operon is **inducible operon** | + | * Enzymes operon makes are inducible enzymes and operon is inducible operon |
| * Bcuz repressor protein is involved → negative regulation | * Bcuz repressor protein is involved → negative regulation | ||
| - | - **Trp Operon: regulatory gene produces inactive repressor that does not bind to operator → RNA pol can transcribe genes to make amino acids for enzyme** | + | - Trp Operon: regulatory gene produces inactive repressor that does not bind to operator → RNA pol can transcribe genes to make amino acids for enzyme |
| - | * When amino acid in environment → cell doesn' | + | * When amino acid in environment → cell doesn' |
| - | * Produced enzymes are **repressible enzymes** and operon is **repressible operon** | + | * Produced enzymes are repressible enzymes and operon is repressible operon |
| - | * Bcuz there is repressor protein → **negative regulation.** | + | * Bcuz there is repressor protein → negative regulation. |
| - | - **Glucose repression: 2nd regulatory process that influences the** **lac** **operon. Glucose is preferred over lactose → lactose only present → process enhances break down of lactose** | + | - Glucose repression: 2nd regulatory process that influences the lac operon. Glucose is preferred over lactose → lactose only present → process enhances break down of lactose |
| - | * Uses **activator** regulatory protein, CAP, that is activated by cAMP → **positive regulation** | + | * Uses activator regulatory protein, CAP, that is activated by cAMP → positive regulation |
| - | | + | * Eukaryotic Gene Expression Regulation |
| * Eukaryotic gene expression regulation is more complicated because… | * Eukaryotic gene expression regulation is more complicated because… | ||
| - | - **Multicellularity: | + | - Multicellularity: |
| - | - **Chromosome complexity: chromosomes are more complex bcuz of their larger size and organization with histone proteins** | + | - Chromosome complexity: chromosomes are more complex bcuz of their larger size and organization with histone proteins |
| * Some metabolic processes require activation of multiple genes, each located on different chromosomes → requires a more sophisticated system of coordination | * Some metabolic processes require activation of multiple genes, each located on different chromosomes → requires a more sophisticated system of coordination | ||
| - | - **Uncoupling of transcription and translation: | + | - Uncoupling of transcription and translation: |
| * Genes are expressed when their nucleotide sequence are transcribed to produce RNAs | * Genes are expressed when their nucleotide sequence are transcribed to produce RNAs | ||
| * Eukaryotes: Coordinately Controlled Genes | * Eukaryotes: Coordinately Controlled Genes | ||
| * Operons not used in eukaryotes | * Operons not used in eukaryotes | ||
| * Genes co-expressed are scattered over different chromosomes and coordinate gene expression & metabolic activity depends on every gene having same transcription factors and combination of control elements | * Genes co-expressed are scattered over different chromosomes and coordinate gene expression & metabolic activity depends on every gene having same transcription factors and combination of control elements | ||
| - | * [[Untitled_a1baf95c2be74fad95ea92c3882c2c8f: | + | * Untitled_a1baf95c2be74fad95ea92c3882c2c8f: |
| * Transcription factors in nucleus bind to control elements → promote simultaneous transcription of genes | * Transcription factors in nucleus bind to control elements → promote simultaneous transcription of genes | ||
| * Coordinate gene regulation often occurs in response to chemical signals from outside the cell, either steroid or protein hormones that activate transcription factors | * Coordinate gene regulation often occurs in response to chemical signals from outside the cell, either steroid or protein hormones that activate transcription factors | ||
| Line 2885: | Line 3009: | ||
| * Genes with same set of control elements are activated by same chemical signals | * Genes with same set of control elements are activated by same chemical signals | ||
| ====Methods of Gene Regulation==== | ====Methods of Gene Regulation==== | ||
| - | - **DNA Methylation: | + | - DNA Methylation: |
| - | - **Histone Acetylation** | + | - Histone Acetylation |
| - | - **Homeotic Genes: master genes that control the pattern of body formation during early embryonic development** | + | - Homeotic Genes: master genes that control the pattern of body formation during early embryonic development |
| * Ex: in flies genes control formation of body structures like body segments and antenna | * Ex: in flies genes control formation of body structures like body segments and antenna | ||
| * Mutant homeotic genes produce body parts in wrong places | * Mutant homeotic genes produce body parts in wrong places | ||
| - | | + | * Homeobox is a specific nucleotide sequence that codes for protein |
| - | | + | * Hox genes contain homeobox and direct development of specific body part |
| * Products of genes act as transcription factors | * Products of genes act as transcription factors | ||
| * Appear in clusters and order on DNA controls order of expression and timing of body part development | * Appear in clusters and order on DNA controls order of expression and timing of body part development | ||
| - | - **X inactivation: | + | - X inactivation: |
| - | - **Transcription Initiation:** | + | - Transcription Initiation: |
| - | - **Coactivators & Mediators: additional proteins that contribute to the binding of transcription complex components** | + | - Coactivators & Mediators: additional proteins that contribute to the binding of transcription complex components |
| - | - **RNA processing/ | + | - RNA processing/ |
| - | - **RNA interference (RNAi): gene silencing caused by short noncoding RNA that bind to complementary sequences of mRNAs & block expression** | + | - RNA interference (RNAi): gene silencing caused by short noncoding RNA that bind to complementary sequences of mRNAs & block expression |
| - | | + | * Short Interfering RNAs (siRNAs): short double-stranded RNA, one strand is degraded → allows remaining strand to complement and inactivate a sequence of mRNA |
| - | | + | * Long noncoding RNA: some condense chromosome |
| - | | + | * PiRNA: reestablishes methylation patterns during gamete formation and block expression of some transposons → induce the formation of heterochromatin → block transcription |
| - | | + | * Dicer: Enzyme that trims small double-stranded RNAs into molecules that can block translation. |
| - | - [[Untitled_a1baf95c2be74fad95ea92c3882c2c8f: | + | - Untitled_a1baf95c2be74fad95ea92c3882c2c8f: |
| - | | + | * MicroRNAs (miRNAs): Functions in RNA silencing and post-transcriptional regulation of gene expression. |
| * Degrades mRNA if bases are completely complementary, | * Degrades mRNA if bases are completely complementary, | ||
| - | - **MRNA degradation: | + | - MRNA degradation: |
| * Poly-A-Tail and 5’ cap maintain mRNA stability but degradation slowly occurs as mRNA ages & degrading enzymes target tail and cap + untranslated UTR regions | * Poly-A-Tail and 5’ cap maintain mRNA stability but degradation slowly occurs as mRNA ages & degrading enzymes target tail and cap + untranslated UTR regions | ||
| * Amount of protein made depends on rate of mRNA degradation | * Amount of protein made depends on rate of mRNA degradation | ||
| - | - **Protein Degradation: | + | - Protein Degradation: |
| - | - **Protein Processing: protein chemical modification can activate/ | + | - Protein Processing: protein chemical modification can activate/ |
| - | - **Translation Initiation: translation can be blocked by regulatory proteins that bind to untranslated sequence (UTR) at 5’ or 3’ end → prevents ribosomal attachment** | + | - Translation Initiation: translation can be blocked by regulatory proteins that bind to untranslated sequence (UTR) at 5’ or 3’ end → prevents ribosomal attachment |
| - | | + | * Epigenetic (above the genes) Changes |
| * Inheritance of traits transmitted by mechanisms not directly involving the nucleotide sequence | * Inheritance of traits transmitted by mechanisms not directly involving the nucleotide sequence | ||
| * Do not alter DNA sequence, | * Do not alter DNA sequence, | ||
| - | | + | * Can affect gene expression through reversible modifications such as… |
| - | | + | * Histone acetylation, |
| - | | + | * Regulation of Chromatin Structures Untitled_a1baf95c2be74fad95ea92c3882c2c8f: |
| - | | + | * Histone modification: |
| * Access to DNA for transcription can be affected by.. | * Access to DNA for transcription can be affected by.. | ||
| - | | + | * Acetylation: |
| - | | + | * Methylation: |
| * Protects against restriction fragments; DNA methylation inactivates genes (long-term) | * Protects against restriction fragments; DNA methylation inactivates genes (long-term) | ||
| - | | + | * Regulation of Transcription Initiation |
| * After chromatin modification, | * After chromatin modification, | ||
| - | | + | * Transcription Initiation Complex: group of proteins associated with RNA pol II and inhibit/ |
| * Proteins assemble on promoter sequence upstream (towards 5’ end) & adjacent to gene to be transcribed | * Proteins assemble on promoter sequence upstream (towards 5’ end) & adjacent to gene to be transcribed | ||
| * Gene expression can be inhibited or activated by binding of repressors or activators to enhancers | * Gene expression can be inhibited or activated by binding of repressors or activators to enhancers | ||
| - | | + | * General transcription factors: proteins required by all transcription events to initiate transcription |
| * Some target the TATA box sequence associated with promoter | * Some target the TATA box sequence associated with promoter | ||
| - | | + | * Specific transcription factors: other proteins associated with regulating specific transcription activities--specific to cell type, genes, or timing of transcription. |
| * 2 kinds which bind to enhancers | * 2 kinds which bind to enhancers | ||
| - | | + | * Activators |
| - | | + | * Repressors: stop transcription & translation |
| - | | + | * Control Elements: segments of noncoding DNA that serve as binding sites for protein transcription factors to regulate transcription |
| * DNA sequences located near (proximal) or far (distal) from the promoter, upstream | * DNA sequences located near (proximal) or far (distal) from the promoter, upstream | ||
| - | | + | * Enhancers: Distal control elements grouped together |
| * Particular combination of control elements in an enhancer associated with a gene | * Particular combination of control elements in an enhancer associated with a gene | ||
| * Diff combination → diff regulation of transcription | * Diff combination → diff regulation of transcription | ||
| - | | + | * Transcription Factors Structure |
| * Usually have DNA binding domains and binding domains for other transcription factors | * Usually have DNA binding domains and binding domains for other transcription factors | ||
| * Transcription factors as repressors: | * Transcription factors as repressors: | ||
| - Bind to enhancers and block activators | - Bind to enhancers and block activators | ||
| - | - **Silencing:** bind to chromatin structure and remove acetyl | + | - Silencing: bind to chromatin structure and remove acetyl |
| - | | + | * The Steps of Regulation of Transcription & Transcription Initiation Complex Untitled_a1baf95c2be74fad95ea92c3882c2c8f: |
| - Enhancers bind to activator | - Enhancers bind to activator | ||
| - Since enhancer can be far from gene, a DNA-bending protein enables activators to bind to mediator proteins and general transcription factors at the promoter | - Since enhancer can be far from gene, a DNA-bending protein enables activators to bind to mediator proteins and general transcription factors at the promoter | ||
| - | - A **transcription initiation complex** is formed → initiate transcription | + | - A transcription initiation complex is formed → initiate transcription |
| - | | + | * Cellular Specialization/ |
| - | | + | * Cell Differentiation: |
| * Always involves master-regulatory genes that produce tissue-specific proteins → give cell structure/ | * Always involves master-regulatory genes that produce tissue-specific proteins → give cell structure/ | ||
| - | | + | * Determination: |
| * 3 Processes of embryonic development: | * 3 Processes of embryonic development: | ||
| - Cell division | - Cell division | ||
| - Cell differentiation: | - Cell differentiation: | ||
| * Example of how gene expression regulation affects cell long-term behaviour | * Example of how gene expression regulation affects cell long-term behaviour | ||
| - | - **Morphogenesis**: pattern formation and shaping of an organism | + | - Morphogenesis: |
| ====Factors That Influence Embryonic Development==== | ====Factors That Influence Embryonic Development==== | ||
| * Specific genes expressed in cell during development determine cell type | * Specific genes expressed in cell during development determine cell type | ||
| Line 2964: | Line 3088: | ||
| * Environment: | * Environment: | ||
| * Internal: signals come from inside cell | * Internal: signals come from inside cell | ||
| - | * Cell signals to itself and **Cytoplasmic Determinants** | + | * Cell signals to itself and Cytoplasmic Determinants |
| - | - **Cleavages don't divide cells equally → cells acquire variations based on orientation of cleavages** | + | - Cleavages don't divide cells equally → cells acquire variations based on orientation of cleavages |
| - | - **Cytoplasmic Determinants: | + | - Cytoplasmic Determinants: |
| * Cytoplasmic determinants not dispersed equally which affect embryonic development | * Cytoplasmic determinants not dispersed equally which affect embryonic development | ||
| * Cytoplasmic axes and substances unique to each cell may turn genes on or off and set cells down specific path | * Cytoplasmic axes and substances unique to each cell may turn genes on or off and set cells down specific path | ||
| - | - **Embryonic Induction: signaling molecules from embryonic cells cause transcriptional changes in nearby target cells** | + | - Embryonic Induction: signaling molecules from embryonic cells cause transcriptional changes in nearby target cells |
| - | | + | * Organizers: cells that exert this influence |
| * Cell-cell communication can occur by ligands or interaction between cell surfaces → leads to specific gene expression and cell differentiation | * Cell-cell communication can occur by ligands or interaction between cell surfaces → leads to specific gene expression and cell differentiation | ||
| * Cells closer receive more than cells farther away | * Cells closer receive more than cells farther away | ||
| - | - **Apoptosis: some cells produced during development have temporary role and are deliberately destroyed** | + | - Apoptosis: some cells produced during development have temporary role and are deliberately destroyed |
| * Ex: during early stages have webbing but later cells undergo apoptosis | * Ex: during early stages have webbing but later cells undergo apoptosis | ||
| ====Differentiation and Stem Cells==== | ====Differentiation and Stem Cells==== | ||
| | | ||
| - | **Stem Cells:** unspecialized cells during early stage of embryonic development that can reproduce indefinitely and differentiate (become any) into specialized cells | + | Stem Cells: unspecialized cells during early stage of embryonic development that can reproduce indefinitely and differentiate (become any) into specialized cells |
| - | [[Untitled_a1baf95c2be74fad95ea92c3882c2c8f: | + | Untitled_a1baf95c2be74fad95ea92c3882c2c8f: |
| * But as development continues → cells differentiate & become specialized → cell divisions make more specialized cells | * But as development continues → cells differentiate & become specialized → cell divisions make more specialized cells | ||
| * Cells become specialized because transcription factors activate some genes while suppressing others | * Cells become specialized because transcription factors activate some genes while suppressing others | ||
| * Process is self-reinforcing as the cell can signal to itself | * Process is self-reinforcing as the cell can signal to itself | ||
| * Genes permanently turned off associated with DNA methylation and histone modification | * Genes permanently turned off associated with DNA methylation and histone modification | ||
| - | * **Embryonic stem cells** **(****ES****)****:** Can become any kind of cell (including sperm and egg) | + | * Embryonic stem cells (ES): Can become any kind of cell (including sperm and egg) |
| - | * **Adult body stem cells****:** can only replace non-reproducing specialized cells (not sperm and egg) | + | * Adult body stem cells: can only replace non-reproducing specialized cells (not sperm and egg) |
| - | * **Pluripotent: | + | * Pluripotent: |
| - | * **Totipotent: | + | * Totipotent: cells that can form new fetus |
| - | * **Unipotent:** a cell that has differentiated and cannot become any type of new cell | + | * Unipotent: a cell that has differentiated and cannot become any type of new cell |
| - | * **Differential Gene Expression:** expression of different genes by cells with the same genome | + | * Differential Gene Expression: expression of different genes by cells with the same genome |
| - | * **Morphogenesis, | + | * Morphogenesis, |
| - | | + | * Pattern Formation: the process of organizing tissues and organs that begins in early embryo |
| * Various genes code for pattern formation of organisms | * Various genes code for pattern formation of organisms | ||
| - | | + | * Positional Information: |
| - | | + | * Maternal effect: offsprings axes encoded by mother’s genes (ie. Cytoplasmic determinants), |
| * So mutations passed to all | * So mutations passed to all | ||
| =====Mutations and Biotechnology===== | =====Mutations and Biotechnology===== | ||
| ====Biotechnology==== | ====Biotechnology==== | ||
| Making Multiple Copies of a Gene or DNA Segment | Making Multiple Copies of a Gene or DNA Segment | ||
| - | | + | * Recombinant DNA: contains DNA segments or genes from diff sources |
| * One part of DNA molecule, chromosome or organism to another | * One part of DNA molecule, chromosome or organism to another | ||
| * Transfer of DNA segments can happen naturally thru viral transduction, | * Transfer of DNA segments can happen naturally thru viral transduction, | ||
| - | * Recombinant DNA can be produced artificially with **biotechnology: | + | * Recombinant DNA can be produced artificially with biotechnology: |
| ====DNA Cloning==== | ====DNA Cloning==== | ||
| * Procedure that allows DNA fragments or genes to be copied | * Procedure that allows DNA fragments or genes to be copied | ||
| - | - **Use a restriction enzyme to cut up the foreign DNA that contains a gene to be copied.** The restriction enzyme produces multiple fragments of foreign DNA with sticky ends | + | - Use a restriction enzyme to cut up the foreign DNA that contains a gene to be copied. The restriction enzyme produces multiple fragments of foreign DNA with sticky ends |
| - | - **Use the same restriction enzyme to cut up the DNA of a cloning vector.** This produces the same strictly ends in both foreign DNA and cloning vector: DNA molecule that can carry foreign DNA into a host cell and be replicated there | + | - Use the same restriction enzyme to cut up the DNA of a cloning vector. This produces the same strictly ends in both foreign DNA and cloning vector: DNA molecule that can carry foreign DNA into a host cell and be replicated there |
| * Plasmid is a common cloning vector bcuz can be introduced into bacteria for transformation | * Plasmid is a common cloning vector bcuz can be introduced into bacteria for transformation | ||
| * Using a plasmid that has one restriction site for restriction enzyme can help with identification of the copied gene | * Using a plasmid that has one restriction site for restriction enzyme can help with identification of the copied gene | ||
| - | | + | * ampR gene: gives bacterial resistance against antibiotic ampicillin |
| - | | + | * GFP gene: makes bacteria fluorescence green |
| - | * **lac****Z | + | * lacZ gene: codes for enzyme that breaks down lactose |
| - | * Also breaks down artificially made **X-gal** | + | * Also breaks down artificially made X-gal |
| * The one restriction site for the restriction enzyme occurs in within the lacZ gene | * The one restriction site for the restriction enzyme occurs in within the lacZ gene | ||
| - | - **Mix the cut foreign DNA with cut plasmids.** This allows base-pairing at the sticky end | + | - Mix the cut foreign DNA with cut plasmids. This allows base-pairing at the sticky end |
| - | - **Apply DNA ligase to stabilize attachments and close up the backbone.** Forms recombinant plasmids (some plasmids will not pair) | + | - Apply DNA ligase to stabilize attachments and close up the backbone. Forms recombinant plasmids (some plasmids will not pair) |
| - | - **Mix plasmids with bacteria to allow transformation.** Some of the bacteria will absorb the plasmids (transformation) | + | - Mix plasmids with bacteria to allow transformation. Some of the bacteria will absorb the plasmids (transformation) |
| * Not all bacteria will be competent enough to take up trait and express traits associated with gene | * Not all bacteria will be competent enough to take up trait and express traits associated with gene | ||
| - | | + | * Competent: change in structure and permeability of cell membrane |
| - | - **Grow the transformed bacteria in the presence of ampicillin and X- gal.** | + | - Grow the transformed bacteria in the presence of ampicillin and X- gal. |
| * Only bacteria that have absorbed a plasmid (transformed bacteria) will grow in presence of ampicillin bcuz contain the resistant genel; they will also be white bcuz lack functioning lacZ gene (foreign DNA was inserted within lacZ gene of the plasmid, making gene dysfunctional ) | * Only bacteria that have absorbed a plasmid (transformed bacteria) will grow in presence of ampicillin bcuz contain the resistant genel; they will also be white bcuz lack functioning lacZ gene (foreign DNA was inserted within lacZ gene of the plasmid, making gene dysfunctional ) | ||
| * Purposes of Gene Cloning: to make many copies/ | * Purposes of Gene Cloning: to make many copies/ | ||
| * Can isolate gene and give product to different organism | * Can isolate gene and give product to different organism | ||
| - | | + | * Using Restriction Enzymes to Make a Recombinant Plasmid |
| - | * Recombinant DNA tech uses **Restriction enzymes (restriction endonucleases)** to cut DNA | + | * Recombinant DNA tech uses Restriction enzymes (restriction endonucleases) to cut DNA |
| * Restriction enzymes obtained from bacteria that manufacture these enzymes to combat invading viruses | * Restriction enzymes obtained from bacteria that manufacture these enzymes to combat invading viruses | ||
| * DNA of a bacterial cell is protected from the cell’s own restriction enzymes by the addition of methyl groups (—CH3) within the sequences recognized by the enzymes | * DNA of a bacterial cell is protected from the cell’s own restriction enzymes by the addition of methyl groups (—CH3) within the sequences recognized by the enzymes | ||
| - | * Restriction enzymes cut the sugar phosphate backbones of the two DNA strands in a staggered manner at short, specific nucleotide sequences (**restriction sites**) → yielding a set of double-stranded | + | * Restriction enzymes cut the sugar phosphate backbones of the two DNA strands in a staggered manner at short, specific nucleotide sequences (restriction sites) → yielding a set of double-stranded restriction fragments with single-stranded sticky ends |
| * Sticky ends can form hydrogen-bonded base pairs with complementary sticky ends of a DNA molecules cut with the same restriction enzyme | * Sticky ends can form hydrogen-bonded base pairs with complementary sticky ends of a DNA molecules cut with the same restriction enzyme | ||
| ====Polymerase Chain Reaction (PCR)==== | ====Polymerase Chain Reaction (PCR)==== | ||
| - | | + | * PCR: a technique that makes large number of DNA copies faster than DNA cloning process |
