Gen Bio Full Course Notes PDF

lOMoARcPSD|46266463 GEN BIO full course notes General Biology I (Rutgers University) Scan to open on Studocu Studocu is not sponsored or endorsed by any college or university Downloaded by Tina Zhu ([email protected]) ...

lOMoARcPSD|46266463 GEN BIO full course notes General Biology I (Rutgers University) Scan to open on Studocu Studocu is not sponsored or endorsed by any college or university Downloaded by Tina Zhu ([email protected])  lOMoARcPSD|46266463 Memory & Learning – Lecture 1 Compare & contrast types of memory Sequence process of memory Neural Development Nervous systems consist of circuits of neurons and supporting cells ○ Neurons send and receive messages in the form of action potential Overall pattern of ns during embryonic development (basic network) ○ Gene expression given this ○ Signal transduction Brain develops throughout entire life (neuronal plasticity)-modified after birth onwards ○ Dynamic, can be remodeled ○ Connections can change (synapses) - junctions bw neurons ○ Remodeling occurs here can add/remove ○ Changes are activity dependent ( do something-synapses stronger & vice versa) ○ High activity-will strengthen but low activity-loose connections Use it/lose it ○ Multiple strong synapses-mutually reinforces; stronger response at all synapses Associating scent w location (together so reinforce each other) ○ Balance with cerebellum and don't lose it with motor things Memory ○ Process occurs at synapses (making and using new synapses) ○ Depends on ability to change connections (neural plasticity) & activity ○ STM-short time (secs/mins) Released if irrelevant/not actively used (most is 7 things) ○ LTM: needs to be retained, use info for long period of time, used indefinitely When needed, retrieved into stm Memory and learning are 2 different things -> learning is using knowledge to decrease the likelihood of negative outcome ( do better as a result of learning) ○ Memory-which parts are electrified, learning-never attack fence twice Workshop- improve ability to form memories and use them to learn and problem solve ○ Develop learning skills & techniques Long-term potentiation: lasting inc in strength of synaptic transmission (signal across synapse due to physiological changes at the synapse) ○ Make synapses work really efficiently ○ Facilitates memory and retrieval Failure to retrieve-dont have synapse thats strong for action potential use->impt->retained Not used->un-important->discarded Discarded no new synapses formed Stimulus -> sensory memory storage (consciously/unconsciously aware of things) but if remember/recognize encoded if not forgotten-> STM aka working Downloaded by Tina Zhu ([email protected])  lOMoARcPSD|46266463 memory but forgotten after few mins-> if intro to STM alot-> encoded into LTM use thing in STM repeatedly (retrieval) Encoding & retrieval= long term potentiation Photographic memo=no sorting (lower barrier/nonexistent) Forget things when old bc brain stops working and synapses are not as good Muscle memory=long term potentiation for a motor circuit ○ New synapses=connections bw neurons ○ Long term potentiation= zoom in to connections and see the strength of connection ○ After ltp-> the signal is sent easily/quickly across synapse Facilitated by Org: associations aid in memo formation (connect related info to remember) Chunking: learn sets of related info rather than 1 at a time activity= practice leads to learning ½ easy ½ synthesis questions BiOs Form ○ Organize material ○ Need to bring to workshop Scientific Process and Chemistry – Lecture 2 Themes in Bio ○ Compare and contrast and sequence levels of organization Evolution: all living things are modified descendants of common ancestors Emergent properties: properties of something that are result of arrangement and interaction of parts (not found in individual components) Whole is more than the sum of parts ○ Ex: bike Levels of Bio Organization: molecules, organelles, cells, tissues, organs, organ systems, organisms, populations, communities, ecosystems, biosphere Methods of Investigating Bio ○ Sequence process of science The scientific method: method of inquiry-finding natural explanations for natural phenomena (process) Want to understand why/how something is happening Inquiry: Limited to observable/measurable structures/process Systematic: method of investigating natural world process, not haphazard Hypothesis: testable proposed explanation based on the information you already know (educated guess) Prediction: expected outcome from when you test hypothesis (directly testable) Theory: broad explanation w lots of support that leads to new hypotheses and accurate predictions Highest level of certainty in science Downloaded by Tina Zhu ([email protected])  lOMoARcPSD|46266463 Laws: descriptive statements of what always occurs under certain conditions Observable pattern “what” not “why” (don’t explain) The scientific Process (not linear) observation/question →background (research -don’t want to repeat past stuff)->generate hypothesis->make predictions-> test predictions (experiments/observations during experiment), collect data-> evaluate (whether you were wrong/correct) -> ○ if predictions were incorrect you can revise hypothesis/predictions or you can redo experiment ○ Correct prediction: repeat and verify your results to show your prediction is correct Sometimes you are unsuccessful, you revise or repeat experiment If successful in repetition, ask a new question and repeat process Basic elements of Chem ○ Compare & contrast chemical bonds Mainly made of four elements: oxygen, hydrogen, carbon, nitrogen (greatest amount of oxygen) Atoms are made of protons, neutrons, & electrons Electron e- (-1 charge, negative) ○ Move rapidly around atomic nucleus Protons and neutrons in the nucleus Potential energy (E) - energy depends on location/structure Once use energy to do work -> work has to be done to restore energy to original state Due to location/arrangement Relation to e-: located in shells diff distances from nucleus ○ More distant e- from nucleus, the more potential energy it has Absorb E to move from lower to higher shell Release E when go from high to low shell ○ Valence e-: outermost shell-> occupy “valence” shell H & He: up to 2 valence e- All others: up to 8 e- valence shell Stable when full Properties of atom depend on atomic structure ○ Number of electrons in valence shell dictate binding properties ELECTRONS IMPORTANCE: bonds & reactions ○ Molecules: a compound of 2/more atoms held together by chemical bonds Chemical formula: tells types of atoms and how many of each ○ Compounds have emergent properties: characteristics of individual atoms differ from the characteristics of actual Downloaded by Tina Zhu ([email protected])  lOMoARcPSD|46266463 compound -> diff properties when creating something/come together Ex: NaCl (less dangerous than both elements) Chemical bonds-result of how atoms share/compete for e- ○ Want full valence shell-> will donate, share or accept e- ○ Energy is stored in chemical bonds Electronegativity: measure of affinity for e- in chemical bonds (how strongly atoms attract e-) ○ Atoms have diff attractive forces ○ More electronegative-> more strongly pull e- towards self Fewer valence e-= less electronegativity More electronegative=more reactive Covalent bonds: sharing e- bw atoms about equally ○ Ex: H2 (2 e- shared bw both) ○ Results in full valence shell ○ Under bio conditions-> strongest type of bond Nonpolar covalent bonds: same/sim electronegativity so e- shared equally (equal attraction to each other) ○ Shape could prevent polarity Polar covalent bonds: ○ Unequal electronegativity (diff in