Complete AP Biology Study Guide

• Credit: Weshe2005 on reddit,
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Useful Links: Cliff Notes: https://kamsc.github.io/assets/links/Cliff_AP_Biology.pdf

Practice Resources

• 2013: https://apcentral.collegeboard.org/pdf/ap-biology-practice-exam-2013.pdf?course=ap-biology|2013 Practice Exam
• 2012: https://web.archive.org/web/20170430191045/https://d3jc3ahdjad7x7.cloudfront.net/SJI5NL7tiTFTL7XcjKnSB4Db6Q8fzIU1qfRT4Y0Z83pajwL6.pdf|2012 Practice Exam

Past FRQs:

• https://apcentral.collegeboard.org/courses/ap-biology/exam/past-exam-questions?course=ap-biology|College Board Past Exam Questions Page
• FRQ 2020: https://youtu.be/fcMniGj9Wmc
• FRQ: 2021: https://secure-media.collegeboard.org/apc/ap21-frq-biology.pdf

Topics 1.1-1.4

KEY OVERVIEWS

• How properties of water that result from its polarity and hydrogen bonding affect its biological function

• Composition of macromolecules

• Description of the properties of the monomers and type of bonds that connect the monomers in biological macromolecules

Trace Elements: required by organisms in minute amounts

Essential elements: C, H, O, N (most abundant)

Atom

• “Smallest unit of an element; consists of nucleus of (+) protons and neutrons”

• Electrons orbit the nucleus
  • Mostly energy, negligible mass
  • Stay at fixed energy level but if absorb energy can move to shell further

• The type of bonds that form between atoms and its strength depends on the electronegativities of atom
  • (low to high) nonpolar covalent → polar covalent → ionic

Ionic Bonds

• Form between atoms when electrons are transferred from one atom to another → Forms ions

• Occurs when there is a great electronegativity difference

Covalent Bonds

• Form when electrons are shared; neither atom completely holds electron

• Single covalent, double covalent, and triple covalent bonds form when two, four, and six electrons are shared respectively

Nonpolar Covalent Bonds

• When electrons are shared equally → atoms have same/similar electronegativity

• No charge = hydrophobic

Polar Covalent Bonds

• When electron are shared unequally → atoms have diff electronegativity

• Single water molecule held by polar covalent bonds

• Yes charge = hydrophilic

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
  • Strong in large numbers

• Bond holds one water molecule to another water molecule

Vocab

Heat of fusion: energy required to change water from a solid to liquid

Heat of evaporation: energy required to change water from liquid to gas

Mass Number: number of protons and neutrons

Isotopes: atoms of same elements with diff mass/number of neutrons

Electronegativity: measure of an atom’s attraction for electrons

• Allows oxygen to form polar and hydrogen bonds

Energy: capacity to do work

Potential energy: energy that matter has because of location

• Electrons have potential energy because of distance from nucleus

Electron Shell: distance from nucleus where electrons found

• Further = more energy

Valence electrons: outermost electrons

• Determine chemical behavior

Molecule: 2 or more atoms held by bonds

• Molecule shape determined by position of valence electrons orbitals

Compound:

two or more different elements joined together chemically

• The subcomponents of biological molecules and their sequences determine the properties of that molecule

Properties of Water

• Water: 2 hydrogen and 1 oxygen bonded together with (Polar) COVALENT bonds bcuz oxygen is more electronegative, so electrons pulled closer to it

• Water is POLAR- overall charge is unevenly distributed (+ & -), allows molecules to form HB

• The hydrogen bonds between water molecules result in cohesion, adhesion, and high surface tension, self-regulation, expansion upon freezing, versatility as a solvent

• Cohesion: water molecules attached to each other (bcuz of HB)
  • Makes water “sticky”
  • 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

• 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

• 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/broken → allows organisms to walk on water

Self-regulation

• Water has high specific heat because lots of energy is absorbed when bonds break and released when hydrogen bonds form
  • So body of water can absorb lots of heat and resist chemical change; needs lots of energy to freeze

• Cool air when it is warm and release heat in the winter

• Stabilizes ocean temperature, climate, and organisms (bcuz they are mostly made up of water)

• When water changes physical state, energy is absorbed but water temp remains constant → absorbed energy just changes HB

Evaporative Cooling

• As water evaporates, cools the surface of the earth & organisms bcuz molecules with more heat energy evaporate quicker
  • Hydrogen bonds need to break for water to vaporize

Expansion Upon Freezing

• Water is less dense/expands as a solid bcuz weak HB stabilize/crystalize, keeping molecules too far apart (also slow) to break them

• So ice floats and insulates water, reducing heat loss from water below → warmer water that is less likely to freeze
  • If sank then all water would freeze over → no aquatic life

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)

• (+) and (-) attraction

• Ionic compounds are soluble because poles of polar water molecules interact with them and separate into ions

• Water helps cell transport substances throughout the body (ex. nutrients, antibiotics)

• Hydrophilic: affinity for water, polar Hydrophobic: repel water, nonpolar

Acids and Bases

• Water molecule can transfer H+ to another water forming OH (hydroxide) and hydronium ion
  • Water is an acid and base

• Hydrogen Ion: Single proton, highly reactive/energy/unstable

• 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+)

• Buffer solutions: maintain a ~constant pH when either acids or bases 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
  • Ex: pH of 3 is ten times more acidic as pH of 4

Water Potential

• “Measure of potential energy of water & eagerness to go from high potential to low”

• Water potential = pressure potential + solute potential
  • High water potential = more water molecules (higher concentration) & will move somewhere else
  • More solutes = increases osmolarity and decreases water potential
    • More likely to gain water

• Water potential explains how water moves from soil → roots → leaves for photosynthesis
  • Plant roots have lots of sugar and low water potential (0 pressure)
  • Water moves into roots cell bcuz of higher water potential in soil but roots will gain pressure from water → increases water potential and limits water gain
    • Pressure increases until water potential on outside equals pressure on inside
      • Add pressure to get same water potential

Water as a Metabolic Mediary

• Process of osmosis allows cells to expel waste products or hormones to maintain internal environment and cell turgidity

• Found in photosynthesis and cellular respiration; provide oxygen for aerobic reactions
  • Photosynthesis: water splits to provide electrons, protons, and releases oxygen

• 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's ability to build long chains of itself, bond to lots of molecules & form a wide variety of compounds (chemical versatility) bcuz has 4 valence electrons
  • Form strong bonds with C, H, O, N

• Organic compound includes carbon; Inorganic compound does not include carbon

• Factors that determine an organic molecules’ properties
  • Carbon Backbone - central part of organic molecule, bonding sites of atoms that determines their structure (function/properties),
    • Rings, linear, branching, single/double bond: shape determines function
    • Carbon atoms bond to other carbon atoms to form very long carbon chains/skeleton
  • Functional Groups branch off carbon backbone & determine chemical properties of an organic compound
    • In a reaction the backbone is unchanged & only functional groups react

Hydrocarbons

• Long chains of covalently bonded carbon and hydrogen
  • Come in many structures which determine properties: single, double, or triple bonds which makes it more rigid

• Make up lipids and contains lots of energy (lots of bonds)

• Nonpolar (Hydrophobic)
  • Only polar if has electronegative charge (O2, Su, F, N – electronegative atoms)

Isomers

• “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
    • Trans: functional groups on opp side

• Enantiomers/Stereoisomers: molecules are mirror images of each other bcuz of asymmetric carbon

Functional Groups Continued

• Affect structure and function
  • Ex: determine if amino acid is polar or nonpolar

• All life does NOT require same elements
  • TRUE for amino acids which always have amino and carboxyl group

Dehydration Synthesis and Hydrolysis

• Used to cleave and form covalent bonds between monomers

• Structure and function of polymers depends on the chemical properties and assembly of their monomers

• Macromolecule: chains of polymers linked together

• Polymers: large molecule made up of monomers joined by covalent bonds

• Monomer: single repeating subunit

Nucleic Acids:

• Biological information is encoded in sequences of nucleotide monomers

• DNA & RNA are polymers of nucleotides; nucleotides named by nitrogenous base

Structural Components of Nucleotides

• Nitrogenous Base: has 2 types;
  • Purines: Adenine and Guanine with double ring structure
  • Pyrimidines: Thymine, Cytosine, Uracil with single ring

* Phosphate Group: (-) charged

• Five-carbon sugar: deoxyribose or ribose; nonpolar

DNA and RNA synthesis

• DNA nucleotides form single-stranded DNA when phosphate group joins to sugar of another nucleotide → covalent

• Two of the strands are paired by weak HB between bases → form double-stranded DNA

• Nucleotides are added to the 3’ end of the strand; nucleotides linked by sugar-phosphate covalent bonds

Sugar-Phosphate Backbone

• Composed of alternating sugar and phosphate groups that defines directionality & structure of nucleic acids

• The sugar-phosphate backbone is polar

Antiparallel

• The DNA Molecule has directionality, otherwise known as Antiparallel ⇒ double helix

• The two strands run in opposite directions
  • One strand is arranged 5’ → 3’ end & other is 3’ → 5’
  • Antiparallel: gives DNA stability and allows for replication–if wasn’t then nucleotides wouldn’t be complementary

* Binding of the nitrogenous bases

• Cytosine + Guanine with 3 hydrogen bonds = stronger
• Adenine + Thymine with 2 hydrogen bonds

• Purine + Pyrimidine = only uniform diameter suitable for double helix

5’ End

The phosphate group is bound to the carbon at the 5th position on sugar

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)

DNA vs 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

• Bases perpendicular to the sugar-phosphate backbone

Proteins

Function:

1. Structural: ex: keratin in hair, collagen in tissues

1. Storage: ex: casein in milk

1. Transport: ex: membrane of cells and oxygen carrying hemoglobin in red blood cells

1. Defensive: Ex: antibodies that protect against foreign substances

1. Enzymes: regulate the rate of chemical reactions

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

• Proteins differ from each other by number and arrangement of 20 types of amino acids that vary in polarity

Always contains amino group (basic), carboxyl (acid), R group, H

• R Group:
  • “Random group” → determine chemical properties & differences of amino acids
    • 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

• Proteins have directionality: one end is a carboxyl group and the other an amino group
  • Amino acid are added onto the carboxyl end thru dehydration synthesis

• Dimer: protein with two tertiary structures

The 4 Structural Levels of Proteins

PRIMARY STRUCTURE

• Order of amino acids connected by covalent bonds which determines the overall shape and function of a protein

SECONDARY STRUCTURE

• Local folding of the amino acid chain (polypeptide) into elements such as alpha-helices and beta sheets thru hydrogen bonding
  • Misfoldings lead to prions

TERTIARY STRUCTURE

• 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

• Components of a tertiary structure:
  • 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
  • Hydrophobic interactions/effect: occurs when hydrophobic R groups move toward the center of protein (away from water in which protein is usually in)

QUATERNARY STRUCTURE

• Arises from non-covalent interactions between multiple polypeptide units (ex: hemoglobin)
  • Basically, two or more polypeptides (2nd) into single protein; not all proteins have it

Most proteins are made of a single polypeptide chain but some have multiple chains called

subunits

that allow for 4th structure.

Carbohydrates

• Function: main source of energy (for ATP) and cell structure
  • Carbs (+fats, lipids) are high energy bcuz have many hydrogen atoms with e-

• 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

• Dehydration synthesis of two monosaccharides makes a disaccharides

• Ex. glucose, frutose, galactose
  • Structural isomers → placement of carbon atoms are diff → different functions
    • Alpha glucose (storage) and beta-glucose (structure) differ by reversal of H and OH

• Monosaccharides provide immediate energy bcuz don’t need hydrolysis

• Simple carbs are polar bcuz of -OH functional group which makes them hydrophilic
  • Some polysacch like cellulose & starch are insoluble

• Disaccharides include…
  • Glucose + Glucose = Maltose
  • Glucose + Fructose = Sucrose
  • Glucose + Galactose = Lactose

Complex: Polysaccharides → energy storage

• 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

• Function: cell membrane (phospho,) insulation, protection, fat is long term and high energy

• Structure: Nonpolar, hydrophobic
  • Not true macromolecules bcuz not large enough

Triglycerides: fats and oils

• 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/double covalent bonds
  • 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
  • Unsaturated Fatty Acids: Two or more double covalent bonds
    • Stops carbon from packing together and hydrogen from saturating them which makes fat more flexible/liquid
  • Monounsaturated Fatty acid: one double bond and each has only one H

• *differences in saturation determine the structure and function of lipids

Steroids: are characterized by four linked carbon rings

• Ex. cholesterol, hormones

• Cholesterol maintain cell structure and cell fluidity, used in nervous system & insulation

• Hormones: long distance, nonpolar molecules that control bodily activities

• Ex: Testosterone & estrogen made with cholesterol

Phospholipids: Like a triglyceride except one of fatty acids chain replaced by phosphate group (PO₄); part of every cell membrane lipid bilayer

• Hydrophilic Head → Has phosphate group with R (random) group attached

• Hydrophobic tail → Nonpolar bcuz made up of carbon and hydrogen atoms

The 4 Carbon Compounds

• 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/competition with other nearby reactions

• Cell can be specialized for specific functions depending on number of specific organelles

Nucleus

• Membrane bound organelle that contains the cell’s DNA/chromosomes
  • Nucleoli/Nucleolus: concentrations of DNA that make rRNA

• Nuclear pores: passageways for proteins and RNA molecules on nucleus surface

Ribosomes

• Structure: Made of ribosomal RNA (rRNA) and protein

• Function: synthesizes protein according to mRNA sequence by assembling amino acids

• Found in all living things, reflecting common ancestry
  • Prokaryotes have ribosomes attached to cytoplasmic surface of plasma membrane

• 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

• Occurs in two forms: rough and smooth

• Rough has small ribosomes attached to the ER
  • Synthesizes proteins using the attached ribosome
    • 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
  • Found in liver cells and detoxifies/breaks down drugs, toxins; metabolizes carbs
  • Synthesizes lipids and steroid hormones

• Helps transport proteins from the ribosome to other parts of the cell

Golgi Complex

Functions: correct folding and chemical modification of proteins

• and packaging in vesicles for protein trafficking
  • Receives, modifies, ships

• Structure: Folded membrane bound sacs (cisternae)
  • Also has vesicles attached to it to ship out proteins to membrane, lysosome, or exterior

• 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

* Function: Site of ATP synthesis and other aerobic processes

Physical Attributes of the Mitochondria

• Double membranes → separates metabolic processes in intermembrane space and inner membrane + increased surface area

• Contains circular mDNA, ATP synthase & own ribosomes

Lysosomes

• Structure: Vesicles from Golgi that contain hydrolytic enzymes (from rough ER)

• Function: Lysosomes hydrolytic enzymes break down food (intracellular digestion), cellular debris/waste (recycle a cell’s organic materials); metabolize lipids and control apoptosis

• Low pH is favorable to hydrolytic enzymes → any enzyme that might escape from lysosomes becomes inactive in neutral pH of cytosol

Vesicles

• Transport Vesicles: membrane enclosed sacs that move materials between organelles and plasma membrane
  • Movement dependent on microtubules and motor proteins

Vacuole

• Fluid-filled, membrane-bound bodies

• 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
  • Has other functions which specializes cell for specific functions
    1. Store starch, nutrients, pigments, waste
    2. Digestion
    3. Helps plants growth by absorbing water; animal cells need nutrients to build macromolecules to grow
    4. Reduces volume of cytoplasm
    5. Act as balancers to maintain homeostasis

Centrioles/Basal Bodies

• Act as microtubule organizing centers

• 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

Peroxisomes

• Contain enzymes that break down hydrogen peroxide (make water and oxygen), fatty acids, and amino acids

• Many in liver and kidney cells to detoxify substances

• In plants, found near chloroplast and modify by-products of photorespiration

Cytoskeleton

• Network of protein fibers and internal structure of cytoplasm

• Function: Cell support, maintain shape, motility
  • Motor proteins use ATP to act on cytoskeleton and move cell along fibers

Parts of Cytoskeleton

• Microtubules: shape cell, guide organelle movement, separate chromosomes in cell division
  • Made of protein tubulin; organized by centrioles
  • Found in spindle apparatus + cilia and flagella

• Microfilaments: muscle contraction (cell division), amoeboid movement, pseudopodia extension
  • Made of protein actin
  • 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

• Intermediate filaments: support cell shape and fix organelles in place

Flagella and Cilia

• 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

CHLOROPLASTS: REFER TO PHOTOSYNTHESIS UNIT DOWN BELOW

• The ER synthesizes proteins, the Golgi modifies/packages it, and then the vesicle will export them

• To be part of EM system must be derived from ER or Golgi
  • Ex: nuclear envelope, plasma membrane, lysosomes

Extracellular Matrix/Glycolax (animal cells)

• A large network of proteins and other molecules in animal cells
  • Molecules ex: oligosaccharides from lipids, recognition proteins, and glycoproteins
  • Has connections to cytoskeleton

• Function: surrounds cell to provide support, structure, attachment, communication, growth, movement, & differentiation

• Membrane Carbs: help with cell-cell recognition → interact w/ other surface molecules so cells can be sorted into tissues
  • Glycoproteins and glycolipids: have carbon chains attached

Key Overview

* Surface area-to-volume ratio of cell/plasma membrane affects the ability of a biological system to obtain & exchange necessary resources with the environment, diffuse materials through volume & eliminate waste products

• 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

• Cells increase in volume/size → surface area ratio decreases → demand for internal resources increases and affects properties like rate of heat exchange with the environment

• More complex cellular structures (ie. organelles, membrane folds, double membranes) are needed to increase surface area by reducing volume of the cytoplasm

• Cells with smaller surface area-to-volume ratio are better for long-term energy storage and slower metabolism

The Phospholipid Bilayer

• 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 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
  • Some are transmembrane

• Phospholipids (and some proteins) are amphipathic
  • Have polar (hydrophilic) and nonpolar (hydrophobic) regions

Fluid Mosaic Model

• Membrane is made up of of amphipathic proteins embedded in fluid bilayer of phospholipids”

• Membrane is fluid bcuz of weak hydrophobic interactions in interior of membrane that allow proteins to move vertically

• Proteins and lipids move in membrane which stays fluid until temp decreases
  • Fluidity of membrane depends on # of saturated and unsaturated fatty acids
    • Fluidity affects permeability and protein transport

• Unsaturated hydrocarbons of some phospholipids help keep membranes fluid at lower temp.
  • Double bonds stop carbons and fatty acids from packing together
  • Cholesterol helps keep membrane fluid at low temp and rigid at high temp
    • Lipids get excited (more energy) at high temp → increased fluidity & permeability

• Functional & structural: lipids provide structure but proteins determine function

Permeability

• The cell membrane is amphipathic with a hydrophobic interior, so only nonpolar molecules can pass through → selective permeability

What Can Pass Through?