| - | - **DNA is heated.** Heating denatures (separates) hydrogen bonding holding the dsDNA together and forms two ssDNA molecules | + | - DNA is heated. Heating denatures (separates) hydrogen bonding holding the dsDNA together and forms two ssDNA molecules |
| - | - **DNA is cooled and ssDNA primers are added.** Two primers are added, each complementary to the 3' end of ssDNA. (ssDNA ~ role of RNA primers) | + | - DNA is cooled and ssDNA primers are added. Two primers are added, each complementary to the 3' end of ssDNA. (ssDNA ~ role of RNA primers) |
| - | - **DNA polymerase is added.** A special, heat-tolerant DNA polymerase derived from bacteria adapted to living in hot springs is added. | + | - DNA polymerase is added. A special, heat-tolerant DNA polymerase derived from bacteria adapted to living in hot springs is added. |
| * DNA polymerase attaches to primers at each end of ssDNA and synthesizes complementary DNA strand | * DNA polymerase attaches to primers at each end of ssDNA and synthesizes complementary DNA strand | ||
| * In the end one initial dsDNA becomes two dsDNA | * In the end one initial dsDNA becomes two dsDNA | ||
| - | - **Repeat the above steps. Increases the number of DNA molecules exponentially** | + | - Repeat the above steps. Increases the number of DNA molecules exponentially |
| - | * **Expressing Cloned Genes** Bacterial Expression Systems | + | * Expressing Cloned Genes Bacterial Expression Systems |
| * For eukaryotic gene to be expressed must have its coding exons and a bacterial promoter | * For eukaryotic gene to be expressed must have its coding exons and a bacterial promoter | ||
| - | | + | * Expression vector: a cloning vector that contains a highly active bacterial promoter just upstream of a restriction site where the eukaryotic gene can be inserted in the correct reading frame |
| * The bacterial host cell will recognize the promoter and proceed to express the foreign gene now linked to that promoter. | * The bacterial host cell will recognize the promoter and proceed to express the foreign gene now linked to that promoter. | ||
| * Bacteria have same mechanisms for replication & transcription so can express eukaryotic genes | * Bacteria have same mechanisms for replication & transcription so can express eukaryotic genes | ||
| * Eukaryotic Expression Systems | * Eukaryotic Expression Systems | ||
| - | | + | * Electroporation: |
| * Introduced DNA is incorporated into a cell’s genome by genetic recombination, | * Introduced DNA is incorporated into a cell’s genome by genetic recombination, | ||
| * Evolution: Because of their common ancestry, all living organisms share the same basic mechanisms of gene expression. | * Evolution: Because of their common ancestry, all living organisms share the same basic mechanisms of gene expression. | ||
| - | | + | * Analyzing Gene Expression & DNA Sequencing |
| - | | + | * When trying to find mRNA for a specific gene can use nucleic acid probe: a short, single-stranded nucleic acid (either RNA or DNA) complementary to the mRNA of interest |
| - | | + | * DNA sequencing: genetic engineering technique that determines the order of nucleotides in DNA to analyze DNA through base-pairing rules |
| * Problems With Gene Expression | * Problems With Gene Expression | ||
| * When eukaryotic DNA are inserted into the genome of a bacterium, introns often prevent translation | * When eukaryotic DNA are inserted into the genome of a bacterium, introns often prevent translation | ||
| * To avoid this problem, reverse transcriptase (from retrovirus) obtains DNA with required genes directly from mRNA | * To avoid this problem, reverse transcriptase (from retrovirus) obtains DNA with required genes directly from mRNA | ||
| - | * DNA obtained in this manner is called | + | * DNA obtained in this manner is called complementary DNA (cDNA) and lack the introns that suppress transcription |
| - | | + | * Medical Applications of Biotechnology & DNA Sequencing |
| * Can use mentioned techniques to compare gene expression in healthy and diseased tissues → researchers are finding genes that are turned on or off in particular diseases | * Can use mentioned techniques to compare gene expression in healthy and diseased tissues → researchers are finding genes that are turned on or off in particular diseases | ||
| * Diagnosis and Treatment of Diseases | * Diagnosis and Treatment of Diseases | ||
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| * Mitochondrial DNA is contributed to the egg only by the mother → trace ancestry | * Mitochondrial DNA is contributed to the egg only by the mother → trace ancestry | ||
| * Personalized Medicine | * Personalized Medicine | ||
| - | * In humans, | + | * In humans, genome-wide association studies identify and use single nucleotide polymorphisms (SNPs) as genetic markers for alleles that are associated with particular conditions |
| * Help ppl minimize risk for disease and better treatment through Genetic profiling | * Help ppl minimize risk for disease and better treatment through Genetic profiling | ||
| * Humans share 99% DNA, differences caused by variation of nucleotide bases | * Humans share 99% DNA, differences caused by variation of nucleotide bases | ||
| * Human Gene Therapy and Gene Editing | * Human Gene Therapy and Gene Editing | ||
| - | | + | * Gene therapy: introduce new genes as a treatment for disease |
| * Goal: insert a normal allele of the mutated gene into the somatic cells of the tissue affected by the disorder → can now make missing protein | * Goal: insert a normal allele of the mutated gene into the somatic cells of the tissue affected by the disorder → can now make missing protein | ||
| * CRISPR-Cas9: | * CRISPR-Cas9: | ||
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| * Human insulin gene cloning: insulin gene is inserted into bacteria; bacteria multiply and reproduce human insulin protein for use in treating diabetes | * Human insulin gene cloning: insulin gene is inserted into bacteria; bacteria multiply and reproduce human insulin protein for use in treating diabetes | ||
| ====Gel Electrophoresis and DNA Fingerprinting==== | ====Gel Electrophoresis and DNA Fingerprinting==== | ||
| - | [[https:// | + | https:// |
| - | | + | <img src=" |
| + | </ | ||
| + | * Gel Electrophoresis: | ||
| - DNA fragments of diff lengths are separated as they diffuse thru a gelatinous material under influence of an electrical field | - DNA fragments of diff lengths are separated as they diffuse thru a gelatinous material under influence of an electrical field | ||
| * DNA has same charge per mass so separated only by lengths | * DNA has same charge per mass so separated only by lengths | ||
| - | - Since DNA is **(-)** charged (bcuz of phosphate groups) it moves towards | + | - Since DNA is (-) charged (bcuz of phosphate groups) it moves towards (+) electrode |
| - Shorter fragments move further thru the gel than longer, heavier fragments | - Shorter fragments move further thru the gel than longer, heavier fragments | ||
| - Uses process to compare DNA fragments of presumed closely related species to determine evolutionary relationships | - Uses process to compare DNA fragments of presumed closely related species to determine evolutionary relationships | ||
| * Forensic Evidence and Genetic Profile | * Forensic Evidence and Genetic Profile | ||
| - | * When restriction fragments between individuals of same species are compared, the fragments differ in length because of **polymorphisms** (slight differences in DNA sequences) | + | * When restriction fragments between individuals of same species are compared, the fragments differ in length because of polymorphisms (slight differences in DNA sequences) |
| - | * Fragments called | + | * Fragments called restriction fragment length polymorphism (RFLP) |
| - | * In **DNA fingerprinting**, compare produced RFLPs to find match | + | * In DNA fingerprinting, |
| ====Concerns About Biotechnology==== | ====Concerns About Biotechnology==== | ||
| - | - **Pharmaceuticals: | + | - Pharmaceuticals: |
| * Ex: human insulin and human growth hormone (HGH) are readily available as products of DNA cloning | * Ex: human insulin and human growth hormone (HGH) are readily available as products of DNA cloning | ||
| * Insulin is used to treat diabetes and HGH for dwarfism but can also be misused by athletes to enhance performance | * Insulin is used to treat diabetes and HGH for dwarfism but can also be misused by athletes to enhance performance | ||
| - | - **Human Disease Profiles: Some diseases are inherited and can be identified before symptoms appear by evaluating the genes thru SNP markers and PCR with specific primers** | + | - Human Disease Profiles: Some diseases are inherited and can be identified before symptoms appear by evaluating the genes thru SNP markers and PCR with specific primers |
| * Sometimes a person can avoid symptoms but other times there are no available treatments (so should the person know?) | * Sometimes a person can avoid symptoms but other times there are no available treatments (so should the person know?) | ||
| * Should medical insurances know they are high-risk patients? | * Should medical insurances know they are high-risk patients? | ||
| - | - **Transgenic organisms have genes taken from other organisms (and species) through genetic engineering** | + | - Transgenic organisms have genes taken from other organisms (and species) through genetic engineering |
| - | | + | * Genetic engineering in plants. Genes have been inserted into plants that provide resistance to pests, insects, herbicides, and drought |
| * Ex: many GM plants have the Bt gene that gives plants insecticide properties. | * Ex: many GM plants have the Bt gene that gives plants insecticide properties. | ||
| * Gene comes from the plasmid of bacteria which makes chemicals toxic to specific insects → but some insects not killed → build up resistance | * Gene comes from the plasmid of bacteria which makes chemicals toxic to specific insects → but some insects not killed → build up resistance | ||
| * Also plants spread genetic information through pollen between different species | * Also plants spread genetic information through pollen between different species | ||
| - | | + | * Genetic engineering in animals. Genes have been inserted into domestic animals to make desirable products or to produce animals that are better at rearing. |
| * Ex: salmon given growth hormone gene (from different species) | * Ex: salmon given growth hormone gene (from different species) | ||
| * Concerned about gene flow into wild populations | * Concerned about gene flow into wild populations | ||
| - | | + | * GMOs in the food chain. Worried that genes that causes allergies might be may be unknowingly inserted into GM organisms |
| - | - **Reproductive/ | + | - Reproductive/ |
| * Selective breeding is slow but reproductive cloning promises to produce copies of a desirable individual within single generation | * Selective breeding is slow but reproductive cloning promises to produce copies of a desirable individual within single generation | ||
| * But so far has had mediocre success with test subjects suffering organ failure, disease, shorter life spans, and low success rates (hundreds of trials before successful clone | * But so far has had mediocre success with test subjects suffering organ failure, disease, shorter life spans, and low success rates (hundreds of trials before successful clone | ||
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| * A change in the sequence of nucleotides in an original DNA molecule | * A change in the sequence of nucleotides in an original DNA molecule | ||
| - | | + | * Mutations are irreversible and the main cause of genetic variation (alleles) |
| - | * Mutations can cause **changes in phenotype** (ex. cystic fibrosis) or disorders | + | * Mutations can cause changes in phenotype (ex. cystic fibrosis) or disorders |
| * Alterations in DNA can lead to changes in type or amount of protein produced | * Alterations in DNA can lead to changes in type or amount of protein produced | ||
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| Causes for Mutations | Causes for Mutations | ||
| - | | + | * Mutagens: radiation or chemicals that cause mutations → damage DNA (ex: deamination, |
| - | | + | * Carcinogens: |
| Environmental: | Environmental: | ||
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| * Errors in DNA replication, | * Errors in DNA replication, | ||
| - | **Point Mutation:** single or few nucleotide errors that include… | + | Point Mutation: single or few nucleotide errors that include… |
| - | - **Substitution: | + | - Substitution: |
| * An amino acid substitution would always alter the primary structure of the protein, sometimes alter the tertiary structure of the protein and its biological activity | * An amino acid substitution would always alter the primary structure of the protein, sometimes alter the tertiary structure of the protein and its biological activity | ||
| - | - **Deletion: when a nucleotide is omitted from the nucleotide sequence → missing amino acid** | + | - Deletion: when a nucleotide is omitted from the nucleotide sequence → missing amino acid |
| * Deletions closer to start point of coding are more harmful | * Deletions closer to start point of coding are more harmful | ||
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| * An amino acid deletion will alter the primary, secondary, and tertiary structure → can’t fold properly → nonfunctional | * An amino acid deletion will alter the primary, secondary, and tertiary structure → can’t fold properly → nonfunctional | ||
| - | - **Insertion: when a nucleotide is added to nucleotide sequence** | + | - Insertion: when a nucleotide is added to nucleotide sequence |
| - | - **Frameshift: result of deletion or insertion & occurs when the number of nucleotides is not divisible by three → alters the way that the genetic messages (mRNA codons) is read** | + | - Frameshift: result of deletion or insertion & occurs when the number of nucleotides is not divisible by three → alters the way that the genetic messages (mRNA codons) is read |
| * All other codons and amino acids (proteins) following mutation will be wrong | * All other codons and amino acids (proteins) following mutation will be wrong | ||
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| * Might change the lvl of protein activity bcuz might substitute an amino acid in the active site. | * Might change the lvl of protein activity bcuz might substitute an amino acid in the active site. | ||
| - | - **Silent Mutation: when new codon still codes for the same amino acid** | + | - Silent Mutation: when new codon still codes for the same amino acid |
| * More common when nucleotide substitution results in a change of last of 3 in a codon nucleotide | * More common when nucleotide substitution results in a change of last of 3 in a codon nucleotide | ||
| - | | + | * Wobble Pairing: relaxed requirement for in the third position nucleotide |
| - | - **Missense Mutation: when new codon codes for** **new** **amino acid** | + | - Missense Mutation: when new codon codes for new amino acid |
| * Effect can be minor or result in the production of a protein that can’t fold into 3D shape and carry out function specific to shape | * Effect can be minor or result in the production of a protein that can’t fold into 3D shape and carry out function specific to shape | ||
| * Ex: hemoglobin protein that causes sickle-cell disease | * Ex: hemoglobin protein that causes sickle-cell disease | ||
| - | - **Nonsense Mutation: when new codon codes for stop codon** | + | - Nonsense Mutation: when new codon codes for stop codon |
| * Causes translation to be terminated early → resulting polypeptide is shorter → usually nonfunctional | * Causes translation to be terminated early → resulting polypeptide is shorter → usually nonfunctional | ||
| - | **Alterations to Chromosome Structure:** | + | Alterations to Chromosome Structure: |
| - | | + | * Chromosomal aberrations occur when chromosome segments are changed, often result of crossing over errors |
| - | | + | * Duplications: |
| - | * Ex: **Huntington’s disease** is caused by insertion of multiple repeats of 3 nucleotides → codes for defective enzyme → death | + | * Ex: Huntington’s disease is caused by insertion of multiple repeats of 3 nucleotides → codes for defective enzyme → death |
| - | | + | * Deletions: during crossing over, one chromosome takes the WHOLE part of the other that crossed over and the other one is left shorter. Usually involve lots of genes |
| * Cri du chat: cry of the cat, caused by deletion in chromosome 5 | * Cri du chat: cry of the cat, caused by deletion in chromosome 5 | ||
| - | | + | * Inversion: piece of chromosome that is crossed over goes on backwards, |
| * So order of the genes matters (usually don’t express abnormalities as long as does not introduce duplications or deletions) | * So order of the genes matters (usually don’t express abnormalities as long as does not introduce duplications or deletions) | ||
| - | | + | * Translocation: |
| * A parent with balanced translocation has chance to produce offspring with deletion or duplication | * A parent with balanced translocation has chance to produce offspring with deletion or duplication | ||
| - | [[https:// | + | https:// |
| + | <img src=" | ||
| + | </ | ||
| * Random mutations = source of new alleles = new phenotypes | * Random mutations = source of new alleles = new phenotypes | ||
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| * Translocations and inversions don't usually alter phenotype | * Translocations and inversions don't usually alter phenotype | ||
| - | **Human Genetic Disorders** | + | Human Genetic Disorders |
| - | - **Point Mutations:** | + | - Point Mutations: |
| - | | + | * Sickle-cell disease: caused by nucleotide substitution → defective hemoglobin → blood cell to become sickle shaped in low-oxygen → cell does not flow through capillaries freely and oxygen not delivered throughout body |
| * Heterozygote generally without symptoms | * Heterozygote generally without symptoms | ||
| - | | + | * Tay-Sachs Disease: nucleotide insertion → lysosomes lack functional enzyme to break down glycolipids → fat accumulate → death |
| - | - **Aneuploidy:** | + | - Aneuploidy: |
| - | | + | * Down Syndrome: when egg or sperm with with extra number 21 chromosome fuses with normal gamete → results in gamete with 3 copies of chromosome 21 (trisomy 21) |
| - | | + | * Turner Syndrome: nondisjunction of the sex chromoosome (monosomy) |
| * Sperm will have either both sex chromosomes (XY) or none (O) | * Sperm will have either both sex chromosomes (XY) or none (O) | ||
| * When normal gamete fuses with (O) gamete will have zygote that is XO → sterile female (45 chromosomes) with abnormalities | * When normal gamete fuses with (O) gamete will have zygote that is XO → sterile female (45 chromosomes) with abnormalities | ||
| * Although absence of single chromosome usually fatal, Y chromosome has such few genes that not too harmful | * Although absence of single chromosome usually fatal, Y chromosome has such few genes that not too harmful | ||
| - | | + | * Klinefelter Syndrome: occurs when XY or XX, produced as result of nondisjunction, |
| * Only affects male → still male as long as you have Y chromosome with the SRY gene | * Only affects male → still male as long as you have Y chromosome with the SRY gene | ||
| * Explains how there can be male calico cats | * Explains how there can be male calico cats | ||
| * Might express female secondary sex characteristics | * Might express female secondary sex characteristics | ||
| - | **Transfer and Sharing of DNA: Prokaryotes Vs. Eukaryotes** | + | Transfer and Sharing of DNA: Prokaryotes Vs. Eukaryotes |
| - | [[https:// | + | https:// |
| + | <img src=" | ||
| + | </ | ||
| - | - **Transduction** | + | - Transduction |
| * Viruses that infect bacteria (bacteriophages) move DNA from one bacterium to another "by accident." | * Viruses that infect bacteria (bacteriophages) move DNA from one bacterium to another "by accident." | ||
| - | - **Transformation** [[https:// | + | - Transformation https:// |
| + | <img src=" | ||
| + | </ | ||
| * Bacteria takes in DNA from its environment, | * Bacteria takes in DNA from its environment, | ||
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| Which can be copied and passed onto descendants | Which can be copied and passed onto descendants | ||
| - | - **Conjugation** | + | - Conjugation |
| - | * DNA is transferred from one bacterium to another. | + | * DNA is transferred from one bacterium to another. https:// |
| + | <img src=" | ||
| + | </ | ||
| * Donor cell (F+) uses pilus to transfer DNA from its cell to recipient cell (F-) → recipient becomes donor | * Donor cell (F+) uses pilus to transfer DNA from its cell to recipient cell (F-) → recipient becomes donor | ||
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| * Donor cells typically act as donors because they have a chunk of DNA called the fertility factor (or F factor) | * Donor cells typically act as donors because they have a chunk of DNA called the fertility factor (or F factor) | ||
| - | | + | * F Factor: codes for the proteins that make up the sex pilus. |
| * also contains a special site where DNA transfer during conjugation begins | * also contains a special site where DNA transfer during conjugation begins | ||
| - | **Horizontal Gene Transfer**: | + | Horizontal Gene Transfer: |
| - | | + | * Horizontal Gene Transfer: transmission of DNA between different genomes |
| * Source of genetic variation in bacteria: horizontal gene transfer & mutations | * Source of genetic variation in bacteria: horizontal gene transfer & mutations | ||
| * Bacteria use horizontal gene transfer used to spread virulent genes to harmless stains | * Bacteria use horizontal gene transfer used to spread virulent genes to harmless stains | ||
| - | | + | * Vertical Gene Transfer transmission of genetic material from parents to offspring during reproduction |
| * Occurs in: eukaryotes, prokaryotes; | * Occurs in: eukaryotes, prokaryotes; | ||
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| Virus Function | Virus Function | ||
| - | | + | * Virus: small nucleic acid genome enclosed in capsid |
| * Penetrates cell → takes over metabolic machinery → assembles new virus copies | * Penetrates cell → takes over metabolic machinery → assembles new virus copies | ||
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| Virus Structure | Virus Structure | ||
| - | [[https:// | + | https:// |
| + | <img src=" | ||
| + | </ | ||
| * DNA/RNA may be double-stranded or single-stranded | * DNA/RNA may be double-stranded or single-stranded | ||
| - | - **Capsid: viral protein coat enclosing genome, determines genomes size/shape and specificity** | + | - Capsid: viral protein coat enclosing genome, determines genomes size/shape and specificity |
| - | - **Viral envelopes: surrounds capsids, comes from host membranes lipids & proteins, help virus infect host** | + | - Viral envelopes: surrounds capsids, comes from host membranes lipids & proteins, help virus infect host |
| * The viral envelope mediates entry into the cell, the capsid enters the nuclear membrane, and the genome is all that enters the nucleus | * The viral envelope mediates entry into the cell, the capsid enters the nuclear membrane, and the genome is all that enters the nucleus | ||
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| * Are specific for types of cell they parasitize: some attack only one kind of cell within single species and others attack similar cells from range of closely related species | * Are specific for types of cell they parasitize: some attack only one kind of cell within single species and others attack similar cells from range of closely related species | ||
| - | | + | * Bacteriophages: |
| * Simpler Viruses | * Simpler Viruses | ||
| - | | + | * Viroids: infect plants, just floaty RNA (no capsids) |
| * Plant infections spread by plasmodesmata | * Plant infections spread by plasmodesmata | ||
| - | | + | * Prion: infectious misfolded proteins that can transmit incorrect shape |
| Viruses and Evolution | Viruses and Evolution | ||
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| Replication of Viruses | Replication of Viruses | ||
| - | **Lytic Cycle:** | + | Lytic Cycle: |