polarity) ○ Unequal e- sharing ○ Causes partial + charge (less electronegative) & partial - charge (more electronegative) Ionic (charged atoms) Bonds ○ High unequal electronegativity e- lost (+) cation or gained (-) anion One accepts and one gains e- Strongest CHEMICAL bond Dissolves in water (not strong in bio) Called salts (form crystals) -> dissolve in water VanDer Waal Interactions ○ (relatively) Short, weak interactions due to electron position and motion ○ Areas w partial +/- charges interact ○ Ex: lizard toes (millions of microscopic fibers that can fit on microscopic grooves of glass) ○ Includes may diff interactions: London dispersion forces & HYDROGEN BONDS Hydrogen bonds: interactions between molecules where hydrogen is usually involved Regions of partial charge on diff molecules attract each other Downloaded by Tina Zhu ([email protected])  lOMoARcPSD|46266463 Partial charges result when H (partial +) binds to electronegative atom (partial -) Emergent properties of water ○ Compare & contrast properties of water Water is a polar molecule bc H is more electronegative than O Form h-bonds w each other (can form 4 bonds with each other) ○ Responsible for many impt properties Cohesion: water molecules stick to each other (form bonds with each other) -> move water up trunk of tree Surface tension: measure how difficult it is to stretch or break surface of liquid (hard to break bc bonds are strong ) Adhesion: water can be attracted to other things with h- bonds Water transport in plants Capillary action: tendency of water to rise against gravity into small spaces of hydrophilic material Moderates temperature: takes high temp to inc temp of water -> high specific heat (good at absorbing heat) H bonds hold water together strongly so it can't move fast ○ Ex: climate-> cities near temp have regulated temperature (colder) ○ Ex: reg body temp thru evaporative cooling: sweating Expansion when freezing (too close to to form h-bonds in water so form crystal structure when move apart so ice floats on top of water because solid form is less dense) Prevents bodies of water from freezing bottom up (things can live under5neath frozen lake Hydrophilic substances: affinity for water (will dissolve) ○ Regions of partial positive/negative ○ Protein will dissolve in solution bc form h bonds w water Hydrophobic substances: “water fearing”, nonpolar, nonionic, cannot form h-bonds ○ Ex: oil (won’t dissolve) ○ Ex: soap-dissolves things that can’t dissolve in water Covalent, ionic, hydrogen Downloaded by Tina Zhu ([email protected])  lOMoARcPSD|46266463 Biological Macromolecules – Lecture 3 Biological importance of carbon ○ Compare & Contrast functional groups Carbon-> organic compounds: c bonded to c or H Chemistry: study of carbon compounds Cell ~ 70%-90% h20; rest are c-based compounds Carbon backbone varies in 4 ways: length, branching, double bond position, presence of rings Carbon can be a backbone and have other elements attached to it Hydrocarbons: simplest organic molecules of only C and H (ex: CH4) ○ Nonpolar, uncharged (nonionic) ○ Hydrophobic ○ Can contain functional groups: diff groups of atoms that can replace 1/more H Key to molecular function Ex: estradiol, testosterone *7 key groups for us ○ Hydroxyl group: OH, called alcohols; name ends in “ol”; polar, hydrophilic ○ Carbonyl group: carbon with double covalent bond to O Polar, hydrophilic-less polar than hydroxyl group ○ Carboxyl group: carbon backbone, double bond to O and single bond to OH (COOH) Can release Hydrogen (H+)-> acidic (carboxylic acids); becomes COO- Polar, hydrophilic impt part of amino acids but ionic in ionized form ○ Amino Group (NH2) N bond to 2 H’s; proton H+ acceptor (basic) becomes NH3+-> in aqueous solution it can pick up protons, impt comp Hydrophilic, ionized/polar ○ Sulfhydryl Group -SH Polar but weakest polarity of all groups Impt in protein structure Weakly polar, so slightly hydrophilic Downloaded by Tina Zhu ([email protected])  lOMoARcPSD|46266463 ○ Phosphate group (-PO4H2) Extremely acidic, so only see in ionized form PO4- O bounded to P, bonded to 1 O and 2 OHs ( 1 double bond) Can release 1 or both H+ exists as ionized or nonionized Acidic, hydrophilic, found in phospholipids and nucleic acids ○ Methyl group CH3 (single bonds) Nonpolar, hydrophobic Affects dna expression (methylation) * know structure, properties, polar/charged, FIGURE 4.9 Biological macromolecules ○ Macromolecules: large molecules-thousands of atoms Many are polymers: produced by linking smaller components (monomers): identical/similar repeating subunits Dehydration reaction/synthesis: adding monomer to polymer by removing a water molecule (OH + H -> H2O), forming new bond Dehydrogenases: proteins that speed up removal of hydrogen Hydrolysis: breaking down polymer (add water molecule, breaking bond) Hydrolases: enzyme that help speed up hydrolysis ○ 4 Classes of biomolecules: carbohydrates, lipids, proteins, nucleic acids Lipids are not polymers but other 3 are made up of repeating subunits Carbohydrates: C, H, O (ration is CH2O) ex: C6H12O6 Monomers: sugars -> contain 3-7 C, hydroxyl groups, carbonyl groups, very hydrophilic ○ Monomers: monosaccharides -> classified by # of C and location of carbonyl ○ Most common: glucose- C6H12O6 (linear & ring (in bio systems) forms) Can form isomers: alpha & beta glucose (due to different ways ring can close) ○ Disaccharides: formed by linking of 2 monosaccharides Mono->Di through dehydration synthesis Dehydration reaction results in covalent bond called glycosidic linkage Ex: maltose: glucose + glucose, Sucrose: glucose + fructose, lactose: glucose + galactose (milk sugar, lactase not made after infancy in lactose intolerant people) Downloaded by Tina Zhu ([email protected])  lOMoARcPSD|46266463 ○ Polysaccharides: compounds of hundreds-thousands monosaccharides Main functions: storage & structure Function: determines by type of monomer and position of glycosidic linkage (orientation relative to ring- easy/not to breakdown) Ex: starch (storage polysaccharide in plant) Alpha-glucose subunits; storage plastids all face the same way in structure (animals have evolved the ability to break down) Ex: glycogen is storage in animals (alpha glucose subunits Larger, more branched than starch Stored in muscles & liver (energy) Plant structural polysaccharides (cellulose) Most abundant organic compound on earth Beta subunits breakdown require different enzymes ○ Can't break down this-fiber ○ Very few organisms can digest-some microbes, fungi, nails ○ Found in cell wall of plant cells Animal structural polysaccharide:Chitin Monomer: glucose w nitrogen group attached In arthropod exoskeletons (insects, arachnids, crustaceans) Fungi cell walls Fuel (energy), structural Tend to end w “-ose” Lipids: diverse, hydrophobic, not polymers Don’t dissolve in water, dissolve in nonpolar solvents (ex: chloroform) Fats ○ Most abundant lipid: energy storage ○ Fat contains 9 cal/g but carbs/proteins contain 4cal/g (fats are better in terms of efficient energy storage) ○ Structure: glycerol: 3 carbon alcohol 3 -OH groups & 1,2, 3 fatty acids ○ Fatty acids: unbranched hydrocarbon ~14-22C, carboxyl group ○ Glycerol & fatty acid )H & hydroxyl group connected via ester linkage ( O C double bond O) ○ Fat synthesis: dehydration reaction ○ Saturated fatty acids: each C bonded to highest possible number of H (saturated with H) Tend to be solid at room temperature Downloaded by Tina Zhu ([email protected])  lOMoARcPSD|46266463 Ex: Most non-fish animal fats ○ Unsaturated fatty acids: double bonds in the hydrocarbon chain fewer H than max capacity Monounsaturated: 1 double bond Polyunsaturated: 2 + double bonds