• Ability of molecule to pass through depends on size, charge, and SP of membrane

• Small, uncharged, nonpolar molecules can freely pass among the membrane bcuz repel water like hydrophobic inside layer
  • Do not need channel or carrier proteins
  • N2, O2, CO2, H2

• Large, polar molecules and all ions (hydrophilic) are impermeable and can only move across the membrane through EMBEDDED CHANNEL AND TRANSPORT PROTEINS
  • Ex: ions, monosaccharides (glucose), amino acids
  • Some uncharged, polar molecules (H2O) can pass thru the membrane in small amounts

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/foreign cells & normal/infected cells
  • 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

Types of Transport Proteins

• Integral proteins: amphipathic, penetrate hydrophobic interior, some transmembrane

• Transmembrane proteins: all across membrane

• Peripheral protein: not in lipid bilayer: bound to membrane surface → hydrophilic

Cell Walls (found in plants)

• Cell walls provide a semipermeable barrier that regulates the movement of molecules into the cell
  • Cell walls stop plants, fungi, some protists, and prokaryotes from bursting in hypotonic solution

• 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

Passive Transport

• 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
  • Includes facilitated diffusion & simple diffusion: the molecule is hydrophobic

• Net movement of molecules is random/constant and independent from other molecules
  • Net = is eventual movement = not all molecules go down gradient

Facilitated Diffusion

• Passive transport sped up by proteins → still down concentration gradient

• 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

Active Transport

• Proteins move molecules from a region of low concentration to region of high concentration
  • It moves AGAINST the gradient
  • It DOES need ATP

• Unlike passive, does NOT result from random movement of molecules → moves specific solutes across a membrane

• ATP hydrolysis causes integral protein to change shape & shuttle molecules across membrane & against the gradient

Bulk Flow

• Movement of substances (solvent & solutes) in the same direction bcuz of pressure

Vesicular Transport (Bulk Transport)

• Uses vesicles to move substances across the plasma membrane; in/out of the cell

• Endocytosis: cell takes in substance outside of cell when plasma membrane merges to engulf it → substance enters cytoplasm enclosed in a vesicle; 3 types
  • Vesicle then merges with lysosome to break down food

1. Phagocytosis: occurs when undissolved (solid) material enters the cell

• Plasma membrane wraps around solid material and engulfs it → forms phagocytic vesicle → phagocytic cells attack and engulf bacteria this way

1. Pinocytosis: occurs when dissolved substances enter cell

1. Receptor-mediated: form of pinocytosis when ligand bind to specific receptors in plasma membrane pits

• Membrane pits, receptors and ligands fold inwards and vesicle forms

Osmosis

• “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

• Higher water potential = less solutes, lose water; Lower water potential = more solutes, gain water

• Plasmolysis: movement of water out of a cell that results in the collapse of a cell

• Cell Lysis: water enters the cell, causing it to swell and burst
  • 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

• 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

• Animal cells prefer isotonic solution; plant cells prefer hypotonic cuz water stored in vacuoles

Ion Pumps:

* Ions diffuse across membranes thru ion channels down their electrochemical gradient

• Ion channels/pumps work together to establish ion gradient across membrane, resulting in negative charge inside membrane

• 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/membrane potential across a cellular membrane

• 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
  • Ex: Sodium-Potassium Pump
  • Plants have proton pump that pumps H+ rather than sodium and potassium and increases potential energy

Cotransport:

• 2 solutes, membrane protein uses downwards diffusion of ion to power upward transport of another against gradient (secondary active transport)

• Ex. Glucose & Sodium transport:

Sodium-Potassium Pump Review

• Keeps cell polarized
  • Has (-) & (+) side

• Cell has higher concentration of K+ and lower Na+ than extracellular solution

• Protein goes back and forth between two forms:
  • An inward-facing form with high affinity for sodium (and low affinity for potassium) and an outward-facing form with high affinity for potassium (and low affinity for sodium)

• The protein can be toggled back and forth between these forms by the addition or removal of a phosphate group (ATP hydrolysis)

• Overall charge of cell is negative because cations (K+) leave cell at faster rate than Sodium (Na+) enters l
  • K+ more permeable

Primary vs Secondary Active Transport

• Primary directly uses energy source (ie ATP) to move molecules against gradient

• Secondary transport (ex: cotransport) uses electrochemical gradient (formed thru active) to move molecules against gradient (no ATP)

• Metabolismthe sum of all chemical reactions that take place in cells ~O2 Consumption
  • Catabolism: reactions break down molecules and release free energy (exergonic)
    • Cellular respiration
  • Anabolism: reactions build up molecules and absorb energy (endergonic)
    • Synthesis of proteins and amino acids, ATP synthase

• Metabolic reactions are controlled by enzymes
  • Higher temp → faster metabolism cuz most enzymes work better

Reactions in Metabolism

Exergonic:

• Net release of free energy, -G, (usually spontaneous)

• Products have less energy than reactants
  • Ex: cellular respiration

Endergonic

* Absorbs free energy, +G, (nonspontaneous)

• Products have more energy than reactants
  • Ex: Photosynthesis

Laws of Thermodynamics

• Thermodynamics: study energy transformations

• 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

• Open system: exchange energy and matter with environment
  • Ex: Organisms and Earth bcuz get energy from sun

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)

• So organisms must get all their resources from the environment

Second Law:

• “Every energy transfer or transformation increases the entropy (disorder) of the universe”
  • 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
  • Means that some energy becomes unusable/unstable (usually heat)

• 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
  • No input → entropy increases, cells deteriorate, death
  • Photosynthesis + Cellular Respiration = cells can maintain order, minimize entropy, and remain alive

• Evolution of complex organisms does not defy 2nd law of entropy → as organisms grow the entropy of the universe increases, not within organisms bcuz heat is released
  • Organisms grow by converting energy into matter (macromolecules)
  • Become more orderly by taking organized forms of matter and replacing them with less organized

• Free Energy: portion of systems energy that can perform work when temperature and pressure are uniform throughout (not heat)

• Formula: G= HTS
  • G= Free energy change
  • H = Enthalpy, change in total energy/heat content
  • 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

• Nonspontaneous: requires energy, decreases entropy, + G
  • Ex. monomer to polymer

Free Energy, Stability, and Equilibrium

• G(result energy) = G (final) - G (initial) ← net energy

• G= system loses free energy and becomes more stable

• More energy/more unstable → lowerG/more stable/less work capacity

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

• System at equilibrium = lowest delta G

• Ex: Chemical reactions where neither reactant or product are used

• A cell at metabolic equilibrium is dead cuz systems can do no work
  • So cells constantly have materials in/out which stops from reaching equilibrium
    • Ex. cellular respiration: the product does not accumulate, instead becomes the reactant in next step

• Reaction at equilibrium will stay that way even if the enzyme is added!

• Principle molecule for storing and transferring energy for cell work and activation energy; converted by enzymes

Structure

• Basically RNA adenine nucleotide with two more phosphates

• Nitrogenous base (adenine) attached

• Ribose sugar (carbohydrate)

• Three phosphate groups
  • All negatively charged groups → VERY unstable/reactive → has lots of potential energy

ATP Hydrolysis

• Releases free energy (-G) by hydrolyzing the last (terminal) phosphate group

• Inorganic phosphate used to add molecule that has phosphate

• Powers cellular work:
  • Chemical Work - making chemical bonds
  • Transport Work - transporting materials in/out cells
  • Mechanical Work - physical movement (e.g. muscle contractions)

ATP Function

• Energy coupling use exergonic reaction of ATP hydrolysis to power endergonic reactions in the cell
  • Energy released is linked by shared/phosphorylated intermediate to endergonic reaction

• ATP Regeneration

• ATP cannot be made by the body, ATP is converted or recycled in the body

• ATP Dehydration Synthesis: Net ATP made by phosphorylation when ADP combines with phosphate group using energy from molecule (ex: glucose)
  • ADP+Pi+free energy→ATP+H2O
    • Cycle recycles ADP and inorganic phosphate

• ATP production increases in low pH cuz provides more H+ (energy)

What are Enzymes?

• Enzyme: globular catalytic protein
  • 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!

Localization of Enzymes

• Some enzymes are grouped into complexes, membranes, & organelles (mitochondria) → increase the efficiency of metabolic process

Activation Energy Barrier

• Reacting molecules must collide and have enough energy (AE) needed to reach transition state and break bonds of reactants
  • Activation energy often heat from environment
    • But bad bcuz speeds up all reactions, denatures proteins & kills cells

Transition State:

reactive (unstable) condition of the substrate after enough energy has been absorbed to start the reaction

How Enzymes Speed Up Reactions

• Stabilizes transition state and lowers Ea Barrier
  • Allow chemical reactions to occur at lower temperatures
  • Speeds up natural reactions ≠ cause them
  • Reactions can occur without enzymes, but would be slower & a lot more energy

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

• 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.

Induced-Fit Model: describes how enzymes work

• Enzyme and substrate not perfect fit → interactions between enzyme’s amino acids and substrate causes enzyme/active site to change shape and bind tighter to substrate → enhances enzymes ability to catalyze the reaction

Enzyme Cycle

1. The enzyme binds to substrate forming enzyme-substrate complex

1. Substrate held by weak bonds

1. Active site lowers Ea barrier and speeds up reactions by…

• Orienting substrates correctly to collide (physically)

• Providing favorable microenvironment

• Straining substrate bonds (breaking bonds, hydrolysis)

• Covalently bonding to the substrate

1. Substates become products

Process Notes

• Enzymes are unchanged by reactions

• Enzyme catalyzes a reaction in both forward and reverse directions
  • Direction of net activity is determined by substrate concentration
    • Net direction of enzyme can be driven forward by keeping product of low (remove it or convert to another product)

Environmental Factors/Local Activity on Enzyme Activity

• Each enzyme has optimal pH and temp
  • Single amino acid substitution mutation can alter optimal pH and temp
  • Temp increases = enzyme activity increases
    • But only until too high temp & then decreases

• 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
  • Most enzymes have optimal pH at 7; digestive proteins (ie pepsin) become active only at low pH

• Saturated enzyme has all active sites engaged → cell might make more enzymes
  • More substrate = increased activity until a certain point

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/reaction

Enzyme inhibitors

• Bind to enzyme and reduce function
  • 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

• Noncompetitive inhibitor: binds to diff site on enzyme, irreversible
  • Changes shape to make active site less effective
    • Ex. Toxins, antibiotics, chemicals

Allosteric Regulation

• Regulatory molecules bind to allosteric sites and affect enzyme shape → function/efficiency
  • Activators - lock enzyme to be active
  • Inhibitors - lock enzyme to be inactive

• Cooperativity: binding of substrate increases catalytic activity at other sites (allosteric activation)
  • 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

Key Overview

• Organisms capture free energy in sunlight to store chemical energy in organic compounds, which can later be released

• Responsible for atmospheric CO2, Oxygen, organic carbon, & ozone layer

• Carbon Dioxide + Water + Light Energy ⇒ Glucose + Oxygen

• Photosynthesis Processes:

1. Noncyclic photophosphorylation use water and energy from sunlight to create ATP, NADPH, and oxygen

1. Calvin Cycle: uses Carbon dioxide and energy in ATP and NADPH to make glucose

Chloroplasts

• The site of photosynthesis in plants
  • Where solar energy is converted into chemical energy
  • Double membrane, circular DNA

• Several membrane systems creates compartments
  • System of compartmentalization increases surface area and allows organelles to finish their tasks faster

Chloroplast Structure

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

• 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

• Chlorophyll a: (green) captures light directly used in light reaction

• Chlorophyll b: accessory pigments (pass to chlorophyll a)

• Carotenoids: broaden spectrum of colors + protects chloroplast from light damage

Wavelengths

• Short wavelengths = more energy
  • Ex. Blue (absorbs heat), violet

• Longer wavelengths = contain less energy.
  • Ex. Red

• Green plants do not absorb green and yellow (500-600)
  • Black absorbs all wavelengths; plants/pigments are the color they reflect/don't absorb

Extra Notes

• Stomata closed at night

• Oxygen in air increases during the day (photosynthesis), and decreases during the day (cellular respiration)

• Captures light energy to form ATP and NADPH (stromal side) which will be used to convert CO2 to sugar

• Takes place in thylakoid membrane
  • First step is transfer of electron to primary electron acceptor

Photosystem

• 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

• Reaction center: proteins with special pair of chlorophyll a
  • Chlorophyll a: have specific max absorb rates & boost/transfer electrons to PEA

Photosystems

Excitation of Chlorophyll by Light

• Pigments absorb photon and incorporate energy into electrons → electrons move to higher energy level and are unstable→ fall back down and give off energy (heat, light) → excite other pigments

• Process of energy absorption and re-emission transfers energy from one pigment to another until it reaches chlorophyll a

Noncyclic Photophosphorylation

1. 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

1. Photosystem II: electrons trapped by P680 are energized by light absorbed by light harvesting complex & passed to PEA

1. Primary Electron Acceptor: first in chain of electron acceptors

1. 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

• Flow of electrons: H₂O → NADPH → Calvin cycle

1. Proton Gradient & Phosphorylation: energized electrons from PSII travel down ETC & lose energy which is captured by cytochromes to pump H+ into thylakoid lumen → used to establish H+ gradient needed for chemiosmosis → powers the production of ATP

1. Photosystem I: P700 absorbs energy and boosts electrons to primary e- acceptor

1. 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 provides energy and NADPH provides reducing power
  • Calvin cycle returns ADP, Pi, and NADP⁺ to the light reactions.

Cyclic Electron Flow: Electrons go thru PSI, not PSII

• Energized electrons from PS I join with protein carriers and make ATP (not NADPH or O2)

• Occurs simultaneously with noncyclic to make extra ATP

Noncyclic Phosphorylation Diagram

Calvin Cycle

• 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

The Process

1. 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

1. Reduction: PGA gets energy (H+) from ATP and electrons from NADPH to make G3P

• CO2 reduced and NADPH oxidized

• G3P: 3 Carbon, used to make other organic compounds like glucose (2 G3P)

1. Regeneration: ATP convert G3P to ribulose: allows cycle to repeat

• 3 CO2 enter to make 6 G3P but only one is net gain because rest are rearranged into ribulose

1. 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

Chemiosmosis in Chloroplasts

Photophosphorylation Process

1. 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

1. 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):

the flow of H+ through ATP synthase provides energy for synthase to phosphorylate ADP to ATP

Photosynthesis Mechanisms and Alternatives

PHOTORESPIRATION

• Wasteful pathway that occurs when the Calvin cycle enzyme rubisco acts on (fixes) oxygen rather than carbon dioxide

• Occurs when STOMATA CLOSES to balance out environment with the guard cells
  • So there is not enough CO2 that can enter → increasing CO2 can reduce photorespiration

• Problems:

1. Wastes NADPH and ATP + decreases output by draining fixed CO2 storage

1. Products from photorespiration are low energy (no sugar)

• Instead peroxisomes (found near chloroplasts) breakdown products

• Possible benefits: point to time where earth had more carbon, protect plants from light radiation

CAM Plants

• Open stomata at night, incorporate CO2 into organic acids stored in mesophyll cells

• During day close stomata and CO2 released for calvin cycle

C4 Plants

• Minimize photorespiration by using PEP Carboxylase (low affinity for O2) to initially fix CO2

• STORE CARBON DIOXIDE→ mesophyll cells always pumping CO2 into bundle sheath cells
  • Doesn't matter if stomata are closed or open cuz of diff process that works in low CO2 and high O2

Similarities between two plants

• Rubisco does not initially fix carbon (C3 plants use rubisco)

• Advantages: Minimize photorespiration, can close stomata to save water & still make sugar

Disadvantage: Both plants compromise cuz spend more ATP; slower photosynthesis & growth

Transpiration

Transpiration and Photosynthesis

• Basically leaf evaporation; water is flowing up a tree → sun shining (providing energy) and water evaporates and leaves thru stomata

• 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

• Plants want water to evaporate out of the plants → no transpirational pull without evaporation

Causes for increased transpiration and dehydration

• Heat (temperature), dryness (humidity), and wind

Key Overview

• 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

• Processes in mitochondria need oxygen

• Photosynthesis uses NADPH but respiration uses NADH

• Lots of ATP made but only ~half are net gain

• Most electrons travel down energy gradient: Glucose→ NADH→ ETC→ Oxygen

• Process that breaks down glucose and releases energy to form:
  • 2 Pyruvate (stores potential energy)
    • Pyruvate is acidic
  • 2 (net) ATP (from ADP)
  • NADH (from NAD+)
  • Inorganic phosphate

• 2 Stages
  • Energy Investment: invests 2 ATP to get glycolysis started
  • Energy Payoff: creates 4 ATP

• Occurs in the cytosol of the cell with or without oxygen

NAD+ ⇒ NADH

• NAD+ combines with 1 proton and 2 electrons to make NADH (reduction)
  • Reverse: NADH broken down to form NAD+

• NADH: reducing agent, carries the electrons to the ETC in mitochondria

Pyruvate Oxidation

• 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

• Occurs in the mitochondrial matrix; cytosol of prokaryotes

• Begins when 2-carbon Acetyl CoA combines with 4-carbon OAA (oxaloacetate) to form citrate
  • Citrate functions as inhibitor of glycolysis

• Result:
  • 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

• 2 ATP created but most energy transferred to NAD+ and FAD

• Is a closed loop bcuz last part of process reforms 1st molecule

• Turns two times for one molecule of glucose (one for each pyruvate)

Substrate Level Phosphorylation

• Glycolysis and Citric Acid Cycle make ATP this way

• Enzyme transfers phosphate from substrate molecule to ADP

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

• Occurs in the inner mitochondrial membrane of eukaryotes; plasma membrane of prokaryotes

• Cytochromes: proteins carriers, function in oxidative phosphorylation

Mitochondria Structure

• Transfers energy from electrons that move down it thru electron carriers that alternate between reduced and oxidized → released energy used to establish an electrochemical gradient of protons (H+) across the

• inner mitochondrial membrane
  • Redox reactions needed for proton gradient
  • Heat allows for hibernation; less ATP made but release heat better
  • Carriers = proteins that act as primary electron acceptors

• Oxygen is ultimate electron acceptor with most affinity→ process needs oxygen
  • Oxygen accepts electrons & protons → forms water

• NADH donates 2 electrons → oxidized, reverts back to NAD+, and goes back to glycolysis/krebs to do it all again

• If NADH couldn't donate electrons → no glycolysis/Krebs/ETC; oxygen can’t accept electrons (not consumed); ATP levels drop

Chemiosmosis

• “Mechanism of ATP generation that occurs when energy is stored in the form of a proton concentration gradient across a membrane”
  • Couples electron transport and energy release to move protons down their energy gradient and through ATP synthase

1. Krebs Cycle produces NADH and FADH2 in matrix

1. 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

1. 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+

1. A proton gradient (proton motive force) and electrical gradient (voltage) is established across the inner membrane: represents potential energy

• As H+ are transferred, the concentration of H+ increases (pH decreases) in the intermembrane space and decreases in the matrix (pH increases).