| - | * Used by **virulent** viruses: builds viral DNA & proteins → self assemble into virus → viruses bust out of the cell and lyse it, releasing lots of viruses → KILLS HOST CELL | + | * Used by virulent viruses: builds viral DNA & proteins → self assemble into virus → viruses bust out of the cell and lyse it, releasing lots of viruses → KILLS HOST CELL |
| - | **Lysogenic Cycle** | + | Lysogenic Cycle |
| - | | + | * Viral DNA incorporated into the cell’s genome by genetic recombination → host cell duplicates viral DNA & proteins |
| - | | + | * Used by temperate viruses DOES NOT KILL HOST CELL |
| - | | + | * Prophage: viral genes inserted into a bacteria |
| - | | + | * Provirus: viral genes inserted into an animal cell |
| * Stays dormant until there are optimal conditions, stress, or external environment stimulus (radiation or chemicals) → releases viruses to create an infection in the lytic cycle | * Stays dormant until there are optimal conditions, stress, or external environment stimulus (radiation or chemicals) → releases viruses to create an infection in the lytic cycle | ||
| * So cycle technically in between phase | * So cycle technically in between phase | ||
| - | * [[Untitled_a1baf95c2be74fad95ea92c3882c2c8f: | + | * Untitled_a1baf95c2be74fad95ea92c3882c2c8f: |
| RETROVIRUS SYNTHESIS: | RETROVIRUS SYNTHESIS: | ||
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| =====Evolution===== | =====Evolution===== | ||
| - | **Review** | + | Review |
| - | * Basic idea: ****“Descent with modification, | + | * Basic idea: “Descent with modification, |
| * Specific: the process by which frequency of heritable traits in population changes from one generation to the next | * Specific: the process by which frequency of heritable traits in population changes from one generation to the next | ||
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| Evolution: Earlier Theories | Evolution: Earlier Theories | ||
| - | - **Use and disuse: describe how body parts of organisms can develop with increased usage while unused parts weaken → idea was correct like among athletes** | + | - Use and disuse: describe how body parts of organisms can develop with increased usage while unused parts weaken → idea was correct like among athletes |
| - | - **Inheritance of acquired characteristics: | + | - Inheritance of acquired characteristics: |
| - | - **Catastrophism: | + | - Catastrophism: |
| - | | + | * Strata: layers of rock |
| - | **Evidence for Evolution** | + | Evidence for Evolution |
| - | - **Paleontology: | + | - Paleontology: |
| * Fossils removed from successive layers of sediment (deeper = older) show gradual changes alternating with rapid changes | * Fossils removed from successive layers of sediment (deeper = older) show gradual changes alternating with rapid changes | ||
| * Large, rapid changes produce new species | * Large, rapid changes produce new species | ||
| * Age of fossils determined using C-14 dating; older = less C-14 | * Age of fossils determined using C-14 dating; older = less C-14 | ||
| - | - **Biogeography: | + | - Biogeography: |
| * Ex: rabbits did not exist in Australia until introduce by humans → native Australian wallaby resembles rabbit both in structure and habit | * Ex: rabbits did not exist in Australia until introduce by humans → native Australian wallaby resembles rabbit both in structure and habit | ||
| - | - **Embryology: reveals similar stages in development among related species → similarities establish evolutionary relationships** | + | - Embryology: reveals similar stages in development among related species → similarities establish evolutionary relationships |
| * Gill sites, arches, and tails are found in mammal embryos | * Gill sites, arches, and tails are found in mammal embryos | ||
| - | - **Comparative Anatomy: describes two kinds of structure used to establish evolutionary relationships among species + there are heritable variations among individuals** | + | - Comparative Anatomy: describes two kinds of structure used to establish evolutionary relationships among species + there are heritable variations among individuals |
| - | - **Homologous Structures (homologies): | + | - Homologous Structures (homologies): |
| * Anatomy may by modified for survival in specific environments→ homologous structures may look different, but will resemble one another in pattern (Similar structure, diff function) | * Anatomy may by modified for survival in specific environments→ homologous structures may look different, but will resemble one another in pattern (Similar structure, diff function) | ||
| * Forelimbs of cats, bats, whales, and humans are homologous bcuz evolved from common mammal | * Forelimbs of cats, bats, whales, and humans are homologous bcuz evolved from common mammal | ||
| - | | + | * Vestigial Structures: body parts that used to serve function in common ancestor but not anymore |
| * Ex: remnants of limbs in snakes, hindlimbs in whales, and wings of flightless birds | * Ex: remnants of limbs in snakes, hindlimbs in whales, and wings of flightless birds | ||
| * More recent homologous characteristics shared by smaller group | * More recent homologous characteristics shared by smaller group | ||
| - | - **Analogous structure (analogies): | + | - Analogous structure (analogies): |
| * Ex: fins and body shapes of sharks, penguins, whales, and poiposies bcuz are adapted to swimming | * Ex: fins and body shapes of sharks, penguins, whales, and poiposies bcuz are adapted to swimming | ||
| - | * Results from **Convergent Evolution:** when similar environmental pressures and natural selection produce similar traits in unrelated organisms | + | * Results from Convergent Evolution: when similar environmental pressures and natural selection produce similar traits in unrelated organisms |
| - | | + | * Homoplasy: trait species share due to convergent evolution |
| - | - **Molecular Biology: examines nucleotide and amino acid sequences of DNA and proteins from diff species** | + | - Molecular Biology: examines nucleotide and amino acid sequences of DNA and proteins from diff species |
| * Closely related species share higher % of sequences than distantly related species | * Closely related species share higher % of sequences than distantly related species | ||
| * More than 98% of sequences in humans and chimpanzees are identical | * More than 98% of sequences in humans and chimpanzees are identical | ||
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| * Process in which individuals with certain inherited characteristics are more likely to survive in an environment, | * Process in which individuals with certain inherited characteristics are more likely to survive in an environment, | ||
| - | * Environment is the main force behind natural selection → controls which traits are most beneficial | + | * Environment is the main force behind natural selection → controls which traits are most beneficial (Selective pressure) |
| - | * Superior traits are **adaptations** to the environment and increase an individual' | + | * Superior traits are adaptations to the environment and increase an individual' |
| * Environment favors a trait = trait increases individuals fitness → selection is said to act for that trait | * Environment favors a trait = trait increases individuals fitness → selection is said to act for that trait | ||
| * Selection also acts against unfavorable traits | * Selection also acts against unfavorable traits | ||
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| Observations for Evolution | Observations for Evolution | ||
| - | - **Populations possess enormous reproductive potential** | + | - Populations possess enormous reproductive potential |
| - | - **Resources are limited. resources don't increase as populations do** | + | - Resources are limited. resources don't increase as populations do |
| - | - **Individuals compete for survival. Overproduction = competition for available resources** | + | - Individuals compete for survival. Overproduction = competition for available resources |
| - | - **There is heritable variation among individuals in a population.** | + | - There is heritable variation among individuals in a population. |
| * Genetic variation is the basis of phenotypic variation that can be acted upon by natural selection → evolution | * Genetic variation is the basis of phenotypic variation that can be acted upon by natural selection → evolution | ||
| - | - **Only most fit individuals survive. “Survival of the fittest%%'' | + | - Only most fit individuals survive. “Survival of the fittest%%'' |
| - | - **Evolution occurs as favorable traits accumulate in the population. Results from the unequal ability of organisms to survive and reproduce** | + | - Evolution occurs as favorable traits accumulate in the population. Results from the unequal ability of organisms to survive and reproduce |
| * As the unsuccessful died off and the successful rises, the adaptations become common | * As the unsuccessful died off and the successful rises, the adaptations become common | ||
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| ====Sources of Variation==== | ====Sources of Variation==== | ||
| - | | + | * Genetic Variation: difference in DNA bases or sequences |
| * Genetic variation enables evolutionary responses to environmental change | * Genetic variation enables evolutionary responses to environmental change | ||
| * Evidence of genetic variation: diff genotypes or phenotypes | * Evidence of genetic variation: diff genotypes or phenotypes | ||
| Line 3462: | Line 3598: | ||
| * Natural selection acts on variation among individuals in the population and arises by… | * Natural selection acts on variation among individuals in the population and arises by… | ||
| - | - **Mutations: are original source of new variation; invent alleles that didn't exist in the gene pool** | + | - Mutations: are original source of new variation; invent alleles that didn't exist in the gene pool |
| * Natural selection and other mechanisms increase variation by rearranging existing alleles & mutations into new combinations | * Natural selection and other mechanisms increase variation by rearranging existing alleles & mutations into new combinations | ||
| * All new alleles are the result of nucleotide variability | * All new alleles are the result of nucleotide variability | ||
| - | - **Sexual Reproduction creates individuals with new combinations of alleles; Genetic recombinations comes from:** | + | - Sexual Reproduction creates individuals with new combinations of alleles; Genetic recombinations comes from: |
| * Crossing Over; Independent assortment of homologous chromosomes; | * Crossing Over; Independent assortment of homologous chromosomes; | ||
| - | - **Diploidy: presence of two copies of each chromosome in a cell** | + | - Diploidy: presence of two copies of each chromosome in a cell |
| * In heterozygous condition, recessive allele is hidden from natural selection → allows variation to be “stored” for future generations → maintains variation in gene pool | * In heterozygous condition, recessive allele is hidden from natural selection → allows variation to be “stored” for future generations → maintains variation in gene pool | ||
| - | - **Outbreeding: | + | - Outbreeding: |
| - | - **Balanced Selection selection itself may preserve variation at some loci → helps maintain multiple phenotypic forms in a population** | + | - Balanced Selection selection itself may preserve variation at some loci → helps maintain multiple phenotypic forms in a population |
| * Often a single phenotype provides the best adaptations while others are less advantageous → favorable allele increases in frequency | * Often a single phenotype provides the best adaptations while others are less advantageous → favorable allele increases in frequency | ||
| * Examples of polymorphism (2 or more diff phenotypes) can be maintained by | * Examples of polymorphism (2 or more diff phenotypes) can be maintained by | ||
| - | - **Hybrid Vigor (Heterosis): | + | - Hybrid Vigor (Heterosis): |
| * Results from the reduction of loci with harmful homozygous recessive conditions and increase with heteroz advantage | * Results from the reduction of loci with harmful homozygous recessive conditions and increase with heteroz advantage | ||
| * Ex: a hybrid of corn in more resistant than either inbred strains | * Ex: a hybrid of corn in more resistant than either inbred strains | ||
| - | - **Heterozygous Advantage** | + | - Heterozygous Advantage |
| - | | + | * When heterozygotes have a greater fitness than either homozygous type→ both alleles and three phenotypes maintained in the population by selection |
| * Ex: heterozygotes for sickle cell disease are ~healthy but oxygen-carrying impaired; provides resistance to malaria = higher % in Africa → both alleles are maintained in gene pool | * Ex: heterozygotes for sickle cell disease are ~healthy but oxygen-carrying impaired; provides resistance to malaria = higher % in Africa → both alleles are maintained in gene pool | ||
| - | - **Frequency-Dependent Selection (minority advantage): the fitness of a phenotype depends on how common it is in the population.** | + | - Frequency-Dependent Selection (minority advantage): the fitness of a phenotype depends on how common it is in the population. |
| * Rare phenotypes are selected → become common → are selected against | * Rare phenotypes are selected → become common → are selected against | ||
| * Ex: rarer prey escape predators | * Ex: rarer prey escape predators | ||
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| Humans Impacting Evolution | Humans Impacting Evolution | ||
| - | - **Monocultures: | + | - Monocultures: |
| * Monocultures have no genetic variation and are susceptible to changing environmental conditions | * Monocultures have no genetic variation and are susceptible to changing environmental conditions | ||
| - | - **Overuse of Antibiotics reduces variation in bacteria population by eliminating certain individuals** | + | - Overuse of Antibiotics reduces variation in bacteria population by eliminating certain individuals |
| * Absence of susceptible individuals decrease competition and allows pathogenic bacteria to increase in number and dominate population | * Absence of susceptible individuals decrease competition and allows pathogenic bacteria to increase in number and dominate population | ||
| - | - **Artificial Selection/ | + | - Artificial Selection/ |
| * Similar to Natural Selection: Needs genetic variation | * Similar to Natural Selection: Needs genetic variation | ||
| * Different to Natural Selection: Humans (not environment) does the selecting | * Different to Natural Selection: Humans (not environment) does the selecting | ||
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| ====Hardy-Weinberg Equilibrium==== | ====Hardy-Weinberg Equilibrium==== | ||
| - | * When the allele frequencies in a population remain constant from generation to generation, the population is said to be in **genetic equilibrium** or **Hardy-Weinberg Equilibrium** | + | * When the allele frequencies in a population remain constant from generation to generation, the population is said to be in genetic equilibrium or Hardy-Weinberg Equilibrium |
| * At genetic equilibrium, | * At genetic equilibrium, | ||
| * But allele representation in generations might differ | * But allele representation in generations might differ | ||
| Line 3523: | Line 3659: | ||
| * But calculations serve as starting point that reveals how allele frequencies are changing, which equilibrium conditions are being violated, and what mechanisms are driving the evolution of a population | * But calculations serve as starting point that reveals how allele frequencies are changing, which equilibrium conditions are being violated, and what mechanisms are driving the evolution of a population | ||
| - | | + | * Population: a group of individuals of the same species that live in the same area and interbreed, producing fertile offspring |
| - | | + | * Gene Pool: consists of all copies of every type of allele at every locus in all members of the population. |
| Conditions for Hardy-Weinberg Equilibrium | Conditions for Hardy-Weinberg Equilibrium | ||
| Line 3557: | Line 3693: | ||
| - Can use q and p to find homozygotes and heterozygotes | - Can use q and p to find homozygotes and heterozygotes | ||
| - | **Causes for Changes in Allele Frequencies** | + | Causes for Changes in Allele Frequencies |
| * Multiple factors, together with natural selection, cause evolution | * Multiple factors, together with natural selection, cause evolution | ||
| - | - **Natural Selection:** increases or decreases allele frequencies bcuz of impact of environment | + | - Natural Selection: increases or decreases allele frequencies bcuz of impact of environment |
| - | - **Mutations** introduce new alleles that may provide selective advantage | + | - Mutations introduce new alleles that may provide selective advantage |
| * WEAK force for changing allele frequencies; | * WEAK force for changing allele frequencies; | ||
| - | - **Gene Flow:** the transfer of alleles between populations | + | - Gene Flow: the transfer of alleles between populations |
| * Movement of individuals between populations resulting in the removal of alleles when they leave (emigration) or introduction of new alleles when they enter (immigration) the population | * Movement of individuals between populations resulting in the removal of alleles when they leave (emigration) or introduction of new alleles when they enter (immigration) the population | ||
| * Ex: pollen transferred from one population to another | * Ex: pollen transferred from one population to another | ||
| * Tends to reduce the genetic differences between populations | * Tends to reduce the genetic differences between populations | ||
| - | - **Genetic Drift:** random increase or decrease of alleles | + | - Genetic Drift: random increase or decrease of alleles |
| * Especially in small (usually <100) chance events can cause allele frequencies to fluctuate and an allele to be disproportionately over or underrepresented in the next generation | * Especially in small (usually <100) chance events can cause allele frequencies to fluctuate and an allele to be disproportionately over or underrepresented in the next generation | ||
| * Decreases genetic variation & evolutionary adaptability and increases homozygosity | * Decreases genetic variation & evolutionary adaptability and increases homozygosity | ||
| - | - **Founder Effect:** “When a few individuals become isolated from a larger population, this smaller group may establish a new population whose gene pool differs from the source population” | + | - Founder Effect: “When a few individuals become isolated from a larger population, this smaller group may establish a new population whose gene pool differs from the source population” |
| * Ex: founding fathers contain mutated allele and established community → reproductive isolation cause mutation to be concentrated in that area | * Ex: founding fathers contain mutated allele and established community → reproductive isolation cause mutation to be concentrated in that area | ||
| * Population tends to have reduced genetic diversity | * Population tends to have reduced genetic diversity | ||
| - | - **Bottleneck:** when the population undergoes dramatic decrease in size (predation, catastrophe, | + | - Bottleneck: when the population undergoes dramatic decrease in size (predation, catastrophe, |
| - | - **Nonrandom Mating:** when individuals choose mates based upon their particular traits | + | - Nonrandom Mating: when individuals choose mates based upon their particular traits |
| * Ex: always choose mates with traits similar to their own or different from their own; only nearby individuals | * Ex: always choose mates with traits similar to their own or different from their own; only nearby individuals | ||
| - | - **Inbreeding:** individuals mate with relatives | + | - Inbreeding: individuals mate with relatives |
| - | - **Sexual Selection:** process in which individuals with certain inherited characteristics are preferred as mates | + | - Sexual Selection: process in which individuals with certain inherited characteristics are preferred as mates |
| - | - **Intrasexual Selection:** Individuals of one sex compe2te directly for mates of the opposite sex. | + | - Intrasexual Selection: Individuals of one sex compe2te directly for mates of the opposite sex. |
| - | - **Intersexual Selection** (mate choice): females choose males based on attractive appearance or behaviour | + | - Intersexual Selection (mate choice): females choose males based on attractive appearance or behaviour |
| - | * Leads to **sexual dimorphosim**: | + | * Leads to sexual dimorphosim: |
| Extra Notes | Extra Notes | ||
| - | | + | * Fixation: when one allele goes extinct and only one remains (becomes fixed) |
| - | | + | * → all individuals will be homozygous for allele |
| ====Speciation==== | ====Speciation==== | ||
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| Species Concept | Species Concept | ||
| - | | + | * Biological species concept: species is a group of populations that can breed and produce viable offspring |
| * Defined by reproductive isolation and gene flow; basis for understanding macroevo. | * Defined by reproductive isolation and gene flow; basis for understanding macroevo. | ||
| - | | + | * Morphological species concept: distinguishes a species by body shape and other structural features. |
| - | | + | * Ecological species concept: defines a species in terms of its ecological niche |
| * Species have diff adaptations to environment | * Species have diff adaptations to environment | ||
| - | | + | * Phylogenetic species concept: set of organisms with unique evolutionary history |
| Notes | Notes | ||
| - | | + | * Speciation: formation of new species |
| * Reproductive isolation is main measure for speciation; can involve changes to 1 gene | * Reproductive isolation is main measure for speciation; can involve changes to 1 gene | ||
| Line 3612: | Line 3748: | ||
| * If two groups are reproductively isolated, they can accumulate allele differences and eventually diverge | * If two groups are reproductively isolated, they can accumulate allele differences and eventually diverge | ||
| - | | + | * Reinforcement: |
| * Selected traits reinforce differences that evolved while the populations were isolated from one another | * Selected traits reinforce differences that evolved while the populations were isolated from one another | ||
| - | | + | * Fusion: two species become one |
| * Likely to occur when an increasing number of viable, fertile hybrids are produced over the course of generations | * Likely to occur when an increasing number of viable, fertile hybrids are produced over the course of generations | ||
| * Reduces species diversity | * Reduces species diversity | ||
| Line 3621: | Line 3757: | ||
| Methods of Speciation | Methods of Speciation | ||
| - | - **Allopatric Speciation:** when a population is divided by a geographic barrier so that interbreeding between two populations is prevented | + | - Allopatric Speciation: when a population is divided by a geographic barrier so that interbreeding between two populations is prevented |
| * Barrier examples: rivers and regions that contain vital resources | * Barrier examples: rivers and regions that contain vital resources | ||
| * Gene flow is interrupted when a population is geographically isolated → reproductive barriers form and maintain speciation → gene pool/allele frequencies in two | * Gene flow is interrupted when a population is geographically isolated → reproductive barriers form and maintain speciation → gene pool/allele frequencies in two | ||
| Line 3629: | Line 3765: | ||
| * Ex: Species that were seperated cannot breed when meet each other again | * Ex: Species that were seperated cannot breed when meet each other again | ||
| - | - **Sympatric Speciation: formation of new species without presence of geographic barrier. Appearance of new species in the same area of the parent population. Can occur bcuz of…** | + | - Sympatric Speciation: formation of new species without presence of geographic barrier. Appearance of new species in the same area of the parent population. Can occur bcuz of… |
| - | - **Sexual Selection:** | + | - Sexual Selection: |
| - | - **Habitat differentiation: | + | - Habitat differentiation: |
| - | - **Balanced Polymorphism** among subpopulations may lead to speciation | + | - Balanced Polymorphism among subpopulations may lead to speciation |
