Bio Final Study Guide PDF

Bio ﬁnal study guide What is science? Science aims to understand the natural world through observation and reasoning Science is both descriptive and hypothesis-driven Science is in a constant state of change as new data, methods, and ideas arise Science uses deductive and inductive reasoning Deductive reasoning uses general principles to make specific predictions ○ big to small ○ Ex: natural selection used to explain changes in population inductive reasoning uses specific observations to make generalizations conclusions ○ Small to big ○ Ex: fossils show life on earth has changed over time Descriptive science vs hypothesis driven science Science begins with observations ○ Much of science is purely descriptive ○ Ex: classifying and describing life in a given habitat ○ Genomic sequencing A systematic approach to understanding the natural world ○ The scientific method observation → question → hypothesis → prediction → conclusion Experiments and variables Control experiment- independent variable is unaltered ○ Purpose: minimize effects of factors other than the one being tested independent variable- what is being changed, x axis dependent variable- what is being measured, y axis Pseudoscience Describes claims, beliefs, or practices that purport to be science Do not use accepted scientific methods to draw conclusions The claims or beliefs often cannot be tested Ex: astrology and intelligent design Key concepts in the practice of science Science vs pseudoscience: can be tested to see if true vs cannot be tested Basic vs applied: expand general knowledge vs solve real world problems Objective vs self correcting: science is directly as stated vs peer review and reproducibility Scientific theories: is supported by substantial direct observation, experimental evidence, and scientific reasoning ○ Expresses idea of which we are most certain ○ Is not guess or conjecture Key concepts of practice in science Reductionism: ○ Breaks a complex process down to its component parts ○ Has an advanced understanding in many areas of biology Systems biology: ○ Focuses on how components work together ○ Relies heavily on modeling biological processes ○ May allow prediction of emergent properties Living systems share several characteristics 1. All living systems consist of cells a. Might just be one cell b. Connection between structure and function is major theme in biology 2. Living systems store and process information a. In the form of DNA 3. Living systems transform energy a. Plants- sun to chemical energy b. Humans- eat their energy 4. Living systems grow and reproduce 5. Living systems adapt and evolve What determines an organism's phenotype Determined by genotype- genetic material and environmental influences Produces phenotype- observable traits Classifying organisms Need to make, label, and organize all of the diversity Each organism is named to binomial system with genus species All descending from one common ancestor Cell theory 1. All organisms are composed of cells 2. Cells are the smallest living things 3. Cells arise only from existing cells a. All cells today represent a continuous line of descent from the first living cell Atoms are the smallest, stable unit of cells Element- substance with one type of atom with the same number of protons, cannot be broken down Atomic number- number of protons in an atom Valence electron- electrons in the outermost energy level Isotope- atoms of the same element that have different numbers of neutrons Atomic mass- sum of mass of protons and neutrons in atom Carbon is the basis for most biological molecules Atoms contain discrete energy levels Greater potential energy moving away from the nucleus The number and arrangement of electrons mediates reactions Octet rule- atoms tend to completely fill outer energy levels Electrical charges and atoms Electronegativity- electrons are not shared equally, distribution of charge is not equal Cation- positively charged ion ○ Formed when an atom loses an electron Anion- negatively charged ion ○ Formed when an atom gains an electron Atoms form molecules from chemical bonds In order from strongest to weakest: Covalent- sharing of electron pairs Ionic- attraction of opposite charges Hydrogen- sharing of a H atom Water structure and properties Cohesion- attraction of water molecules to each other ○ Maintains liquid state, surface tension Adhesion- attraction of water molecules to charged (polar) surfaces ○ Capillary action High specific heat- amount of heat required to change 1 g of substance by 1 C ○ Maintains internal temps, absorbs heat from chemical reactions Water properties High heat of vaporization- amount of energy required to change 1 gram of substance from liquid to gas Water as a solvent- Water clusters around charged and polar molecules Solid water is less dense than liquid water Organization of nonpolar- Cluster in water and do not dissolve ○ Cannot form hydrogen bonds Ionization- Water rarely and spontaneously form ions pH scale Measured hydrogen ion concentration Higher pH value means lower hydrogen ion concentration (more