1. 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
  • Oxidative phosphorylation in cellular respiration
  • Photophosphorylation in photosynthesis

The Proton Gradient

• Proton gradient = pH gradient = electrochemical (voltage) gradient = stored/potential energy

• Proton Motive Force: force exerted on protons by H+ gradient

The ATP Synthase enzyme

• Channel protein that translocates the hydrogen ions from high concentration to low concentration
  • Cellular Respiration: From intermembrane to matrix
  • Photosynthesis: from thylakoid lumen to stroma

• Protons move onto binding sites on the rotor, making it spin in a way that catalyzes ATP
  • The active sites in the enzyme create 34 ATP

Role of Oxygen and Anaerobic Respiration

• Last electron acceptor in ETC; accepts electrons and protons to form water

• Without oxygen…
  • No electron acceptor so electrons can’t pass thru and no proton gradient established
  • NADH and FADH cannot transfer electrons and H+ → NAD+ and FAD not made → stops the citric acid cycle and glycolysis → no new ATP made → death

• Anaerobic respiration used by prokaryotes in low oxygen; sulfate or nitrate as final e-acceptor

• 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)

• Uses substrate-level-phosphorylation
  • Makes 2 ATP (less but quicker), 2 pyruvate and 2 NADH

• Occurs in cytosol NOT in the mitochondria (no oxygen present, no ETC).

Alcohol Fermentation

• Pyruvate loses 2 carbon dioxide molecules and then reduced by NADH
  • Result: NAD+ regeneration & ATP Waste: Ethanol and CO2

• Pyruvate directly reduced by NADH
  • Result: NAD+ regeneration & ATP Waste: lactate (no CO2)

• In animals, lactic acid often transported to the liver to be turned into pyruvate when there is enough ATP

Fermentation vs Anaerobic vs Aerobic

• Diff: methods of oxidizing NAD+, amount of ATP made

• Same: all use glycolysis and NAD+ as oxidizing agent

Versatility of Catabolism

• Glycolysis can break down diff macromolecules
  • Carbs, proteins, and fats give lots of energy bcuz of high energy electrons (C–H)

• Carbs: all end up being hydrolyzed into glucose for glycolysis

• Proteins: fuel, broken down into amino acids to make enzymes for cell respiration (biosynthesis/anabolic)
  • Eaten proteins are digested to amino acids; body proteins can be hydrolyzed to amino acids
  • Deamination: amino group leaves amino acid as waste so amino acid can enter cell R
  • 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)
  • 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

• Controlled by allosteric enzymes at key points of glycolysis and citric acid cycle

• ATP builds up → turns off phosphofructokinase (first enzyme in pathway) → stops glycolysis
  • Citrate also inhibits PFK

• AMP turns back→ forces pathway on

• Can speed up catabolic process: work hard + less ATP = more cell respiration

Similarities

Differences

Key Overview

• Cells communicate by generating, transmitting, receiving and responding to chemical signals that can pass electrically or use hormones

• Cells ALSO communicate through direct contact with other cells

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
  • Using ligands that can diffuse through the space between the cells

• Does NOT go thru bloodstream

• Allows cells to locally coordinate activities with their neighbors

Key Overview

• Cells communicate by generating, transmitting, receiving and responding to chemical signals that can pass electrically or use hormones

• Cells ALSO communicate through direct contact with other cells

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
  • Using ligands that can diffuse through the space between the cells

• Does NOT go thru bloodstream

• Allows cells to locally coordinate activities with their neighbors
  • Especially important during development, when they allow one group of cells to tell the neighboring group of cells what “cellular identity” to take on

• 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

AUTOCRINE SIGNALING

• A cell signals to itself, releasing a ligand that binds to receptors on its own surface
  • Important during development, where it helps cells take on and reinforce their correct identity and shape (ie. cancer, and its role in metastasis)

https://lh7-us.googleusercontent.com/0f2dS70bFeBdHymbWBe8AdyWHDqq3MOk9N_khWVLMnYXxdUWDm3A_7JG1ahLARfX-Qmp23t-eMlktQCSggVhaJN7eBQ-dn1qE4jItRJbWwtE-lz61EOcs6iFl6iTL6-fIALnKltW4taJoGMTNbCC6w| ENDOCRINE SIGNALING

• 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

• Hormones: long-distance, non-polar signals that travel thru bloodstream & control bodily activities
  • 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

https://lh7-us.googleusercontent.com/uaA6qgAE4HAnsBr0_v8_dipiM1ju0cgrZPG9_hZU9pguZl15muYhD00t0MJnF7IUvn-tzrW0xc0Ft7rZ-0L3GOZEIaSHcCx2e6Jtml2O15QqkXyURgky7H5XA46EkYf3lSMdxYwJ3PFXVRSOUqTjjQ| DIRECT/LOCAL: CELL TO CELL

• Between animal cells → allow proteins, carbs, and lipids of the plasma membrane to transmit information
  • 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

• 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

• 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

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
  • Basically channel proteins of two cells that are closely aligned

• Plasmodesmata: tunnels of cytoplasm in the cell wall that connect plants cells
  • Regulates molecule transfer and gene expression

• Cell-Cell Recognition:

• 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.
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• 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
• Ligand: signaling molecule that acts as first messenger
• 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)

• Signaling Molecules: small molecules that bind to larger receptors of specific target cells

1. Hydrophilic ligands: cannot cross membrane and bind to membrane receptors
   • Ex: proteins that are both large and polar
2. Hydrophobic ligands: non-polar signaling molecules that can cross membrane and bind to intracellular receptors https://lh7-us.googleusercontent.com/L5z9ZlMnoZx6G9RCRH-_hr3bBKaZYBPJu91ROPa57HdCWprw1pjDu4ux0aT4y31TNE0AO0clIyXYWZk3lcdmuka_pfXaaJHtqYGKFbqRhOdnkGc1JzdGPb-_d9GOlTRxrFju1Qw5FlfGUSoSqFTimw|
   • Receptors: specific proteins that receive ligands and trigger transduction
3. Membrane receptors: transmembrane & amphipathic; consists of an extracellular ligand-binding site and an intracellular domain that initiates transduction pathway
4. Intracellular receptors: proteins in cytoplasm or nucleus
   • 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

• G Protein-Coupled Receptors
• GPCRs: amphipathic, transmembrane protein that activates a G protein → which activates another membrane protein → triggers cellular response or activates second messenger
• G protein inactive with GDP and activated when GDP is replaced with GTP
• Process Summary

1. GPCR receives signal: specific messenger ligand binds to outward surface of receptor
2. GPCR activates G protein: ligand binding activates GPCR → GPCR exchanges a GTP for the GDP on a nearby G protein → activates G protein
3. G protein binds to and activities [membrane] effector protein:
4. Effector protein initiates cellular response:
   • Enzymatic activity: effector protein may be enzyme that catalyzes specific substrate → ex: protein kinase and initiate kinase cascade
   • Produce second messenger cAMP:
     • If effector protein is adenylyl cyclase, enzyme makes cAMP
       • Pathway activates cytoplasmic protein (ex: protein kinase)
       • Response may be stimulatory or inhibitory
   • Produce second messenger IP3 and DAG:
   • Produce second messenger CA2+:
5. GPCR signaling/pathway is deactivated when GTP is hydrolyzed:

• 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
• Can receive growth factor → cell division → malfunctions = cancer
• Process summary

1. RTK receives signal: ligand binds to its outer surface
2. RTK forms a dimer: two RTKs associate → form a pair (dimer)
3. RTK is activated by autophosphorylation: many phosphates can attach
4. Relay proteins are phosphorylated by RTK
5. 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
6. RTK pathway deactivated by dephosphorylation or receptor protein packaged in vesicle (endocytosis)

• GPCRs vs RTKs Pathways

1. RTK directly responsible for initiating transduction pathway; GPCR indirectly activates transduction pathway via G protein and effector molecule
2. RTK can trigger multiple transduction pathway → direct lots of coordinated responses;

• GPCR triggers single pathway → single response Ligand-Gated Ion Channels
• Gated Ion receptor: transmembrane channel protein that opens/closes in response to ligand binding to allow ions to pass thru

1. Ligand-gated ion receptor receives signal: ligand binds to outward face
2. 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
3. Ions initiate chemical response:
4. 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
  • 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)
• Ligand can block binding to stop diseases or open channel to allow flow of CA+, NA+, or K+
• Example:
• Acetylcholine: neurotransmitter that transmits nerve impulses between nerve cells (neurons)
  • 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

• After the ligand binds, the intracellular domain of the receptor protein changes shape, initiating transduction of the signal by converting it into a form that causes cell response
  • Main Idea: molecules interact with each other to relay/amplify signal
• SECOND MESSENGERS
• Small, non-protein molecules that spread through cell via diffusion and relay/amplify the intracellular signal
• 2nd Messenger: Cyclic AMP (cAMP)
• Created using adenylyl cyclase by cutting ATP and two phosphates
  • Can activate protein kinase→ Cell response
• 2nd messenger: Ca+
• Ca+ levels stimulate cellular response
• Cell regulates concentration by actively transporting into ER and mitochondria
• Signaling Cascade
• 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/control
• 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
• https://lh7-us.googleusercontent.com/HzHUsV5KJopPrnSPVhfC0kZavpxAWUdTpkailME5ZjiQ4HIuOmZCTv55Z02_ZQlG4GTR8qTgJ4SekFHfokL2XFZ0idSfU3sZ7WDekvc9I-l8QX--4T60aYFNhwEtBrld5CjMF-K3vN2W96FPIlop3w| https://lh7-us.googleusercontent.com/6uTR1OjKeEZYCpntUkaSi_vXRA_k-z5OCcvn9of4Il5295KdRwT4tjCJbUsuHp2Kb-MbpOKGVoLBZgI6BbLhII867c4VKwyqOaHIXB3vUzlooTj7Ph5hvvuI0qr-ETJXj2j91TMPXPmjyevBea8rbg| THE PROCESS - PART 3: Response
• Cell carries out specific behavior in response to an extracellular signal
  • Cell response depends on pathway taken that leads to nuclear or cytoplasmic response
• Cellular response can change its behavior
  • Ex. yeast cells change shape when mating
  • Release Pheromones: externally released ligands for communication
  • Muscle contraction, inhibit/promote transcription, molecule/waste secretion, protein activity, cell growth/division
• Gene expression depends on cell type and gender
  • Males: testosterone activates genes in testes that direct development of sperm cells but in muscle cells stimulates production of muscle fibers
  • Females: estrogen activates genes that direct cells in the uterus to prepare for pregnancy but in mammary cells inactivates the same genes.
• INTRACELLULAR RECEPTORS
• Small, hydrophobic/ NONPOLAR molecules can easily diffuse thru cell and bind to proteins in cytosol or nucleus of target cells
• Ex. steroids: testosterone, estrogen bind to intracellular receptors → activated complex (hormone + receptor protein) moves to nucleus → bind to DNA and promotes transcription of genes that direct cell activities
• Process Summary

1. Signaling molecule enters the cytoplasm: must be nonpolar
2. Signaling molecule binds to intracellular receptor, activating it: sometimes activation triggers release of inhibitor that prevents receptor from functioning
3. Receptor-signaling molecule complex acts as a transcription factor: receptor-signal complex binds to DNA → promote or suppress transcription of genes
4. 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
• 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
• Benefits of Signal Transduction Pathways

1. Amplification: Enzyme cascade amplifies cells response so number of activated products is greater than last step; rate of amplification depends on pathway molecules

• Small amount of ligand results in large response, relay proteins amplify response and activate many enzymes

1. 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
2. Multiplicity: single signaling molecule can activate multiple cytoplasmic proteins → each can generate a different response

• 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.
  • Variety and combination of different genes in cells & different structure of receptor result in different pathways taken
• Pathway taken within cell determines response from ligand
  • Cell can only respond if has receptor but pathway determines what response is
• Some cells have more complex pathways but still have similar molecules
• Disease
• 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
• 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
• Expression of the SRY gene triggers the male sexual development pathway in animals
• HOX genes and their role in development
• Ethylene levels cause changes in the production of different enzymes allowing fruit to ripen

• 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
• Caspases: main proteases, enzymes that cut up proteins and carry out apoptosis.
• 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't leak digestive enzymes
  • 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
  • Protein misfolding in the nucleus (ex. alzheimers)
• Mutations cause cancer, so apoptosis helps prevent this
• Regulation
• Ced-9 prevents apoptosis by inhibiting caspases

• A change/mutation in the structure of a receptor protein or signaling molecule affects the activity of the signaling pathway and can alter the cellular response
  • Chemicals that interfere with any component of the signaling pathway may activate or inhibit it: toxins, antibiotics
• https://lh7-us.googleusercontent.com/_b_80JAQDkQHH-A5OPGqsJP7vUiTik4PfzRG1t1W70Jut9FsVUdMyUjN-RcTkNPnTTq1IuDz65TSyR1A4i9hBhv6QA7ANct5JZKXjPVDCujcq92avrBq8owGOrGJ2ONuUb8bRwlnlDxzYtj9-ltyQw| figure: on the left, the hedgehog would not create a signal transduction pathway because the inhibition prevents it from going any further. Feedback Mechanisms Negative Feedback and Homeostasis
  • Organisms use feedback mechanisms to maintain their internal environments and respond to internal and external environmental changes.
  • Negative feedback mechanisms maintain homeostasis
    • Tend to push to stability after abnormality, counteracts change, processes that need to be maintained
      • Processes operate at the molecular and cellular levels.
  • Ex. Temperature regulation, blood glucose & calcium levels,
  • Product accumulates, process that makes it slows down and less is made or output inhibits
• Positive Feedback and Homeostasis
  • Positive feedback mechanisms amplify responses and processes in organisms.
  • 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
    • Ex. pregnancy contractions, fruit ripening, blood clotting
• https://lh7-us.googleusercontent.com/RtYG2qp51y9vFR-IyDIPzkefJ3cxgvcn8IOzCuynFm2Puc66-MTN5uqVDNkoW6qQLF0lLxLfCz75CrOL_dIl7AjUQ_MBFAQZUGbgthTgw1ONPqU7P_cYwpT_CzSJ0UZ9n3aH2YhMpRjyyDMjCv5FCQ| Example: Blood Vessel Injury If there is an injury to a cell, molecules are released and trigger previously inactive clotting factors. Clotting factors activated → activated more clotting factors → amplification continues until injury healed Alterations in Loops
  • 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
  • Usually exchanges hydroxyl R group with phosphate
  • Switches proteins on → increases potential energy and ability for chemical work
• Protein phosphorylation involved with regulation of transcription, enzymes and TRKs
• The transfer of the phosphate group is catalyzed by the kinase enzyme
  • Cells contain many different kinases that phosphorylate different targets
• The reverse: after a protein has been “activated”, the enzyme phosphatases switches them back into non-phosphorylated state by catalyzing removal of phosphates
  • Turns of kinase cascades

4.6: Cell Cycle Key Overview

• Eukaryotic cells divide and transmit genetic information via two highly regulated processes:
  • Mitosis and Meiosis

• 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
• Cytokinesis: the division of the cytoplasm GENOME & DNA Replication
  • 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
  • DNA packaged into chromosomes which makes replication/distribution of DNA easy and prevents breakage
    • 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: protein and DNA structure at each chromatid
  • Every diploid organism has homologous chromosomes: two copies of same chromosome
    • One from mom and one from dad

• Cell Cycle: is a highly regulated series of events for the growth and reproduction of eukaryotic cells
  • Three stages: Interphase, Mitosis, & Cytokinesis
• Smaller cells better because easier to coordinate chromosomes and microtubules with less ATP
• DNA content doubles during Interphase (S phase) and halves during mitosis
• https://lh7-us.googleusercontent.com/Wr_RWeygrHz7T8nmFVecQQObXPpnTefdgyTFS0XJjvVUCIE5MVHSUBHUqgkJO99_15aeSoHkJAB0dPS91ywQHPjqoJnnF0NUWnM9vomV3WZDxFJLISG-kvBeAMihgw-Upg0B4hHGz7qvyJZLLVMZSg| Cell Cycle: Summary Interphase
• Majority of cell cycle, split into 3 phases
  • All have metabolic activity & growth
• G1 Phase
• Metabolic activity and growth; one chromatid
• S Phase
• DNA replication; two chromatids
• G2 Phase
• Prepares for cell division
• M phase
• 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.
  • 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
• How Does Mitosis Produce 2 Identical Daughter Cells https://lh7-us.googleusercontent.com/L4kzRrHgJKc4tynvqddI6MMQm1Nm6x7xyIn2yUt7fraKuniDcqz055p6rZOV3UGmDR8FgJx_o6J1jUZ7fwP1WFhF82ixUYklwI5qaAm7pD6FnRTkoXjfocziUKGeCpWARPwQm68fjKU0euTZJRmrtQ|
• DNA Replication (Interphase) and separation of chromatids (Anaphase)
• 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/identical set of chromosomes
• 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
• MITOTIC SPINDLE
• Consists of mitotic fibers, centrosomes, and asters
  • Fibers made up of microtubules and proteins: control chromosome movement
    • Elongate by adding tubulin
  • Asters: microtubules that hold together two centrioles to make a centrosome
    • Spindle is complete when asters elongate and touch membrane
• Two kinds of microtubules:
  • Kinetochore Microtubules: attach to kinetochores → move chromosomes to metaphase plate → jerk chromosomes back and form
• Non-kinetochore microtubules: interact/overlap → elongate the cell as motor proteins push them from opposite poles using ATP