More than 1 double bond: kinks in molecules- less dense packing (bent) Tend to be liquid at room temp Ex: Plant, fish fats ○ Trans fatty acids (double bonds like unsaturated) but , opposite orientation-> linear fatty acid, few Phospholipids ○ Glycerol + 2 fatty acids + phosphate group Amphiphatic: hydrophobic & hydrophilic regions Fatty acid tails (inside) & phosphate head (outer sticking out) Steroids ○ 3 6-C rings & 1 5-C ring ○ Differ only in functional groups ○ Ex: cholesterol, sex horomones Cholesterol: membrane component precursor to other steroids Proteins (polymers): ○ Monomers: amino acids All have the same basic structure All have basic structure: central carbon, hydrogen atom, an amino group (basic), a carboxyl group (acidic), R- group (side chain/variable) 20 amino acids Side chains: nonpolar (hydrocarbon), polar (hydroxyl group), charged (acidic/basic) Amino acids linked with peptide bonds bw carboxyl and amino groups; formed via dehydration reaction Long chain of amino acids=polypeptide ○ Not a protein yet, req correct shape 4 levels of protein structure Primary: seq of amino acids Secondary: localized folding-accomplished w h- bonds Tertiary: long-dist folding held together with many diff types of bonds (side chains vs. backbone that are involved) Quaternary: 2/more polypeptides working together (ex:hemoglobin) Downloaded by Tina Zhu ([email protected])  lOMoARcPSD|46266463 Protein denaturation: loss of protein's native structure (loose structure->loose function) Caused by changing pH, salt concentration, high temp Protein function: structure, signaling, enzymes, defense, transport (everything but heredity) ○ Nucleic Acids: polymers of nucleotides, DNA, RNA Store and transmit genetic info ○ Sequence process of polymerization ○ Compare & contrast classes of biological molecules The Origin of Life – Lecture 4 Process of Abiogenesis ○ C&C requirements for life ○ C&C abiotic synthesis hypotheses ○ SEQ abiogenesis History of Life ○ SEQ timeline of early life ○ SEQ endosymbiosis Many hypotheses about the origin of life: Fossil evidence: ~3.7bi yrs ago Process of abiogenesis: ○ Abiotic (non living) synthesis of monomers First life developed from non-living organic molecules (abiogenesis) Molecules formed spontaneously (abiotic synthesis) Requirements: low free O2 energy source inorganic precursors (building blocks) ○ chemical components: CO2, H2O, CO, H2, N2, maybe NH3, H2S, CH4, liquid water Lots of time Abiotic synthesis hypothesis: process is same but diff location Oparin-Haldane Hypothesis: life formed near earth’s surface-shallow water ○ Test: Miller Urey (biochemists) Experiment (1953) Generated early earth environment: found amino acids & other organic compounds ○ Recent work: same conditions and molecules produced: DNA/RNA nucleic acid bases, all amino acids, several lipids & sugars, ATP if phosphate is added Original samples reanalyzed Downloaded by Tina Zhu ([email protected])  lOMoARcPSD|46266463 Iron-Sulfur Hypothesis: organic molecules created at hydrothermal vents ○ Hot H20, CO, iron & nickel sulfides released ○ Hot springs produce precursors to biomolecules ○ Recent work inc support ○ Formation of organic macromolecules Can form on clay or rock surfaces Negative ions bind monomers Zn2+, Fe2+ catalyze polymerization Experimentally see: polypeptides, polynucleotides, vesicles ○ Formation of protocells Vesicle: fluid-filled compartment surrounded by membrane Form from lipids in water (ex: liposome) Protocells: aggregates of abiotically produced organic macromolecules Not cells but have characteristics of cells (exhibit attributes of living cells) ○ Electrical potential across surface: absorb materials, osmotic swelling, unique internal chem environment, divide if sufficiently large ○ No mechanism of heredity ○ Appearance of self-replication Living cells: Genetic info in dna Transmit via mRNA (capable of being genetic info and do reactions) ○ Think RNA was first nucleic acid in living things ○ RNA world hypothesis: first cells used RNA to store and copy genetic info DNA & proteins incorporated later ○ Ribozymes: RNA molecule w enzyme props: can cleave RNA & catalyze RNA polymerization Translated into protein (do reactions) Protocells & self-replicating RNA: ○ RNA polymers within vesicle -> high osmotic pressure -> vesicle grows -> growing vesicles take up lipids -> RNA from environment/other vesicles -> RNA gets rewritten -> vesicle continues to grow, eventually splits ○ Experimental support: Thought RNA came first (single stranded) -> become ds (more stable and better for info storage) -> DNA (more stable) Why isn’t life constantly forming: Already exist Anything useful doesn’t accumulate Brief history of life on earth: ○ First cells: prokaryotes-nucleus ○ Anaerobic: don’t use O2 ○ Heterotrophic: obtain organic nutrients from environment Downloaded by Tina Zhu ([email protected])  lOMoARcPSD|46266463 ○ Fermentation: no O2 req, relatively inefficient ○ Autotrophs appeared later: use energy from sunlight to make food 1st released S2 Later released O2 by splitting H2O (cyanobacteria) ○ O2 apocalypse: rise in O2 due to oxygenic photosynthesis & killed off most organisms Know when it happened bc of banded iron formation Aerobic respiration (turn 02 to CO2)-common today Higher ATP yield Eukaryotes: cells with membrane-bound nuclei & organelles Generated 02 thru endosymbiosis (larger cell engulfed smaller cells and the smaller cell becomes a component of larger cell) ○ Evidence of endosymbiosis: mitochondria, plastids: have double membrane, sim size, enzymes, ribosomes to bacteria, DNA seq sim to living bacteria, divide by binary fission ○ All euk have mitochondria but few have chloroplasts-> it appeared before plastids Cell Structure – Lecture 5 Diversity & Characteristics of Cells ○ C & C prokaryotic & eukaryotic cells ○ Cell: the smallest unit that carries out all the activities of life Either does everything/specialized Share common features & evolutionary history Cellular Structures & Diversity (classified by structure/morphology) ○ Prokaryotes No nucleus (“before the nucleus”) -> domains bacteria & archaea (prokaryotes bc no nucleus but disagreement) Appeared 4 bi years ago 1-10 micrometers ○ Eukaryotes “True nucleus”: domain eukarya 1.8 bi years go 10-100 micrometers Cell graphics show all features but may not all look the same ○ Common features of all cells: surrounded by plasma membrane distinct internal environment store & replicate genetic info divide/reproduce Metabolism interact w & respond to external environment limited in size Plasma membrane: all material must pass through membrane to entire cell Downloaded by Tina Zhu ([email protected])  lOMoARcPSD|46266463 ○ SA limits rate of enter/exit Advantageous to max surface area to volume ratio ○ Smaller is better because it takes less time to get to places (efficiency) ○ Big=lots of small cells rather than 1 big cell Components of Eukaryotic cells ○ C & C cellular components ○ Nucleus: contains most of DNA (mitochondria or chloroplasts also contain DNA) & often highly visible Nuclear envelope: double membrane surrounding nucleus (separates nucleoplasm from cytoplasm) Membrane fused -> nuclear pores 2 phospholipid bilayers Nuclear pores: Protein complexes ○ Regulate passage bw cytoplasm and nucleus Nucleolus: where ribosomes are made in nucleus Dense in RNA & proteins ○ Mitochondria & Chloroplasts Created through endosymbiosis (antagonistic relationship-> stuck inside big cell because it can’t break down-> mutualistic relationship (gets ATP & nutrients) Mitochondria: Does aerobic respiration Present in eukaryotic lineages- plants & animals * look at structure * Folding to increase