| * Ex: a population of insects have polymorphism for color → each color provides camouflage to specific substrate → under these circumstances only insects with same color can associate and mate → similarly colored insects are reproductively isolated | * Ex: a population of insects have polymorphism for color → each color provides camouflage to specific substrate → under these circumstances only insects with same color can associate and mate → similarly colored insects are reproductively isolated | ||
| - | - **Polyploidy:** have more than the normal two sets of chromosome found in diploid (2n) cells | + | - Polyploidy: have more than the normal two sets of chromosome found in diploid (2n) cells |
| * Occurs as result of nondisjunction of all chromosomes during meiosis | * Occurs as result of nondisjunction of all chromosomes during meiosis | ||
| * Unlike animals, plants more tolerant to changes in chromosome sets | * Unlike animals, plants more tolerant to changes in chromosome sets | ||
| - | * [[https:// | + | * https:// |
| + | <img src=" | ||
| + | </ | ||
| * Ex: Tetraploid plant produces gamete (2n) that fuses with normal gamete from same species (n) → nonviable/ | * Ex: Tetraploid plant produces gamete (2n) that fuses with normal gamete from same species (n) → nonviable/ | ||
| * Bcuz tetraploid & diploid species cannot produce viable offspring = diff species | * Bcuz tetraploid & diploid species cannot produce viable offspring = diff species | ||
| * Thus speciation can occur over single generation | * Thus speciation can occur over single generation | ||
| - | - **Hybridization: | + | - Hybridization: |
| + | <img src=" | ||
| + | </ | ||
| * Sometimes genetic variation of hybrids is greater than either parent so hybrid population can evolve adaptations to environmental conditions in hybrid zone beyond parent range | * Sometimes genetic variation of hybrids is greater than either parent so hybrid population can evolve adaptations to environmental conditions in hybrid zone beyond parent range | ||
| * Hybrids become new species when exposed to different selection pressures or can only breed among themselves | * Hybrids become new species when exposed to different selection pressures or can only breed among themselves | ||
| - | | + | * Hybrid Zone: place where two different species meet and mate |
| * Form when two species do not have complete reproductive barriers | * Form when two species do not have complete reproductive barriers | ||
| - | - **Adaptive Radiation:** rapid evolution of many species from single ancestor | + | - Adaptive Radiation: rapid evolution of many species from single ancestor |
| * Occurs when ancestral species is introduced to an area where diverse geographic conditions are available | * Occurs when ancestral species is introduced to an area where diverse geographic conditions are available | ||
| * Ex 1: 14 species of Darwin' | * Ex 1: 14 species of Darwin' | ||
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| Maintaining Reproductive Isolation | Maintaining Reproductive Isolation | ||
| - | | + | * Reproductive barriers: prevent interbreeding & maintain reproductive isolation when species are not physically separated by geographic barrier |
| * Often single genes control phenotypic traits that can lead to reproductive isolation → speciation | * Often single genes control phenotypic traits that can lead to reproductive isolation → speciation | ||
| * Ex diff species of hummingbird prefer one type of coloured flower and thus only pollinate those | * Ex diff species of hummingbird prefer one type of coloured flower and thus only pollinate those | ||
| - | - **Prezygotic Isolating Mechanisms: block fertilization from occurring** | + | - Prezygotic Isolating Mechanisms: block fertilization from occurring |
| * If populations do not attempt to breed, then is not considered prezygotic mechanism | * If populations do not attempt to breed, then is not considered prezygotic mechanism | ||
| - | - **Genetic Incompatibility: | + | - Genetic Incompatibility: |
| * Sometimes when occurs in plants, they can self-pollinate and become new species | * Sometimes when occurs in plants, they can self-pollinate and become new species | ||
| - | - **Habitat isolation: occurs when species do not encounter one another** | + | - Habitat isolation: occurs when species do not encounter one another |
| - | - **Timing Isolation: occurs when species mate, flower, or are active during different times** | + | - Timing Isolation: occurs when species mate, flower, or are active during different times |
| * Ex: nocturnal and diurnal animals | * Ex: nocturnal and diurnal animals | ||
| - | - **Behavioral Isolation: when species do not recognize another species as a mating partner because does not perform courtship rituals, release proper chemicals (scents, pheromones) or have appropriate appearance** | + | - Behavioral Isolation: when species do not recognize another species as a mating partner because does not perform courtship rituals, release proper chemicals (scents, pheromones) or have appropriate appearance |
| - | - **Mechanical/ | + | - Mechanical/ |
| - | - **Gametic Isolation: when male gametes do not survive females environment or failed recognition** | + | - Gametic Isolation: when male gametes do not survive females environment or failed recognition |
| - | **2. Postzygotic Isolating Mechanisms:** mechanisms that prevent formation of viable progeny | + | 2. Postzygotic Isolating Mechanisms: mechanisms that prevent formation of viable progeny |
| - | - **Hybrid Inviability: | + | - Hybrid Inviability: |
| - | - **Hybrid sterility:** when hybrids grow to be adults but are sterile | + | - Hybrid sterility: when hybrids grow to be adults but are sterile |
| * Hybrid sterile bcuz chromosomes can’t pair up correctly during meiosis. | * Hybrid sterile bcuz chromosomes can’t pair up correctly during meiosis. | ||
| - | - **Hybrid breakdown:** when hybrids produce offspring with reduced viability or fertility | + | - Hybrid breakdown: when hybrids produce offspring with reduced viability or fertility |
| Directional, | Directional, | ||
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| * Tip: If FRQ about natural selection involves changing phenotype will probs involve one of these vocab | * Tip: If FRQ about natural selection involves changing phenotype will probs involve one of these vocab | ||
| - | | + | * Directional selection: when environment favors individuals with one extreme of a phenotypic |
| * Ex: Moth case study; an increase number of large seeds over small seeds led to an increase in beak depth | * Ex: Moth case study; an increase number of large seeds over small seeds led to an increase in beak depth | ||
| - | | + | * Disruptive selection: when environment favors individuals at both extremes of a phenotypic range over individuals with intermediate phenotypes |
| * Ex: Small-billed birds feed on small, soft seeds, large-billed birds feed on large, hard seeds; intermediate can't eat either | * Ex: Small-billed birds feed on small, soft seeds, large-billed birds feed on large, hard seeds; intermediate can't eat either | ||
| * Increases genetic variation | * Increases genetic variation | ||
| - | | + | * Stabilizing selection: favors intermediate variants and acts against both extreme phenotypes → reduces variation |
| * Ex: human babies at intermediate range tend to be healthier and have higher survival rates | * Ex: human babies at intermediate range tend to be healthier and have higher survival rates | ||
| Patterns of Evolution | Patterns of Evolution | ||
| - | - **Divergent Evolution: species that originate from a common ancestor become increasingly different over time** | + | - Divergent Evolution: species that originate from a common ancestor become increasingly different over time |
| * Might happen because of allopatric speciation or sympatric speciation | * Might happen because of allopatric speciation or sympatric speciation | ||
| - | - **Parallel Evolution: species that originate from a common ancestor have made similar evolutionary changes after divergence** | + | - Parallel Evolution: species that originate from a common ancestor have made similar evolutionary changes after divergence |
| * Species from marsupial mammals and placental mammals have independently evolved similar adaptations | * Species from marsupial mammals and placental mammals have independently evolved similar adaptations | ||
| - | - **Convergent Evolution:** | + | - Convergent Evolution: |
| - | - **Coevolution: | + | - Coevolution: |
| - | **Microevolution vs Macroevolution** | + | Microevolution vs Macroevolution |
| - | - **Microevolution: | + | - Microevolution: |
| - | - **Macroevolution: | + | - Macroevolution: |
| * Different interpretations of fossil evidence have led to 2 contrasting theories for the pace of macroevolution | * Different interpretations of fossil evidence have led to 2 contrasting theories for the pace of macroevolution | ||
| Patterns in Fossil Record | Patterns in Fossil Record | ||
| - | - **Phyletic Gradualism: argues that evolution occurs by the gradual accumulation of small changes** | + | - Phyletic Gradualism: argues that evolution occurs by the gradual accumulation of small changes |
| * Individual speciation events occur of long periods | * Individual speciation events occur of long periods | ||
| * Fossils then reveal only major changes in groups → intermediate stages of evolution not represented and shows incompleteness | * Fossils then reveal only major changes in groups → intermediate stages of evolution not represented and shows incompleteness | ||
| - | - **Punctuated equilibrium: | + | - Punctuated equilibrium: |
| * Most new species accumulate their unique features rapidly as they come into existence, then change little for the rest of their duration as a species. | * Most new species accumulate their unique features rapidly as they come into existence, then change little for the rest of their duration as a species. | ||
| * Most of species in first static event have become extinct or changed enough to be considered a new species | * Most of species in first static event have become extinct or changed enough to be considered a new species | ||
| Line 3733: | Line 3873: | ||
| * “Evolutionary history of a species” | * “Evolutionary history of a species” | ||
| * Determined through fossils, homologous structures, morphology, & molecular biology | * Determined through fossils, homologous structures, morphology, & molecular biology | ||
| - | - **Taxonomy:** classification of organisms; organisms are classified into categories called taxa Hierarchical Classification | + | - Taxonomy: classification of organisms; organisms are classified into categories called taxa Hierarchical Classification |
| * Each taxon more inclusive than the other | * Each taxon more inclusive than the other | ||
| - | * “**D**umb **K**ings **P**lay **C**hess **O**n **F**ine **G**reen **S**and” [[https:// | + | * “Dumb Kings Play Chess On Fine Green Sand” https:// |
| + | <img src=" | ||
| + | </ | ||
| - Species: group of closely related organisms that can reproduce | - Species: group of closely related organisms that can reproduce | ||
| - Genus: phylogenetically closely related species | - Genus: phylogenetically closely related species | ||
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| - Phylogenetic Trees | - Phylogenetic Trees | ||
| * “Evolutionary history of an organism represented by a branching diagram” (Hypothesis!) | * “Evolutionary history of an organism represented by a branching diagram” (Hypothesis!) | ||
| - | | + | * Branch Point: represents common ancestry of 2 evolutionary lineages diverging from it |
| - | | + | * Sister taxa: species that share immediate common ancestor not shared by other groups |
| * Represents a genus | * Represents a genus | ||
| - | | + | * Basal taxon: group that diverges early on |
| * Tree shows pattern of descent, NOT phenotypic similarity | * Tree shows pattern of descent, NOT phenotypic similarity | ||
| * Branch length = estimated amount of evolutionary change or time | * Branch length = estimated amount of evolutionary change or time | ||
| - | - Cladistics | + | - Cladistics https:// |
| + | <img src=" | ||
| + | </ | ||
| * Uses common ancestry and traits to place species into groups called clades | * Uses common ancestry and traits to place species into groups called clades | ||
| - | | + | * Clades: ancestral species & all of descendents |
| * Cladogram shows relationships between diff organism from common ancestor | * Cladogram shows relationships between diff organism from common ancestor | ||
| * Branches determined by comparing number of derived characters in each taxon | * Branches determined by comparing number of derived characters in each taxon | ||
| * More primitive = earlier branching | * More primitive = earlier branching | ||
| * Fewer derived = later branching | * Fewer derived = later branching | ||
| - | | + | * Outgroup: species closely related but not part of the group we are studying (ingroup) |
| * Is the most divergent (different) and least closely related | * Is the most divergent (different) and least closely related | ||
| - | * 1 [[https:// | + | * 1 https:// |
| + | <img src=" | ||
| + | </ | ||
| + | <img src=" | ||
| + | </ | ||
| + | <img src=" | ||
| + | </ | ||
| * Node represents species → all three species are descended from it | * Node represents species → all three species are descended from it | ||
| - Types of Clades | - Types of Clades | ||
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| - Shared Ancestral & Shared Derived Characteristics | - Shared Ancestral & Shared Derived Characteristics | ||
| * Descent with modification has resulted in organisms with shared and diff characteristics from common ancestor | * Descent with modification has resulted in organisms with shared and diff characteristics from common ancestor | ||
| - | | + | * Shared Ancestral: character that originated from ancestor of a taxon (ex: backbone) |
| - | | + | * Derived: novelty unique to clade |
| * Can be loss or gain of a characteristic | * Can be loss or gain of a characteristic | ||
| - | - [[https:// | + | - https:// |
| + | <img src=" | ||
| + | </ | ||
| * Most parsimonious tree is the one with the less amount of changes | * Most parsimonious tree is the one with the less amount of changes | ||
| * This tree is less parisomus bcuz assumes that jaw evolved twice | * This tree is less parisomus bcuz assumes that jaw evolved twice | ||
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| * rRNA changes slowly→ investigate events that happened long time ago | * rRNA changes slowly→ investigate events that happened long time ago | ||
| * mDNA evolves rapidly→ investigate recent events | * mDNA evolves rapidly→ investigate recent events | ||
| - | | + | * Orthologous genes: homologous genes found is diff species as a result of speciation |
| - | | + | * Paralogous genes: homologous genes in a species that results from gene duplication |
| * May diverge and take on new functions; useful cuz extra copy of genes permits modification w/o loss of original copy | * May diverge and take on new functions; useful cuz extra copy of genes permits modification w/o loss of original copy | ||
| * Pseudogenes: | * Pseudogenes: | ||
| Line 3793: | Line 3945: | ||
| * Mutations in genes make it accurate and natural selections makes inaccurate | * Mutations in genes make it accurate and natural selections makes inaccurate | ||
| | | ||
| - | - **The earth and its atmosphere formed** | + | - The earth and its atmosphere formed |
| * Primordial atmosphere made mostly of CO2 and N2 but little O2 → lots free energy | * Primordial atmosphere made mostly of CO2 and N2 but little O2 → lots free energy | ||
| - | - **Primordial seas formed** | + | - Primordial seas formed |
| * As the earth cooled, gasses condensed to form seas | * As the earth cooled, gasses condensed to form seas | ||
| - | - **Organic molecules were synthesized** | + | - Organic molecules were synthesized |
| * Theory 1: Primitive earth provided inorganic precursor from which organic molecules could have been made | * Theory 1: Primitive earth provided inorganic precursor from which organic molecules could have been made | ||
| * Theory 2: organic molecules could have been transported to earth by meteorite or celestial event | * Theory 2: organic molecules could have been transported to earth by meteorite or celestial event | ||
| Line 3804: | Line 3956: | ||
| * Organic molecules were able to form only bcuz oxygen was absent | * Organic molecules were able to form only bcuz oxygen was absent | ||
| * Oxygen is very reactive and would have prevented formation by replacing reactants in chemical reactions | * Oxygen is very reactive and would have prevented formation by replacing reactants in chemical reactions | ||
| - | | + | * Stanley Miller: simulated primordial conditions by applying electrical sparks to simple gasses (no oxygen) connected to a flask of heated water |
| * After one week, water contained organic molecules (ex: amino acids) | * After one week, water contained organic molecules (ex: amino acids) | ||
| - | - **Polymers and self-replicating molecules were synthesized** | + | - Polymers and self-replicating molecules were synthesized |
| * Organic molecules (monomers) served as building blocks for formation of more complex molecules (polymers) that could replicate, store and transfer information | * Organic molecules (monomers) served as building blocks for formation of more complex molecules (polymers) that could replicate, store and transfer information | ||
| - | | + | * RNA world hypothesis: argues that RNA came first |
| * Based on new discoveries of diverse functions of RNA | * Based on new discoveries of diverse functions of RNA | ||
| * RNA can act as carrier of genetic material and catalyst (ex: ribozymes) → is like protein and DNA | * RNA can act as carrier of genetic material and catalyst (ex: ribozymes) → is like protein and DNA | ||
| * RNA can self-replicate w/o proteins, but DNA always needs proteins | * RNA can self-replicate w/o proteins, but DNA always needs proteins | ||
| - | - **Primitive heterotrophic prokaryotes formed** | + | - Primitive heterotrophic prokaryotes formed |
| * Organic “soup” was the source of organic material | * Organic “soup” was the source of organic material | ||
| - | - **Primitive autotrophic prokaryotes were formed** | + | - Primitive autotrophic prokaryotes were formed |
| - | * Bcuz of mutations, heterotrophs gained the ability to produce their own food → became | + | * Bcuz of mutations, heterotrophs gained the ability to produce their own food → became autotroph |
| - | - **Oxygen and ozone layer formed and abiotic chemical evolution ended** | + | - Oxygen and ozone layer formed and abiotic chemical evolution ended |
| * Bcuz of photosynthetic activity of autotrophs, oxygen was released and accumulated in the atmosphere | * Bcuz of photosynthetic activity of autotrophs, oxygen was released and accumulated in the atmosphere | ||
| * Formation blocked UV light and energy source for abiotic synthesis of organic molecules and primitive cells | * Formation blocked UV light and energy source for abiotic synthesis of organic molecules and primitive cells | ||
| - | - **Eukaryotes formed (endosymbiotic theory)** | + | - Eukaryotes formed (endosymbiotic theory) |
| ====Endosymbiotic Events==== | ====Endosymbiotic Events==== | ||
| * “Describes how organelles formed when free-living prokaryotic cells engulfed another prokaryotic cell” → formed eukaryotes | * “Describes how organelles formed when free-living prokaryotic cells engulfed another prokaryotic cell” → formed eukaryotes | ||
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| ====Common Ancestry==== | ====Common Ancestry==== | ||
| * It is believed that all organisms share a common ancestor, There are FOUR features that support common ancestry: | * It is believed that all organisms share a common ancestor, There are FOUR features that support common ancestry: | ||
| - | | + | * DNA and RNA are carriers of genetic information |
| - | | + | * Ribosomes are found in all forms of life |
| - | | + | * Universality of the genetic code and gene expression |
| - | | + | * Core metabolic pathways are conserved across all currently recognized domains |
| * Ex: DNA replication, | * Ex: DNA replication, | ||
| * All living things consist of one or more cells; all cells have plasma membranes | * All living things consist of one or more cells; all cells have plasma membranes | ||
| * All living things are categorized into 3 Domains: Bacteria, Archaea, and Eukarya | * All living things are categorized into 3 Domains: Bacteria, Archaea, and Eukarya | ||
| ====Prokaryotes vs Eukaryotes==== | ====Prokaryotes vs Eukaryotes==== | ||
| - | | + | * Prokaryotes: |
| * Archaea & bacteria | * Archaea & bacteria | ||
| - | - **Cell Type** **Prokaryote** **Eukaryotes** **Size** Smaller Bigger | + | - Cell Type Prokaryote Eukaryotes Size Smaller Bigger Multi or Uni Uni Multi Organelles No (Nucleus) Yes (Nucleus) Cell Wall Yes Plants, Fungi, and some Protists Cytoplasm No cytoskeleton Cytoplasm streaming Ribosomes Yes: smaller, diff proteins Yes: bigger DNA Yes: singular, short, circular chromosome w/o histones \ Usually no introns\ Less DNA that is in the nucleoid/ |
| ====Modes of Nutrition==== | ====Modes of Nutrition==== | ||
| Autotrophs: make their own organic molecules | Autotrophs: make their own organic molecules | ||
| - | | + | * Photoautotrophs Use light energy (as in photosynthesis) |
| - | | + | * Chemoautotrophs Use energy obtained from inorganic substances (as in chemosynthesis) |
| - | | + | * Heterotrophs: |
| - | | + | * Parasites Obtain energy from their hosts while living on or in their tissues |
| - | | + | * Decomposers Obtain energy from dead, decaying matter |
| ====Domain Bacteria==== | ====Domain Bacteria==== | ||
| - | [[https:// | + | https:// |
| + | <img src=" | ||
| + | </ | ||
| * Small size and rapid reproduction | * Small size and rapid reproduction | ||
| * High genetic variation → live in diverse environments | * High genetic variation → live in diverse environments | ||
| - Bacteria Structure and Review | - Bacteria Structure and Review | ||
| - | | + | * Cell wall: made with peptidoglycan (carb polymer with amino acid) |
| * Function: protects cell, stops from bursting in hypotonic solution, structure determines rate of transformation | * Function: protects cell, stops from bursting in hypotonic solution, structure determines rate of transformation | ||
| * Structure either gram positive and negative | * Structure either gram positive and negative | ||
| * (+) = simple | * (+) = simple | ||
| * (-) = more complex, less peptidoglycan | * (-) = more complex, less peptidoglycan | ||
| - | | + | * Capsule: layer of polysaccharides and proteins that surround cell wall |
| * Protect against dehydration, | * Protect against dehydration, | ||
| - | | + | * Endospores: resistant cells |
| - | | + | * Plasmids: small, circular independently replicating (circular) DNA molecules |
| * Can be exchanged with other bacteria introducing genetic variation and promoting the transfer of antibiotic or pathogenic genes to harmless strains | * Can be exchanged with other bacteria introducing genetic variation and promoting the transfer of antibiotic or pathogenic genes to harmless strains | ||
| - | | + | * Quorum sensing: some bacteria release signalling molecule that recruits other bacteria → evaluate the local density of bacteria → bacteria respond and aggregate → form biofilms |
| - | | + | * Biofilms: dense populations of bacteria linked by adhesive proteins |
| * Adhesive proteins help bacteria attach to substrates | * Adhesive proteins help bacteria attach to substrates | ||
| - Groups of Bacteria | - Groups of Bacteria | ||
| * Can be categorized by how they obtain energy and carbon (include 4 modes) | * Can be categorized by how they obtain energy and carbon (include 4 modes) | ||
| - | - **Cyanobacteria: | + | - Cyanobacteria: |
| - | - **Purple sulfur bacteria:** photosynthetic but split H₂S (instead of water) to get electrons | + | - Purple sulfur bacteria: photosynthetic but split H₂S (instead of water) to get electrons |