• G2 of Interphase The last part of interphase:
  • A nuclear envelope encloses the nucleus.
  • Nucleoli usually present in nucleus
  • Two centrosomes have formed by duplication
  • Each centrosomes contain two centrioles
  • duplicated chromosomes but not condensed/visible
• https://lh7-us.googleusercontent.com/S0uNPrThKmFd25lscWukvU2PipBrvEx_jK13jt150rFhpJLQCe3sRSf4uReVVfgUEpCDxHPFSO01SXAgABG23s1M2uxf8sWqFY5-eV7fZvlLRL5XD2RTMgpTuSn-rVLeRbPIc15hatgxiZuzb4Em4Q| Prophase (condensation)
  • Nucleoli gone, nuclear envelope thinning
  • Chromatin fibers condense into tightly coiled and visible chromosomes
  • Mitotic spindle begins to form by adding tubulin units to microtubules
  • Centrosomes move away by lengthening microtubules
• https://lh7-us.googleusercontent.com/xKeCANDNvVg8VlT66vW5Acva4sDwF59qyEPF5qEfdUFSalYXNrD9ULJW10SCxCJPtDGiK1cbFpwNuCHcWFVN_CzTFHilCGYCG_ZNV2CzBVxi2NovucgcPZ9XEwCXI7hpxLrJ8BVBZww5ZaJPmqqJHw| Prometaphase
  • Nuclear envelope gone
  • Kinetochores form at centromere of each chromatid
  • 2 types of microtubules form and go into nuclear area
• https://lh7-us.googleusercontent.com/HyIUlvnyj5JqF41m1gkXsSACqCunvv62t-ypSnrwi2ATSLulbstL2UzpsIO81akipR8RWyiU0-9zhxwEcdsc2DK2prgdZ55KWdZogQvVhs3boa20edBJNMTbEk7eoKMx2uuojNaVAtESxYRhjWu3OQ| Metaphase (middle)
  • Chromosomes line up at metaphase plane (equidistant between spindles two poles)
• https://lh7-us.googleusercontent.com/9n-cjXjqn0uYusvNSZngv5i7v19_d1dhhCsUgAzLVJUQi4LgUymZvbceSLUxGjdZfzsRmzPMg92-4kx5tbEoTHKfqLxnH9a8jWcgNPG8eG6BBwKsN6kGd1Ix61gR1Hhb3MTafkpJHiV8ae1naV0QbA| Anaphase (seperation)
  • Shortest stage
  • Sister chromatids become individual chromosomes when cohesion proteins are cleaved → are reeled to opposite poles as microtubules shorten by uncoupling tubulin units
• https://lh7-us.googleusercontent.com/Zj56AUwzmU8OAjRIQLfqUSCzhbpDo1Yl0GsVxfrGIPpnmw0PCgLw_2W0IM0rv3lgL6ZBm2ip2Bs6Mm9MxdpBcCN-CAA_xJycgNth1YcHvoy0h95jKziV9uTZJp0xqgFgl5cXeBL8rtTo7-WqjXCHLQ| Telophase (restoration) and Cytokinesis
  • Two daughter nucleoli form from parent fragments and endomembrane system; one at each pole
  • chromo decondense & become chromatin, microtubules depolymerize
  • nucleoli & envelope reappears
  • cleavage furrow begins to separate the two into sister cells
• https://lh7-us.googleusercontent.com/PRA2c7dK46x4aEqcD02tEiv5iTpnzWn807YmZoBSrHGmO27C9WEA6h2SZY9xJeviuAsJs5Yw7VtVEIToo4ts2IAbxCEopqCPTsY4_vVZ8nDyBpaeHrr0Tj1VLIbT-R3etmNsqE3dRozK97CRvs3vkw| Cytokinesis
  • 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
• https://lh7-us.googleusercontent.com/l-ur3zN4RoxSJs7-vO12A3bZ8bM4XBAxX1HzHQg9oFsEJvRYH5rKMY5pE59iWPRqEf8RyH5E0blS5QA2DM1AHKZGj1L54Rk2RsRp6MJmDD-C2ONd3AyInAXuyuSxawS8T-bz8I2693FZUzLcpdzoeA|
  • 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://lh7-us.googleusercontent.com/l-ur3zN4RoxSJs7-vO12A3bZ8bM4XBAxX1HzHQg9oFsEJvRYH5rKMY5pE59iWPRqEf8RyH5E0blS5QA2DM1AHKZGj1L54Rk2RsRp6MJmDD-C2ONd3AyInAXuyuSxawS8T-bz8I2693FZUzLcpdzoeA| Mitosis Function:
  1. Asexual Reproduction: only unicellular organism
  2. Growth and development: get bigger by adding more cells
  3. Tissue repair: replace old cells, injuries to a cell can be repaired by replicating the cell in a healthy form

• Internal Regulation of the Cell Cycle

Functional Limitations

1. Surface-to-volume ratio: when surface area is small compared to volume → cell growth stops or cell division begins
2. 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
• Factors that regulate cell cycle become distorted → can lose control of production of growth enzymes → cells become cancerous
• Molecular Regulation of Cell Cycle

1. 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
• 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
• CDKs + Cyclins= Cyclin-CDK complexes such as Maturation Promoting Factor (MPF)
  • CDKs increase in lvls with cyclins
• https://lh7-us.googleusercontent.com/tVv3c6Dx1zSbwVQka5rbmulum_uSv0auRxWMdsI23N4r_6PnmG3vQWFQQl_pmIFsO5-DHTaUHZvt_neJIuun1kyckyDWvXM0ZsfqIheKRPuFxyS1R7qJqWP7G9gHDvmKKC_n-llT-8b6r3Y3U8FmOg| Purple Line: MPF activity
• Shows that it peaks at mitosis & drops again at every checkpoint
• Red Line: Cyclin
• It “cycles”: builds up prior to mitosis, at its peak, then sharply drops
• Maturation Promoting Factor
• Cyclin-CDK complex that advances cell cycle through G2 checkpoint by phosphorylating and activating proteins involved with chromosome condensation, nuclear envelope breakdown, spindle assembly and MPF self destruction (signals end of G2)
  • Is self-regulating because starts process that destroys its own cyclin

1. Checkpoints: specific points during cell cycle where cell evaluates internal and external conditions to determine whether or not to continue thru cell cycle

• 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: external and internal controls that affect it\ \ If passed:\ Enter S phase → synthesize DNA, prepares to divide successfully\ \ If failed:\ Moves into G0\ G2 checkpoint\ • Checks if all DNA is replicated and repaired\ \ If passed:\ Enters M phase (mitosis)\ M Checkpoint\ - in metaphase and before anaphase\ - checks if all of the chromosomes are lined up properly in the middle of the cell and kinetochores are attached\ - ensures that you get equal distribution of chromosomes between the two cells\ \ If Passed:\ Enters Anaphase\ \ If Failed: \ Can pause stage until stray chromosomes corrected or trigger apoptosis\ External Factors that regulate cell cycle/production of cdks
• 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
• Anchorage dependence: cells must be attached to a substrate in order to divide
  • Ex: flat surface of neighboring cell or dish
• Cancer cells exhibit neither density dependence or anchorage dependence

• Disruptions to cell cycle or inability to carry out apoptosis can lead to cancer
• Cancer Cells
• Cancer: unregulated/out of control cell division, results from genetic changes affecting genes whose proteins regulate the cell cycle
  • 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
• Abnormalities of cancer cells:
  • Do not move through cell cycle in a regulated way; if stop dividing, only at random checkpoints
  • Can divide forever with given nutrients
  • Do not display anchorage dependence of density-dependence (divide past one layer)
  • Evade signals that trigger apoptosis when something goes wrong
• Proto-oncogenes: normal version of genes that code for protein that stimulate cell growth (growth-stimulating)
• Oncogenes: dysfunctional, cancer-causing genes
• Transformation: When gene becomes oncogene
• Causes for Oncogenes

1. Gene Translocations: Chromosome broken and rejoined incorrectly; Errors may place gene close to control regions and then expression of wrong gene products can make cancer worse

• Untitled_a1baf95c2be74fad95ea92c3882c2c8f:Untitled_5|

1. Gene Amplification: too many copies of gene → excess growth-stimulating proteins
2. Epigenetic: abnormal chromatin condensation → proto-oncogene expressed at the wrong time or amount
3. Point Mutations:
4. In promoter, enhancer/control element → could increase expression → excess growth-stimulating proteins
5. Within gene → could code for protein that is more/less to degradation

• Tumors
• 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/cancers is a number of mutations
• 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: part breaks off, enters the bloodstream, divides and creates a tumour elsewhere in the body
  • 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
• Treatments
• Radiation that harms localized tumours more than normal cells
• Chemotherapy: a toxin that kills all dividing cells by destroying spindle fibres that splits cell
• GENES AND CANCER
• Each cancer is caused by a different set of mutated genes, so there is no possible cure-all
• 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
  • 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.
• Interference with Normal Cell Signaling Pathways factor With P53 Transcription Factor: Untitled_a1baf95c2be74fad95ea92c3882c2c8f:Untitled_6|
• Activated by signal transduction pathway when DNA is damaged from external factors and promotes transcription of cycle-inhibiting proteins
• Without P53 Transcription Factor: https://lh7-us.googleusercontent.com/ydiVlqkvcqxXXqE73gI1Yebo5JuL_Ke6aZg17wa5IUnjg2P_N3XM_jJ-2S5CB86_HtkHz-N4bJ5Sps1CiwibdB-z8WASXNjWF-kqJHSC-erR-xFO8PyuQyy4U083TsR8EIeiBHEB7crCrpojZ6_MRg|
• If gene mutates, damaged cells can proliferate and spread, becoming tumor
• Increased cell division
• Ras gene: Untitled_a1baf95c2be74fad95ea92c3882c2c8f:Untitled_7|
• 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

* In sexual reproduction two parents produce offspring with a unique combination of genes.

• In eu. results in gamete formation
• Increases genetic variation bcuz random mutations can be shuffled between organisms

* Zygote: fertilized egg, diploid

• 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) * 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
• Number of alleles determines how many different types of gametes

* 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): pair of chromosomes with same size, shape, centromere, and same genes that control specific inheritance pattern but different versions https://lh7-us.googleusercontent.com/HKSBmyMJhWsFtm3DryyYTR7yv33irXyquq3ohKPFqU00_rbgJlZNCpmXkZaD3gYV4jVk5GiRsRF7BTdrIid06GPiwWkaKCZBnTmEXPItaO5NXTea6qIPcCn5LWc2aQMuOlQCa5sEzifCg1ZNctiYgw|

• One maternal and other paternal

* 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

* Locus (loci): exact location of a gene on a chromosome * Tetrad: Made up of two pairs of sister chromatids that have synapsed * 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: * 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 * 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

* Plant Life Cycle: both haploid and diploid split equally so there is no dominant stage (multicellular)

• Alternation of generations: one gen is haploid and the next may be diploid, it flips every generation
• Sporophyte: multicellular diploid plant Gametophyte: multicellular haploid
• 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

alteration of halving and doubling chromosome count in each generation * In sexual reproduction two parents produce offspring with a unique combination of genes.

• In eu. results in gamete formation
• Increases genetic variation bcuz random mutations can be shuffled between organisms

* Zygote: fertilized egg, diploid

• 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) * 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
• Number of alleles determines how many different types of gametes

* 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): pair of chromosomes with same size, shape, centromere, and same genes that control specific inheritance pattern but different versions https://lh7-us.googleusercontent.com/HKSBmyMJhWsFtm3DryyYTR7yv33irXyquq3ohKPFqU00_rbgJlZNCpmXkZaD3gYV4jVk5GiRsRF7BTdrIid06GPiwWkaKCZBnTmEXPItaO5NXTea6qIPcCn5LWc2aQMuOlQCa5sEzifCg1ZNctiYgw|

• One maternal and other paternal

* 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

* Locus (loci): exact location of a gene on a chromosome * Tetrad: Made up of two pairs of sister chromatids that have synapsed * 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: * 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 * 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

* Plant Life Cycle: both haploid and diploid split equally so there is no dominant stage (multicellular)

• Alternation of generations: one gen is haploid and the next may be diploid, it flips every generation
• Sporophyte: multicellular diploid plant Gametophyte: multicellular haploid
• 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

Untitled_a1baf95c2be74fad95ea92c3882c2c8f:Untitled_8|

• Meiosis: specialized cell division that yields 4 nonidentical, haploid gametes in sexually reproducing diploid organisms
  • Only occurs specialized (diploid) cells like testes & ovaries in humans to make sperm and egg
  • 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
• Meiosis 1 and Meiosis 2: Process Overview
• Meiosis 1: focuses on the separation of homologous chromosomes
• 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/tetrads line up along the metaphase plate\ • Alignment determines independent assortment \ • The same apparatus moves the pairs: microtubules, spindle fibers, asters\ • Diff to mitosis bcuz they line up in pairs\ • One pole attaches to one of homologs kinetochore\ Anaphase 1 Telophase/Cytokinesis 1 Homologous pairs separate and move to opposite sides of the cell, guided by the spindle apparatus \ Cohesins are not cleaved so sister chromatids remain attached at the centromere and move as one unit toward the pole\ Each half of the cell has a haploid set of chromosomes \ Cytokinesis: two haploid daughter cells\ Meiosis 2: Detailed Processes Prophase 2 Metaphase 2 No synapsis, chiasmata or crossing over of homologs\ A spindle apparatus forms.\ In late prophase 2, chromosomes (made up of two chromatids) move towards metaphase plate\ Sister chromatids line up in single file line at middle of the cell Anaphase 2 Telophase/Cytokinesis 2 Sister chromatids are separated and move to opposite sides of the cell, now as two newly individual chromosomes.\ Because of crossing over in meiosis 1, the two sister chromatids of each chromosome are no longer identical.\ Chromosomes arrive at opposite poles.\ Nuclei form, and the chromosomes begin decondensing.\ \ Result: FOUR haploid cells that are not identical to each other or parent Meiosis and Genetic Diversity Crossing Over Specifically Occurs in Prophase 1
• 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/unwinds pieces of genetic material on a chromosome & attaches it to non-sister chromatids on homolog (recombines) → exchanges DNA segments
• Physical constraints: probability of crossing over between genes is proportional to distance between two genes (increases as distance becomes larger)
• Chiasmata (sing. Chiasma): Point of contact between two nonsister chromatids where crossing over will occur https://lh7-us.googleusercontent.com/mVA2d7m0EBKdoLRVoLkXBjfdhDx8Zpv5ky_sxN6F-P7seO3lTVRJ74pLoqZF4-r2nqRR_lb-nwnr1Jf9B9XiqYCH4siYAOn-SwRDzHWqZbRVmXTLwuxtmG9H0wL20fcC52yfsZB2yvxvAcQPEmbI_A|
  • Holds homologous pairs together due to sister chromatid cohesion
  • Absence leads to aneuploidy
• Chromosomes that look like its parent (1 and 4) parental
• Chromosomes that are crossed over: ( 2 and 3): recombinant
• Mitosis vs Meiosis
• Both have separation of sister chromatids
• Untitled_a1baf95c2be74fad95ea92c3882c2c8f:Untitled_9| https://lh7-us.googleusercontent.com/23-t2oHzqSgT9YFM7H3k8Niel1vHpH14WGgbQHKzcT7qMj6hfdRqyA0qg1eXVWl9iUpQb4KRnT104DB-N3rawirNnimAO5__rd-BTPyXnuUXPn0R6OzbumydDuAKiLGfLcHhv8JRokGrc7CK_L-8DQ| Genetic Variation Contributes to Evolution
• 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
    • 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
• Random fertilization: random chance of any sperm and egg fusing is astronomical
• 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
  • 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

Unit 5.3 Mendelian Genetics

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

• Dominant: always expressed

• Recessive: masked by dominant

• Hybrid: cross of two “true-breeding”; combination of two organisms

• 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
    • Rare bcuz crossover between genes close together are uncommon

Homozygous Dominant: two dominant alleles

Homozygous Recessive: two recessive alleles

Heterozygous:

one dominant allele, one recessive allele

• P generation: Parental generation, Mendel crossed a purebred purple with a purebred white plant
  • People used to believe in blending inheritance: traits are mixed
    • 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

Types of Crosses

https://lh7-us.googleusercontent.com/WZ7166RNIbldE7U0Qv6dwvJqn13kmU7r_bveufyeByRsK_jjDgiZ15ZG-Ftybushms86QfsTpn08I9otMECqFuNBREmcGbU2sNxy9bAiQn1Lw-x0apJUte47i6Yw_zX2bvlGyK9zxF-6qo_A1TEENQ| - Monohybrid cross: only one trait (ex: stem length)

1. 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

• 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)

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

4:4:4:4

→ Heterozygous x Homozygous dihybrid cross

Mendel's Law of Inheritance

Law of Segregation

• Describes how alleles are segregated into different gametes and reunited after fertilization

• During anaphase I, homologs separate randomly to opposite poles so that each gamete only receives one copy of each allele
  • Describes alleles of same gene

• Process in meiosis that ensures gametes get both maternal and paternal chromosomes

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.
  • In other words, the allele a gamete receives for one gene does not influence the allele received for another gene
    • Ex. Brown hair doesn’t mean you will get brown eyes

• The behavior of one homolog doesn’t affect that of another

• Assumes every gene is found (or behave like they are) on different chromosomes and are not inherited together
  • Describes alleles of different genes

https://lh7-us.googleusercontent.com/LhBI_9rsjh4UkO8V2csjSjCTOq40dBF-CseKWXVqzWirJQFmGWiNkFdCiujKgB2tBH2Kmbt69Oc9aUHSHUN8SXgGFkr1qSVa5QBXyDXJlELGlsfJqQIKQkWL71N4gSy7Jy_YpbmK_vwoRZz5FzufRA| * Rules of probability can be applied to analyze passage of single-gene traits from the parent to the offspring.