surface area Chloroplasts: Only found in some eukaryotic lineages (only in some plants & algae) Outer membrane, intermembrane space, inner membrane Have stroma: thylakoids, thylakoid space *LOOK AT STRUCTURE* ○ Ribosomes: Structures responsible for photosynthesis Not membrane-bound -> not considered organelles Made of protein & RNA Found in cytoplasm and ER surface ○ Endomembrane system: Internal membrane system Membrane: lipid bilayer, closed (compartment surrounded by phospholipid bilayer) Divides cell into compartments -> create membrane-bound organelles (part of endomembrane system) Allows specialization & efficiency Components of endomembrane system: nuclear envelope, ER, Golgi apparatus, plasma membrane, lysosomes, vacuoles Downloaded by Tina Zhu ([email protected])  lOMoARcPSD|46266463 ○ Plasma Membrane: selectively permeable phospholipid bilayer Not a cell wall Encloses cell contents Controls flow of material flow in/out ○ ER: internal membrane complex Single cont. Lumen (internal space) Connected to outer membrane of nuclear envelope Rough ER: ribosomes attached to outer surface Involved in protein synthesis Proteins made -> transfer through translocon -> into lumen Smooth ER: lipid synthesis & metabolism Very little except in specific cells (ex: liver) ○ Golgi Apparatus: many membranes; modify & transport proteins Take in vesicle & package vesicle Cis face (recieving) & trans face (exports) No contiguous lumen ○ Vacuoles: large vesicles (smaller, temporary vacuoles from endomembrane system) & (big compartments) Many functions: food vacuoles, contractile vacuoles, storage in plant cells ○ Lysosomes: compartments containing hydrolytic enzymes (digestive enzymes bc hydrolysis to break down molecules) Primary lysosome: made in RER, processed in Golgi where modified and activated -> ready/inactive Secondary lysosome: 1st lysosome fuses with vacuole & (actively) digesting Ex: phagocytosis If enzymes released in cytoplasm, it will be bad but not terrible Compartmentalization: prevents cell from damaging itself ○ Membrane Communication: Direct continuity: once inside membrane compartment-> can go anywhere Vesicular transport: transfer of membrane segments (within cells) One membrane blobs off -> fuses with next membrane -> materials get inside other cell -> blob becomes part of next membrane ○ SEQ transport pathway Membranes & Transport – Lecture 6 Membrane Components ○ C & C membrane components ○ HD (hypothesize & diagnose-> what would happen if you change the system) Fluid Mosaic Model Downloaded by Tina Zhu ([email protected])  lOMoARcPSD|46266463 ○ Membrane Structure: Impt features: fluid mosaic model, phospholipids, proteins, carbohydrates Phospholipids: primary component (hydrophobic tails, phosphate group- hydrophilic, tails are away from aqueous environment) Bilayer formation: forms spontaneously, due to phospholipid shape (amphipathic nature), held together by hydrophobic interactions (Van der Waals) Membrane Proteins Many membrane functions Peripheral (hydrophilic) vs. integral (amphipathic) ○ (often transmembrane -> span membrane) Some can move (membrane proteins fuse together into a hybrid cell and move together) ○ Generally can’t flip Some proteins can’t move because they are bound to something on the other side of the membrane Functions of membrane proteins: transport, enzymatic activity, signal transduction, cell-cell recognition, intercellular joining, attachment to cytoskeleton & extracellular matrix (ECM) Carbohydrates Polysaccharides attached to protein (glycoprotein) or lipid (glycolipid) Primarily cell identification ○ Fluid Mosaic model Fluid: membrane components that can move laterally within 1 layer of the membrane (not locked in place) Depends on many factors: temp chain length-carbons in tail (shorter hydrocarbons -> smaller van der waal interactions) Saturation-double bonds in tail (unsaturated tails prevent packing of dense membrane) Cholesterol (moderate fluidity of membrane & reduces fluidity at higher temps Mosaic Membrane Transport ○ C & C types of membrane transport Membrane Transport: memn=brane is selectively permeable ○ 2 types of transport: passive (does not use ATP), active (req. metabolic energy/ATP) ○ Passive Transport: simple diffusion, osmosis, facilitated diffusion Net movement down concentration gradient (no ATP required) Downloaded by Tina Zhu ([email protected])  lOMoARcPSD|46266463 results in dynamic equilibrium DIffusion: tendency for molecules to fill available space; all molecules are in constant random motion so they are eventually evenly distributed in available space Dynamic equilibrium: no net movement at equilibrium (motion on each side but concentration is not changing) ○ Different substances diffuse independently of each other Things that can diffuse across membrane: membrane fluidity, solute hydrophobicity ○ Small, non-charged gases (ex: 02, C02, N2) ○ Small nonpolar molecules (hydrophobic), inc. hydrocarbons ○ Small polar uncharged molecules (hydrophilic) inc. h20 Osmosis: diffusion of h20 across selectively permeable membrane Solvent: substance that dissolves other substances solute: dissolved substance Direction of osmosis is determined by diff in total solute ○ Type of solute doesn’t affect osmosis ○ Water diffuses from lower solute to higher solute (higher h20 to lower h20 concentration) ○ Result: in more similar solute (equalize solute concentration on each side of the membrane) Tonicity: ability of solution to cause cell to gain/lose water ○ Isotonic solution: solute concentration outside cell =solute concentration inside cell No net h20 movement ○ Hypertonic solution: solute concentration outside > solute concentration inside (cell loses h20) ○ Hypotonic solution: solute concentration outside < solute concentration inside (cell gains h20) ○ Terms are relative (in comparison to eachother) Osmosis & cells *picture* What can’t cross a membrane: large molecules, polar molecules (hydrophilic-that are too big), ions (+/-) Cells evolved means to transport materials-involve transport proteins ○ Facilitated diffusion: passive transport thru a transport protein Doesn’t require ATP Specific 2 channels: channel, carrier * down concentration gradient, don’t involve ATP* ○ Active Transport: req ATP, agst concentration gradient, transport thru carrier protein The sodium-potassium pump: 3 Na out, 2 K in (establishes electrical gradient) Downloaded by Tina Zhu ([email protected])  lOMoARcPSD|46266463 Bulk Transport – Lecture 7 ○ C & C, SEQ Bulk Transport Transport large number of molecules at once Type of active transport but not using carrier proteins Always require ATP Exocytosis: vesicle containing waste or secretory products fuses w plasma membrane ○ Releases contents from cell ○ Adds lipids to PM- primary mechanism for growing plasma membrane Endocytosis: material taken from outside by forming vesicles derived from plasma membrane ○ 3 types: Phagocytosis: cell eating Engulfs large particle; fuses with lysosome and particle digested Pinocytosis: cell drinking Ingestion of fluid and dissolved material; forms vesicle and slowly transferred to cytoplasm Non-specific ○ Takes any volume of fluid from outside Receptor-mediated Endocytosis: receptor proteins in plasma membrane bind specific macromolecules outside cell form coated pits Fold inward to form vesicles Main mechanism for uptake of macromolecules More efficient because specific Photosynthesis – Lecture 8 Outcomes: Compare and contrast photosynthesis and cellular respiration Follow energy from the sun through the light reaction ○ Energy +6C02+6H20----> C6H12O6 + 6O2 Compare and contrast cyclical and linear electron flow in light dependent reaction