| - | - **Nitrogen-fixing bacteria:** convert/fix N2 to ammonia (NH₃) → used to make nitrogen-containing amino acids and nucleotides | + | - Nitrogen-fixing bacteria: convert/fix N2 to ammonia (NH₃) → used to make nitrogen-containing amino acids and nucleotides |
| * Some have mutualistic relationships with plants and bacteria | * Some have mutualistic relationships with plants and bacteria | ||
| - | - **Heterotrophic bacteria:** obtain carbon and energy from organic molecules | + | - Heterotrophic bacteria: obtain carbon and energy from organic molecules |
| * Ex: parasites, pathogens, decomposers, | * Ex: parasites, pathogens, decomposers, | ||
| - Motility | - Motility | ||
| * Use flagella | * Use flagella | ||
| * Pro and eu. flagella have diff proteins, molecular composition, | * Pro and eu. flagella have diff proteins, molecular composition, | ||
| - | - [[https:// | + | - https:// |
| + | <img src=" | ||
| + | </ | ||
| * Asexual→ no genetic variation | * Asexual→ no genetic variation | ||
| * Rapid reproduction + no proofreading enzymes → high rate of mutation = main method of creating variation for evolution (fast) | * Rapid reproduction + no proofreading enzymes → high rate of mutation = main method of creating variation for evolution (fast) | ||
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| - Extremophiles | - Extremophiles | ||
| * Thrive in extreme conditions | * Thrive in extreme conditions | ||
| - | | + | * Halophiles: highly saline |
| - | - **Thermophiles: | + | - Thermophiles: |
| * Evidence for common ancestry of eukaryotes | * Evidence for common ancestry of eukaryotes | ||
| * Organelles, linear chromosomes, | * Organelles, linear chromosomes, | ||
| Line 3906: | Line 4062: | ||
| * Extremely diverse: can be algae-like, animal-like, | * Extremely diverse: can be algae-like, animal-like, | ||
| * Evolutionary relationships are weak, poorly understood, or both | * Evolutionary relationships are weak, poorly understood, or both | ||
| - | * Features shared by two or more groups may represent | + | * Features shared by two or more groups may represent convergent evolution |
| - | - **Algae-Like** | + | - Algae-Like |
| * All obtain energy by photosynthesis, | * All obtain energy by photosynthesis, | ||
| - | - **Protozoa/ | + | - Protozoa/ |
| * Heterotrophs: | * Heterotrophs: | ||
| - | - **Fungus-Like** | + | - Fungus-Like |
| * Resemble fungus bcuz they form filaments or spore-bearing bodies | * Resemble fungus bcuz they form filaments or spore-bearing bodies | ||
| ====Kingdom Fungi==== | ====Kingdom Fungi==== | ||
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| * Grow as filaments called hyphae; mass of hyphae is called mycelium | * Grow as filaments called hyphae; mass of hyphae is called mycelium | ||
| * Some have septa (cross walls) which divide the filament into compartments containing single nucleus | * Some have septa (cross walls) which divide the filament into compartments containing single nucleus | ||
| - | * Cell walls consist of **Chitin**: nitrogen-containing polysaccharide | + | * Cell walls consist of Chitin: nitrogen-containing polysaccharide |
| - Ecological Interaction | - Ecological Interaction | ||
| - | * Most either parasites or **decomposers: | + | * Most either parasites or decomposers: |
| - Mutualistic Arrangements | - Mutualistic Arrangements | ||
| - | - **Mycorrhizae**: mutualistic relationships between fungi and plants | + | - Mycorrhizae: |
| * Fungus grows on the roots of plants → facilitate movement of water & nutrients | * Fungus grows on the roots of plants → facilitate movement of water & nutrients | ||
| * Plants provides sugar | * Plants provides sugar | ||
| - | - **Lichens:** relationship between fungi and algae | + | - Lichens: relationship between fungi and algae |
| * Fungus provides water and protection | * Fungus provides water and protection | ||
| ====Kingdom Plantae==== | ====Kingdom Plantae==== | ||
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| - Rooted in the ground | - Rooted in the ground | ||
| - Organs & Interactions with the Environment | - Organs & Interactions with the Environment | ||
| - | - **Roots:** anchor plants to the ground; absorb water and nutrients. Water capacity of roots improved by increasing absorbing surface area through… | + | - Roots: anchor plants to the ground; absorb water and nutrients. Water capacity of roots improved by increasing absorbing surface area through… |
| - | | + | * Root hairs: extensions of epidermal cells into substrate |
| - | | + | * Mycorrhizae |
| ====Kingdom Animalia==== | ====Kingdom Animalia==== | ||
| Similarities among all members | Similarities among all members | ||
| Line 3942: | Line 4098: | ||
| =====Animal Behavior===== | =====Animal Behavior===== | ||
| Review | Review | ||
| - | | + | * Behavior: reaction of living things to stimuli (either from the physical environment or other living things) |
| * Behaviors may be encoded in DNA or learned; group behaviors or individual | * Behaviors may be encoded in DNA or learned; group behaviors or individual | ||
| * Behavior used to maintain homeostasis, | * Behavior used to maintain homeostasis, | ||
| - | | + | * Proximate causation: how a behavior occurs or is modified |
| - | | + | * Ultimate causation: why a behavior occurs in the context of natural selection |
| * Do it to increase fitness → find mates or survive | * Do it to increase fitness → find mates or survive | ||
| - Kinds of Animal Behavior | - Kinds of Animal Behavior | ||
| - | - **Instinct: behaviour that is innate/ | + | - Instinct: behaviour that is innate/ |
| * Ex: in mammals, care for offspring by the female parent is innate | * Ex: in mammals, care for offspring by the female parent is innate | ||
| - | - **Fixed Action Patterns (FAPs) innate behaviors that follow a regular, fixed pattern** | + | - Fixed Action Patterns (FAPs) innate behaviors that follow a regular, fixed pattern |
| * Initiated by specific stimulus and usually carried out to completion | * Initiated by specific stimulus and usually carried out to completion | ||
| - | | + | * Sign stimulus: external cue thats acts as a trigger for the behavior |
| * Ex: if goose sees egg outside nest will roll back to nest → egg is stimulus → anything that looks like the egg will be treated same | * Ex: if goose sees egg outside nest will roll back to nest → egg is stimulus → anything that looks like the egg will be treated same | ||
| * Male stickleback fish defend territory against other males → red belly of a male is a stimulus for aggressive behaviour → any object with red initiates aggressive FAP | * Male stickleback fish defend territory against other males → red belly of a male is a stimulus for aggressive behaviour → any object with red initiates aggressive FAP | ||
| - | - **Imprinting: an innate program for acquiring a specific behaviour only if have correct stimuli experienced during critical/ | + | - Imprinting: an innate program for acquiring a specific behaviour only if have correct stimuli experienced during critical/ |
| * Ex: geese goslings will accept any moving object as mothers, salmon imprint odors associated with birthplace so that they can return | * Ex: geese goslings will accept any moving object as mothers, salmon imprint odors associated with birthplace so that they can return | ||
| - | - **Learning** | + | - Learning |
| - | | + | * Learning: the modification of behavior as a result of specific experiences |
| * Capacity for learning depends on nervous system organization established during development following instructions encoded in the genome | * Capacity for learning depends on nervous system organization established during development following instructions encoded in the genome | ||
| - | - **Associative Learning (association) occurs when animal recognizes (learns) that two or more events are connected** | + | - Associative Learning (association) occurs when animal recognizes (learns) that two or more events are connected |
| - | * One form called | + | * One form called classical conditioning when an animal performs a behavior in response to substitute stimulus rather than normal stimulus |
| * Ex: dogs salivate when presented with food → bell rung before giving food → dogs salivate in response to bell ringing alone; associated ringing of bell (substitute stimulus) with presentation of food (normal stimulus) | * Ex: dogs salivate when presented with food → bell rung before giving food → dogs salivate in response to bell ringing alone; associated ringing of bell (substitute stimulus) with presentation of food (normal stimulus) | ||
| - | - **Trial-and-error learning (operant conditioning): | + | - Trial-and-error learning (operant conditioning): |
| * If response is desirable (positive reinforcement) animal will repeat behavior | * If response is desirable (positive reinforcement) animal will repeat behavior | ||
| * If response is undesirable, | * If response is undesirable, | ||
| * Learning acquired by association can be forgotten or reversed if performed behavior does not result in expected response | * Learning acquired by association can be forgotten or reversed if performed behavior does not result in expected response | ||
| - | | + | * Extinction: loss of acquired behavior |
| - | - **Spatial learning: form of associative learning when an animal associates attributes of a location (landmarks) with reward it gains by going back there** | + | - Spatial learning: form of associative learning when an animal associates attributes of a location (landmarks) with reward it gains by going back there |
| * Ex: wasps were able to associate nearby markers (pine cones) with location of nests; removed markers and couldn' | * Ex: wasps were able to associate nearby markers (pine cones) with location of nests; removed markers and couldn' | ||
| - | - **Habituation: | + | - Habituation: |
| * Sea anemones tentacles can ignore nonfood items after repeated attempts to grab food | * Sea anemones tentacles can ignore nonfood items after repeated attempts to grab food | ||
| - | - **Observational learning: when animals copy behaviors of another animal** | + | - Observational learning: when animals copy behaviors of another animal |
| * One monkey learned that could more easily clean potatoes in water and soon all monkeys did same | * One monkey learned that could more easily clean potatoes in water and soon all monkeys did same | ||
| - | - **Cognition and Problem Solving** | + | - Cognition and Problem Solving |
| - | | + | * Cognition: the process of knowing that involves awareness, reasoning, recollection, |
| - | | + | * Problem solving: the cognitive ability to overcome obstacles |
| - | - **Insight: when an animal, exposed to new situation with no experience, performs behavior with desirable outcome** | + | - Insight: when an animal, exposed to new situation with no experience, performs behavior with desirable outcome |
| * Ex: monkey will stack boxes to climb and access previously unreachable bananas | * Ex: monkey will stack boxes to climb and access previously unreachable bananas | ||
| - | - **Signaling behavior: response and communication between organisms that can change behavior and reproductive success** | + | - Signaling behavior: response and communication between organisms that can change behavior and reproductive success |
| * Organisms exchange info in response to internal and external signals | * Organisms exchange info in response to internal and external signals | ||
| * Cooperative behavior increases fitness of individuals and survival of the population | * Cooperative behavior increases fitness of individuals and survival of the population | ||
| - Notes | - Notes | ||
| - | * Some behaviors that appear learned may be innate but need **maturation** | + | * Some behaviors that appear learned may be innate but need maturation |
| * Ex: birds appear to learn to fly by trial and error or observational learning but birds raised in isolation will fly on first try if are physically capable | * Ex: birds appear to learn to fly by trial and error or observational learning but birds raised in isolation will fly on first try if are physically capable | ||
| * Inherited behaviors and learning capabilities have evolved because increase individual fitness | * Inherited behaviors and learning capabilities have evolved because increase individual fitness | ||
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| * Habituation allows them to ignore repetitive events which have learned (from experience) are inconsequential → can focus on more important events | * Habituation allows them to ignore repetitive events which have learned (from experience) are inconsequential → can focus on more important events | ||
| * Observational learning and insight allows animals to learn new behaviors in response to unexpected events without receiving reinforcement | * Observational learning and insight allows animals to learn new behaviors in response to unexpected events without receiving reinforcement | ||
| - | | + | * Game Theory: The fitness of a particular behavior is influenced by other behavioral phenotypes in a population |
| - | - **General Animal Behaviors** | + | - General Animal Behaviors |
| * Animal always encountering different situations so respond to each in way that maximizes survival and reproductive success (fitness) | * Animal always encountering different situations so respond to each in way that maximizes survival and reproductive success (fitness) | ||
| - Survival responses: when encounters dangerous situation | - Survival responses: when encounters dangerous situation | ||
| - | - **Fight-Flight response:** animal encounters situation where must either fight or run | + | - Fight-Flight response: animal encounters situation where must either fight or run |
| * Response is triggered by stress and stimulates nervous system to produce adrenaline → prepares body by dilating blood vessels, increasing heart rate, and increasing release of sugar from liver into blood | * Response is triggered by stress and stimulates nervous system to produce adrenaline → prepares body by dilating blood vessels, increasing heart rate, and increasing release of sugar from liver into blood | ||
| - | - **Avoidance response: when animal avoids encountering a stressful situation → associative learning bcuz recognizes that is stressful** | + | - Avoidance response: when animal avoids encountering a stressful situation → associative learning bcuz recognizes that is stressful |
| * Ex: avoid predator habitats, unfamiliar objects, scents, or sound | * Ex: avoid predator habitats, unfamiliar objects, scents, or sound | ||
| - | - **Alarm response: triggered when animal detects threat so warns group** | + | - Alarm response: triggered when animal detects threat so warns group |
| * Ex: monkeys emit distinctive alarms for intruders, with special calls for snakes, birds and leopards | * Ex: monkeys emit distinctive alarms for intruders, with special calls for snakes, birds and leopards | ||
| - | - **Foraging Behaviors:** **Optimal foraging model**: natural selection should favor a foraging behavior that maximizes the benefits (food eaten) & minimizes the costs (energy extended and risk) + behaviors that increases survival of populations | + | - Foraging Behaviors: Optimal foraging model: natural selection should favor a foraging behavior that maximizes the benefits (food eaten) & minimizes the costs (energy extended and risk) + behaviors that increases survival of populations |
| - | - **Flower color and flower scent are signals that animals use to locate flowers (and that plants use to attract them)** | + | - Flower color and flower scent are signals that animals use to locate flowers (and that plants use to attract them) |
| * Often vision and olfactory abilities of animals have coevolved with flower color and scents | * Often vision and olfactory abilities of animals have coevolved with flower color and scents | ||
| * Flowers provide animals protein (from pollen) and carbs (sugar in nectar) ←→ animals disperse pollen | * Flowers provide animals protein (from pollen) and carbs (sugar in nectar) ←→ animals disperse pollen | ||
| * Ex: bees attracted to blue or yellow flowers with sweet smell | * Ex: bees attracted to blue or yellow flowers with sweet smell | ||
| - | - **Fruit color: a signal that animal uses to locate fruit and know if are ripe/edible or toxic** | + | - Fruit color: a signal that animal uses to locate fruit and know if are ripe/edible or toxic |
| * Sometimes fruit color is warning that is poisonous; chemical signals provide cues that is edible | * Sometimes fruit color is warning that is poisonous; chemical signals provide cues that is edible | ||
| * Food toxic to one animal may be nutritious for another and many animals have evolved metabolic pathways to detoxify plant materials | * Food toxic to one animal may be nutritious for another and many animals have evolved metabolic pathways to detoxify plant materials | ||
| * Ex: monarch butterflies use milkweeds to make themselves toxic | * Ex: monarch butterflies use milkweeds to make themselves toxic | ||
| - | - **Body scents: signals presence of predators** | + | - Body scents: signals presence of predators |
| * Ex: zebras increase vigilance when detect body odor | * Ex: zebras increase vigilance when detect body odor | ||
| - | - **Herds, flocks, and schools provide advantages when foraging** | + | - Herds, flocks, and schools provide advantages when foraging |
| * Concealment: | * Concealment: | ||
| * Vigilance: more ppl watching | * Vigilance: more ppl watching | ||
| * Defense: can shield or mob attack | * Defense: can shield or mob attack | ||
| - | - **Packs: corner and attack large prey** | + | - Packs: corner and attack large prey |
| - | - **Search Images: look for abbreviated forms of of object to find favored or plentiful food** | + | - Search Images: look for abbreviated forms of of object to find favored or plentiful food |
| - | - **Social Behavior** May live in group or alone; always make contact to reproduce | + | - Social Behavior May live in group or alone; always make contact to reproduce |
| - | - **Agonistic behavior (aggression and submission) originates from competition for food, mates, or territory** | + | - Agonistic behavior (aggression and submission) originates from competition for food, mates, or territory |
| - | - **Parental Care: innate behavior in response to producing offspring** | + | - Parental Care: innate behavior in response to producing offspring |
| * Paternal behavior exists because it has been reinforced over generations by natural selection | * Paternal behavior exists because it has been reinforced over generations by natural selection | ||
| - | - **Dominance Hierarchies: | + | - Dominance Hierarchies: |
| - | | + | * Pecking order |
| - | - **Territoriality: | + | - Territoriality: |
| - | - **Eusocial (truly social) consists of members divided into castes** | + | - Eusocial (truly social) consists of members divided into castes |
| * One caste will forage, other will feed and care | * One caste will forage, other will feed and care | ||
| - | - **Altruistic behavior: seemingly unselfish behavior that appear to reduce fitness of an individual** | + | - Altruistic behavior: seemingly unselfish behavior that appear to reduce fitness of an individual |
| * Often occurs when animal risks safety in the face of another to help another individual (of same species) rear its young | * Often occurs when animal risks safety in the face of another to help another individual (of same species) rear its young | ||
| - | * This behavior increases | + | * This behavior increases inclusive fitness: fitness of individual plus fitness of relatives (share % DNA) |
| - | * Evolution of these behaviors occurs by **kin selection:** form of natural selection that increases inclusive fitness | + | * Evolution of these behaviors occurs by kin selection: form of natural selection that increases inclusive fitness |
| * Altruistic behavior can be maintained by evolution because furthers survival of population | * Altruistic behavior can be maintained by evolution because furthers survival of population | ||
| - Ground squirrels give alarm calls that warns other squirrels of predators but risks own safety by revealing presence | - Ground squirrels give alarm calls that warns other squirrels of predators but risks own safety by revealing presence | ||
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| - Bees live in colonies made of queen and female daughters (worker bees) → only queen reproduces so fitness of workers is zero | - Bees live in colonies made of queen and female daughters (worker bees) → only queen reproduces so fitness of workers is zero | ||
| * Kin selection favors sterile workers in haplodiploid society because all sister bees share 75% genes and fitness of worker bees (by how much genes contributes to the next gen) is greater if it promotes production of sisters by nurturing queens rather than by themselves. | * Kin selection favors sterile workers in haplodiploid society because all sister bees share 75% genes and fitness of worker bees (by how much genes contributes to the next gen) is greater if it promotes production of sisters by nurturing queens rather than by themselves. | ||
| - | | + | * Reciprocal Altruism: exchange of aid between unrelated individuals |
| * Do it bcuz think they will receive something in return in future | * Do it bcuz think they will receive something in return in future | ||
| - | - **Animal Movement** Animals can respond to external stimuli by moving → allows them to seek food, shelter, safety, or mates | + | - Animal Movement Animals can respond to external stimuli by moving → allows them to seek food, shelter, safety, or mates |
| - | - **Kinesis:** **undirected** **change in** **speed** **of an animal' | + | - Kinesis: undirected change in speed of an animal' |
| * Animal slows down in favorable environment (stay longer) & speed up in unfavorable | * Animal slows down in favorable environment (stay longer) & speed up in unfavorable | ||
| * Ex: animal will suddenly scurry about in response to light, touch, or air temp | * Ex: animal will suddenly scurry about in response to light, touch, or air temp | ||
| - | - **Taxis: directed movement in response to stimulus; either toward or away from stimulus** | + | - Taxis: directed movement in response to stimulus; either toward or away from stimulus |
| - | | + | * Phototaxis: movement in response to light; Chemotaxis: movement in response to chemicals |
| * Ex: bacteria move toward oxygen or nutrients (positive chemotaxis) or away from taxis | * Ex: bacteria move toward oxygen or nutrients (positive chemotaxis) or away from taxis | ||
| * Moths move toward light at night, sharks move toward when food odors reach them by diffusion or bulk flow (ocean current) | * Moths move toward light at night, sharks move toward when food odors reach them by diffusion or bulk flow (ocean current) | ||
| - | - **Migration: long-distance, | + | - Migration: long-distance, |
| ====Animal Rhythms==== | ====Animal Rhythms==== | ||
| - | | + | * Circadian rhythm: pattern of behavioral activity aligned with 24 hour cycle (AKA biological clock); daily cycle of rest and activity |
| * Can persist without external cues but cues can help → light can maintain synchronization | * Can persist without external cues but cues can help → light can maintain synchronization | ||
| * Biological rhythms can be linked to light/dark and lunar cycles | * Biological rhythms can be linked to light/dark and lunar cycles | ||
| - | - **Day/Night Rhythms** found in all animals in response to predator habits or environment | + | - Day/Night Rhythms found in all animals in response to predator habits or environment |
| - | | + | * Diurnal animals are active during day and sleep at night |
| * Communicate mostly with auditory and visual signals | * Communicate mostly with auditory and visual signals | ||
| - | | + | * Nocturnal animals are active at night and rest during day |
| * Communicate mostly with auditory and olfactory signals | * Communicate mostly with auditory and olfactory signals | ||
| - Changes to Behavioral Rhythms in Response to Season Changes | - Changes to Behavioral Rhythms in Response to Season Changes | ||
| * Causes for changes in behavioral rhythms → seasonal changes → changes in weather, length of day, availability of food | * Causes for changes in behavioral rhythms → seasonal changes → changes in weather, length of day, availability of food | ||