For harder problems, where there are 2 alleles (AaBb)

• Mutually exclusive (can’t happen at same time) = or

Multiplication Rule

• Two or more independent events (and)

• Find the probability of each individual alleles, then multiply the two by each other

• 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

• Aa=2, AA=1, aa= 1
  • Add up. Ex AaBbCCDdEE =

• 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

Relationship Among Alleles of a Single Gene

Untitled_a1baf95c2be74fad95ea92c3882c2c8f:Untitled_10|Untitled_a1baf95c2be74fad95ea92c3882c2c8f:Untitled_11|Untitled_a1baf95c2be74fad95ea92c3882c2c8f:Untitled_12| - Complete dominance: Heterozygous phenotype is the same as the dominant

1. Incomplete dominance of either allele: heterozygous phenotype is intermediate between two homozygous
   • Dominant allele doesn't make that much protein, recessive makes none, so heterozygous makes weaker amount

1. Codominance: both inherited alleles are completely expressed in heterozygotes
   • 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

1. Pleiotropy: one gene affects multiple phenotypic characters
   • Ex: sickle cell disease

1. 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
     • Superscripts used because the two alleles, A and B, are codominant; lowercase i is recessive when expressed with others
     • There are six possible genotypes representing all possible combinations of 2 alleles: [I^A, I^A] and[ I^A, i] (A blood type), [I^B, I^B and I^B, i] (B blood type), [I^A, I^B] (AB blood type) and [ii] (O blood type)
     • 4 phenotypes correspond to presence/absence of an A or B sugar component attached to plasma membrane of red blood cells (A sugar, B sugar, I^A, I^B both sugar, and ii no sugar)

Relationships Among Multiple Genes

1. Epistasis: Expression of one gene affects/masks another
   • 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)

1. Polygenic Inheritance:
   • 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
     • Any human character that is polygenic, cannot be predicted (like eye color)

Environmental Impact on Phenotype

• 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:
  • At high temp & pH enzymes & transcription factors become denatured
  • Environment might contain a molecule that acts as a repressor or activator

Case Study: Identical Twins

• Although have same DNA, expression of DNA influenced by environmental factors

• Before are born → experience slightly different environments in uterus → affect gene expression → different phenotypic expressions

Examples

1. Nutrition: not enough nutrients can inhibit growth and plants without enough nitrogen may not flower
   • 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
     • Organisms w/ mutation so cant syhtnesize amino acid can grow in environment w/ amino acid

1. Temperature:

• Influences sex dertermination in some reptiles
  • 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)

1. Soil pH:

• Influences flower color; blue in low pH and pink in high pH

1. Released Chemicals

• Chemical signals can affect gene expression and often needed to elicit mating
  • Ex: bacteria secrete signaling molecules that stimulate nearby bacteria to aggregate & form biofilms
  • 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

Behavior of Recessive Alleles

• 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

• Cystic Fibrosis: caused by a mutated channel gene that causes ppl with two recessive to not have chloride transport
  • 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

Dominantly Inherited Disorders

Lethal Dominant:

only needs one copy to kill (heteroz)

• “Genes have specific loci along chromosomes & undergo segregation and independent assortment”
  • Chromosomal inheritance generates genetic variation in sexual reproduction.
  • Evidence: parallels between genes during meiosis and behavior of chromosomes

• Autosomal Inheritance: gene is located on one of autosomes
  • Male and female equally likely to inherit the gene

T. H. Morgan:

• Discovered sex-linkage of genes

Fly Case Study

• Have mutations affecting body color and wing structure which are linked:
  • Normal (wild) body color is gray (B) while mutation is black (b)
  • The normal wing (V) and vestigial wings (v, small, nonfunctional)

• Heterozygous would be BbVv with BV on one chromosome and bv on another
  • Since genes are linked and cant assort independently can only make BV and bv gametes

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
  • 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 https://lh7-us.googleusercontent.com/POiUEIVLNI_CIQ7jA3OjYJ21cvHka0xg4Zqz_2bUdbom1FLenI5g4S60fh_QD8FjkMVwChNzWZuP1_tMRntv8sWMv9_-3Tt0-cb5qGNJKum4Riot7826Fg69MSPllfAKG0R2Pe27z_2cO58_h9uKfw|
  • Expected: parental & recombinant type are equal
  • More than 50% offspring look the same as parent = genes are linked

https://lh7-us.googleusercontent.com/0nGKJqi6V86j8sUhk8JEoQ2oR0Mvn0nkBPlY_AB0xrVAZ7_vMGzGHB1E61FgNCbf-FSGW5_cG582oB3sYId2_y9SxY7RfY25R7MbQ1SAKghfKOE5m-vhBEXPlRl_phmysKm-DW54WtV718zxMPRW9A| Percent Recombination

• “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 closer together → more likely to be inherited https://lh7-us.googleusercontent.com/1rnmGMPaECcJo-LH92DpCHj6pha8Uwz3FgevZW7WmgV3JeFvKt00ywtUGGS9aJ_OjnePAORMZEpLP6PxYH9O72A3dwqzbqqe1FnDba20SckM-dzqv46tvXQ8612cMnrYQw9jX8RZFNxl8baL2lfzWw|

• Percent Recombination: add up the recombinants → divide by total number of offsprings
  • 50% RF is max, < 25% = genes are close

• Divide percent recombination by 2 to get map units distance btwn. genes
  • (high map units = high percent recombination = independent assortment & crossing over more likely)

Sex Chromosomes

• X chromosome is bigger and contains more genes than y
  • So most disorders are found on the X chromosome & less disorders passed father → son because of so few y-linked genes

• 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
  • SRY Gene: found on Y, makes males male, directs development of male anatomical features

• X chromosome contains genes for more than reproduction
  • Nervous system, light receptors in eyes (color blindness)

Inheritance of Sex-Linked Genes

• Sex-Linked Genes: gene located on either sex chromosomes, either X-linked or Y-linked

• Males and females inherit diff number of X chromosomes which results in pattern of inheritance
  • Females have two copies of sex-linked genes (23 homologous chromosomes) but males only get one copy (22 homologous chromosomes)

• Father passes Y-linked alleles to all sons but NOT daughters; mother passes X to both
  • Son can ONLY receive X chromosome from mother
    • 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

• Nondisjunction: occurs when chromosomes or chromatids fail to separate to opposite poles during meiosis or mitosis → daughter cells (or gametes) with extra or missing chromosomes https://lh7-us.googleusercontent.com/Ysg28XAi3rRqcsPv-yQcPHnkOU4faV2l7gJnch9_-7rTcHSwjc0BczUsEaNNW8vop8euw6Anbv0keykNDy2HAd_m2eY3t6fcjYTz3n3QuN5Sqicro4QpnotYbti2QzfNGCVAukAbhG_vicvEl9OvKg|

1. Meiosis: failure for two homologous chromosomes (maternal and paternal migrate along spindle fibers together) or two chromatids

1. 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

1. 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)

• Aneuploidy: genome with extra or missing chromosomes; usually caused by nondisjunction
  • Can result in monosomic zygotes (missing a chromosome) or trisomic (extra)
  • Mitosis will then spread abnormality; almost always lead to genetic disorders

X Inactivation

• During embryonic development of female mammals, one of the 2 X chromosomes does not uncoil into chromatin.

• 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

• 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

• One of X chromosome randomly is inactivated through DNA methylation and removal of acetylation on histone structure
  • After X is inactivated, mitosis results in body cells with same inactive X

• In a developed fetus, some groups with have one X inactivated and while others will have other
  • SO all cells in a female mammal are not functionally identical

X-Inactivation & Sex-Linked Genetic Disorders

• If a trait is X-linked then a male produced from a homozygous mother will always express the trait

• A carrier female (X^N X^n) should normally be normal because some of the cells will have activated X^N
  • But in (rare) case where all cells with X^N inactivated, carrier female should express same symptoms for trait as male (ex: color blindness)

https://lh7-us.googleusercontent.com/YZBM6cNqWKJ9LoQWkJx0khlLo86sCpO6SzHSNLf6HGiQHIJU3fj2gfmqcgtwlykem4n9HsG-Y6zHzNGG30GWR-bjAnaaE9wpjZukPMB4QN1T0-WIOUVt9sFFjAxQzoK1oaUvhgn2J_5EATnmaG0o-w| Case Study: Calico Cats

• Calico cats female bcuz heterozygotes inherit two X-linked alleles for hair color → some cells will express red and other black color

• Males inherit only one x-linked allele controlling hair color

Genomic Imprinting

• Only one gene is expressed and the other is silenced

• GOES AGAINST EVERYTHING: sometimes you only use the allele inherited from mom or from the dad, doesn’t deal with dominance

• Occurs during gamete formation & results in one allele silenced thru methylation (not expressed in offspring)
  • Reversed in gonads during meiosis https://lh7-us.googleusercontent.com/FlPgo4_y33Gw3XQHZIw9Zav9MSD9oMVTUVfYSBt-bUIaKOPY_8BhRQPrlvtmpsgc6rI7nVMVGX4SP5GsOAN8l06oYHqet3dkSNx7Uu37tSGdMwRsvMDepM1etABEjh0GXKJ6cN3cOnePpTfCUU3MXg|

Inheritance of Organelle Genes

• 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

• This Maternal Inheritance can trace specific genome from progeny back thru generation

 Unit 6: DNA Structure and Replication

Molecular Biology

• Chromosomes are a condensed complex of DNA & proteins that contain the genetic information passed from parent to offspring
  • Genetic material = DNA & proteins
  • Structure: chromosome → gene → DNA → nucleosome → histone proteins

• Central Dogma: DNA → RNA → proteins/enzymes → traits, metabolism, homeostasis

• Some proteins: form basic cell structure and appearance, enzymes that regulate chemical reactions that direct metabolism for cell development, growth and maintenance

• 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

Prokaryotes Vs. Eukaryotes

Replication Similarities

• Contain double-stranded DNA, RNA primers, origin of replication

Differences

Packing of Eukaryotic DNA:

• DNA usually so densely packed that it’s largely inaccessible to the replication machinery Untitled_a1baf95c2be74fad95ea92c3882c2c8f:Untitled_13|
  • Acts as a way of regulating gene expression

• Euchromatin: uncoiled, less compact interphase chromatin where DNA can be used for transcription and replication in S phase

• Heterochromatic: more dense

Untitled_a1baf95c2be74fad95ea92c3882c2c8f:Untitled_14| * Histones: proteins that pack chromatin in the nucleus of eukaryotes & condense into chromosomes; chemical modifications to histones change chromatic organization.

• Bind tightly to DNA bcuz histones amino acids are (+) charged and DNA is (-)

Nucleosomes

:tight complexes of DNA double helix in chromatin wrapped around bundle of eight histone molecules

Early Experiments

1. 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
   • Showed evidence for transformation: bacteria can absorb and express genetic info (DNA) obtained from surroundings

1. 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

1. The Hershey and Chase experiments established that DNA was the genetic material of phages
   • 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 phosphorous for phosphorus in bacteria DNA → same procedure → bacteria–not culture– was radioactive → phage DNA had entered the bacteria

1. 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)
   • Proposed that sugar-phosphate material (hydrophilic) formed the outside while nitrogenous bases (hydrophobic) were located inside the molecule

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

DNA Replication

• DNA Replication ensures continuity of genetic info

• Is made possible by base-pairing rules and uniform diameter that forms double helix

• DNA replication occurs in the 5’ - 3’ direction bcuz DNA pol can only attach to 3’ end

DNA Replication Proteins & Their Functions

“Semiconservative”

• Before duplication, hydrogen bonds between bases are broken → double strands unwind and separate into single strands → each strand serves as a template for new, complementary strand → replicated DNA consists of a single strand of old DNA (template strand) and a single strand of new replicated DNA (complementary strand) https://lh7-us.googleusercontent.com/RvCWn1GzvXNoLgLmSix-34Z9KZc1mcnWTePbA9BHLQB5PgK4kyqZiqBb7HUvcPmKtlCNTB9y-vtSF5PhKxUi9OThGGmPanj6Fhm27A9Uxvd4M6GlREnoiHAb28do-A5OkskLzR2Tk48DOsltQZEspQ|
  • This ensures that the DNA replication is identical.

• A new DNA strand is the product of both continuous and discontinuous synthesis bcuz DNA synthesis only occurs in a 5′ to 3′ direction → synthesis of a DNA strand in a replication bubble is continuous at one replication fork and discontinuous at the other replication fork

The Elegant Experiment

• After two rounds of semi-conservative replication, half the double helices will be half 15N and half 14N while the other helices will be all 14N

The Role of DNA Polymerase

DNA Polymerase I vs. III

• Both can only add DNA to 3 end

Summary: The Process of DNA Replication

1. Helicase unwinds the parental double helix at the origin of replication→ forms a Y-shaped replication fork
   • Origin of replication: short, stretch of DNA with a specific sequence of nucleotides

1. Single-stranded binding protein attaches to each strand of uncoiled DNA to keep separate

1. 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

1. 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
   • 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

1. Since DNA consists of two opposing DNA strands, uncoiled DNA consists of 3’ → 5’ template strand and 5’ → 3’ template strand

1. Leading strand: For the 3’ → 5’ strand, replication occurs continuously DNA polymerase moves towards the replication fork

1. 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
2. https://lh7-us.googleusercontent.com/TtET1WWg-NCgqb20h6jXmK591ZPns9QR7N9xLvxj-PxHEgdml3vPrZKSt4TjQLw27JNnbVVh-p1a56LsvFimh4kahIKOcPEe_A_l-UqkLJnMep3t8NfG-VP6929O0mBqnRhYXT5_otKUX8CR6dBmqQ|
   • 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'

1. RNA nucleotides of RNA Primer are later replaced with DNA by DNA pol 1

1. DNA ligase joins the sugar-phosphate backbones of Okazaki fragments and closes up gaps thru covalent bonds

Antiparallel Elongation

• 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

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

• Result: DNA loss → shorter and shorter DNA molecules with uneven ends → can trigger apoptosis

Untitled_a1baf95c2be74fad95ea92c3882c2c8f:Untitled_15| * To solve this problem telomerase attaches to the end of the template strand and extends template by adding telomeres

• 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
  • Telomerase activity declines as cells age → once stops, chromosome becomes shorter with each replication → eventually important DNA at end of the chromosome is lost → nonfunctional daughter cells
  • Telomerase activity high in cancer cells and tumors → prolongs life

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

• w/o mechanisms → accumulate cancer-causing errors https://lh7-us.googleusercontent.com/XNl68oCXOxY5yu9NmbaRjMzsR7BjzxBnKz8mZA0FOH4tElbogxTgYdNieMaK2zB_3NyZaoHS25evwSBjVS8aS6_6iDQKzixsM4a2XrDzqSveN5VvMryVMppVPfO5ka9eKtDb15k59LGTGmC1vO8zcA|

1. Proofreading: Polymerase proofreads newly made DNA, replacing any incorrect nucleotides with the correct ones

1. Mismatch Repair Proteins: other enzymes correct errors in base pairing

1. 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

• Mutations may be passed onto next generations

• Leads to genetic variation ⇒ natural selection

Helpful Images

Replication Proteins:

Untitled_a1baf95c2be74fad95ea92c3882c2c8f:Untitled_16|Leading Strand

Untitled_a1baf95c2be74fad95ea92c3882c2c8f:Untitled_17|Lagging Strand

Untitled_a1baf95c2be74fad95ea92c3882c2c8f:Untitled_18|

Overview

• 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
  • 3 Steps: Transcription ⇒ mRNA processing ⇒ Translation!

Types of RNA molecules

• The sequence of RNA bases + structure of the RNA molecule = RNA function

The Genetic Code

• Identifies amino acid specified by each of possible 64 codons combination
  • 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
    • Codon cannot code for more than one amino acid
  • 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; does not code for amino acid

• 64 ways that 4 nucleotides can be arranged = there are 64 possible codons

• Unity/Common ancestry: ~all organisms use the same genetic code for amino acids

• Aminoacyl tRNA synthetases: enzyme that recognizes the tRNAs (and their anticodons) and catalyzes transfer of specific amino acid (by acetyl group) to tRNA

• Transcription is where DNA strands are turned into RNA strands for translation to use.

1. 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, often TATA box which transcription factors bind to
   • 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

1. Elongation: occurs as RNA polymerase unzips the DNA and assembles RNA nucleotide using one strand of the DNA as a template
   • Unlike DNA replication: new nucleotides are RNA, uracil not thymine, only one and part of DNA strand is transcribed, and primers are not needed (bcuz RNA pol II can initiate synthesis)
   • Like DNA replication: nucleotides are synthesized in the 5’ to 3’ direction

1. Termination: occurs when RNA polymerase reaches a special sequence of nucleotides that serve as termination point

• In Eukaryotes, mRNA transcript must be processed before can exit the nucleus and be used for translation → Pre-mRNA longer than post mRNA

1. 5’ Cap: is added to the 5’ end of mRNA
   • Guanine nucleotide with 2 additional phosphate groups (forms GTP)
   • Capping provides stability, protection from nucleases, and a point of attachment for small ribosomal subunit

1. Poly-A-tail: attached to 3’ end of mRNA
   • Consists of many adenine nucleotides
   • 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
     • It is transcribed into an RNA sequence that signals where the transcript is cleaved and the poly-A-tail is added https://lh7-us.googleusercontent.com/C1Jxx_GMSEgcWXBd5qGpI6KYEsGh5DVcf-ue_4CxinQ5Dmb8WIT4PIOw630YimeQJfsl0H7as7T0YT3H37F6xTOVMwLLxzLOZmYyLfuV3qe7T-CoddRbmC4TgUhjJST3iF-c_WnVt-uOfKlAnJiY9Q|

1. RNA splicing: removes nucleotide segments from mRNA
   • mRNA (and DNA) contain two kinds of sequences
     • Exons: express code for polypeptide
     • Introns: intervening sequences that are noncoding
       • Allow for exon shuffling/alternative splicing
   • Uses spliceosomes: a large RNA-protein complex made on snRNA and proteins (snRNPs) that catalyzes the removal of introns & join exons

1. 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_19| * So single gene can code for proteins that are specific to cell type & developmental stage

• Often diff exon combinations code for diff subunits (4th) of same protein

• Translation is where RNA is turned into proteins for the cell to use.

• In Eukaryotes, after transcription & processing mRNA, tRNA, and ribosomal subunits are transported across the nuclear envelope and into the cytoplasm
  • In cytoplasm, a specific amino acid attaches to each of tRNAs using energy from ATP

• In organisms that lack a nucleus/nuclear envelope, like bacteria and archaea, transcription and translation can happen at the same time → quicker

• Proteins that will stay in the cytoplasm are translated into the cytoplasm.

• 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/guide polypeptides across ER membrane

Details Prelude

1. Translation has three steps: initiation, elongation, termination
   • Sequence of codons on mRNA determines the sequence of amino acids in polypeptide to be synthesized

1. Ribosome has three binding sites for tRNA
   • A site (amino acid/acceptor): accepts incoming tRNA carrying an amino acid
   • P site (polypeptide): the second position, holds tRNA with a growing chain of amino acids
   • E site (exit): in the third position, tRNA and polypeptide exit ribosome

1. Wobble: rules for base pairing between the third base of a codon and tRNA is flexible https://lh7-us.googleusercontent.com/cmOVzlWnl1-AiIjhk6UqoOrwckCQno8y64SrnyqIAut-LB65rE8Cu7y9SgzwWodpGa1r4bKcg9grIbstC_0ZH7nW66E1Oenb-HoEsHlJ2gpZjaqSDXy2_BHujctUEkGM5KQ0a494CNrvtNe4Fq3KTQ|
   • So there are fewer tRNAs than possible amino acid codons

1. Energy for translation is provided by GTP at each stage
   • GTP energizes the formation of the initiation complex, using initiation factors.

1. Once polypeptide is completed, interactions among amino acids give it its secondary and tertiary structures + processes by ER or Golgi body may make final modification before the protein can function
   • A protein’s size and function is determined by the size and chemical properties of its amino acids

Process Steps

1. 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
   • Large ribosomal subunit attaches to the mRNA with the tRNA → ribosome fully assembled with tRNA occupying the P site

1. Elongation: continues as each tRNA delivers an amino acid one by one according to mRNA sequence Untitled_a1baf95c2be74fad95ea92c3882c2c8f:Untitled_20|
   • 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
     • Removes the polypeptide from the tRNA in the P site and attaches it to the amino acid on the tRNA in the A site
   • Ribosome translocates the empty tRNA in the P site to the E site & tRNA in the A site to the P site
     • This leaves the A binding site empty → new tRNA can arrive

Termination:

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, last tRNA, and two ribosomal subunits are released

• Ribosomal subunits can attach to same or another mRNA and repeat the process

Process Efficiency

• Transcription: Multiple RNA polymerase complexes can transcribe the same gene all at once, → cells can make many mRNA copies of a single gene.

• Translation: Multiple ribosomes can translate the same mRNA all at once, lined up one behind the other → cell can make many copies of the same protein at a time
  • Hydrolysis of GTP increases the accuracy and efficiency

Ribozymes

• RNA molecules that function as an enzyme!