Trace carbon and sugar creation in Calvin cycle # ATP # NADPH # ATP used # NADPH Point of this produced produced used step Light Dependent Calvin Cycle --------------------------------------------------------------------------------------------------------------------------- Downloaded by Tina Zhu ([email protected])  lOMoARcPSD|46266463 Introduction to photosynthesis ○ Photoautotrophs: fix inorganic carbon (CO2) PRODUCERS ○ Heterotrophs: obtain their carbon material from organic sources (other organisms) CONSUMERS ○ Ecological Importance Redox: H20 is oxidized and CO2 reduced Endergonic process→ energy boost from light energy ΔG + ENERGY + 6C02 + 6H20→ C6H12O6 + 602 CO2 reduced (more electrons) H20 oxidized (less electrons) ○ The Nature of Light light= form of electromagnetic energy All radiation travels in waves photon= small particle of light energy E in photon: Shorter wavelength= more energy/photon Longer wavelength= less energy/ photon ○ Effect of Photon on Electrons Electron become energized→ shifts to high energy Absorbs photon Can return to lower energy orbital or leave atom → captured by an electron acceptor→ acceptor is reduced Structures in Photosynthesis ○ Plant organization Plants absorb visible light Leaves are green because chlorophyll reflects and transmits green light chloroplasts= photosynthetic organelles The only color that is not used by plants is the green wavelength which is why it is bounced back and reflected/transmitted ○ Structure of Chloroplasts 2 membranes in a chloroplast Inner membrane= thylakoid Inner “cytosol” = stroma Result of endosymbiosis because they were eaten through phagocytosis, but not digested ○ Photosynthetic pigments Chlorophyll is a pigment: a substance that absorbs visible light Chlorophyll a: main one (should recognize the basic structure) CH3 in A and CHO in B Porphyrin ring: light-absorbing: “head” of molecule Hydrocarbon tail: interacts with hydrophobic regions of proteins inside thylakoid membranes of chloroplasts Downloaded by Tina Zhu ([email protected])  lOMoARcPSD|46266463 AMPHIPATHIC The Process of Photosynthesis ○ Overview of Photosynthesis REDOX reactions: H20 is oxidized, CO2 is reduced Endergonic, E input from sunlight FOLLOW THE ATOMS: ○ Light-dependent reactions Light reactions (in thylakoid): Split H20 and releases O2 Reduce NADP+ to NADPH Generate ATP from ADP Occur in the thylakoid membrane 2 photosystems (PSII and PSI) ○ Trap the sun's energy and convert it to NADPH and ATP ○ most reactions use a linear electron flow Photosystem Parts 2 Light- harvesting complexes ○ Capture light Linear electron flow ○ Light dependent ○ PSII and PS I ○ Produces ATP and NADPH and O2 ○ More recent - cause of O2 rev Cyclic electron flow ○ Produces only ATP ○ older→ predate O2 rev Linear electron Flow Steps ○ Both photosystems involved, same 3 things happen in each other Boost electrons Use energy in electrons Replace electrons ○ Steps include redox reactions Boost PSII electrons Photon hits pigment in PS II E passed to P680 (chlorophyll molecule reaction center) ○ Absorbs wavelength of slightly orange Electron transferred to first electron acceptor from P680 (REDOX REACTION) ○ P680 is oxidized, electron acceptor is reduced, P680+ Use energy in electrons (to make ATP) Downloaded by Tina Zhu ([email protected])  lOMoARcPSD|46266463 ○ Electrons from the 1st acceptor goes through the electron transport chain ○ Generate a H+ gradient inside thylakoid space ○ H+ diffuses through ATP synthase (facilitated diffusion) ○ ATP synthesis Replace PSII electrons (from water) ○ P680+ is an extremely strong oxidizing agent→ H20 is oxidized (photolysis) ○ Electron is transferred to P680+ ○ P680+ reduced back to P680 ○ O2 is released as byproduct ○ This is where atmospheric O2 comes from Boost PSI electrons ○ Light energy excites electrons in pigments Excited P700 Oxidized to P700+, 1 degree electron acceptor reduced Use E in electrons (this time to make NADPH) ○ Electrons moves through PS 1 ETC to ferredoxin (Fd) ○ Electrons transferred to NADP+ → NADPH synthesized Catalyzed by NADP+ reductase Replace P ○ ○ ○ Cellular Respiration – Lecture 9 I. Introduction SEQ, HD general respiration processes and pathway A. Overview of eukaryotic respiration Respiration: e in chem bonds of food -> E in ATP Occurs in all cells Anaerobic and aerobic Catabolic Respiration is a series of redox reactions ○ Coupled reactions: Carbon is oxidized while Oxygen gets reduced ○ Form of energy (follow pathway of electrons) Downloaded by Tina Zhu ([email protected])  lOMoARcPSD|46266463 Summary of metabolic pathway ○ C6H12Og + 6O2 -> 6CO2 + 6H2O + E (ATP-> exergonic because energy released) ○ aerobic ○ Reverse of photosynthesis II. 4 Stages CC, SEQ, HD steps of respiration I. Glycolysis “Sugar splitting”-breakdown glucose 1 Glucose 6C -> 2 pyruvate (3C) Doesn’t require 02 Occurs in cytoplasm 2 phases: ○ energy investment phase (uses ATP) Endergonic: requires ATP 6C (glucose) -> use ATP to phosphorylate glucose into 6C with 2 phosphate -> break into 2 * 3C (G3P) ○ energy payoff phase (makes ATP) Generates ATP & NADH Do redox reaction to add another inorganic phosphate -> 3C with 2 phosphates -> generate ATP at series of actions that remove phosphates -> end with 3C molecule called pyruvate Happens twice for glucose so get 4 ATP and 2 NADH ATP synthesis in glycolysis ○ substrate-level phosphorylation: enzymatic transfer of phosphate to ADP -> ATP Glycolysis summary ○ Start w 1 glucose and end with 2 pyruvate ○ Also have 2 ATP and 2 NADH ○ After: can go to aerobic pathway of pyruvate oxidation or anaerobic pathway of fermentation B. Pyruvate Oxidation Takes place inside mitochondria Pyruvate Import: ○ Pyruvate diffuses through pores in outer membrane ○ Active transport across inner membrane Pyruvate oxidation reaction ○ Catalyzed by pyruvate dehydrogenase ○ No atp used or produced ○ 2x per glucose molecule bc each glucose generates 2 pyruvate ○ Pyruvate + NAD+ + CoA -> CO2 + NADH + Acetyl CoA ○ End of step causes 2 of original 6C to be released as CO2 ○ Net gain so far: ATP, NADH C. Citric Acid Cycle/ Kreb’s Cycle Takes place in the matrix of mitochondria Downloaded by Tina Zhu ([email protected])  lOMoARcPSD|46266463 Starts w Acetyl CoA from pyruvate oxidation and oxaloacetate (4C) Oxaloacetate (4C) + Acetyl CoA (2C) -> Citrate (6C) -> 5C + CO2 (released as waste) + NADH ○ 5C oxidized again and creates 4C and CO2 & NADH ○ 4C creates GTP & ATP is created indirectly ○ * figure pic* Citric Acid cycle summary: ○ Acetyl CoA completely oxidized to CO2 ○ 1 glucose -> 2 “turns” (bc of 2 pyruvate) ○ Each turn generates: 2 CO2, ATP, NADH, FADH2 ○ Each glucose generates: 4CO2, ATP, NADH, FADH2 ○ By end of cycle, carbon is entirely oxidized (had 4 CO2 and lost 4CO2) ○ After Citric Acid Cycle: *figure* D. Oxidative Phosphorylation (ETC and Chemiosmosis) Energy (electrons) stored in NADH and FADH2 used to create proton gradient Proton diffusion across inner membrane (chemiosmosis) drives ATP synthesis ETC ○ Series of electron carriers in the inner mitochondrial membrane ○ Series of redox reactions ○ Electrons from electron carriers -> thru ETC -> O2 ○ Energy used to make H+ gradient via active transport ○ Proton pumped with active transport (using electron energy) into Intermembrane space O2 is a terminal electron acceptor Aerobic respiration evol benefit use toxic energy (O2) and make water *proton gradient*=potential energy ETC Energy ○ Energy in reaction mostly goes into heat ○ Do reaction slowly (ETC and “slow combustion” of glucose have the same purpose -> minimize E lost as heat) Chemiosmosis ○ E coupling mechanism used to synthesize ATP ○ Convert potential E