| * So animals adjust behavior to maximize fitness and take advantage of benefits | * So animals adjust behavior to maximize fitness and take advantage of benefits | ||
| - | - **Hibernation: | + | - Hibernation: |
| * Hibernating reduces energy & metabolic maintenance by lowering body temperature and using fat as energy | * Hibernating reduces energy & metabolic maintenance by lowering body temperature and using fat as energy | ||
| - | - **Estivation: dormancy during summer** | + | - Estivation: dormancy during summer |
| * Protect from drying out by burrowing or climbing in plants | * Protect from drying out by burrowing or climbing in plants | ||
| - | - **Courtship and mating: often during spring with warmer weather and more food → provide energy and nourishment** | + | - Courtship and mating: often during spring with warmer weather and more food → provide energy and nourishment |
| - | - **Migration** | + | - Migration |
| ====Communication in Animals==== | ====Communication in Animals==== | ||
| - | | + | * Signal: A stimulus transmitted from one organism |
| - | | + | * Communication: |
| * Common modes of animal communication: | * Common modes of animal communication: | ||
| * Uses: indicate dominance, find food, establish territory, ensure reproductive success, species recognition, | * Uses: indicate dominance, find food, establish territory, ensure reproductive success, species recognition, | ||
| - | - **Chemical: release pheromones (chemicals for communication) that elicit response when smelled or eaten** | + | - Chemical: release pheromones (chemicals for communication) that elicit response when smelled or eaten |
| - | | + | * Releaser pheromones: chemicals that trigger immediate and specific behavior changes |
| - | | + | * Primer pheromones: cause developmental changes |
| - | * Ex: queen bee pheromones stop workers from being able to reproduce, ants use to guide other ants, male animals exhibit | + | * Ex: queen bee pheromones stop workers from being able to reproduce, ants use to guide other ants, male animals exhibit territoriality when spray urine |
| - | - **Visual: often during acts of aggression (agonistic behavior) or courtship** | + | - Visual: often during acts of aggression (agonistic behavior) or courtship |
| * Ex: stickleback fishes where red bellies, head-up posture, zigzag motions, and swimming to nest are visual cues | * Ex: stickleback fishes where red bellies, head-up posture, zigzag motions, and swimming to nest are visual cues | ||
| - | * Some male birds assemble into groups called | + | * Some male birds assemble into groups called leks in which make courtship to female who chooses |
| - | - **Auditory: sounds often used to communicate over long distances, thru water, and at night** | + | - Auditory: sounds often used to communicate over long distances, thru water, and at night |
| * Use to ward off male rivals, attract female, species recognition, | * Use to ward off male rivals, attract female, species recognition, | ||
| - | - **Tactile: use of touch for social bonding, infant care, and mating** | + | - Tactile: use of touch for social bonding, infant care, and mating |
| * Ex: bees perform dances that provide info about location of food | * Ex: bees perform dances that provide info about location of food | ||
| * Bees make body contact (tactile) during dance | * Bees make body contact (tactile) during dance | ||
| - Mating Behavior and Mate Choice | - Mating Behavior and Mate Choice | ||
| * In some animal species, mating is promiscuous, | * In some animal species, mating is promiscuous, | ||
| - | * In others, mates form a relationship that is **monogamous** (one male mating with one female) or **polygamous** (an individual of one sex mating with several of the other) | + | * In others, mates form a relationship that is monogamous (one male mating with one female) or polygamous (an individual of one sex mating with several of the other) |
| - | | + | * Sexual Dimorphism: Physical differences between male and females; resuls from sexual selection & mating systems |
| * In monogamous species, males and females often look very similar while in polygamous species the mate that attracts multiple partners is usually showier | * In monogamous species, males and females often look very similar while in polygamous species the mate that attracts multiple partners is usually showier | ||
| * Often master-regulatory genes control courtship because products regulate other genes controlling sexual reproduction | * Often master-regulatory genes control courtship because products regulate other genes controlling sexual reproduction | ||
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| * Change in level of receptor can alter development | * Change in level of receptor can alter development | ||
| =====Ecology===== | =====Ecology===== | ||
| - | **Review** | + | Review |
| * Ecology is the study of the distribution of organisms, their interactions with other organisms, and their interactions with their physical environment | * Ecology is the study of the distribution of organisms, their interactions with other organisms, and their interactions with their physical environment | ||
| * Vocab | * Vocab | ||
| - | - A **population** is a group of individuals of the same species living in the same area | + | - A population is a group of individuals of the same species living in the same area |
| - | - A **community** is a group of populations living in the same area | + | - A community is a group of populations living in the same area |
| - | - An **ecosystem** describes the interaction between organisms and the environment | + | - An ecosystem describes the interaction between organisms and the environment |
| - | - The **biosphere** is composed of all regions of the earth that contain living things | + | - The biosphere is composed of all regions of the earth that contain living things |
| - | - The **habitat** of an organism is the type of place it usually lives | + | - The habitat of an organism is the type of place it usually lives |
| * Described by organisms that live there (often the dominant vegetation) and physical and chemical characteristics of the environment (like temp, soil quality, or water salinity). | * Described by organisms that live there (often the dominant vegetation) and physical and chemical characteristics of the environment (like temp, soil quality, or water salinity). | ||
| - | - The **niche** of an organism describes all the biotic (living) and abiotic (nonliving) resources in the environment used by an organism | + | - The niche of an organism describes all the biotic (living) and abiotic (nonliving) resources in the environment used by an organism |
| * An organism occupies a niche → changes factors in a way | * An organism occupies a niche → changes factors in a way | ||
| ====Climate==== | ====Climate==== | ||
| * Long-term conditions in an area | * Long-term conditions in an area | ||
| * Four physical factors— temperature, | * Four physical factors— temperature, | ||
| - | | + | * Climograph: plot of the annual mean temperature and precipitation in a particular region |
| * Global Climate Patterns | * Global Climate Patterns | ||
| * Determined largely by the input of solar energy (differential heating of Earth' | * Determined largely by the input of solar energy (differential heating of Earth' | ||
| Line 4124: | Line 4280: | ||
| * Forests dark in color absorb more and reflects less solar energy → warm Earth' | * Forests dark in color absorb more and reflects less solar energy → warm Earth' | ||
| * Warming effect balanced by transpiration | * Warming effect balanced by transpiration | ||
| - | * **Aquatic Biomes** | + | * Aquatic Biomes |
| * Unlike terrestrial biomes, aquatic biomes are characterized by their physical environment rather than by climate and are often layered with regard to light penetration & temperature | * Unlike terrestrial biomes, aquatic biomes are characterized by their physical environment rather than by climate and are often layered with regard to light penetration & temperature | ||
| * Very big, so impact biosphere | * Very big, so impact biosphere | ||
| * ex: produce oxygen, source of rainfall, effects on ocean temp on global climate and wind patterns | * ex: produce oxygen, source of rainfall, effects on ocean temp on global climate and wind patterns | ||
| * Zonation | * Zonation | ||
| - | | + | * Photic zone: region where there is sufficient light for photosynthesis |
| - | | + | * Aphotic zone: little light |
| - | | + | * Abyssal zone: deep in aphotic zone |
| - | | + | * Benthic zone: bottom of all zones |
| * Where light penetrates = warm. No light = cold | * Where light penetrates = warm. No light = cold | ||
| - | | + | * Thermocline: |
| - | | + | * Turnover: semiannual mixing of lake waters as a result of seasonal changing of water density |
| * Sends oxygenated water from a lake’s surface to the bottom and brings nutrient-rich water from the bottom to the surface in both spring and autumn | * Sends oxygenated water from a lake’s surface to the bottom and brings nutrient-rich water from the bottom to the surface in both spring and autumn | ||
| - | * **Dispersal and Distribution** | + | * Dispersal and Distribution |
| - | | + | * Dispersal: movement of individuals or gametes away from their area of origin or from centers of high population density |
| * Contributes to global distribution of organisms | * Contributes to global distribution of organisms | ||
| - | | + | * Range expansion: when organisms reach an area where they did not exist previously |
| * Successful = potential range is larger than actual range | * Successful = potential range is larger than actual range | ||
| * Increasing greenhouse gas concentrations in the air are warming Earth and altering the distributions of many species. | * Increasing greenhouse gas concentrations in the air are warming Earth and altering the distributions of many species. | ||
| * Some species will not be able to shift their ranges quick enough to reach suitable habitat in the future | * Some species will not be able to shift their ranges quick enough to reach suitable habitat in the future | ||
| - | * **Effects on Organism Distribution** Biotic & Abiotic Factors | + | * Effects on Organism Distribution Biotic & Abiotic Factors |
| - | | + | * Abiotic (nonliving) factors like temp, light, water, and nutrients & biotic factors influence organism distribution, |
| - | * **Biotic Factors** | + | * Biotic Factors |
| * Ability of a species to survive and reproduce is reduced by its interactions with other species, such as predators or herbivores | * Ability of a species to survive and reproduce is reduced by its interactions with other species, such as predators or herbivores | ||
| * Also presence/ | * Also presence/ | ||
| Line 4152: | Line 4308: | ||
| * Primary Producers: Provide food, shelter, reduce erosion | * Primary Producers: Provide food, shelter, reduce erosion | ||
| * Predators: keep prey populations in control, diverse diets that don't put too much pressure | * Predators: keep prey populations in control, diverse diets that don't put too much pressure | ||
| - | * **Abiotic Factors** Temperature | + | * Abiotic Factors Temperature |
| * Cells may rupture if the water they contain freezes; at higher temp → more radiation → damage DNA and denature proteins | * Cells may rupture if the water they contain freezes; at higher temp → more radiation → damage DNA and denature proteins | ||
| * More sunlight & nutrients → more primary production; also more water more species | * More sunlight & nutrients → more primary production; also more water more species | ||
| Line 4162: | Line 4318: | ||
| * Salinity | * Salinity | ||
| * Affects water balance bcuz of osmosis | * Affects water balance bcuz of osmosis | ||
| - | * **Biomes** | + | * Biomes |
| - | | + | * Biomes: regions of the biosphere that exhibit common environmental characteristics. |
| * Each has unique communities or ecosystems of plants and animals that share adaptations to survive | * Each has unique communities or ecosystems of plants and animals that share adaptations to survive | ||
| * Major Biomes | * Major Biomes | ||
| - | - **Tropical rain forests:** characterized by high temperature and heavy rainfall; tall trees that from thick canopy that reduces light penetration | + | - Tropical rain forests: characterized by high temperature and heavy rainfall; tall trees that from thick canopy that reduces light penetration |
| - | - **Savannas** are grasslands with scattered trees. | + | - Savannas are grasslands with scattered trees. |
| * Tropical → high temp but lot less water than rain forests | * Tropical → high temp but lot less water than rain forests | ||
| - | - **Temperate grasslands** receive less water and lower temperatures than savannas. | + | - Temperate grasslands receive less water and lower temperatures than savannas. |
| - | - **Temperate deciduous forests** have warm summers, cold winters, and moderate precipitation. | + | - Temperate deciduous forests have warm summers, cold winters, and moderate precipitation. |
| * Deciduous trees shed their leaves during the winter → adaptation to poor growing conditions (short days and cold temperatures). | * Deciduous trees shed their leaves during the winter → adaptation to poor growing conditions (short days and cold temperatures). | ||
| - | - **Deserts** are hot and dry → located where air masses are descending | + | - Deserts are hot and dry → located where air masses are descending |
| * Adaptations: | * Adaptations: | ||
| - | - **Taigas** are characterized by coniferous forests (vegetation with needles for leaves). Long and cold winters with precipitation is in the form of snow. | + | - Taigas are characterized by coniferous forests (vegetation with needles for leaves). Long and cold winters with precipitation is in the form of snow. |
| - | - **Tundras** have winters so cold that the ground freezes | + | - Tundras have winters so cold that the ground freezes |
| * During summer, the upper topsoil thaws and supports grassland community (vegetation tolerant to soggy soil) | * During summer, the upper topsoil thaws and supports grassland community (vegetation tolerant to soggy soil) | ||
| - | * But the deeper soil, the **permafrost**, stays frozen (growth limiting factor) | + | * But the deeper soil, the permafrost, stays frozen (growth limiting factor) |
| - | - **Freshwater** biomes include ponds, lakes, streams, and rivers. | + | - Freshwater biomes include ponds, lakes, streams, and rivers. |
| - | - **Marine biomes** include estuaries (where oceans meet rivers), intertidal zones (where oceans meet land), continental shelves (shallow oceans that border continents), | + | - Marine biomes include estuaries (where oceans meet rivers), intertidal zones (where oceans meet land), continental shelves (shallow oceans that border continents), |
| - | * **Trophic Levels** [[https:// | + | * Trophic Levels https:// |
| - | | + | <img src=" |
| + | </ | ||
| + | * Trophic Levels: position organism is in food chain | ||
| * Way of illustrating energy flow and production & utilization of energy | * Way of illustrating energy flow and production & utilization of energy | ||
| - | - **Primary produces: photoautotrophs that convert sun energy into chemical energy → ecosystem’s initial source of energy** | + | - Primary produces: photoautotrophs that convert sun energy into chemical energy → ecosystem’s initial source of energy |
| - | - **Primary consumers: (herbivores) heterotrophs that eat primary producers** | + | - Primary consumers: (herbivores) heterotrophs that eat primary producers |
| - | - **Secondary consumers: (primary carnivores) heterotrophs that eat primary consumers** | + | - Secondary consumers: (primary carnivores) heterotrophs that eat primary consumers |
| - | - **Tertiary consumers: (secondary carnivores/ | + | - Tertiary consumers: (secondary carnivores/ |
| - | - **Detritivores: | + | - Detritivores: |
| - | | + | * Decomposers: |
| * Recycle chemical elements to producers and important bcuz convert organic matter from all trophic levels to inorganic compounds usable by primary producers. | * Recycle chemical elements to producers and important bcuz convert organic matter from all trophic levels to inorganic compounds usable by primary producers. | ||
| * If decomposition stopped, life would cease as detritus piled up and the supply of ingredients needed to synthesize organic matter was exhausted. | * If decomposition stopped, life would cease as detritus piled up and the supply of ingredients needed to synthesize organic matter was exhausted. | ||
| - | * **Trophic Interactions** Certain species in community can influence the dynamics of that community | + | * Trophic Interactions Certain species in community can influence the dynamics of that community |
| - | - **Foundation Species: strong effects on communities bcuz of large size or abundance** | + | - Foundation Species: strong effects on communities bcuz of large size or abundance |
| - | - **Dominant Species: most abundant species that contributes greatest biomass to a community** | + | - Dominant Species: most abundant species that contributes greatest biomass to a community |
| * Species dominant bcuz is best able to compete for resources & escape predators/ | * Species dominant bcuz is best able to compete for resources & escape predators/ | ||
| - | - **Keystone species: have strong, disproportionate influence on the health of a community or ecosystem their relative to abundance** | + | - Keystone species: have strong, disproportionate influence on the health of a community or ecosystem their relative to abundance |
| * Removal of keystone species results in collapse in food webs and ecosystems; leads to decrease in species diversity | * Removal of keystone species results in collapse in food webs and ecosystems; leads to decrease in species diversity | ||
| * May eat species that eat another species | * May eat species that eat another species | ||
| - | - **Invasive Species: introduced species that proliferates and displaces native species bcuz it is a better competitor and/or because natural predators/ | + | - Invasive Species: introduced species that proliferates and displaces native species bcuz it is a better competitor and/or because natural predators/ |
| - | | + | * Kudzu: climbing vine that kills vegetation by blocking sun |
| - | | + | * Potato blight: caused by fungus-like protist |
| * Influences on Number and Size of Trophic Levels in Ecosystems | * Influences on Number and Size of Trophic Levels in Ecosystems | ||
| - | - **Size of bottom trophic levels: bcuz primary producers provide initial source of energy to the ecosystem, their number and generated biomass control how many trophic lvls can be supported** | + | - Size of bottom trophic levels: bcuz primary producers provide initial source of energy to the ecosystem, their number and generated biomass control how many trophic lvls can be supported |
| * So ecosystem with small tier of primary producers cannot sustain many tiers above it | * So ecosystem with small tier of primary producers cannot sustain many tiers above it | ||
| - | - **Efficiency of energy transfer between trophic levels: ~10% of energy passed from one lvl to another → energy loss limits number/size of trophic lvls and abundance of top carnivores** | + | - Efficiency of energy transfer between trophic levels: ~10% of energy passed from one lvl to another → energy loss limits number/size of trophic lvls and abundance of top carnivores |
| * Ecosystems (like in tropical rainforests) have higher photosynthetic efficiency → longer food chains → more complex food webs | * Ecosystems (like in tropical rainforests) have higher photosynthetic efficiency → longer food chains → more complex food webs | ||
| - | - **Stability of trophic levels: ecosystems with long food chains have less stable trophic levels bcuz bcuz there are more lvls below them that can be weakened by environmental changes** | + | - Stability of trophic levels: ecosystems with long food chains have less stable trophic levels bcuz bcuz there are more lvls below them that can be weakened by environmental changes |
| - | - **Requirements of top predators: top tier size is limited bcuz of less biomass available and high energy requirements of large, top predators** | + | - Requirements of top predators: top tier size is limited bcuz of less biomass available and high energy requirements of large, top predators |
| * Trophic Levels Models | * Trophic Levels Models | ||
| * Size of trophic levels can also be regulated by interactions between the levels | * Size of trophic levels can also be regulated by interactions between the levels | ||
| * Organisms can be controlled by what they eat (“bottom-up” control) or by what eats them (“top-down” control). | * Organisms can be controlled by what they eat (“bottom-up” control) or by what eats them (“top-down” control). | ||
| - | - **Bottom-up model: structure of trophic lvls are regulated by changes in the** **bottom** **trophic lvl** | + | - Bottom-up model: structure of trophic lvls are regulated by changes in the bottom trophic lvl |
| * Ex: primary productivity low → few supported trophic lvls | * Ex: primary productivity low → few supported trophic lvls | ||
| - | - **Top-down model: structure of trophic levels are regulated by changes in the** **top** **trophic level** | + | - Top-down model: structure of trophic levels are regulated by changes in the top trophic level |
| * Ex predator removed → herbivores increase → primary producers decrease → total biomass decreases | * Ex predator removed → herbivores increase → primary producers decrease → total biomass decreases | ||
| * Top down regulation can become irregular when humans remove top predators | * Top down regulation can become irregular when humans remove top predators | ||
| * Ecological Pyramids | * Ecological Pyramids | ||
| * Used to show relationship between trophic levels | * Used to show relationship between trophic levels | ||
| - | * [[Untitled_a1baf95c2be74fad95ea92c3882c2c8f: | + | * Untitled_a1baf95c2be74fad95ea92c3882c2c8f: |
| * Tiers represent sizes of trophic levels | * Tiers represent sizes of trophic levels | ||
| * Each represented in terms of energy (A.K.A productivity), | * Each represented in terms of energy (A.K.A productivity), | ||
| Line 4224: | Line 4382: | ||
| * Aquatic ecological pyramids are often inverted because biomass of consumers exceeds that of producers | * Aquatic ecological pyramids are often inverted because biomass of consumers exceeds that of producers | ||
| ====Energy Flow in an Ecosystem==== | ====Energy Flow in an Ecosystem==== | ||
| - | - **Food chain:** linear flow chart of who eats whom and direction of nutrient and energy transfer | + | - Food chain: linear flow chart of who eats whom and direction of nutrient and energy transfer |
| - | - **Food web:** linked group of food chains (animals have more than one food source) | + | - Food web: linked group of food chains (animals have more than one food source) |
| * Conservation of Mass | * Conservation of Mass | ||
| - | | + | * Matter, like energy, cannot be created or destroyed. |
| * But elements can cycle--be gained or lost by an ecosystem | * But elements can cycle--be gained or lost by an ecosystem | ||
| * Ecosystems are open systems, absorbing energy and mass and releasing heat and waste products | * Ecosystems are open systems, absorbing energy and mass and releasing heat and waste products | ||
| * Ecosystems depend on constant input of energy | * Ecosystems depend on constant input of energy | ||
| - | * **Ecological/ | + | * Ecological/ |
| * “Proportion of energy represented at one trophic lvl that is transferred to the next lvl” | * “Proportion of energy represented at one trophic lvl that is transferred to the next lvl” | ||
| * Always less than production efficiency | * Always less than production efficiency | ||
| Line 4254: | Line 4412: | ||
| * Ex: sunlight can affect number and size of trophic levels | * Ex: sunlight can affect number and size of trophic levels | ||
| * Energy Flow and Chemical Cycling | * Energy Flow and Chemical Cycling | ||
| - | | + | * Chemical Cycling: plants take chemicals from soil & air → chemicals passed to herbivores → decomposers break down dead matter, releasing chemicals back to the soil https:// |
| - | | + | <img src=" |
| + | </ | ||