Structure and Functions:

1. Have specific catalyst activity bcuz of HB and functional groups

1. Catalyze formation of peptide bonds and removal of introns

Prokaryotes vs. Eukaryotes

Transcription

Translation

• Both need tRNAs, amino acids, ribosomal subunits, polypeptide factors, and GTP

Untitled_a1baf95c2be74fad95ea92c3882c2c8f:Untitled_21|Big Idea: How can Two Cells With Same Genome Function Differently

• 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
  • The unique expression of genes allow cells to carry out their specific function

• Cells are always modifying activities to respond to internal and external conditions → so exist mechanisms to turn genes on and off at appropriate times

Bacteria

• Coordinately controlled genes clustered in operon regulated by one promoter

• Prokaryotic regulation mostly at transcriptional level
  • Prokaryotes don’t have RNA splicing or chromatin modification

Operon

• “Unit of DNA that contains functionally related genes that can be coordinately controlled by “on/off” switch”

• Benefit of Operons: better coordination and control → can regulate cluster of functionally related genes with single on/off switch
  1. Promoter: sequence of DNA to which RNA polymerase attaches to begin transcription
  2. 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
  3. 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
  4. Regulatory gene: lies outside operon region → produces a regulatory protein that binds to operator region and controls whether RNA polymerase can begin transcription
  5. Regulatory proteins are allosteric, can be one of two kinds
     • Repressor protein: blocks attachment of RNA polymerase to promoter region
       • 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
  6. Corepressor: small molecule that binds to and activates a repressor protein to switch an operon off
• Untitled_a1baf95c2be74fad95ea92c3882c2c8f:Untitled_22| Types of Regulation Negative Regulation: Repressible and Inducible Operons
  • 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_23|
  • 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.
• Positive Gene Regulation
  • Gene regulation positive bcuz activator regulatory protein directly interacts with operon to increase transcription
  • 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
  • Glucose lvls high → cAMP lvls are down → CAP is inactive
  • Glucose lvls low → cAMp lvls are high → CAP is activated
• 3 Examples of Gene Regulation
  1. 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.
  • 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
  • Bcuz repressor protein is involved → negative regulation
  1. 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't need to make it → amino acid acts as a corepressor by binding to and activating the repressor → repressor binds to operator → prevents transcription
  • Produced enzymes are repressible enzymes and operon is repressible operon
    • Bcuz there is repressor protein → negative regulation.
  1. 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
• Eukaryotic Gene Expression Regulation
  • Eukaryotic gene expression regulation is more complicated because…
  1. Multicellularity: requires different gene regulation for diff cell types
  2. 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
  1. Uncoupling of transcription and translation: Allows for a greater range to control gene expression.
  • Genes are expressed when their nucleotide sequence are transcribed to produce RNAs
• Eukaryotes: Coordinately Controlled Genes
  • 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
• Untitled_a1baf95c2be74fad95ea92c3882c2c8f:Untitled_24|
  • 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
    • Steroid hormones act directly
    • Protein hormones act indirectly via a signal transduction pathway
  • Genes with same set of control elements are activated by same chemical signals

1. DNA Methylation:
2. Histone Acetylation
3. 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
• 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
  • Appear in clusters and order on DNA controls order of expression and timing of body part development

1. X inactivation:
2. Transcription Initiation:
3. Coactivators & Mediators: additional proteins that contribute to the binding of transcription complex components
4. RNA processing/Alternative Splicing:
5. 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.
6. Untitled_a1baf95c2be74fad95ea92c3882c2c8f:Untitled_25|
   • MicroRNAs (miRNAs): Functions in RNA silencing and post-transcriptional regulation of gene expression.
     • Degrades mRNA if bases are completely complementary, If the match is less than complete, then translation is blocked
7. MRNA degradation: occurs bcuz of RNAi and bcuz mRNA are unstable molecules
   • 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
8. Protein Degradation: final stage of proteins; as proteins age, they lose functionality as 3D shape changes → nonfunctional proteins marked for destruction with protein ubiquitin
9. Protein Processing: protein chemical modification can activate/inactivate protein by adding/removing phosphate
10. 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
  • Do not alter DNA sequence,
• Can affect gene expression through reversible modifications such as…
  • Histone acetylation, DNA methylation, genomic imprinting, X-inactivation
• Regulation of Chromatin Structures Untitled_a1baf95c2be74fad95ea92c3882c2c8f:Untitled_26|
• Histone modification: change in the organization of histone proteins with DNA.
• Access to DNA for transcription can be affected by..
• Acetylation: enzymes add acetyl to histones → histones loosen grip on DNA → DNA uncoils → activated transcription
• Methylation: enzymes attach methyl groups (-CH3) to histone proteins → histones tighten grip on DNA → preventing DNA from uncoiling and being expressed → repressed transcription
• Protects against restriction fragments; DNA methylation inactivates genes (long-term)
• Regulation of Transcription Initiation
• After chromatin modification, transcription is next point of regulation
• Transcription Initiation Complex: group of proteins associated with RNA pol II and inhibit/promote activity → make region of DNA more/less able to bind to transcription machinery
  • 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
• General transcription factors: proteins required by all transcription events to initiate transcription
  • 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
    • 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
• Enhancers: Distal control elements grouped together
• Particular combination of control elements in an enhancer associated with a gene
  • Diff combination → diff regulation of transcription
• Transcription Factors Structure
• Usually have DNA binding domains and binding domains for other transcription factors
• Transcription factors as repressors:

1. Bind to enhancers and block activators
2. Silencing: bind to chromatin structure and remove acetyl

• The Steps of Regulation of Transcription & Transcription Initiation Complex Untitled_a1baf95c2be74fad95ea92c3882c2c8f:Untitled_27|

1. Enhancers bind to activator
2. 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
3. A transcription initiation complex is formed → initiate transcription

• Cellular Specialization/Differentiation
• Cell Differentiation: Process in which cells decide what kind of cells as cells become tissues, tissues become organs, and organs become organisms (us)
  • Always involves master-regulatory genes that produce tissue-specific proteins → give cell structure/function and commit cells as specific types
• Determination: Embryonic cells become committed to a certain type/fate
• 3 Processes of embryonic development:

1. Cell division
2. Cell differentiation: results from genes being regulated differently in each cell type
   • Example of how gene expression regulation affects cell long-term behaviour
3. Morphogenesis: pattern formation and shaping of an organism

• Specific genes expressed in cell during development determine cell type
• Cell can receive external and internal cues that cause regulation of gene expression by turning genes on/off
• External: cells receive signals from extracellular environment
  • Adjacent cells: ex: binding of growth factors
  • Environment: temperature can trigger cellular response
• Internal: signals come from inside cell
  • Cell signals to itself and Cytoplasmic Determinants

1. Cleavages don't divide cells equally → cells acquire variations based on orientation of cleavages
2. Cytoplasmic Determinants: eggs cytoplasm contains RNA, protein, and nutrients encoded by mum DNA
   • 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
3. 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
     • Cells closer receive more than cells farther away
4. Apoptosis: some cells produced during development have temporary role and are deliberately destroyed
   • Ex: during early stages have webbing but later cells undergo apoptosis

Stem Cells: unspecialized cells during early stage of embryonic development that can reproduce indefinitely and differentiate (become any) into specialized cells Untitled_a1baf95c2be74fad95ea92c3882c2c8f:Untitled_28|

• 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

• Process is self-reinforcing as the cell can signal to itself
• 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) * Adult body stem cells: can only replace non-reproducing specialized cells (not sperm and egg) * Pluripotent: can become any type of cell * Totipotent: cells that can form new fetus * 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 * Morphogenesis, Pattern Formation, and Axis Development

• Pattern Formation: the process of organizing tissues and organs that begins in early embryo
  • Various genes code for pattern formation of organisms
• Positional Information: molecular cues that control pattern formation, tells a cell its location relative to the body’s axes and to other cells
• Maternal effect: offsprings axes encoded by mother’s genes (ie. Cytoplasmic determinants),
  • So mutations passed to all

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
• Transfer of DNA segments can happen naturally thru viral transduction, bacterial conjugation, or transposons & regular event in eukaryotes they crossing over
• Recombinant DNA can be produced artificially with biotechnology: use of biological systems to modify organisms or produce desired products

• Procedure that allows DNA fragments or genes to be copied

1. 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
2. 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
   • 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
   • lacZ gene: codes for enzyme that breaks down lactose
     • Also breaks down artificially made X-gal
     • The one restriction site for the restriction enzyme occurs in within the lacZ gene
3. Mix the cut foreign DNA with cut plasmids. This allows base-pairing at the sticky end
4. Apply DNA ligase to stabilize attachments and close up the backbone. Forms recombinant plasmids (some plasmids will not pair)
5. 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
  • Competent: change in structure and permeability of cell membrane

1. 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 )
• Purposes of Gene Cloning: to make many copies/amplify particular gene and to produce a protein product from it
• 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
  • 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
  • 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

• PCR: a technique that makes large number of DNA copies faster than DNA cloning process

1. DNA is heated. Heating denatures (separates) hydrogen bonding holding the dsDNA together and forms two ssDNA molecules
2. 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)
3. 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
   • In the end one initial dsDNA becomes two dsDNA
4. Repeat the above steps. Increases the number of DNA molecules exponentially

* Expressing Cloned Genes Bacterial Expression Systems

• 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.
• Bacteria have same mechanisms for replication & transcription so can express eukaryotic genes
• Eukaryotic Expression Systems
• Electroporation: Method of introducing recombinant DNA into eukaryotic cells → electrical pulse applied to cell → creates temporary holes in its plasma membranes so DNA can pass thru
• Introduced DNA is incorporated into a cell’s genome by genetic recombination, then it can be stably expressed by the cell
  • 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
• 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
  • 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
• Diagnosis and Treatment of Diseases
• Can use PCR with primers that target the genes associated with these disorders → amplified DNA product is then sequenced to reveal the presence or absence of the disease-causing mutation
• Personal Genome Analysis
• Mitochondrial DNA is contributed to the egg only by the mother → trace ancestry
• Personalized Medicine
• 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
  • Humans share 99% DNA, differences caused by variation of nucleotide bases
• 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
• CRISPR-Cas9: edited cells from sickle-cell proteins with some success
• Small Molecules and Drugs
• Some drugs that combat tumor cells are small molecules that can inhibit a tyrosine kinase
• But bcuz tumor cell have random mutations bcuz of high rate of division → drug resistance
• Protein Synthesis
• Scientists can use organisms to produce lots of protein products
  • Human insulin gene cloning: insulin gene is inserted into bacteria; bacteria multiply and reproduce human insulin protein for use in treating diabetes

https://lh7-us.googleusercontent.com/QI-JIPiZly-gmvSk3mWeUetRbV1Qp1-FFn77jDQTItNiW_g9Q-grbpFNE8APXLGfI_M-LzfyFvpUgBDMFykkrAvkdBBB5WtoI5ZzxeU2bfHFpa9yoKK-qu2blGV03CJCM_VMTgJUS_Bl7frF5l0NaQ|

• Gel Electrophoresis: a procedure that separates restriction fragments

1. 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
2. Since DNA is (-) charged (bcuz of phosphate groups) it moves towards (+) electrode
3. Shorter fragments move further thru the gel than longer, heavier fragments
4. Uses process to compare DNA fragments of presumed closely related species to determine evolutionary relationships

• 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)
  • Fragments called restriction fragment length polymorphism (RFLP)
• In DNA fingerprinting, compare produced RFLPs to find match

1. Pharmaceuticals: DNA cloning allows quick and inexpensive production of pharmaceuticals

• 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

1. 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?)
  • Should medical insurances know they are high-risk patients?

1. 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.
       • 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
   • 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)
       • 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

1. Reproductive/Gene Cloning: process uses somatic cell nuclear transfer → Nucleus from a somatic cell taken from differentiated adult cell of desired animal replaces nucleus of unfertilized egg cell→ creates a clone of desired animal
   • 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

Reasons for Cloning problems

• Changes in the genome of nuclei of a fully differentiated cell from donor animal must be reversed for genes to be expressed
  • Can result in abnormal regulation due to variant methylation

• 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
  • Alterations in DNA can lead to changes in type or amount of protein produced

• DNA mutations can be positive, negative, or have no consequence; effect is determined by environmental conditions (usefulness of a mutated phenotype determined by natural selection)

Causes for Mutations

• Mutagens: radiation or chemicals that cause mutations → damage DNA (ex: deamination, double strand breaks)
  • Carcinogens: mutagens that activate uncontrolled cell growth (cancer)

Environmental:

• UV light → forms dimers; radiation (X-rays); chemical mutagens

Internal:

• Errors in DNA replication, proofreading, or repair

Point Mutation: single or few nucleotide errors that include…

1. Substitution: when DNA sequence contains an incorrect nucleotide instead of the correct one

• 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

1. Deletion: when a nucleotide is omitted from the nucleotide sequence → missing amino acid

• Deletions closer to start point of coding are more harmful

• Can occur when homologs don’t align properly

• An amino acid deletion will alter the primary, secondary, and tertiary structure → can’t fold properly → nonfunctional

1. Insertion: when a nucleotide is added to nucleotide sequence

1. 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

Effects of Point Mutations

• Point mutations may or may not have a significant phenotypic effect.
  • Depends on whether amino acid had important chemical properties or part in proteins structure
    • Might change the lvl of protein activity bcuz might substitute an amino acid in the active site.

1. 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

• Wobble Pairing: relaxed requirement for in the third position nucleotide

1. 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
  • Ex: hemoglobin protein that causes sickle-cell disease

1. Nonsense Mutation: when new codon codes for stop codon

• Causes translation to be terminated early → resulting polypeptide is shorter → usually nonfunctional

Alterations to Chromosome Structure:

• Chromosomal aberrations occur when chromosome segments are changed, often result of crossing over errors

• Duplications: broken DNA fragment reattached as an extra to chromatid resulting in repeating segment
  • 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

• 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)

• Translocation: two nonhomologous chromosomes cross over which shouldn’t
  • A parent with balanced translocation has chance to produce offspring with deletion or duplication

https://lh7-us.googleusercontent.com/fIVBaHLN-0-0u3Qeie3rYXTxPWdy57y4qmm3MVtgyTtCwVi3HUFVmiP23hb2RyktosGpNZ_-FtI15jiFvwcJ1tJ4DA51JnIjvh_BfRX9DRhI7R8CnjauGSL8geQkYiylFoRcEbO0ESRUHOvEpn_tNQ| Notes

• Random mutations = source of new alleles = new phenotypes

• Deletion and duplication more common during crossing over when non-sister chromatids exchange unequal amounts of DNA

• Translocations during mitosis can cause some cancers

• Deletions and translocations more lethal
  • Syndrome = not as lethal, group of traits caused by gene mutation or chromosome alteration

• Translocations and inversions don't usually alter phenotype

Human Genetic Disorders

1. 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

• Tay-Sachs Disease: nucleotide insertion → lysosomes lack functional enzyme to break down glycolipids → fat accumulate → death

1. 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)
  • 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

• Klinefelter Syndrome: occurs when XY or XX, produced as result of nondisjunction, combines with normal gamete to form XXY zygote (male with extra X)
  • Only affects male → still male as long as you have Y chromosome with the SRY gene
    • Explains how there can be male calico cats
    • Might express female secondary sex characteristics

Transfer and Sharing of DNA: Prokaryotes Vs. Eukaryotes

https://lh7-us.googleusercontent.com/o-Ouk4M64uSRy97ehKQS48RCpg0i37TB7EO8I6MtJZIhZXZAxjCcoGPw9LbLqe242WvhDYIWAmr7Wxd3m2M2dXBmf75oHIWp6ITRMQIGsQ_SmFpzD0rLpVf_oHL8flfTlmuMwwhG5zffvToFiq3tYQ| Bacteria: 3 Methods of Transferring DNA

1. Transduction

• Viruses that infect bacteria (bacteriophages) move DNA from one bacterium to another “by accident.”

1. Transformation https://lh7-us.googleusercontent.com/rfjo1I7vqBppXqW8kT0FldG_YGQlu4_sIdAfFunUJN_avM3t9htBW2e5EJQVAnLhSQiiFBCbz_DLcoBWzphEPD3muuVpGkSf6orkq7KfJZ-ReH4AGajSgAOB1dmKBaakwXbHq6R1_HtqKnybHk_CrA|

• Bacteria takes in DNA from its environment,

• DNA often from other bacteria as a plasmid

Which can be copied and passed onto descendants

1. Conjugation

• DNA is transferred from one bacterium to another. https://lh7-us.googleusercontent.com/c9sRo-qBm34jQnm7gDyqi6y-brJVzOTkJ4inWzTHJfiKuodSUIhVWvzdKVfsnuj9fhL7bbysEV1Gp6qqXxmyT2olwP7RYWygyyX0OAZ9MGnaxwSyeloiRSRvUx6I7QC3XG5-AHHnJI9-3ep87480Wg|

• Donor cell (F+) uses pilus to transfer DNA from its cell to recipient cell (F-) → recipient becomes donor
  • Usually DNA is in the form of a plasmid

• 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

Horizontal Gene Transfer:

• Horizontal Gene Transfer: transmission of DNA between different genomes
  • Source of genetic variation in bacteria: horizontal gene transfer & mutations
    • 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; chloroplasts, nucleus, & mitochondrion

Virus Function

• Virus: small nucleic acid genome enclosed in capsid

• Penetrates cell → takes over metabolic machinery → assembles new virus copies

Virus Structure

https://lh7-us.googleusercontent.com/spN336V0HMmovdccgZ05exqiu4ny9RFeELYggAUQ1LjQPxPv6-Ih_s1cZ4ZdJYg8HayEzRPgm-aqLIgj1Gxm4vkbmyll9-umb2vqDhmg8aXmSgC4OWg7bJ7KsCoNSTh75gHvW95b_fid8XO3a04W_w| - Nucleic Acid: either RNA or DNA which contains viruses information to make progeny

• DNA/RNA may be double-stranded or single-stranded

1. Capsid: viral protein coat enclosing genome, determines genomes size/shape and specificity

1. 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

• Antibiotics don’t work on viruses bcuz don't have a cell wall that can be targeted

Types of Viruses

• 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: infect bacteria, most complex

• Simpler Viruses
  • Viroids: infect plants, just floaty RNA (no capsids)
    • Plant infections spread by plasmodesmata
  • Prion: infectious misfolded proteins that can transmit incorrect shape

Viruses and Evolution

• Rapid evolution bcuz produce many copies over short time & less proofreading → mutations can be passed on

• High rate of mutation increase pathogenicity bcuz host populations don’t evolve defense as fast as viruses evolve
  • Viruses mutate and evolve quickly → new strains on regular/seasonal basis

• Genetic material of different but related viruses can combine when present in host cell → produce new virus

Living or Nonliving?