in gradient (proton motive force) to potential E in ATP (diffuse through ATP synthase) ○ Protons diffuse thru ATP synthase (facilitated diffusion) which generates ATP ○ ATP Synthase: Protein complex Inner mitochondrial membrane “Molecular mill” H+ diffuse thru (exergonic) Causes rotation & energy used for ATP synthesis Oxidative Phosphorylation overview ○ *figure* Downloaded by Tina Zhu ([email protected])  lOMoARcPSD|46266463 ATP production by Oxidative Phosphorylation ○ Glucose -> NADH or FADH2 -> ETC -> PMF -> ATP ○ Each NADH Prokaryotic Respiration ○ Same stages as eukaryotes ○ No mitochondria so do aerobic respiration in cytosol ○ ETC in plasma membrane ○ Electron carriers don’t need to cross membranes -> more ATP Respiration Summary Big Picture ○ Energy comes in photosynthesis as sunlight and leaves in cell respiration as ATP Start of Exam II Cell Cycle: Mitosis – Lecture 10 I. Organization of Genetic Material A. Introduction 1. Cell division is an integral part of the cell cycle 2. What are the three functions of cell division a) Reproduction b) Growth and development c) Tissue renewal B. Genetic material of the cell 1. Genome- all dna in a cell (gene instructions) a) Prokaryotic cells- single circular dna molecule b) Eukaryotic cells- several dna molecules 2. Dna molecules in a cell are packaged into chromosomes 3. Eukaryotic chromosomes consist of chromatin (DNA and proteins) a) Condenses during cell division DNA wound around histone proteins into nucleosomes C. Chromosome number 1. Humans- 46 chromosomes 2. Every eukaryotic species has a characteristic number of chromosomes in each cell nucleus Downloaded by Tina Zhu ([email protected])  lOMoARcPSD|46266463 a) Not about how complex it looks but how dna is organized into the body that determines chromosome number 3. Ploidy- number of sets of chromosomes a) Haploid cell (n)- 1 copy of each chromosome b) Gametes- sex cells (n) c) Diploid cells(2n)- 2 sets of each chromosome 4. Chromosome structure a) Gene instructions for a protein b) Centromere- pinched in part c) Steps (1) Prior to mitosis dna is doubled (2) Sister chromatids form (3) Ploidy does not change (4) Same genetic information, just two times the mass II. Phases of the cell cycle A. Introduction 1. All cells must divide 2. Goals- make identical copies 3. During cell cycle: starting ploidy= ending ploidy 4. So a) n-> n b) 2n-> 2n c) 100n-> 100n 5. Prokaryotes ( what 2 domains) a) Binary fission- double in size and split b) Why (1) 1 circular chromosome (2) No nucleus 6. Eukaryotes- the cell cycle a) Interphase (growth and dna replication) (1) Time between division (2) Longest time b) Mitotic phase (M) (mitosis and cytokinesis) B. Events of interphase 1. 90 percent of cell cycle 2. 3 sub phases a) G1- first gap b) S- synthesis c) G2- second gap (1) Cell grows during all three 3. Chromosome duplicated only during S phase 4. GI phase a) Most of cell life b) No dna synthesis Downloaded by Tina Zhu ([email protected])  lOMoARcPSD|46266463 c) Cell functions, communication d) Protein manufacture e) How many chromosomes? (1) Diploid (a) 2 sets from mom dad (4 chromosomes) 5. S phase a) Chromosome duplicate (2n→ 2n) ploidy does not change (1) Diploid to diploid (2) Form identical sister chromatids (3) Held together at the centromere (a) By cohesion proteins (i) Kinetochores- proteins handles that grow from centromere 6. G2 Phase a) Cell doubles in mass b) Centrosomes duplicate (1) Star shaped c) 2 centrioles per centrosome d) Function=move chromosomes C. Events of M Phase (goes wrong→ cancer) 1. Eukaryotic cell division is divided into 4 phases(PMAT): a) Prophase (1) Chromosomes condense (2) Mitotic Spindles form (a) Lines (3) Centrosomes move to opposite poles (4) Nuclear envelope breaks down (5) Spindle fibers attach to kinetochore handles b) Metaphase (1) LONGEST stage of mitosis (2) Chromosomes align on the metaphase plate c) Anaphase (1) SHORTEST stage of Mitosis (2) Cohesion proteins cleaved by enzyme- disjunction (3) Chromosomes begin to move to opposite sides (4) Now 2 complete sets of chromosomes (5) (2N) on each side d) Telophase (1) About separating the chromosomes (2) 2 new daughter cells form (3) Nuclear envelope reforms (4) Cytokinesis will divide cytoplasm (a) Occurs at the same time as telophase (b) Not part of mitosis Downloaded by Tina Zhu ([email protected])  lOMoARcPSD|46266463 (c) About separating the cells, cytoplasm divides (d) How: animals for a cleavage furrow (e) Plants form a cell plate (i) Due to the fact they have a cell wall made up of cellulose, so form a cell plate which is basically a cell wall in the making (f) Each daughter cell gets: (i) Full set of chromosomes organelles (ii) What happens next? GO BACK TO INTERPHASE (a) Cell cycle is a cycle Meiosis – Lecture 11 I. Intro to Heredity CC sexual & asexual reproduction Heredity: transmission of traits from 1 generation to the next (inheritance) Variation: differences bw individuals Genetics: study of heredity and heriditary variation Gametes: reproductive cells that transmit genes from 1 generation to the next Reproduction is asexual A. Asexual reproduction Single parent produces offspring Unicellular: split Multicellular: budding or fragmentation Eukaryotes-> via mitosis (dividing nucleus) -> produces clones: offspring genetically identical to parent ○ 1 haploid (2n) parent -> 2 diploid offspring ○ 1 haploid (n) parents -> 2 haploid offspring Advantages: Fast, low E required, safe, lots of offspring, well adapted/ don’t change (clones) B. Sexual Reproduction Fusion of 2 gametes (haploids) form zygote (diploid) Gamete (n) + gamete (n) -> fertilization -> zygote (2n) ○ Gametes are usually from different parents but not always ○ Offspring not genetically identical to each other or their parents Disadvantages: slow, high E required, dangerous: predation (mating ritual can be seen by predators), disease, often fewer offspring, offspring only get half of your genes-genome dilution Downloaded by Tina Zhu ([email protected])  lOMoARcPSD|46266463 Advantage: genetic variation- offspring get new combos of genes from parents’ genes; better able to respond to change/stress Why variation is good: ○ Low variation -> new predator introduced -> many of species are killed ○ High variation -> selection for traits because less of species killed when new predator introduced If gametes has same # of chromosomes as parents -> chromosome # doubles (can’t be sustained) ○ Solution: meiosis (reduction division) ○ Cell divides twice ○ 1 diploid (2n) cell -> 4 haploid (n) cells C. Chromosomes in Heredity Karyotype: orderly display of chromosomes ○ Mitotic chromosomes; stained Human Karyotype ○ Somatic cells: 46 chromosomes (2n=46) ○ 22 pairs of autosomes (non sex chromosomes) ○ Sex Chromosomes: X & Y (determine sex) Female: XX Male: XY ○ Small homologous region in X and Y chromosomes Homologous chromosomes ○ Same length, centromere position staining pattern ○ Homologous chromosomes contain the same genes * Figure 13.4* II. Life Cycles SEQ, CC sexual life cycles Life cycle: seq of changes from generation to generation Fertilization and meiosis: ○ occur in all sexual life cycles ○ Alternate bw fertilization and meiosis ○ Timing varies A. Human Life cycle Haploid gametes fuse in fertilization -> results in diploid zygote grows into humans thru mitosis B. Variety in Sexual life cycles N and 2n cells can undergo mitosis Only 2n cells can undergo meiosis *pic* III. Four Stages of Meiosis SEQ, CC, HD process of meiosis Reduction division 4 stages & involves 2 cell divisions Downloaded by Tina Zhu ([email protected])  lOMoARcPSD|46266463 ○ Interphase ○ Meiosis I ○ Interkinesis ○ Meiosis II A. Interphase