OH-) logarithmic scale- difference of 1 is ten-fold change in hydrogen ion concentration Acidity- as pH decreases Basic- as pH increases More protons (H+), lower pH (1,2,3), more acidic Carbon is the framework Carbon atoms may bind to other carbon atoms, or to atoms of hydrogen, oxygen, nitrogen, phosphorus, or sulfur Hydrocarbons- hydrogens bonded to chain of carbons Different atoms bond to form amino acids ○ Have electronegativities associated with each, forming polar regions Functions of macromolecules Carbs- energy storage and structural support Proteins- enzyme and structural support Nucleic acids- storage of genetic information in form of RNA Lipids- energy storage, membrane structure, cell communication Nucleotide strands and bonds DNA 5’ group look for phosphate group DNA 3’ group look for hydroxyl group Phosphodiester bonds- linkage between 3’ carbon atom of one sugar and the 5’ carbon atom of another molecule Types of bases Purines- adenine and guanine ○ Double ringed Pyrimidines- cytosine, thymine, uracil ○ Single ringed Linked together for form a nucleic acid C and G and A and T (U in RNA) ○ Hydrogen bonds between the nitrogenous bases Amino acids Each amino acid has a different R group 20 total amino acids 4 main types: ○ Non polar and neutral ○ Polar and neutral ○ Acidic and polar ○ Basic and polar Linked together via a peptide bond ○ Covalent bond created through dehydration reaction protein structure N terminus- 5’ C terminus- 3’ Denaturation Changes in chemical and physical conditions in the environment Protein unfolds and deactivates Can restore if conditions are right, renaturation Extreme conditions cause to adapt Common features and differences between P and E Plasma membrane separates the cell interior (cytoplasm) from the extracellular environment DNA is genetic material Control of gene expression Metabolic pathways (glycolysis, respiration, photosynthesis) Eukaryotes have internal, membrane enclosed compartments Prokaryotes tend to be smaller Prokaryotes are unicellular Have different propulsion systems Cellular compartments and functions Nucleus: Protects DNA and separate rna synthesis from protein synthesis Nuclear envelope- separate inside from outside Nuclear pores- opening for protein and RNA movement Nucleus- synthesis of RNA components in ribosome Lysosomes: Digestive enzymes to help cell recycle building blocks for its own reactions Cellular compartments and function Golgi apparatus: Protein and lipid modification from ER Protein sorting and packaging Peroxisomes: Oxidation of fatty acids Biosynthetic reactions Detoxification ER: Calcium storage and detoxification Rough ER: Protein synthesis Smoother ER: lipid synthesis Cytoplasm vs cytosol Cytoplasm- everything inside cell membrane Cytosol- just the liquid portion of the cytoplasm Exocytosis and endomembrane systems ER to golgi to either: ○ Lysosomes ○ Plasma membrane or environment Exocytosis- outward movement Chloroplast and mitochondria comparisons Similarities: Synthesize ATP Reproduce by binary fission Multiple membrane structures Circular DNA Ribosomes Differences: Mitochondria metabolize sugar to synthesis ATP Chloroplast only found in plants using light energy to make ATP and sugars Mitochondria has 2 membrane structures Chloroplasts have 3 membrane structures The theory of endosymbiosis Mitochondria and chloroplasts originated from bacteria that were engulfed by ancestral eukaryotes Mitochondria: came from bacteria that performed oxidative metabolism Chloroplasts: came from bacteria that performed photosynthesis Explains why both have circular dna, ribosomes, divide within cell by binary fission Cytoskeletal ﬁlaments Actin: Muscle contraction (along with myosin filaments) Cell shape, cell crawling cytokinesis Microtubules: Organization, cell swimming, mitosis Intermediate filaments: Structural support Extracellular matrix vs cell wall Extracellular matrix: Meshwork of secreted carbs and proteins Fibrous nature Cell wall: Outside of plasma membrane for protection and structural support Molecular composition of cell membranes Lipids- provide structure of membrane Carbs- outer surface of plasma membrane form a sugar coat ○ Provides protection and facilitates cell-cell recognition Proteins- membrane-specific functions Phospholipid structure Polar hydrophilic head group Two non-polar hydrophobic tails Fatty acid- long chain hydrocarbons with a carboxylic acid group at one end Saturated: no double bonds are present Unsaturated: double bonds between one or more pairs of successive carbons Selective permeability Small, nonpolar molecules- o2, co2, n2 ○ Readily diffuse through bilayer Small, uncharged, polar molecules- h20, ethanol ○ Diffuse at slower rate Large, uncharged polar molecules- glucose, amino acids Fluid mosaic model Two dimensional fluid in which proteins are inserted or dissolved and gives the membrane a fluid character Membrane proteins: integral and peripheral Cholesterol, proteins, carbs, phospholipids Evidence from x rays and neutron scattering Membrane proteins Integral membrane proteins: Embedded in phospholipid bilayer