| + | * Energy Flow: Energy enters most ecosystems as sunlight → converted to chemical energy by autotrophs → passed to heterotrophs in the organic compounds of food → dissipated as heat when energy used for work | ||
| * Both energy and chemicals are transformed in ecosystems through photosynthesis and feeding relationships. But unlike chemicals, energy cannot be recycled. | * Both energy and chemicals are transformed in ecosystems through photosynthesis and feeding relationships. But unlike chemicals, energy cannot be recycled. | ||
| - | * **How do Organisms Regulate Body Temp and Metabolism?** | + | * How do Organisms Regulate Body Temp and Metabolism? |
| - | | + | * Endotherms use thermal energy generated by metabolism |
| * Ex: changes in heart rate, fat storage, muscle contractions (shivering) | * Ex: changes in heart rate, fat storage, muscle contractions (shivering) | ||
| * Metabolic Rate/O2 consumption rate increases with decreasing temperature | * Metabolic Rate/O2 consumption rate increases with decreasing temperature | ||
| * Spend more energy to maintain internal temp | * Spend more energy to maintain internal temp | ||
| - | | + | * Ectotherms lack efficient body temperature regulating mechanisms |
| * Rely on behavior: moving in and out sun, eating | * Rely on behavior: moving in and out sun, eating | ||
| * Metabolic Rate/O2 consumption rate increases with increasing temperature | * Metabolic Rate/O2 consumption rate increases with increasing temperature | ||
| - | * **Primary Productivity** | + | * Primary Productivity |
| * Organisms use energy to grow and reproduce | * Organisms use energy to grow and reproduce | ||
| - | | + | * Primary productivity: |
| - | - **Gross primary productivity (GPP): rate at which producers acquire chemical energy before any of this energy is used for metabolism** | + | - Gross primary productivity (GPP): rate at which producers acquire chemical energy before any of this energy is used for metabolism |
| - | - **Net primary productivity (NPP): rate at which producers acquire the chemical energy minus the rate at which they consume energy thru respiration** | + | - Net primary productivity (NPP): rate at which producers acquire the chemical energy minus the rate at which they consume energy thru respiration |
| * NPP represents the biomass available to herbivores | * NPP represents the biomass available to herbivores | ||
| - | - **Respiratory/ | + | - Respiratory/ |
| * Most of energy is lost as heat | * Most of energy is lost as heat | ||
| * Larger organisms = higher rate | * Larger organisms = higher rate | ||
| Line 4277: | Line 4437: | ||
| * Net Gain = energy storage or growth | * Net Gain = energy storage or growth | ||
| * Net Loss = mass loss or death | * Net Loss = mass loss or death | ||
| - | * **Regulation of Primary Productivity** | + | * Regulation of Primary Productivity |
| * Aquatic Biomes: Light and nutrients | * Aquatic Biomes: Light and nutrients | ||
| * Terrestrial Biomes: Temperature and moisture | * Terrestrial Biomes: Temperature and moisture | ||
| Line 4283: | Line 4443: | ||
| * Solar energy exposure controls extent of photosynthesis and biomass of primary producers | * Solar energy exposure controls extent of photosynthesis and biomass of primary producers | ||
| * Nutrient Limitation | * Nutrient Limitation | ||
| - | | + | * Limiting nutrient is the element that must be added for production to increase |
| * Usually nitrogen and phosphorous | * Usually nitrogen and phosphorous | ||
| * If a nutrient’s outputs exceed its inputs, that nutrient will eventually limit production in that ecosystem | * If a nutrient’s outputs exceed its inputs, that nutrient will eventually limit production in that ecosystem | ||
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| ====Population Ecology==== | ====Population Ecology==== | ||
| “Study of the growth, abundance, and distribution of populations” Population abundance and distribution are described by… | “Study of the growth, abundance, and distribution of populations” Population abundance and distribution are described by… | ||
| - | - **Size (****N****): total number of individuals in the population** | + | - Size (N): total number of individuals in the population |
| - | - **Density: total number of individuals per area occupied** | + | - Density: total number of individuals per area occupied |
| * Adding = thru birth or immigration; | * Adding = thru birth or immigration; | ||
| * Resource availability affects population density | * Resource availability affects population density | ||
| * More food → population can become denser → higher reproductive rates & limited space | * More food → population can become denser → higher reproductive rates & limited space | ||
| - | - **Dispersion: how individuals in a population are distributed** | + | - Dispersion: how individuals in a population are distributed |
| * May be clumped (like humans in cities), uniform (like trees in an orchard), or random (trees in a forest) | * May be clumped (like humans in cities), uniform (like trees in an orchard), or random (trees in a forest) | ||
| - | - **Age structure: description of individuals of each age** | + | - Age structure: description of individuals of each age |
| * Rapidly growing population is indicated when the large proportion is young | * Rapidly growing population is indicated when the large proportion is young | ||
| * Pyramid-shaped = rapidly growing populations | * Pyramid-shaped = rapidly growing populations | ||
| - | * Tiers of equal width = stable populations with little/no population growth (**zero population growth**) | + | * Tiers of equal width = stable populations with little/no population growth (zero population growth) |
| - | - **Survivorship curves: Describes mortality rates of individuals in a species** | + | - Survivorship curves: Describes mortality rates of individuals in a species |
| - | | + | * Type I: species in which most individuals survive to middle age and after that age mortality is high |
| * Ex: humans | * Ex: humans | ||
| - | | + | * Type II: die randomly (any age) |
| * Ex: many rodents | * Ex: many rodents | ||
| - | | + | * Type III: most individuals die young; only a few survive to reproductive age |
| - | - **Biotic potential: maximum growth rate of a population under ideal conditions (unlimited resources and no growth restrictions) → rMax** | + | - Biotic potential: maximum growth rate of a population under ideal conditions (unlimited resources and no growth restrictions) → rMax |
| * Ex: some bacteria can divide every 20 minutes | * Ex: some bacteria can divide every 20 minutes | ||
| - Factors that contribute to the biotic potential & reproductive success of a species | - Factors that contribute to the biotic potential & reproductive success of a species | ||
| * Age at reproductive maturity | * Age at reproductive maturity | ||
| - | | + | * Clutch size (number of offspring produced at each reproductive event) |
| * Frequency of reproduction | * Frequency of reproduction | ||
| * Reproductive lifetime | * Reproductive lifetime | ||
| * Survivorship of offspring to reproductive maturity | * Survivorship of offspring to reproductive maturity | ||
| - | - **Carrying capacity: max number of individuals of a population that can be sustained by a particular habitat** | + | - Carrying capacity: max number of individuals of a population that can be sustained by a particular habitat |
| * Largely contributed by competition for resources | * Largely contributed by competition for resources | ||
| - | - **Limiting factors: factors that prevent a population from attaining its biotic potential and determine carrying capacity → can be density-dependent or density-independent factors** | + | - Limiting factors: factors that prevent a population from attaining its biotic potential and determine carrying capacity → can be density-dependent or density-independent factors |
| * Energy, shelter, nutrient & water availability can all be limiting factors | * Energy, shelter, nutrient & water availability can all be limiting factors | ||
| * Limited quantities of these resources result in intraspecific competition | * Limited quantities of these resources result in intraspecific competition | ||
| - | | + | * Density-dependent factors: abiotic and biotic factors whose limiting effects become more intense as the population density increases |
| * Ex: competition for resources, territoriality, | * Ex: competition for resources, territoriality, | ||
| * Process that maintains a stable population | * Process that maintains a stable population | ||
| * Factors are a negative feedback which stops population growth by reducing birth rates or increasing death rates | * Factors are a negative feedback which stops population growth by reducing birth rates or increasing death rates | ||
| - | | + | * Density-independent factors: occur independently of the density of the population |
| * Ex: Natural disasters, pollution, and extremes of climate | * Ex: Natural disasters, pollution, and extremes of climate | ||
| - | * **Population Growths** Equation for Growth of Population | + | * Population Growths Equation for Growth of Population |
| - | - **Growth of Populations: | + | - Growth of Populations: |
| + | <img src=" | ||
| + | </ | ||
| * R is the reproductive rate (or growth rate), N is the population size, numerator is net increase in individuals | * R is the reproductive rate (or growth rate), N is the population size, numerator is net increase in individuals | ||
| * When deaths exceed births, r will be negative and population size will decrease | * When deaths exceed births, r will be negative and population size will decrease | ||
| - | | + | * Intrinsic rate of growth: when reproductive rate (r) is at maximum (biotic potential) |
| * Patterns of Population Growth | * Patterns of Population Growth | ||
| - | - **Exponential growth: occurs whenever the reproductive rate is greater than one. Results from reproduction w/o constraints** [[https:// | + | - Exponential growth: occurs whenever the reproductive rate is greater than one. Results from reproduction w/o constraints https:// |
| + | <img src=" | ||
| + | </ | ||
| * A population will usually exhibit exponential growth when they have more resources and space that they need | * A population will usually exhibit exponential growth when they have more resources and space that they need | ||
| - | * Formula: | + | * Formula: https:// |
| + | <img src=" | ||
| + | </ | ||
| * ΔN is the change in population size → add to original N to find total population | * ΔN is the change in population size → add to original N to find total population | ||
| * ΔT is change in time | * ΔT is change in time | ||
| - | | + | * A population’s growth rate stays the same regardless of population size |
| - | - **Logistic growth: when limiting factors restrict size of the population to the carrying capacity of the habitat** | + | - Logistic growth: when limiting factors restrict size of the population to the carrying capacity of the habitat |
| * Cause for logistic growth: density-dependent factor becomes limiting and then population stabilizes (population at carrying capacity = stable) | * Cause for logistic growth: density-dependent factor becomes limiting and then population stabilizes (population at carrying capacity = stable) | ||
| * Population will usually switch to logistic growth bcuz of competition for resources (food, space, mates) | * Population will usually switch to logistic growth bcuz of competition for resources (food, space, mates) | ||
| - | * Formula: | + | * Formula: https:// |
| + | <img src=" | ||
| + | </ | ||
| * K = carrying capacity. | * K = carrying capacity. | ||
| * If question gives you max population, use logistic formula | * If question gives you max population, use logistic formula | ||
| Line 4347: | Line 4515: | ||
| * A population’s growth rate gets smaller as population reaches K | * A population’s growth rate gets smaller as population reaches K | ||
| * A population is stable when it is not growing/at carrying capacity | * A population is stable when it is not growing/at carrying capacity | ||
| - | | + | * Population cycles: fluctuations in population size in response to varying effects of limiting factors |
| * Population may grow exponentially beyond carrying capacity of the habitat before limiting factors inhibit growth | * Population may grow exponentially beyond carrying capacity of the habitat before limiting factors inhibit growth | ||
| * Population increases above carrying capacity → N decreases → factors ease → renew population grow | * Population increases above carrying capacity → N decreases → factors ease → renew population grow | ||
| Line 4353: | Line 4521: | ||
| * When the population size is small, limiting factors exert little negative feedback → population growth | * When the population size is small, limiting factors exert little negative feedback → population growth | ||
| * Ex: since many limiting factors are density-dependent, | * Ex: since many limiting factors are density-dependent, | ||
| - | - [[Untitled_a1baf95c2be74fad95ea92c3882c2c8f: | + | - Untitled_a1baf95c2be74fad95ea92c3882c2c8f: |
| - | | + | * Life History of an organism is its strategy for maximum fitness. |
| - | - **R-selected species** exhibit rapid (exponential) growth | + | - R-selected species exhibit rapid (exponential) growth |
| * Opportunistic species that quickly invade a habitat, reproduce and die | * Opportunistic species that quickly invade a habitat, reproduce and die | ||
| * Produce many offspring that are small, mature quickly, and require little parental care | * Produce many offspring that are small, mature quickly, and require little parental care | ||
| - | - **K-selected species** exhibit logistic growth as they remain at K | + | - K-selected species exhibit logistic growth as they remain at K |
| * Species (ex: humans) produce a small number or large offering that require extensive parental care until they mature | * Species (ex: humans) produce a small number or large offering that require extensive parental care until they mature | ||
| * Key Idea: What maintains a stable population ? | * Key Idea: What maintains a stable population ? | ||
| Line 4368: | Line 4536: | ||
| * “Number of species in an ecosystem or across the biosphere” | * “Number of species in an ecosystem or across the biosphere” | ||
| * Species Diversity depends on: | * Species Diversity depends on: | ||
| - | - **Species Richness: number of different species** | + | - Species Richness: number of different species |
| - | - **Relative Abundance:** | + | - Relative Abundance: |
| * Benefits of species diversity: ecosystem with higher species diversity can better resist environmental change | * Benefits of species diversity: ecosystem with higher species diversity can better resist environmental change | ||
| - | * Increased productivity and stability of communities (can survive better), produce more **biomass** (total mass of all organisms in a habitat), more resistant to introduced species | + | * Increased productivity and stability of communities (can survive better), produce more biomass (total mass of all organisms in a habitat), more resistant to introduced species |
| - | * Structure of Communities: | + | * Structure of Communities: |
| - | | + | <img src=" |
| + | </ | ||
| + | * Simpson’s Diversity Index: measures species diversity | ||
| * Higher index value = more diverse | * Higher index value = more diverse | ||
| - | * Based on random samples of environment | + | * Based on random samples of environment https:// |
| - | * **Interactions in Communities** | + | <img src=" |
| - | | + | </ |
| - | | + | * Interactions in Communities |
| - | | + | * Competitive Exclusion principle (Gause’s principle): Two species cannot occupy the same niche (when resources are limiting) |
| + | * When two species compete for the same resources or occupy the same niche, one is probs gonna be more successful and 2nd is eliminated | ||
| + | * Ex: when two species of Paramecium competed for same resources, one outcompeted other and grew more rapidly | ||
| * Competition is an interaction that can affect how populations access energy and matter | * Competition is an interaction that can affect how populations access energy and matter | ||
| * Can result in change in community structure | * Can result in change in community structure | ||
| - | * One form of interaction is **interspecific competition** (competition between different species). Different ways to resolve competition & enable similar species to coexist in a community | + | * One form of interaction is interspecific competition (competition between different species). Different ways to resolve competition & enable similar species to coexist in a community |
| - | - **Resource partitioning: | + | - Resource partitioning: |
| - | - **Realized niche: the actual space an organism inhabits as a result of competition → allows two species to coexist** | + | - Realized niche: the actual space an organism inhabits as a result of competition → allows two species to coexist |
| - | | + | * Fundamental niche: niche that an organism occupies w/o competing species |
| - | | + | * Ecological niche: specific set of biotic and abiotic resources that an organism uses in its environment |
| * Ex: temp tolerance range, habitat, time of eating | * Ex: temp tolerance range, habitat, time of eating | ||
| * Species can partition their niches in space & time | * Species can partition their niches in space & time | ||
| - | - **Character displacement (niche shift): natural selection favours a divergence of characteristics when two similar species inhabit the same environment** | + | - Character displacement (niche shift): natural selection favours a divergence of characteristics when two similar species inhabit the same environment |
| * Ex: finches with diff beaks (thru evolution) suited to diff food → minimize competition | * Ex: finches with diff beaks (thru evolution) suited to diff food → minimize competition | ||
| * Predation Form of community interaction when an animal hunts another organism | * Predation Form of community interaction when an animal hunts another organism | ||
| - | - **True predator** kills and eats other animals | + | - True predator kills and eats other animals |
| - | - **Parasite** feeds and lives on host’s tissues, weakening it | + | - Parasite feeds and lives on host’s tissues, weakening it |
| - | - **Parasitoid** is an insect that lays its eggs in a host | + | - Parasitoid is an insect that lays its eggs in a host |
| - | - **Herbivore** is an animal that eats plants | + | - Herbivore is an animal that eats plants https:// |
| + | <img src=" | ||
| + | </ | ||
| * Predator-Prey Interactions | * Predator-Prey Interactions | ||
| * Increase/ | * Increase/ | ||
| * Increase in predator → decrease in prey | * Increase in predator → decrease in prey | ||
| - | | + | * Trophic cascade: negative effect of removal of key species |
| - | * **Symbiosis** | + | * Symbiosis |
| * When two species live together in close contact during a portion of their lives; examples of interactions among populations include | * When two species live together in close contact during a portion of their lives; examples of interactions among populations include | ||
| * Positive | * Positive | ||
| - | - **Mutualism: when both species benefits (+,+)** | + | - Mutualism: when both species benefits (+,+) |
| - | | + | * Lichens: symbiotic associates of fungi and algae |
| * Algae produce sugar and fungi provide water & protection | * Algae produce sugar and fungi provide water & protection | ||
| * Can also be parasitic | * Can also be parasitic | ||
| - | | + | * Mycorrhizae: |
| * Plants provide sugar and filaments of fungi increase surface area of roots, facilitate absorption of water and minerals (especially phosphorus) | * Plants provide sugar and filaments of fungi increase surface area of roots, facilitate absorption of water and minerals (especially phosphorus) | ||
| - | - **Commensalism: | + | - Commensalism: |
| * Birds build nests in trees | * Birds build nests in trees | ||
| * Negative Interactions | * Negative Interactions | ||
| - | - **Parasitism: parasite benefits, host is harmed (+, -)** | + | - Parasitism: parasite benefits, host is harmed (+, -) |
| * Tapeworms in digestive tract of animals | * Tapeworms in digestive tract of animals | ||
| - | - **Predator-Prey (+/-)** | + | - Predator-Prey (+/-) |
| - | - **Competition: | + | - Competition: |
| * Ex: weeds compete for nutrients | * Ex: weeds compete for nutrients | ||
| * Although negative for one species, might benefit another species by providing new niches or freeing up resources | * Although negative for one species, might benefit another species by providing new niches or freeing up resources | ||
| * Disturbances | * Disturbances | ||
| - | | + | * Disturbances: |
| * Ex: Humans have altered much of Earth’s surface by replacing natural terrestrial communities with urban and agricultural one | * Ex: Humans have altered much of Earth’s surface by replacing natural terrestrial communities with urban and agricultural one | ||
| * Some organisms depend on periodic disturbances | * Some organisms depend on periodic disturbances | ||
| * Ex: pine that depend on burning for reproduction | * Ex: pine that depend on burning for reproduction | ||
| * Disturbances that threaten stability include fires, floods, disease, and human effects | * Disturbances that threaten stability include fires, floods, disease, and human effects | ||
| - | - **El Nino: trade winds and upwelling that promote bottom up effect stop; algae declines → then consumers → collapse in food webs** | + | - El Nino: trade winds and upwelling that promote bottom up effect stop; algae declines → then consumers → collapse in food webs |
| - | - **Meteor Impacts and volcanic eruptions: increase amount of matter → reduce solar radiation → less primary production** | + | - Meteor Impacts and volcanic eruptions: increase amount of matter → reduce solar radiation → less primary production |
| - | - **Plate tectonics (continental drift): describes movement of land masses (plates) over surface of earth** | + | - Plate tectonics (continental drift): describes movement of land masses (plates) over surface of earth |
| * Plates collide and move to new latitudes → earthquakes, | * Plates collide and move to new latitudes → earthquakes, | ||
| * Environmental conditions change → create new niches for speciation | * Environmental conditions change → create new niches for speciation | ||
| - | * **Characterizing Disturbance** | + | * Characterizing Disturbance |
| * Vary in frequency and severity among communities | * Vary in frequency and severity among communities | ||
| * High level of disturbance = frequent or intense disturbance | * High level of disturbance = frequent or intense disturbance | ||
| * Low disturbance levels = low frequency or low intensity of disturbance. | * Low disturbance levels = low frequency or low intensity of disturbance. | ||
| - | | + | * Intermediate disturbance hypothesis: moderate levels of disturbance → open up habitats for less competitive species → greater species diversity than high or low levels of disturbance |
| * Small-scale disturbances can create patches of different habitats across a landscape, which help maintain diversity in a communitys | * Small-scale disturbances can create patches of different habitats across a landscape, which help maintain diversity in a communitys | ||
| - | * **Coevolution** | + | * Coevolution |
| * The tit-for-tat evolution in one species in response to adaptation in another species | * The tit-for-tat evolution in one species in response to adaptation in another species | ||
| * Results from natural selection of characteristics that promote most successful predators and most elusive prey leads to coevolution of predator and prey | * Results from natural selection of characteristics that promote most successful predators and most elusive prey leads to coevolution of predator and prey | ||
| - | - **Secondary Compounds:** toxic chemicals produced in plants that discourage herbivores; some herbivores have adaptations that allow them to tolerate them | + | - Secondary Compounds: toxic chemicals produced in plants that discourage herbivores; some herbivores have adaptations that allow them to tolerate them |