Like before mitosis, chromosomes (dna in S) and centrioles duplicate (G2) Each chromosome now has 2 sister chromatids (still chromatin) Diploid-2 sets of chromosomes -> 8 chromatids still 2n=4 Humans- 2n=46 so 92 chromatids enter meiosis B. Meiosis I (and cytokinesis) First meiotic division: homologous chromosomes separate, ploidy reduced (end w haploid cells) First and second meiotic divisions are indicated in the name of each stage ○ Prophase I, Metaphase I, Anaphase I, Telophase I ○ Prophase II, Metaphase II, Anaphase II, Telophase II Prophase I: crossing over (causes genetic variation) happens ○ Synapsis occurs: homologous chromosomes pair up ○ Genes in chromosome align ○ Synaptonemal complex forms- protein structure ○ Results in tetrad: 2 homologous chromosomes (4 chromatids) held together Crossing over (homologous recombination) Enzymes break and rejoin DNA Exchanges bw non-sister chromatids ○ Crossing over at gene level: Dna physically breaks and is reattached to the same chromosome -> point is to generate new combos (new variation within population) ○ Chromatin condenses, centromeres and kinetochores of homologous chromosomes separate Sister chromatids still attached Nuclear envelope breaks down; spindle forms ○ At end of prophase I in humans: Humans: 2n=46 (46 chromosomes) 23 tetrads 92 chromatids Metaphase I ○ Tetrads align at the metaphase plate ○ Homologous chromosomes orient towards opp poles ○ Both sister kinetochores of 1 chromosome -> spindle for same pole ○ Kinetochores of homologous chromosomes -> spindle for opp poles Anaphase I ○ Disjunction: homologous chromosomes separate ○ Sister chromatids still connected ○ Chromosomes act independently ○ Direction depends on orientation of tetrad ○ Nondisjunction: homologs fail to separate 2 homologs go to same pole Downloaded by Tina Zhu ([email protected])  lOMoARcPSD|46266463 Relatively common in meiosis I Telophase I ○ Chromosomes may decondense ○ Nuclear envelope reforms (may/may not) ○ Cytokinesis occurs ○ Results in 2 haploid cells (each has duplicated chromosomes) ○ 2n=4 -> 2 n=2 cells (diploid to haploid cells) ○ At the end of telophase I in humans -> Start w 2n=46 23 chromosomes 46 chromatids No homologous pairs so 0 tetrads Meiosis I ○ Start w 1 cell (2n-duplicated chromosomes) ○ End w 2 cells (n-duplicated chromosomes) ○ Crossing over in prophase I ○ Homologous pairs line up in metaphase I, separate in anaphase I ○ Ploidy reduced IN MEIOSIS I C. Interkinesis Time bw 1st & 2nd meiotic divisions Short (usually) interphase-like stage No S phase, no DNA synthesis occurs D. Meiosis II 2nd meiotic division Chromatids separate into daughter cells Very similar to mitosis *pic* End w 4 daughter cells Start w 2 cells, n, duplicated chromosomes End w 2 cells, n, unduplicated chromosomes Each daughter cell is genetically unique No crossing over in meiosis II Amount of DNA per cell reduced but PLOIDY DOESN’T CHANGE *figure 13.8* * CC mitosis vs. meiosis* Mendelian Genetics – Lecture 12 Outcomes List and detail the four concept in Mendel's model that support discrete inheritance Set up and solve both a monohybrid cross using a punnett square from a word problem Solve problems using the multiplication rule and the addition rule, this means solve genetic problems without using a punnett square CC and calculate probability independent events vs mutually exclusive events Downloaded by Tina Zhu ([email protected])  lOMoARcPSD|46266463 ------------------------------------------------------------------------------------------------------------------------------- I. Mendel’s Experimental Approach A. Background 1. Gregor Mendel (1822-1884) 2. Why pea plants? a) Inexpensive b) Many varieties c) Easy to grow, short generation time d) Lots of offspring e) Clearly identifiable traits f) Easy to control pollination B. Testing Blending Hypothesis 1. Testing the blending inheritance hypothesis a) Mendel crossed true-breeding plants with contrasting traits (1) P= parental generation (2) CONTROL- pollination b) Crossing 2 different flowers in the P generation results in the first generation (F1) c) “True-breeding” = all individuals of line have the same characteristics 2. EXPERIMENT: a) P generation (true breeding parents) → Purple Flowers + White Flowers b) F1 generation (hybrids) → All plants had purple flowers (1) 100% purple c) F2 generation→ 705 purple flowers, 224 white flowers (1) 3:1 ratio (a) 75% purple (b) 25% white d) Conclusions: (1) No intermediate phenotype (2) Lost phenotypes reappear (3) Blending of fluids cannot explain either observation 3. MENDEL REJECTED BLENDING HYPOTHESIS C. Mendel’s Model 1. New hypothesis= particulate inheritance 2. “Heritable factors” = genes, determine characteristics a) They are discrete units b) Each characteristic is controlled by 2 factors (genes) from parents 3. Mendel’s particulate inheritance explains the 3:1 inheritance pattern in F2 offspring 4. 4 related concepts make up this model a) Alleles (1) Allele- alternate version of a gene (2n means 2 of each allele) Downloaded by Tina Zhu ([email protected])  lOMoARcPSD|46266463 (2) Each allele has the same locus (location) on homologous chromosomes b) Two Alleles, 1 From each Parent (1) The 2 alleles: (a) May be identical (like the P generation)= homozygous (b) May be different (like F1 hybrid)= heterozygous c) Dominant and recessive alleles (1) If heterozygous (a) Dominant allele- determines the organism’s appearance (b) Recessive allele- has no effect on appearance d) Mendel’s 2 Laws (1) Law of segregation- each gamete gets 1 allele (a) * only pass on half the genetic material* (b) 2 alleles segregate during MEIOSIS (c) Egg/Sperm only get 1 of the 2 alleles (2) Law of independent assortment- alleles assort independently (action of sorting) (a) Genes on different chromosomes assort independently during gamete formation due to random orientation of tetrads during metaphase 1 (b) Each chromosome is equally likely, which leads to genetic recombination II. Genetic Crosses A. Introduction 1. Punnett squares- illustrate mendel’s laws, show possibile babies a) Phenotype- physical/expressed type (white or purple) b) Genotype- genetic type (PP, Pp, pp) 2. Monohybrid- cross of one characteristic a) Practice: Monohybrid cross F1 x F1 (1) Start by drawing a box (2) Make a key and determine genotypes (3) Place genes (4) Determine possible offspring III. Probability in Genetics A. Introduction a. Probability- use math to solve squares faster , percent chance that something is going to happen b. Genetic ratios expressed in terms of probability c. Event is certain to occur- probability= 1 d. Event is certain not to occur→ probability= 0 B. Multiplication Rule a. Predicts combined probabilities of independent events b. Independent events= one event does not affect the probability of other Downloaded by Tina Zhu ([email protected])  lOMoARcPSD|46266463 i. P(this) and P(that) ii. Word “and” means to multiply sep. probabilities iii. INDEPENDENT- one event does not affect the other iv. KEY WORDS- and v. EX) So I hope to have veggie burgers AND wine 1. P(eating veggie burger)= 50% 2. P(drinking wine)= 25% a. 0.5 * 0.25= 0.125= 12.5% chance of having veggie burgers and wine vi. EX) if the mother is Bb and father is Bb what is the probability that first child will be homozygous recessive (bb)? 