Must destroy bilayer structure to isolare peripheral membrane proteins: Non-covalently bound to transmembrane proteins or phospholipid heads Can be removed from membrane without destroying membrane structure Cell membranes are asymmetric Two faces are different in composition and function Each face has: ○ Different types of phospholipids ○ Different types of proteins ○ Different domains of TM proteins ○ Only outer face has carbs Membrane proteins classiﬁed by function Receptors- detect signal molecules and initiate the cells response to that signal Identity markers- give cell identity and allow cell recognition Enzymes- associate with different membranes and promote specific chemical reactions Cell adhesion- one cell to attach to another or to extracellular matrix Cytoskeletal attachment- transmit changes in cytoskeleton to changes in plasma membrane, controls cell shape Transport- facilitate movement of small hydrophilic molecules from one membrane side to the other Transport by channel proteins Creates a pore in the membrane Many involved in ion transport Function by passive transport Can be specific for certain molecules Are always open or are gated Active transport by carrier proteins Use energy to create and/or maintain a concentration gradient Molecules are transported or pumped up (against) the concentration gradient Many active transported are ATPases ○ Use energy from ATP hydrolysis to power movement Active transport vs passive transport Passive- move down gradient thru channel and carrier proteins Active- use energy to make or maintain gradient from low to high concentrations Use ATP hydrolysis for energy Coupled transport: symporters and antiporters Symporters- ion and molecule move in same direction Antiporters- use energy from ion moving down gradient to transport molecule in opposite direction osmosis Water will move down its concentration gradient Solute concentration differ on two sides of cell membrane; influences movement of water Move towards higher solute concentration Types of tonics Hypertonic: higher concentration on outside, skinny cell Isotonic: equal concentration Hypotonic: higher concentration on inside, fat cell Pinocytosis- cell drinking Non Selective uptake of water and macromolecules Constant inward budding of plasma membrane to form endocytic vesicles ○ Eventually to be delivered to lysosomes Constant inward budding of plasma membrane to form endocytic vesicles Receptor-mediated endocytosis Receptor protein binds specific molecule (target) Receptor and target are collected in clathrin-coated vesicles Provides selective uptake of necessary molecules Phagocytosis- cell eating Selective engulfment of another cell Not all cells capable of this ○ Ex- white blood cells destroying invaders Energy basics Flows into the world from the sun Forms: mechanical, heat, sound, electric current, light, radioactivity Two states: ○ Kinetic- energy of motion ○ Potential- stored energy Energy- ability to do work, most commonly measured in joule Reduction- gain of electrons, negative charge Oxidation- loss of electrons, positive charge First law of thermodynamics Energy cannot be created or destroyed ○ Can only change from one form to another ○ Some energy is lost as heat during the energy conversion ○ Total amount of energy in the universe is constant Energy continuously flows thru biological systems from from sun to heat second law of thermodynamics Entropy (disorder) is continuously increasing Energy transformations proceed spontaneously to convert matter from a more ordered/ less stable form to a less ordered/ more stable form Free energy (gibbs free energy) G= energy available to do work G= H-TS ○ H: enthalpy- energy in a molecules chemical bonds ○ T: absolute temperature (degrees C+273) ○ S= entropy Delta G= change in free energy Delta G= delta D- T delta S Endergonic (Positive) reactions Products of reaction have more free energy than the reactants Not spontaneous Require input of energy (endergonic) Bond energy H is higher, entropy S is lower Energy level of reactions less than products Exergonic (negative) reactions Proceed spontaneously Contain less free energy than the reactants Lower bond energy H, higher entropy S, or both Exergonic- release energy Not instantaneous- may still need energy input to start Energy level of reactants greater than products Activation energy Extra energy required to destabilize existing bonds and initiate a chemical reaction An exergonic reaction rate depends on the activation energy required ○ Larger activation energy= slower reaction rate To increase ration rate, either: ○ Increase energy of reacting molecules (heating) ○ Use a catalyst to lower activation energy catalysts Substances that influence chemical bonds in a way that lowers activation energy of a reaction Cannot violate laws of thermodynamics ○ Cannot make an endergonic reaction Do not alter the proportion of reactant turned into product Enzymes are biological catalysts Many proteins and some RNA molecules act as enzymes Enzyme shape stabilizes transient association between substrates Enzyme is not changed