• Living characteristics: have DNA or RNA, can reproduce/replicate, metabolic activity, and genetic recombination but only in hosts cell

• Nonliving: are not cellular

Replication of Viruses

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

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
  • So cycle technically in between phase
• Untitled_a1baf95c2be74fad95ea92c3882c2c8f:Untitled_29|

RETROVIRUS SYNTHESIS:

• Retrovirus: ssRNA animal virus

1. Glycoprotein plasma membrane of virus fuses with that of the cell (virus enters cell)

1. The virus contains protein capsids, RNA, & reverse transcriptase which it releases into the cytoplasm of the host cell

1. Reverse transcriptase makes DNA complement strand from RNA

1. dsDNA strand transcribed immediately to manufacture mRNA (lytic) or be incorporated into the host genome (lysogenic)

• Ex. HIV: makes an envelope and leaves through exocytosis

• Over time eats up the host’s membrane destroying the immune system

Review

• Basic idea: “Descent with modification, change in genetic composition over time from generation to generation”

• Specific: the process by which frequency of heritable traits in population changes from one generation to the next

• A population is evolving if their allele frequencies are changing
  • Model for evolution: survival and reproduction

Evolution: Earlier Theories

1. Use and disuse: describe how body parts of organisms can develop with increased usage while unused parts weaken → idea was correct like among athletes

1. Inheritance of acquired characteristics: described how body features acquired during an organism’s lifetime (ex: muscle bulk) could be passed onto offspring → idea was incorrect bcuz only genetic material of cells can be passed on

1. Catastrophism: The reason for different fossils in different strata of rocks was because of mass extinction events (true)

• Strata: layers of rock

Evidence for Evolution

1. Paleontology: provides fossils of extinct species → changes in species and formation of new species can be studied
   • Fossils removed from successive layers of sediment (deeper = older) show gradual changes alternating with rapid changes
     • Large, rapid changes produce new species
   • Age of fossils determined using C-14 dating; older = less C-14

1. Biogeography: the study of the distribution of species → reveal that unrelated species in different regions in the world look like when found in similar environments
   • Ex: rabbits did not exist in Australia until introduce by humans → native Australian wallaby resembles rabbit both in structure and habit

1. Embryology: reveals similar stages in development among related species → similarities establish evolutionary relationships
   • Gill sites, arches, and tails are found in mammal embryos

1. Comparative Anatomy: describes two kinds of structure used to establish evolutionary relationships among species + there are heritable variations among individuals

1. Homologous Structures (homologies): body parts that resemble one another in different species because have evolved from a common ancestor
   • 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
   • 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
   • More recent homologous characteristics shared by smaller group

1. Analogous structure (analogies): body parts that resemble one another in different species, not because evolved from common ancestor, but because evolved independently as adaptations to similar environment (similar structure and function)
   • 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
     • Homoplasy: trait species share due to convergent evolution

1. 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
     • More than 98% of sequences in humans and chimpanzees are identical
       • Shows how morphology is not only way
     • Distantly related species have different DNA bases and lengths bcuz of deletions & insertions
   • Molecular data more accurate/reliable bcuz directly shows genetic makeup
   • Bcuz of redundancy of the genetic code, gene bases in different species can differ slightly and produce same protein

Use base sequences NOT base-pair percentages to infer relatedness

• Process in which individuals with certain inherited characteristics are more likely to survive in an environment, reproduce and pass on those traits → traits have selective advantage
  • 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's fitness (relative ability to survive and leave offspring)
  • Environment favors a trait = trait increases individuals fitness → selection is said to act for that trait
    • Selection also acts against unfavorable traits

Observations for Evolution

1. Populations possess enormous reproductive potential

1. Resources are limited. resources don't increase as populations do

1. Individuals compete for survival. Overproduction = competition for available resources

1. 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

1. Only most fit individuals survive. “Survival of the fittest'' occurs because individuals with traits adapted for survival and reproduction are able to out-compete other individuals for resources and mates

1. 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

Key Features of Natural Selection

• Natural selection acts on phenotypic variation

• Overtime can increase the frequency of desirable traits → adaptive evolution

• If environment changes or individual moves → apply new selective pressures → the process may result in new adaptations & species

• Individuals DO NOT evolve – populations do

• Process of editing species, not creating

• Evolution by natural selection can occur quickly in fast multiplying species bcuz mutations are common → produces genetic variation

• Natural selection limited to modifying structures already present → not perfect

• Evolution by natural selection is a blend of chance and “sorting”
  • Chance in the creation of new genetic variations (as in mutation) and sorting as natural selection favours some alleles over others.
  • Because of this favouring process, the outcome of natural selection is not random.

• Genetic Variation: difference in DNA bases or sequences
  • Genetic variation enables evolutionary responses to environmental change
  • Evidence of genetic variation: diff genotypes or phenotypes

• Natural selection acts on variation among individuals in the population and arises by…

1. 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
     • All new alleles are the result of nucleotide variability

1. Sexual Reproduction creates individuals with new combinations of alleles; Genetic recombinations comes from:
   • Crossing Over; Independent assortment of homologous chromosomes; Random joining of gametes

1. 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

1. Outbreeding: mating with unrelated partners increases the possibility of mixing different alleles and creating new combinations

1. 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
   • Examples of polymorphism (2 or more diff phenotypes) can be maintained by

1. Hybrid Vigor (Heterosis): superior quality of offspring resulting from crosses between two diff inbred strains of plants
   • 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

1. 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

1. 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
     • Ex: rarer prey escape predators
       • Maintain multiple phenotypes (and their alleles) that alternate between high and low frequencies

What Decreases Variation

• Stabilizing selection, sexual selection/nonrandom mating, genetic drift

Neutral Variation

• Not all variation has selective variation → some (especially at molecular level in DNA and proteins) is neutral variation
  • Ex: differences in fingerprint patterns

• Environment determines whether variation is neutral or has selective value

Humans Impacting Evolution

1. Monocultures: only grow one type of crop → reduce genetic variation bcuz only a few varieties of many wild varieties of plants are used
   • Monocultures have no genetic variation and are susceptible to changing environmental conditions

1. 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

1. Artificial Selection/Selective Breeding: breed individuals to produce desired traits
   • Similar to Natural Selection: Needs genetic variation
   • Different to Natural Selection: Humans (not environment) does the selecting

• 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, there is no evolution
    • But allele representation in generations might differ

• In most natural populations, the conditions of hardy-Weinberg equilibrium are not obeyed
  • 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

• If allele frequencies are changing then one of these are likely being violated

1. No natural selection (all traits are selectively neutral)
2. No mutations
   • Gene pool modified by mutations
3. No gene flow (the population must be isolated from other populations)
   • Moving alleles in and out of a population can alter allele frequency
4. No genetic drift (The population is large)
   • In small populations, allele frequencies fluctuate by chance
5. No sexual selection (mating must be random)

Values of Genetic Equilibrium

1. Allele frequencies for each allele (p,q)
2. Frequency of homozygous dominant (p^2) and homozygous recessive ( q^2)
3. Frequency of heterozygous [2 diff alleles] (2pq)

2 Equations

1. p + q = 1 (all alleles sum to 100%)
2. p^2 + 2pq + q^2 = 1 (all individuals sum to 100%)

Steps

1. Find percentage of homozygous recessive
2. Square root q% (as decimal) → q
3. 1 - q = p
4. Can use q and p to find homozygotes and heterozygotes

Causes for Changes in Allele Frequencies

• Multiple factors, together with natural selection, cause evolution

1. Natural Selection: increases or decreases allele frequencies bcuz of impact of environment
2. Mutations introduce new alleles that may provide selective advantage
   • WEAK force for changing allele frequencies; STRONG force for creating new alleles
3. 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
     • Ex: pollen transferred from one population to another
     • Tends to reduce the genetic differences between populations
4. 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
     • Decreases genetic variation & evolutionary adaptability and increases homozygosity
5. 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
     • Population tends to have reduced genetic diversity
6. Bottleneck: when the population undergoes dramatic decrease in size (predation, catastrophe, disease) → becomes susceptible to genetic drift
7. 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
8. Inbreeding: individuals mate with relatives
9. Sexual Selection: process in which individuals with certain inherited characteristics are preferred as mates
10. Intrasexual Selection: Individuals of one sex compe2te directly for mates of the opposite sex.
11. Intersexual Selection (mate choice): females choose males based on attractive appearance or behaviour
    • Leads to sexual dimorphosim:

Extra Notes

• Fixation: when one allele goes extinct and only one remains (becomes fixed)
  • → all individuals will be homozygous for allele

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.

• 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

• Phylogenetic species concept: set of organisms with unique evolutionary history

Notes

• Speciation: formation of new species
  • Reproductive isolation is main measure for speciation; can involve changes to 1 gene

• In order for speciation to happen, there must be something that prevents interbreeding between closely related population or species → Reproductive Barriers

• If two groups are reproductively isolated, they can accumulate allele differences and eventually diverge

• Reinforcement: Natural selection for traits that prevent interbreeding among populations
  • 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
  • Reduces species diversity

Methods of Speciation

1. 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
   • Gene flow is interrupted when a population is geographically isolated → reproductive barriers form and maintain speciation → gene pool/allele frequencies in two
   • populations can diverge bcuz of diff selective pressures
     • If gene pool diverges enough then interbreeding will not occur if barrier removed
   • Geographic barriers lead to reproductive isolation & barriers that prevent interbreeding:
     • Ex: Species that were seperated cannot breed when meet each other again

1. 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…
   1. Sexual Selection:
   2. Habitat differentiation: When subpopulation exploits habitat not used by parent → natural selection can act
   3. 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
   4. 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
        • Unlike animals, plants more tolerant to changes in chromosome sets
      • https://lh7-us.googleusercontent.com/mC8jsW3mhio7rCxAcMdXE9W8k9_PGj18V83LGgw6TfcNM7RFDqefVWAlOTL41FBJNY09-UYLfx9ptJukLh83uMVAyCpAdl9cCFiXvUz2fArE9Rzk-X0ajZbm8xo66z01DAzycE1HshpIW7NuTesLqg|
      • Ex: Tetraploid plant produces gamete (2n) that fuses with normal gamete from same species (n) → nonviable/infertile triploid plant
        • Bcuz tetraploid & diploid species cannot produce viable offspring = diff species
          • Thus speciation can occur over single generation
   5. Hybridization: two different species mate and produce offspring along geographic barrier called hybrid zone https://lh7-us.googleusercontent.com/2Pzz5IT73e3KpsUsVLKgIj7ln6r_m0h0BP65alUig92w7RBK2Q2K4MWkiAg91fDaf0oFpvW7J2UkxWICgZcJ4ugummabNwOj1A7niI24OElVHZK4a9il8cgta8yY8fdUMCGMTnIioWxgY7wQDv8vPA|
      • 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
      • Hybrid Zone: place where two different species meet and mate
        • Form when two species do not have complete reproductive barriers

1. 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
   • Ex 1: 14 species of Darwin's finches on galapagos islands evolved from single ancestor
   • Ex 2: adaptive radiation occurred after mass extinctions → many species go extinct → periods with ecological opportunities for species to colonize → colonization led to competition → promotes speciation

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
  • Ex diff species of hummingbird prefer one type of coloured flower and thus only pollinate those

1. Prezygotic Isolating Mechanisms: block fertilization from occurring
   • If populations do not attempt to breed, then is not considered prezygotic mechanism

1. Genetic Incompatibility: can't reproduce bcuz proteins or chromosomes incompatible
   • Sometimes when occurs in plants, they can self-pollinate and become new species

1. Habitat isolation: occurs when species do not encounter one another

1. Timing Isolation: occurs when species mate, flower, or are active during different times
   • Ex: nocturnal and diurnal animals

1. 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

1. Mechanical/Anatomical isolation: when male and female genitalia are structurally incompatible or flower structures select diff pollinators

1. Gametic Isolation: when male gametes do not survive females environment or failed recognition

2. Postzygotic Isolating Mechanisms: mechanisms that prevent formation of viable progeny

1. Hybrid Inviability: when zygote fails to develop properly and dies before reaching reproductive maturity

1. Hybrid sterility: when hybrids grow to be adults but are sterile
   • Hybrid sterile bcuz chromosomes can’t pair up correctly during meiosis.

1. Hybrid breakdown: when hybrids produce offspring with reduced viability or fertility

Directional, Disruptive, and Stabilizing Selection

• Different ways environment/natural selection can act on a phenotype

• 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

• 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
  • 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

Patterns of Evolution

1. Divergent Evolution: species that originate from a common ancestor become increasingly different over time
   • Might happen because of allopatric speciation or sympatric speciation

1. 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

1. Convergent Evolution:

1. Coevolution:

Microevolution vs Macroevolution

1. Microevolution: describes how the population of organisms change from generation to generation (how allele frequencies change)

1. Macroevolution: describes general patterns of change in groups of related species that have occurred over broad geological time; evolution of new species
   • Different interpretations of fossil evidence have led to 2 contrasting theories for the pace of macroevolution

Patterns in Fossil Record

1. Phyletic Gradualism: argues that evolution occurs by the gradual accumulation of small changes
   • Individual speciation events occur of long periods
   • Fossils then reveal only major changes in groups → intermediate stages of evolution not represented and shows incompleteness

1. Punctuated equilibrium: argues that evolutionary history consists of long periods of with little evolution, then interrupted/punctuated by short periods of rapid evolution (new 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

• “Evolutionary history of a species”
  • Determined through fossils, homologous structures, morphology, & molecular biology

1. Taxonomy: classification of organisms; organisms are classified into categories called taxa Hierarchical Classification

• Each taxon more inclusive than the other
• “Dumb Kings Play Chess On Fine Green Sand” https://lh7-us.googleusercontent.com/U-dZ8yQXFguTIy2AYtI40u25XaRLtXHwcWpcZW8IHC_5MXxy3lECWU_cttwHUte8WlnsHszJ8kOj2tDQi1bCSyXVvqAQTnrJHmYvqmSFrfHrJIJyrPaHjg7o-FU6GN7HQqtZ_GCmXdU7p17K3zs67Q|

1. Species: group of closely related organisms that can reproduce
2. Genus: phylogenetically closely related species
3. Family: Genera that share same features
4. Order
5. Classes:
6. Phyla:
7. Kingdom
8. Domain
9. Phylogenetic Trees

• “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
• Basal taxon: group that diverges early on
• Tree shows pattern of descent, NOT phenotypic similarity
• Branch length = estimated amount of evolutionary change or time

1. Cladistics https://lh7-us.googleusercontent.com/J8E-WBOpkilaMzUjyd0thN5HX5lEdBe3Umh7DkoAL34ouUFb-XFOaGKjsllTTbKRk4C7V3Z0OcrGpKxiCcA5K1vbFC2zXgAfzkGhgVJAg8rOo2v2eS6aN3VwYhCWFx8rBkzYG3Nr-aBNQfvNa5Rorw|

• 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
  • Branches determined by comparing number of derived characters in each taxon
    • More primitive = earlier 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
• 1 https://lh7-us.googleusercontent.com/03J3d1KYL3dEC879aEPpn6h9PMrjhx2qikfVDouEFkNx8JDImp76voqAH43A5spUaFasENqJzBHVvOHVin-b81lkalNccykCVnYLwAh2enYS3Lf5mA0fa0eJtd-3GMbQQkaIOpQ-f4BpIAjpISROHg| https://lh7-us.googleusercontent.com/sdooiUd99_5b2qtuR8ENIB2SdZ2Bv3hcTczeHKTXOfxsqLlahBZS-WlevXqTmug0nv5_vcdUHsP94YsIUb4frzjFJj1T78rZV-0fJwvkMQ5VytAYs07K1Ny30YyTZR4Xo8cT-9RqG1Ivae4GoLqOlg| https://lh7-us.googleusercontent.com/Ga6V9aahWEwE46ufyXa-hyqqxlqLe19AgkpOL7fDhovAeElWGQkbLrHFN-NVE8TWTqItw986pKDwSZ9vpFgJOTK1cRBIvJ9blnEhy3MfL5KPyUpjRoExJY6URRJNq6lMdnf4x-dwF7YFbgUTdFRUGQ|
• Node represents species → all three species are descended from it

1. Types of Clades

• Monophyletic: ancestral species & all of its descendents (best!)
• Paraphyletic: ancestral species & some of its descendents
• Polyphyletic: includes distantly related species but not recent common ancestor

1. Shared Ancestral & Shared Derived Characteristics

• 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

1. https://lh7-us.googleusercontent.com/3qwOvHEzF-ERhKqPVl84fjE9wzRUBNIr5uveBC5Rp7dIWGINLLA1TFNguhqU-z8k-BpKT5MI7XJhD6-jnJDRQJ-M92JMk-sCrPu9ce5xd94bmj30BujGnPsJ9zt3EErvL4dORd1PkzDiMyqHW8fDLw| Maximum Parsimony: simplest explanation is usually most correct one

• Most parsimonious tree is the one with the less amount of changes
• This tree is less parisomus bcuz assumes that jaw evolved twice

1. Evolution and Genome

• Comparison of nucleic acids can show relatedness
  • Ex: between humans and fungi
• Diff genes evolve at diff rates = molecular trees represent short/long period of time
  • rRNA changes slowly→ investigate events that happened long time ago
  • 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
  • Pseudogenes: Paralogous genes that have lost function of coding for functional gene product (vestigial)
    • Over evolution will have high mutations
• Nucleic acids are poorly conserved
  • Conserved = few changes over time
  • Poorly conserved homologous genes used to relate distant species

1. Molecular Clocks

• “Method of estimating past evolution events based on pattern of neutral mutations”
  • Mutations in genes make it accurate and natural selections makes inaccurate

1. The earth and its atmosphere formed
   • Primordial atmosphere made mostly of CO2 and N2 but little O2 → lots free energy
2. Primordial seas formed
   • As the earth cooled, gasses condensed to form seas
3. Organic molecules were synthesized
   • 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
   • Energy catalyzed formation of organic molecules like amino acids & nucleotides
     • Provided by UV, light, heat etc
   • 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
   • 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)
4. 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
   • RNA world hypothesis: argues that RNA came first
     • 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 self-replicate w/o proteins, but DNA always needs proteins
5. Primitive heterotrophic prokaryotes formed
   • Organic “soup” was the source of organic material
6. Primitive autotrophic prokaryotes were formed
   • Bcuz of mutations, heterotrophs gained the ability to produce their own food → became autotroph
7. Oxygen and ozone layer formed and abiotic chemical evolution ended
   • 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
8. Eukaryotes formed (endosymbiotic theory)

• “Describes how organelles formed when free-living prokaryotic cells engulfed another prokaryotic cell” → formed eukaryotes
  • So bacteria earliest descendent; says that mitochondria & chloroplast used to be prokaryotes
• Single endosymbiotic event more likely to have resulted in a two-membrane structure
• Double endosymbiotic event more likely to have resulted in a three-membrane structure.