| - | - **Camouflage (cryptic coalition):** physical characteristics or behavior that allows prey or predator to hide | + | - Camouflage (cryptic coalition): physical characteristics or behavior that allows prey or predator to hide |
| - | - **Aposematic coloration (warning coloration): | + | - Aposematic coloration (warning coloration): |
| * Associate yellow and black body of bees with danger | * Associate yellow and black body of bees with danger | ||
| - | - **Mimicry :** when species resemble one another in appearance. 2 kinds | + | - Mimicry : when species resemble one another in appearance. 2 kinds |
| - | | + | * Mulelerian mimicry: animals with similar defense mechanism share same coloration |
| * Mutualistic: | * Mutualistic: | ||
| * Ex: 2 diff species of butterflies, | * Ex: 2 diff species of butterflies, | ||
| - | | + | * Batesian mimicry: harmless animal mimics the coloration of an animal that does have a defense |
| * Parasitic relationship: | * Parasitic relationship: | ||
| * Ex: harmless beetle mimics noxious beetle | * Ex: harmless beetle mimics noxious beetle | ||
| - | - **Pollination: | + | - Pollination: |
| * Red, tubular flowers coevolved with hummingbird who attracted to red & have long beaks | * Red, tubular flowers coevolved with hummingbird who attracted to red & have long beaks | ||
| ====Ecological Succession==== | ====Ecological Succession==== | ||
| Line 4457: | Line 4631: | ||
| * Succession can occur over long periods as climate changes and shorter periods when species alter habitat | * Succession can occur over long periods as climate changes and shorter periods when species alter habitat | ||
| * Both times, characteristics of an ecosystem that supported resident species no longer exist and habitat become favorable to new species | * Both times, characteristics of an ecosystem that supported resident species no longer exist and habitat become favorable to new species | ||
| - | | + | * Pioneer species: plants and animals that are first to colonize new habitat |
| * Usually opportunistic, | * Usually opportunistic, | ||
| * As physical characteristics change, r-selected species gradually replaced by more stable k-selected species | * As physical characteristics change, r-selected species gradually replaced by more stable k-selected species | ||
| * Live longer so environmental effects slow down rate of succession | * Live longer so environmental effects slow down rate of succession | ||
| - | | + | * Climax community: Final successional stage where organisms remain stable |
| * Two Kinds of Succession | * Two Kinds of Succession | ||
| - | - **Primary succession: in habitats that never previously supported living things** | + | - Primary succession: in habitats that never previously supported living things |
| * Start with protists and prokaryotes and end with grass | * Start with protists and prokaryotes and end with grass | ||
| - | - **Secondary Succession: in habitats where communities destroyed by disturbance** | + | - Secondary Succession: in habitats where communities destroyed by disturbance |
| ====Biodiversity==== | ====Biodiversity==== | ||
| * “Describes the number of species, niches, and trophic levels in the ecosystem and the complexity of its food web” | * “Describes the number of species, niches, and trophic levels in the ecosystem and the complexity of its food web” | ||
| * Factors that influence biodiversity… | * Factors that influence biodiversity… | ||
| - | - **Climate: influences abundance and type of primary producers and number of species primary production can support** | + | - Climate: influences abundance and type of primary producers and number of species primary production can support |
| * Climate is major factor in determining location of biomes and where terrestrial organisms live | * Climate is major factor in determining location of biomes and where terrestrial organisms live | ||
| - | - **Latitude: correlated with climate but also determines solar energy exposure** | + | - Latitude: correlated with climate but also determines solar energy exposure |
| * Areas at middle/ | * Areas at middle/ | ||
| * Also, seasonal variations are minimized at lower latitudes bcuz each day earth strikes at same angle; more constant environment (stable) can support more species | * Also, seasonal variations are minimized at lower latitudes bcuz each day earth strikes at same angle; more constant environment (stable) can support more species | ||
| * So tropical ecosystems are very diverse, have many species but with smaller numbers of each species; polar ecosystems have few species but with many individuals | * So tropical ecosystems are very diverse, have many species but with smaller numbers of each species; polar ecosystems have few species but with many individuals | ||
| - | - **Habitat size and diversity: influence how many different kinds of organisms can be supported** | + | - Habitat size and diversity: influence how many different kinds of organisms can be supported |
| * Larger the ecosystem, likely to have more diverse habitats that can support a greater variety of species | * Larger the ecosystem, likely to have more diverse habitats that can support a greater variety of species | ||
| - | - **Evolutionary History: Tropical communities are generally older than temperate or polar communities, | + | - Evolutionary History: Tropical communities are generally older than temperate or polar communities, |
| * So, species diversity usually highest in the tropics bcuz there has been more time for speciation to occur | * So, species diversity usually highest in the tropics bcuz there has been more time for speciation to occur | ||
| - | - **Elevation: temp and precipitation strongly correlated with elevation (temp decreases & rain increases as elevation increases)** | + | - Elevation: temp and precipitation strongly correlated with elevation (temp decreases & rain increases as elevation increases) |
| - | * **Stability Of Ecosystems** | + | * Stability Of Ecosystems |
| * Stability of an ecosystem increases with increases in biodiversity | * Stability of an ecosystem increases with increases in biodiversity | ||
| * Occurs bcuz in highly diverse system, disturbances may adversely affect only a few species which can be replaced by more unaffected species | * Occurs bcuz in highly diverse system, disturbances may adversely affect only a few species which can be replaced by more unaffected species | ||
| * In systems with low biodiversity, | * In systems with low biodiversity, | ||
| - | * **Island Equilibrium Model** | + | * Island Equilibrium Model |
| * Islands closer to mainland and larger are more diverse | * Islands closer to mainland and larger are more diverse | ||
| * Small island = fewer resources, less diverse habitats, smaller populations, | * Small island = fewer resources, less diverse habitats, smaller populations, | ||
| * Number of species gets larger → immigration rate decreases while extinction rate increases | * Number of species gets larger → immigration rate decreases while extinction rate increases | ||
| ====Biogeochemical Cycles==== | ====Biogeochemical Cycles==== | ||
| - | | + | * Biogeochemical cycles: describe flow of essential elements from the environment to living things and back to environment |
| * Studies the rate of element movement between reservoirs & interaction of the current cycle with other cycles | * Studies the rate of element movement between reservoirs & interaction of the current cycle with other cycles | ||
| - | | + | * FRQ: if question asks about flow of cycle, describe the input, use of element, and output |
| * Decomposition on land slower in temperate bcuz less rain (so have more nutrients in soil) | * Decomposition on land slower in temperate bcuz less rain (so have more nutrients in soil) | ||
| * Net primary production greatly exceeds the rate of decomposition in such ecosystems, causing them to store large amounts of organic matter. | * Net primary production greatly exceeds the rate of decomposition in such ecosystems, causing them to store large amounts of organic matter. | ||
| - | | + | * Reservoirs: where elements/ |
| * Ex: organisms, fossil fuels, water, soil, air, rocks (not directly available to organisms but slowly thru erosion) | * Ex: organisms, fossil fuels, water, soil, air, rocks (not directly available to organisms but slowly thru erosion) | ||
| * Nutrients in organisms & detritus are available to other organism | * Nutrients in organisms & detritus are available to other organism | ||
| - | | + | * Assimilation: |
| - | | + | * Release: processes which return elements to environment |
| * Major Cycles | * Major Cycles | ||
| - | - **Nitrogen cycle:** nitrogen is required for the manufacture of all amino acids and nucleic acids | + | - Nitrogen cycle: nitrogen is required for the manufacture of all amino acids and nucleic acids |
| * Reservoirs: atmosphere (N2); soil (ammonium [NH4] or ammonia [NH3], nitrite) | * Reservoirs: atmosphere (N2); soil (ammonium [NH4] or ammonia [NH3], nitrite) | ||
| * Assimilation: | * Assimilation: | ||
| - | | + | * Nitrogen fixation: nitrogen-fixing bacteria transform atmospheric nitrogen to fixed nitrogen which is absorbed by plants |
| - | | + | * Nitrification: |
| - | * Release: | + | * Release: denitrification: |
| - | - **Hydrologic cycle** (water cycle) | + | - Hydrologic cycle (water cycle) |
| * Reservoirs: oceans, groundwater, | * Reservoirs: oceans, groundwater, | ||
| * Assimilation: | * Assimilation: | ||
| - | - [[Untitled_a1baf95c2be74fad95ea92c3882c2c8f: | + | - Untitled_a1baf95c2be74fad95ea92c3882c2c8f: |
| * Release: plants transpire; animals and plants decompose | * Release: plants transpire; animals and plants decompose | ||
| - | - **Carbon cycle** | + | - Carbon cycle |
| * Reservoirs: atmosphere, sediments, fossilized plant and animal remains (coal, oil, and natural gas), plant and animal biomass (as carbon) bodies of water, fossil fuels | * Reservoirs: atmosphere, sediments, fossilized plant and animal remains (coal, oil, and natural gas), plant and animal biomass (as carbon) bodies of water, fossil fuels | ||
| * Assimilation: | * Assimilation: | ||
| * Release: plants and animals release carbon thru respiration and decomposition; | * Release: plants and animals release carbon thru respiration and decomposition; | ||
| * compounds back to NH4 (ammonification); | * compounds back to NH4 (ammonification); | ||
| - | - **Phosphorus cycle:** phosphorus is required for ATP & nucleic acids; involves weathering of rocks | + | - Phosphorus cycle: phosphorus is required for ATP & nucleic acids; involves weathering of rocks |
| * Reservoirs: ocean sediment, soil | * Reservoirs: ocean sediment, soil | ||
| * Assimilation: | * Assimilation: | ||
| * Release: plants and animals release phosphorus when they decompose; animals excrete in waste products | * Release: plants and animals release phosphorus when they decompose; animals excrete in waste products | ||
| * %%---------------------%% | * %%---------------------%% | ||
| - | * **Extinction risks in small populations** | + | * Extinction risks in small populations |
| * Small populations particularly vulnerable threats to biodiversity such as overharvesting, | * Small populations particularly vulnerable threats to biodiversity such as overharvesting, | ||
| * Inbreeding often reduces fitness because offspring are more likely to be homozygous for harmful recessive traits | * Inbreeding often reduces fitness because offspring are more likely to be homozygous for harmful recessive traits | ||
| - | * **Environmental Factors that Affect Biodiversity** Fragmentation and Edges | + | * Environmental Factors that Affect Biodiversity Fragmentation and Edges |
| - | | + | * Edges: boundaries between ecosystems |
| * Can provide both types of resources | * Can provide both types of resources | ||
| - | | + | * Fragmentation: |
| * Can help some species and harm others: benefit disturbance-adapted and invasive species | * Can help some species and harm others: benefit disturbance-adapted and invasive species | ||
| * Corridors That Connect Habitat Fragments | * Corridors That Connect Habitat Fragments | ||
| - | | + | * Movement corridor: a narrow strip of habitat connecting otherwise isolated patches |
| * Important for conserving biodiversity in fragmented habitats; can be man-made | * Important for conserving biodiversity in fragmented habitats; can be man-made | ||
| * Movement corridors can also promote dispersal and reduce inbreeding in declining populations | * Movement corridors can also promote dispersal and reduce inbreeding in declining populations | ||
| * Can be harmful by helping to spread disease | * Can be harmful by helping to spread disease | ||
| - | * **Human Population Growth** | + | * Human Population Growth |
| * The following factors have increased the carrying capacity of the environment and made exponential growth possible | * The following factors have increased the carrying capacity of the environment and made exponential growth possible | ||
| - | - **Increases in food supply: domesticating animals and plants + increased food output bcuz of tech advances (ex: fertilizers and pesticides)** | + | - Increases in food supply: domesticating animals and plants + increased food output bcuz of tech advances (ex: fertilizers and pesticides) |
| - | - **Reduction in disease & human waste:** | + | - Reduction in disease & human waste: |
| - | - **Habitat expansion: immigrating to new areas** | + | - Habitat expansion: immigrating to new areas |
| - | * **Human Impact on Ecosystems:** | + | * Human Impact on Ecosystems: |
| * Human activity damages biosphere | * Human activity damages biosphere | ||
| * Ex: exponential population growth, destruction of habitats for agriculture and mining, pollution from industry and transportation. | * Ex: exponential population growth, destruction of habitats for agriculture and mining, pollution from industry and transportation. | ||
| * Consequences of Human Impact on Ecosystems | * Consequences of Human Impact on Ecosystems | ||
| - | - **Global climate change:** | + | - Global climate change: |
| - | * Some wavelengths of light reflected while rest absorbed by earth; earth re-emits some of radiation back to atomposhere → absorbed by CO2 and other **greenhouse gasses** | + | * Some wavelengths of light reflected while rest absorbed by earth; earth re-emits some of radiation back to atomposhere → absorbed by CO2 and other greenhouse gasses |
| * Population increase → so does human activity (burning of fossil fuels) → increase greenhouse gasses→ absorb more energy → temp of atmosphere & earth increases | * Population increase → so does human activity (burning of fossil fuels) → increase greenhouse gasses→ absorb more energy → temp of atmosphere & earth increases | ||
| * Warming temp = rising sea levels, decade agricultural output (affect weather patterns), increase human disease (by broadening range of tropical disease vectors), and threaten extinction to species (disrupting environmental conditions to which species are adapted) | * Warming temp = rising sea levels, decade agricultural output (affect weather patterns), increase human disease (by broadening range of tropical disease vectors), and threaten extinction to species (disrupting environmental conditions to which species are adapted) | ||
| - | - **Ozone depletion:** ozone layer forms when as UV radiation reacts with oxygen to form ozone | + | - Ozone depletion: ozone layer forms when as UV radiation reacts with oxygen to form ozone |
| * Absorbs UV radiation and stops reaching surface of earth (would damage DNA of organisms) | * Absorbs UV radiation and stops reaching surface of earth (would damage DNA of organisms) | ||
| - | * Air pollutants break down layer → **ozone holes** → UV reaches surface | + | * Air pollutants break down layer → ozone holes → UV reaches surface |
| - | - **Acid rain:** burning of fossil fuels release into air pollutants with sulfur dioxide and nitrogen dioxide → react with water vapor → produce sulfuric acid and nitric acid → acids return to surface of the earth as rain → acidify soil and oceans | + | - Acid rain: burning of fossil fuels release into air pollutants with sulfur dioxide and nitrogen dioxide → react with water vapor → produce sulfuric acid and nitric acid → acids return to surface of the earth as rain → acidify soil and oceans |
| - | - **Desertification: | + | - Desertification: |
| - | - **Deforestation: | + | - Deforestation: |
| - | - **Pollution:** contaminate materials essential to life | + | - Pollution: contaminate materials essential to life |
| * Pollutants remain for long time; toxins concentrate in plants and animals | * Pollutants remain for long time; toxins concentrate in plants and animals | ||
| - | * **Biological magnification: | + | * Biological magnification: |
| - | * **Algal blooms:** massive growths of algae and other phytoplankton when lake polluted with runoff fertilizer or sewage → add nutrients | + | * Algal blooms: massive growths of algae and other phytoplankton when lake polluted with runoff fertilizer or sewage → add nutrients |
| - | * **Eutrophication: | + | * Eutrophication: |
| * Results in oxygen depletion, fishes dying, and growth of anaerobic bacteria that produce foul-smelling gasses | * Results in oxygen depletion, fishes dying, and growth of anaerobic bacteria that produce foul-smelling gasses | ||
| - | | + | - Reduction in species diversity: human impacts are causing plant and animals to become extinct at a faster rate |
| * Reduction in plants that could become useful to humans as medicines or food | * Reduction in plants that could become useful to humans as medicines or food | ||
| =====Statistics===== | =====Statistics===== | ||
| ====Chi-Squared Tests==== | ====Chi-Squared Tests==== | ||
| - Calculation Based: Chi-Squared Tests | - Calculation Based: Chi-Squared Tests | ||
| - | [[https:// | + | https:// |
| + | <img src=" | ||
| + | </ | ||
| + | <img src=" | ||
| + | </ | ||
| * This means that you are 95% sure of it being accurate (if you pick 0.05) | * This means that you are 95% sure of it being accurate (if you pick 0.05) | ||
| - | - Degrees of freedom: number of “choices” that you could possibly have minus 1 If the chi squared value is higher than the critical value on the table, then you reject the null hypothesis. If it’s lower than the critical value, then you accept it \ \ **Graphs** Bar Graphs | + | - Degrees of freedom: number of “choices” that you could possibly have minus 1 If the chi squared value is higher than the critical value on the table, then you reject the null hypothesis. If it’s lower than the critical value, then you accept it \ \ Graphs Bar Graphs |
| * Units: when looking at graph always figure out the units | * Units: when looking at graph always figure out the units | ||
| - | | + | * Margin of Errors: |
| * there' | * there' | ||
| * When question includes margins of error, always look to see if they overlap | * When question includes margins of error, always look to see if they overlap | ||
| - Steps to Drawing Graph | - Steps to Drawing Graph | ||
| - | - **Name the graph:** Dependent variable (y-axis) vs Independent variable (x-axis) | + | - Name the graph: Dependent variable (y-axis) vs Independent variable (x-axis) |
| - | - **Label x-axis:** will be the independent variable (units!) | + | - Label x-axis: will be the independent variable (units!) |
| - | - **Label y-axis:** will be the dependent variable | + | - Label y-axis: will be the dependent variable |
| - | - If included, | + | - If included, label the margins of error/ |
| - | - **Null Hypothesis: states that here is no statistical difference or correlation (observed diff is by chance alone)** | + | - Null Hypothesis: states that here is no statistical difference or correlation (observed diff is by chance alone) |
| * The null hypothesis can be rejected if test group is different from the control group | * The null hypothesis can be rejected if test group is different from the control group | ||
| * Says that there is a similarity between two explanations or things | * Says that there is a similarity between two explanations or things | ||
| * Key words: resemble, like, similar | * Key words: resemble, like, similar | ||
| - | - **Alternative Hypothesis (of a test) says there is an effect/ | + | - Alternative Hypothesis (of a test) says there is an effect/ |
| * Also says that there is another explanation; | * Also says that there is another explanation; | ||
| - | - **Dependent Variable: The thing you are measuring** | + | - Dependent Variable: The thing you are measuring |
| * Changes in response to the independent variable | * Changes in response to the independent variable | ||
| - | - **Independent variable: the thing that you are changing/ | + | - Independent variable: the thing that you are changing/ |
| - | - **Positive Control: is not exposed to experimental treatment but is expected to have effect (Ex: positive control for movement, growth, be active)** | + | - Positive Control: is not exposed to experimental treatment but is expected to have effect (Ex: positive control for movement, growth, be active) |
| - | - **Negative Control: not exposed to experimental treatment or expected to have an effect** | + | - Negative Control: not exposed to experimental treatment or expected to have an effect |
| * Ex: denatured enzyme, inactive gene…. | * Ex: denatured enzyme, inactive gene…. | ||
| - | - **Control: group that does not receive the independent variable (what you are testing)** | + | - Control: group that does not receive the independent variable (what you are testing) |
| * Control group will have everything the same as experimental group, but will not receive independent variable | * Control group will have everything the same as experimental group, but will not receive independent variable | ||
| * So you know that any change/ | * So you know that any change/ | ||
| - | - **Experimental Control:** | + | - Experimental Control: |
| * A control can also be a benchmark which is used to determine something | * A control can also be a benchmark which is used to determine something | ||
| * Ex: (thing) is a control for (process) | * Ex: (thing) is a control for (process) | ||
| - | | + | * Justify: |
| - | | + | * “All variables must be held constant” |
| * Since control has not experienced the variable you are testing, any effect observed in both groups cannot be attributed to independent variable | * Since control has not experienced the variable you are testing, any effect observed in both groups cannot be attributed to independent variable | ||
| * Know that any response/ | * Know that any response/ | ||
| - | - **Environmental Factors: vary them** | + | - Environmental Factors: vary them |
| * Ex: vary light, temp, duration of experiment, location | * Ex: vary light, temp, duration of experiment, location | ||
| * Justify: know that any change is only because of independent variable | * Justify: know that any change is only because of independent variable | ||
| Line 4611: | Line 4789: | ||
| * ONLY IDENTIFY THAT MANY! DO NOT GO OVER THE ASSIGNED NUMBER | * ONLY IDENTIFY THAT MANY! DO NOT GO OVER THE ASSIGNED NUMBER | ||
| * Use specific words from the question | * Use specific words from the question | ||
| - | - **CALCULATION QUESTIONS** “Calculate total efficiency” | + | - CALCULATION QUESTIONS “Calculate total efficiency” |
| * If you have %%___%% amount of energy, but you only use %%____%% amount, then the amount that you actually used was the efficient part | * If you have %%___%% amount of energy, but you only use %%____%% amount, then the amount that you actually used was the efficient part | ||
| * Divide the amount that you ACTUALLY used by the amount available | * Divide the amount that you ACTUALLY used by the amount available | ||
| - | - **Most Missed** | + | - Most Missed |
| * When question involves phenotypes changing, answer will probs include either directional, | * When question involves phenotypes changing, answer will probs include either directional, | ||
| - | | + | * Graph Questions: |
| * When describing trend, specifically point out when the line increased/ | * When describing trend, specifically point out when the line increased/ | ||
| - | | + | * Explain: only need to give one answer |
| * Don't need to explain the explanation; | * Don't need to explain the explanation; | ||
| - | | + | * Predict: only need to predict, no explanation |
| | | ||