1. (CHANCE THAT CHILD WILL GET A b from mom AND a b from dad?) 2. Probability (bb)- P(b from Mom) and P(b FROM DAD)= 0.5 * 0.5= 0.25 a. Independent because meiosis in one gamete is independent of meiosis the other gamete C. Addition Rule a. Predicts combined probabilities of mutually exclusive events b. Mutually exclusive events= events that cannot occur simultaneously c. Stated as: i. P(this) or P(that) ii. Word “or” in equation means to add separate probabilities d. EX) If mother is Bb and father is Bb what is the probability that the first child will be heterozygous? What is chance? i. b from Mom AND a B from Dad ii. OR iii. B from Mom AND a b from Dad iv. \ Chromosomes – Lecture 13 I. Chromosomal Theory of Inheritance (SEQ Morgan’s Experiments) Figure 15.2 (review of Meiosis and Genetics) Mendel didn’t know about genes and chromosomes Genes have specific loci on chromosomes Chromosomes undergo segregation and independent assortment A. Thomas Morgan and D. melanogaster Early 20th century, experimental embryologist 1860s-1900s: Cytologist- chromosomes behave like Mendel’s “heritable factors” Originally a skeptic of Mendel’s work and chromosome theory 1st experimental support for genes on chromosomes Downloaded by Tina Zhu ([email protected])  lOMoARcPSD|46266463 Chromosomal theory fit what was known about Mendel’s “heritable factors” Drosophila Melanogaster: fruit fly-Morgan’s model organism ○ Advantages: Lots of offspring Short generations of ~2 weeks 4 pairs of chromosomes-3 pairs of autosomes, 1 pair of sex chromosomes Describing traits ○ Wild type: most common phenotype for character in natural populations Wild type is not dominant (ex: red eyes in fruit flies) ○ Mutant phenotype: alternative to wild type (ex: white eyes in fruit flies) Notation ○ Conventions differ ○ In drosophila, symbol based on 1st observed mutant ○ Ex: allele for white eyes (w) ; allele for red eyes (w^+) + indicates wild type B. Correlating Allelic and Chromosome behavior P: Red-eyed female x white-eyed male F1: All offspring have red eyes ○ Red eyes dominant over white eyes Red-eyed female F1 x Red-eyed male F1 F2: 3:1 phenotypic ratio but ALL MALE Sex Determinantion ○ Y chromosome doesn’t determine male (only states make sperm) ○ Ratio of X chromosomes compared to sets of autosomes (A) ○ Ex: XX:AA -> 1:1 -> female ○ Ex: XY:AA -> 1:2 -> male ○ Ex: XO:AA -> 1:2 -> sterile male ○ Ex: XXX:AAA -> 1:1 -> female ○ Ex: XXY:AA -> 1:1 -> female Why no white-eyed females ○ Eye-color gene located on the X chromosome ○ No corresponding locus on the Y chromosome Eye-color Monohybrid Cross ○ *pic* Morgan’s Findings ○ Show how specific gene is carried on a specific chromosome ○ Unique inheritance patterns for genes on sex chromosomes ○ Strong support for chromosome theory of inheritance II. Inheritance Patterns on Sex Chromosomes (CC, HD sex linkage) A. Sex Chromosomes 1 pair (2 chromosomes-1 from each parent) Sex-determining genes Heteromorphic Act homologous during meiosis Downloaded by Tina Zhu ([email protected])  lOMoARcPSD|46266463 Contain genes unrelated to sex determination Sex-linked genes: gene on either sex chromosomes Human Sex determination ○ Males - XY -> heterogametic Half of sperm get X, half get a Y Y chromosome has genes for male development ○ Females - XX -> homogametic All eggs have X Female phenotype due to absence of Y Sex Determination Varies *pic* B. X-linked Genes X-chromosome-many genes, many required X-linked traits- controlled by genes on x-chromosome ○ Unique inheritance ○ Ex: hemophilia, color-blindness, male pattern blindness Inheritance of Sex Chromosomes ○ XX * XY Gametes: X or X x X or Y Half XX and Half XY Males are significantly less likely to survive childhood but more common at birth than females (5%) Males ○ Just 1 x-chromosome ; all alleles are expressed ○ Hemizygous: having just 1 allele for a gene ○ Recessive alleles are never masked! ○ Ex: Red-green color blindness Recessive trait Female can be: homozygous dominant (normal vision) Heterozygous (carrier-normal vision) Homozygous recessive (color blindness) Males can be Hemizygous dominant (normal vision) Hemizygous recessive (color blindness) *pic* ○ Ex: carrier female x unaffected male Offspring: multiplication rule 0.5 * 0.5 P (male): 0.5 P (colorblind male): 0.25 P (female): 0.5 P (colorblind female): 0 ○ A father with hemophilia has a daughter with hemophilia The mom has to be a carrier (unaffected) Downloaded by Tina Zhu ([email protected])  lOMoARcPSD|46266463 C. X Inactivation Genes on X chromosomes expressed in females and males Females=2 copies Males=1 copy Females don’t make 2X proteins from X-linked genes Barr Bodies ○ 1 X chromosomes inactivated during development ○ Make a dense structure: Dna and protein coiled along inside of nuclear envelope (can’t express genes) ○ Involves modification of DNA and histone proteins (often methylation) ○ Inactivation is random- different X in different cells Tortoiseshell cat ○ Some genes for fur color are x-linked ○ Heterozygous females -> mosaic expression pattern Sex Chromosome Summary ○ Traits on sex chromosomes have unique inheritance patterns ○ Due to: hemizygosity in heterogametic sex; X inactivation III. Violations of Independent Assortment (SEQ, HD patterns of inheritance) A. Linked Genes Genes on same chromosome Humans: ~ 20k genes; 23 homologous pairs Many genes on each chromosome Unlinked Genes ○ A and B on non-homologous chromosomes; assort independently ○ Parent genotype: AaBb Possible gametes: AB ab Ab aB Linkage ○ Tendency for groups of genes on the same chromosome to be inherited together Chromosomes inherited as units Genes B and C are not independent Mendel’s traits were all unlinked ○ Ex: B & C on same chromosome -> don’t assort independently ○ Parent genotype: BbCc (dominant alleles linked) Possible gametes: BC, bc *pic* B. Recombination Mechanism J and K are linked and recombine via crossing over Parent genotype: JjKk (dominant alleles linked) Possible gametes: JK, jK, Jk, jk ○ *pic* Genetic Recombination: 2 mechanisms ○ Unlinked genes: independent assortment ○ Linked genes: crossing over ○ *pic* Downloaded by Tina Zhu ([email protected])  lOMoARcPSD|46266463 DNA – Lecture 14 Outcomes CC major experiments and the scientist Diagram a single nucleotide and then diagram a fragment of DNA including all 4 nitrogenous bases CC DNA replications for a prokaryote and eukaryote Flow chart the process of DNA replication DNA REPLICATION How do we replicate DNA? Want to go from chromosomes to fat chromosomes (make sister chromatids) When? During S phase Why? So we can separate sister chromatids later Midterm: ask about polymers and monomers in DNA replication I. DNA is the genetic material 1. Chromosomes have: a) DNA (deoxyribonucleic acid)--> 4 nucleotides b) Proteins→ 20 amino acids c) Which of these 2 are genes? (1) early research hypothesis→ genes made of protein B. A. Griffith’s experiment 1. 2 strains of the bacterium Streptococcus pneumoniae 2. EXPERIMENT ( S cells- smooth, R cells= rough) a) Living S cells (pathogenic control) injected in mouse, mouse dies b) Living R cells (nonpathogenic control) mouse healthy c) Heat-killed S (nonpathogenic control), mouse healthy Downloaded by Tina Zhu ([email protected])  lOMoARcPSD|46266463 d) Mixture of heat-killed S cells and living R cells (1) MOUSE DIES and forms LIVING S CELLS (2) DNA falls out of S cells and R cells pick this up and incorporate and use it this is what bacteria can do this e) He called this phenomenon transformation C. B. Avery, MacLeod, McCarthy Experiment 1. Lysed S cells 2. Separated contents into-lipids, proteins, polysaccharides, and nucleic acids 3. Tested each for transforming ability 4. Only DNA could transform R bacteria to S bacteria out of all contents 5. Many scientists still skeptical a) Still believed it was protein→ no one believed them D. C. Hershey-Chase Experiment 1. bacteriophages(or phages)- viruses that infect bacteria a) Virus is just DNA (or RNA) and protein (1) No lipids or carbs b) Conclusio