1. Evidence
2. Prokaryotes, mitochondria, chloroplasts and plastids have their own DNA
   • Are circular and without histone proteins
3. Ribosomes of mitochondria and chloroplasts resemble those of bacteria and cyanobacteria → similar in size and nucleotide sequence
4. Mitochondria and chloroplasts reproduce independently in a process similar to binary fission of bacteria
5. Mitochondria and chloroplasts have two membranes
   • 2nd membrane could have formed when host prokaryotic wrapped engulfed prokaryotic in a vesicle (endocytosis)
6. The thylakoid membranes of chloroplasts resemble photosynthetic membranes of cyanobacteria

• 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, cellular respiration, protein synthesis
• 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

• Prokaryotes: unicellular, microorganisms that lack organelles
  • Archaea & bacteria

1. 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/cytoplasm\ Some contain plasmids\ Yes: multiple linear packaged with histone proteins & capped w/ telomeres  \ Usually has introns \ Chromosome enclosed in  nucleus → large genome\ Cell Division Binary Fission Meiosis or Mitosis Transfer of DNA Only fragments Thru meiosis Flagella and Cilia When present are made from globular protein flagellin & not microtubules enclosed by plasma membrane When present are of protein tubulin “9 + 2” array

Autotrophs: make their own organic molecules

• Photoautotrophs Use light energy (as in photosynthesis)
• Chemoautotrophs Use energy obtained from inorganic substances (as in chemosynthesis)
• Heterotrophs: obtain carbon & energy from other organisms
• Parasites Obtain energy from their hosts while living on or in their tissues
• Decomposers Obtain energy from dead, decaying matter

https://lh7-us.googleusercontent.com/4KGI5F1QB5JtzDk5aOKFIUOtQ5EJCW0hEpFZwDRyfzroZsiAhItlKgKVepFM4ZK2d2iRbr-doZQcmbKSYP3qdROIkAoqErIwp54yQnGr3I4zQOL-3bYspbuLmJQC1wuFkYTPsrlo-kUfKTUNTbba1g| Characteristics of Prokaryotes:

• Small size and rapid reproduction
• High genetic variation → live in diverse environments

1. 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
  • Structure either gram positive and negative
  • (+) = simple
  • (-) = more complex, less peptidoglycan
• Capsule: layer of polysaccharides and proteins that surround cell wall
  • Protect against dehydration, cell adherence, resist host organism defenses
• 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
• 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

1. Groups of Bacteria

• Can be categorized by how they obtain energy and carbon (include 4 modes)

1. Cyanobacteria: photosynthetic
2. Purple sulfur bacteria: photosynthetic but split H₂S (instead of water) to get electrons
3. 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
4. Heterotrophic bacteria: obtain carbon and energy from organic molecules
   • Ex: parasites, pathogens, decomposers, and bacteria in the digestive tract that also compete with pathogenic bacteria
5. Motility

• Use flagella
  • Pro and eu. flagella have diff proteins, molecular composition, and method

1. https://lh7-us.googleusercontent.com/B2pdtlM_J9Sxuhpg_cvMorhCDEVb3rp0mFpQHDc9L6SrtzW1rdvfcsSarmmBg0FVsvRMphjnkx4RnH58L9rDUo1RlLl_RNqLoF8dG7M-9itJjHjnHaTIFd98HeBET9b2FA038dYayfwuVsWARcRVuw| Reproduction: Binary Fission

• Asexual→ no genetic variation
• Rapid reproduction + no proofreading enzymes → high rate of mutation = main method of creating variation for evolution (fast)

1. Metabolism

• Obligate aerobes require O2; obligate anaerobes are poisoned by O2; Facultative anaerobes can survive with or without
• Some antibiotics disable the activity of bacterial ribosomes or break down cell wall

What makes Archaea Different?

• Cell walls contain diff polysaccharides, not peptidoglycans, cellulose, or chitin
• Plasma membrane contain different phospholipids

1. What Makes Archaea Similar

• Like bacteria, are prokaryotes
• Like eukaryotes, are not inhibited by antibiotics and some have introns
  • Bacteria don't have ribosomes & ribosome activity is inhibited by antibiotics

1. Extremophiles

• Thrive in extreme conditions
• Halophiles: highly saline

1. Thermophiles: very hot Domain Eukarya

• Evidence for common ancestry of eukaryotes
  • Organelles, linear chromosomes, histone proteins

• Extremely diverse: can be algae-like, animal-like, fungus-like; unicellular, multicellular
• Evolutionary relationships are weak, poorly understood, or both
  • Features shared by two or more groups may represent convergent evolution

1. Algae-Like

• All obtain energy by photosynthesis, have chlorophyll a

1. Protozoa/Animal like

• Heterotrophs: Consume living cells or dead organic matter

1. Fungus-Like

• Resemble fungus bcuz they form filaments or spore-bearing bodies

Structure

• 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
• Cell walls consist of Chitin: nitrogen-containing polysaccharide

1. Ecological Interaction

• Most either parasites or decomposers: absorb breakdown products from excreted digestive enzymes

1. Mutualistic Arrangements
2. Mycorrhizae: mutualistic relationships between fungi and plants
   • Fungus grows on the roots of plants → facilitate movement of water & nutrients
   • Plants provides sugar
3. Lichens: relationship between fungi and algae
   • Fungus provides water and protection

Similarities among all plants

1. Multicellular; cell wall
2. Autotrophic
3. Rooted in the ground
4. Organs & Interactions with the Environment
5. 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

Similarities among all members

1. Multicellular & heterotrophic
2. Dominant generation in the life cycle is diploid
3. Most are motile during at least some part of life

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
  • Behavior used to maintain homeostasis, find mates and nutrients
• 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

1. Kinds of Animal Behavior
2. Instinct: behaviour that is innate/inherited (genetically controlled)
   • Ex: in mammals, care for offspring by the female parent is innate
3. Fixed Action Patterns (FAPs) innate behaviors that follow a regular, fixed pattern
   • 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
   • 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
4. Imprinting: an innate program for acquiring a specific behaviour only if have correct stimuli experienced during critical/sensitive period (limited time interval during life of an animal) → irreversible
   • Ex: geese goslings will accept any moving object as mothers, salmon imprint odors associated with birthplace so that they can return
5. 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
6. Associative Learning (association) occurs when animal recognizes (learns) that two or more events are connected
   • 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)
7. Trial-and-error learning (operant conditioning): form of associative learning when an animal connects its own behavior with environmental response.
   • If response is desirable (positive reinforcement) animal will repeat behavior
   • If response is undesirable, animal will avoid behavior

• Learning acquired by association can be forgotten or reversed if performed behavior does not result in expected response
  • Extinction: loss of acquired behavior

1. 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't identify
2. Habituation: learned behavior that allows animal to disregard meaningless stimuli
   • Sea anemones tentacles can ignore nonfood items after repeated attempts to grab food
3. 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
4. Cognition and Problem Solving
   • Cognition: the process of knowing that involves awareness, reasoning, recollection, and judgment
   • Problem solving: the cognitive ability to overcome obstacles
5. 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
6. Signaling behavior: response and communication between organisms that can change behavior and reproductive success
   • Organisms exchange info in response to internal and external signals
   • Cooperative behavior increases fitness of individuals and survival of the population
7. Notes

• 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
• Inherited behaviors and learning capabilities have evolved because increase individual fitness
  • Innate behaviors improve fitness by providing dependable mechanic for animal to respond to expected behavior
• Associative learning allows individuals to benefit from unexpected events
  • Once form association can respond appropriately next time
• 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
• Game Theory: The fitness of a particular behavior is influenced by other behavioral phenotypes in a population

1. General Animal Behaviors

• Animal always encountering different situations so respond to each in way that maximizes survival and reproductive success (fitness)

1. Survival responses: when encounters dangerous situation
2. 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
3. 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
4. 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
5. 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
6. 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
   • 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
7. 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
   • 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
8. Body scents: signals presence of predators
   • Ex: zebras increase vigilance when detect body odor
9. Herds, flocks, and schools provide advantages when foraging
   • Concealment: most individuals hidden from view
   • Vigilance: more ppl watching
   • Defense: can shield or mob attack
10. Packs: corner and attack large prey
11. Search Images: look for abbreviated forms of of object to find favored or plentiful food
12. Social Behavior May live in group or alone; always make contact to reproduce
13. Agonistic behavior (aggression and submission) originates from competition for food, mates, or territory
14. Parental Care: innate behavior in response to producing offspring
    • Paternal behavior exists because it has been reinforced over generations by natural selection
15. Dominance Hierarchies: indicate power and status among individuals in group → minimize fighting
    • Pecking order
16. Territoriality: possession and defense of territory → ensure enough food and safety
17. Eusocial (truly social) consists of members divided into castes
    • One caste will forage, other will feed and care
18. 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
    • 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
    • Altruistic behavior can be maintained by evolution because furthers survival of population
19. Ground squirrels give alarm calls that warns other squirrels of predators but risks own safety by revealing presence
    • These squirrels live in groups of closely related females so is example of kin selection
20. 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.
    • Reciprocal Altruism: exchange of aid between unrelated individuals
    • Do it bcuz think they will receive something in return in future
21. Animal Movement Animals can respond to external stimuli by moving → allows them to seek food, shelter, safety, or mates
22. Kinesis: undirected change in speed of an animal's movement in response to stimulus
    • 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
23. 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
    • Moths move toward light at night, sharks move toward when food odors reach them by diffusion or bulk flow (ocean current)
24. Migration: long-distance, seasonal movement of animals; response to seasonal availability of food or degradation of environmental conditions

• 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
  • Biological rhythms can be linked to light/dark and lunar cycles

1. 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
   • Nocturnal animals are active at night and rest during day
   • Communicate mostly with auditory and olfactory signals
2. 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
  • So animals adjust behavior to maximize fitness and take advantage of benefits

1. Hibernation: extended period of sleep to avoid hostile environment during winter
   • Hibernating reduces energy & metabolic maintenance by lowering body temperature and using fat as energy
2. Estivation: dormancy during summer
   • Protect from drying out by burrowing or climbing in plants
3. Courtship and mating: often during spring with warmer weather and more food → provide energy and nourishment
4. Migration

• Signal: A stimulus transmitted from one organism
• Communication: the transmission and reception of signals between animals of same species
  • Common modes of animal communication: visual, chemical, tactile, auditory,
  • Uses: indicate dominance, find food, establish territory, ensure reproductive success, species recognition, mating behavior, and social behavior. Occurs by…

1. 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 territoriality when spray urine
2. 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
   • Some male birds assemble into groups called leks in which make courtship to female who chooses
3. Auditory: sounds often used to communicate over long distances, thru water, and at night
   • Use to ward off male rivals, attract female, species recognition, warn of territorial boundaries, infrasound for greeting, singing songs that announce reproduction
4. Tactile: use of touch for social bonding, infant care, and mating
   • Ex: bees perform dances that provide info about location of food
   • Bees make body contact (tactile) during dance
5. Mating Behavior and Mate Choice

• In some animal species, mating is promiscuous, with no strong pair-bonds
• 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
• Often master-regulatory genes control courtship because products regulate other genes controlling sexual reproduction
• In some species, neurotransmitters or hormones are needed for partnering and parental behavior
  • Ex: antidiuretic hormone (ADH) or vasopressin: a peptide that binds to specific receptors on nervous system
  • Change in level of receptor can alter development

Review

• Ecology is the study of the distribution of organisms, their interactions with other organisms, and their interactions with their physical environment
• Vocab

1. A population is a group of individuals of the same species living in the same area
2. A community is a group of populations living in the same area
3. An ecosystem describes the interaction between organisms and the environment
4. The biosphere is composed of all regions of the earth that contain living things
5. 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).

1. 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

• Long-term conditions in an area
• Four physical factors— temperature, precipitation, sunlight, and wind
• Climograph: plot of the annual mean temperature and precipitation in a particular region

* Global Climate Patterns

• Determined largely by the input of solar energy (differential heating of Earth's surface) and Earth’s movement in space

* Effects on Climate Seasonality

• Changes in wind pattern affect ocean current

* Bodies of Water

• Water’s high specific heat helps regulate local temp → less extreme temp
• Ocean currents influence climate along the coasts of continents by heating or cooling overlying air masses that pass across the land.
• Ex: Coastal regions are also generally wetter than inland areas at the same latitude.

* Mountains

• Affect amount of sunlight that reach ground → affect local temp, air flow, and rainfall
• When warm, moist air approaches a mountain, the air rises and cools, releasing moisture on the windward side of the peak
• On the leeward side, cooler, dry air descends, absorbing moisture and producing a “rain shadow” → determine where deserts are found
• South-facing slopes in the Northern Hemisphere receive more sunlight than north-facing slopes and are therefore warmer and drier → determine local distribution

* Vegetation

• Forests dark in color absorb more and reflects less solar energy → warm Earth's surface in forested areas
• Warming effect balanced by transpiration

* 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
• Very big, so impact biosphere
• ex: produce oxygen, source of rainfall, effects on ocean temp on global climate and wind patterns

* 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
• Thermocline: layer of abrupt temperature change which separates uniform warm upper layer from cold deeper layer
• 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

* 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
• Range expansion: when organisms reach an area where they did not exist previously
• 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.
• 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

• Abiotic (nonliving) factors like temp, light, water, and nutrients & biotic factors influence organism distribution, size, and biodiversity

* Biotic Factors

• Ability of a species to survive and reproduce is reduced by its interactions with other species, such as predators or herbivores
• Also presence/absence of pollinators, food resources, parasites, pathogens, and competing organisms
• Primary producers & dominant predators support diversity in ecosystems
• Primary Producers: Provide food, shelter, reduce erosion
• Predators: keep prey populations in control, diverse diets that don't put too much pressure

* Abiotic Factors Temperature

• 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
• All increase diversity
• Organisms typically function best within a specific range of environmental temperature
• Temp outside range = more energy

* Water and Oxygen

• Water affects oxygen availability in aquatic environments; more water → more species

* Salinity

• Affects water balance bcuz of osmosis

* 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

* Major Biomes

1. Tropical rain forests: characterized by high temperature and heavy rainfall; tall trees that from thick canopy that reduces light penetration
2. Savannas are grasslands with scattered trees.

• Tropical → high temp but lot less water than rain forests

1. Temperate grasslands receive less water and lower temperatures than savannas.
2. 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).

1. Deserts are hot and dry → located where air masses are descending

• Adaptations: plants with leathery leaves or spines (cacti); animals have thick skins and restrict their activity to nights.

1. Taigas are characterized by coniferous forests (vegetation with needles for leaves). Long and cold winters with precipitation is in the form of snow.
2. Tundras have winters so cold that the ground freezes

• 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)

1. Freshwater biomes include ponds, lakes, streams, and rivers.
2. Marine biomes include estuaries (where oceans meet rivers), intertidal zones (where oceans meet land), continental shelves (shallow oceans that border continents), coral reefs (masses of corals that reach the ocean surface), and the pelagic ocean (the deep oceans)

* Trophic Levels https://lh7-us.googleusercontent.com/Zwzo-Hi8sy6hHUkb5R8NapUW-cFUMJALutxR8KZiymSaxc41Bv4pZIBzHbFdsq_AXGdZSmtkPAR9Gtal37LuZcsfdWdtmibOcORK70kv_TB-VJ-amCJX6HXeSsSzT9gz08YzNU9Mvo0jFQQ2EYe-AQ|

• Trophic Levels: position organism is in food chain
• Way of illustrating energy flow and production & utilization of energy

1. Primary produces: photoautotrophs that convert sun energy into chemical energy → ecosystem’s initial source of energy
2. Primary consumers: (herbivores) heterotrophs that eat primary producers
3. Secondary consumers: (primary carnivores) heterotrophs that eat primary consumers
4. Tertiary consumers: (secondary carnivores/Apex) heterotrophs that eat secondary consumers
5. Detritivores: heterotrophs that get energy by consuming dead plants and animals (detritus)

• Decomposers: smallest detritivores (ex: fungi and bacteria)
  • 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.

* Trophic Interactions Certain species in community can influence the dynamics of that community

1. Foundation Species: strong effects on communities bcuz of large size or abundance
2. Dominant Species: most abundant species that contributes greatest biomass to a community

• Species dominant bcuz is best able to compete for resources & escape predators/disease

1. 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
  • May eat species that eat another species

1. Invasive Species: introduced species that proliferates and displaces native species bcuz it is a better competitor and/or because natural predators/pathogens are absent

• 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

1. 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

1. 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

1. 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
2. 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

• 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).

1. Bottom-up model: structure of trophic lvls are regulated by changes in the bottom trophic lvl

• Ex: primary productivity low → few supported trophic lvls

1. 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
• Top down regulation can become irregular when humans remove top predators

* Ecological Pyramids

• Used to show relationship between trophic levels

* Untitled_a1baf95c2be74fad95ea92c3882c2c8f:Untitled_30|

• Tiers represent sizes of trophic levels
• Each represented in terms of energy (A.K.A productivity), biomass, or number of organisms
• Tiers are stacked upon one another in order of which energy is transferred between levels
• Aquatic ecological pyramids are often inverted because biomass of consumers exceeds that of producers

1. Food chain: linear flow chart of who eats whom and direction of nutrient and energy transfer
2. Food web: linked group of food chains (animals have more than one food source)

* Conservation of Mass

• Matter, like energy, cannot be created or destroyed.
• 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 depend on constant input of energy

* Ecological/Trophic Efficiency

• “Proportion of energy represented at one trophic lvl that is transferred to the next lvl”
• Always less than production efficiency
• ~1% of the solar energy that reaches the surface of the earth is converted into organic matter
• Transfer of energy between trophic lvls is inefficient → ~only 10% of the productivity of one trophic lvl is transferred to the next lvl
• Remaining 90% is used for metabolic activities, passed thru feces, or transferred to detritivores
• Most energy for respiration and other metabolic activities is ultimately lost as heat
• Heat is energy that cannot be harnessed by organisms to do work → represents energy lost from the ecosystem
  • So ultimately all energy originally gained through NPP is lost as heart
• BUT chemicals, nutrients and matter recycled in an ecosystem (unlike heat)
• Bcuz ecological efficiency is so low, almost all animals used for food/work are herbivores
• Carnivores require more energy to sustain themselves
• Changes in energy availability can result in…
• Changes in population size & density
• Disruptions to an ecosystem: Species have adaptations that aid survival when energy availability changes
  • Ex: fat as energy, lose/grow leaves, migration, hibernation, lower metabolic rate
  • Exist reproductive strategies in response to energy availability
  • Produce lots of offspring at one
    • Energy efficient when not enough resources
  • Some produce few offspring at one
    • Energy efficient in stable environments
  • Ex: sunlight can affect number and size of trophic levels

* 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://lh7-us.googleusercontent.com/vQa_TYH4x0q0j-vG6rOD5BzUIoUwLo-b_U9KzUQG3mJTs8WC9rSz47o7w6rTswMkU9XM5iaVgF_1so-P29GZbAoKaiPFbZvENjsqxBC_-1Swa6z2s3fHuS2pruT7ewcuTgMzwBwQ5E1Go7k82i-Mcw|
• 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.

* 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)
• Metabolic Rate/O2 consumption rate increases with decreasing temperature
  • Spend more energy to maintain internal temp
• Ectotherms lack efficient body temperature regulating mechanisms
• Rely on behavior: moving in and out sun, eating
• Metabolic Rate/O2 consumption rate increases with increasing temperature