or consumed in reaction ○ Can be used again and again Different types of cells contain different enzymes: ○ Enzymes specify cell structure and function Enzymes may be soluble or associated with membranes The active site A pocket or cleft for substrate binding Allows precise fit of substrate Applies stress to distort bond(s) to lower activation energy Enzymes may change shape to maximize contact with the substrate ○ Induced fit Factors that inﬂuence enzyme function Concentration of substrate Concentration of enzyme Any chemical or physical condition that impacts enzymes structure ○ Temperature ○ pH ○ Regulatory molecules Enzyme regulatory molecules Allow cells to control enzyme activities (for allosteric enzymes) Inhibitors- molecule that binds to and decreases the activity of an enzyme Competitive inhibitor- competes with substrate for active site Noncompetitive inhibitor- binds the enzyme at a site (allosteric site) other than active site ○ Causes shape change that makes energy unable to bind to substrate Metabolism Total of all chemical reactions carried out by an organism Anabolic reaction (anabolism)- expand energy to synthesis molecules Catabolic reaction (catabolism)- harvested energy by the breakdown of molecules Biochemical pathways Reactions occur in a sequence Product of one reaction is the substrate for the next reaction Many occur within organelle or within certain membranes ○ Ex- inner mitochondrial membrane needed for ATP synthesis Feedback inhibition End product of pathway binds allosteric site on first enzyme in pathway Shuts off pathway so raw materials and energy are not wasted The atp cycle Is main energy currency for all cells stored in muscles ATP is constantly synthesized and used ○ Cells only store ATP for a few seconds In coupled reactions, an exergonic reaction (atp hydrolysis) is combined with an endergonic reaction ○ Overall net negative delta G ATP synthesis depends on: energy from exergonic cellular reactions ATP hydrolysis provides: energy for endergonic cellular processes ATP is also used to control the activity of proteins phosphorylation/ dephosphorylation is a molecular light switch To turn on: ○ enzyme kinase binds and hydrolyzes ATP ○ covalently attaches the released phosphate group to target protein To turn off ○ Enzyme phosphatase removes phosphate group from relevant amino acid side chain How organisms obtain energy Organisms can be classified based on how they obtain energy: Autotrophs: ○ Produce own ATP and organic molecules thru photosynthesis ○ Plants, algae, photosynthetic bacteria Heterotrophs (95% species) ○ Live on organic molecules made by autotrophs ○ Convert that energy into ATP ○ Animals, fungi, most protists Transfer often involves cofactors working as electron carriers Transfer of electrons always has some loss of energy All are easily and reversibly oxidized and reduced NAD+ accepts 2 electrons and 1 proton to become NADH NADH donates 2 electrons and loses 1 proton to become NAD+ NADH has higher energy ○ More electrons carrying more energy is present in NADH The aerobic respiration of glucose Glucose is oxidized in the presence of molecular oxygen (02) Final electron acceptor is oxygen (02) Energy must be harvested in small steps ○ More energy harvested from using more steps ○ Involve electron carriers ○ Convert half of energy stored in glucose to ATP Glucose oxidation proceeds in four stages 1. Glycolysis (in cytosol) 2. Pyruvate oxidation (in matrix) 3. Krebs cycle (in matrix) 4. Electron transport chain and chemiosmosis (inner membrane) a. Bulk of ATP synthesis occurs b. Cytoplasm or plasma membrane for prokaryotes Steps 2, 3, 4 need oxygen to work Glycolysis converts one glucose to two pyruvates Multi-step biochemical pathway Two phases: Energy input ○ ATP must be supplied by cell ○ Glucose is converted into 2 G3P molecules Energy production ○ ATP ○ Electrons accepted by NAD+ to produce NADH ○ Each G3P molecule is converted into pyruvate Glucose in ﬁrst converted into two g3p molecules Generation of glyceraldehyde-3-phosphate (G3P) (split of glucose) requires energy input Endergonic process ○ Hydrolysis of 2 ATP molecules ○ Needed to prime cleavage of glucose backbone Split into 2, 3 carbon molecules Each g3p molecule is converted into pyruvate G3P is oxidized- NAD+ into NADH ○ Transfers 1 proton and 2 electrons NAD+ is reduced to NADH Substrate level phosphorylation- transfer of Pi from ADP to form ATP Products of glycolysis: ○ 2 ATP (net) ○ 2 NADH Pyruvate oxidation during aerobic respiration (oxygen) Occurs in: ○ Mitochondrial matrix of eukaryotes ○ Plasma membrane of prokaryotes ○ Catalyzed by pyruvate dehydrogenase Causes the removal of co2 from pyruvate Coenzyme- small organic molecule used as cofactor Each pyruvate is used to make: ○ 1 co2 (x2) ○ 1 NADH (x2) ○ 1 acetyl-CoA (x2) Krebs cycle Oxidizes the acetyl group generated by pyruvate oxidation Occurs in the matrix of the mitochondria Pathway of 9 steps divided into 3 parts: 1. Acetyl-CoA + oxaloacetate to citrate a. CoA cycles out and can be reused by oxidation 2. Citrate rearrangement and decarboxylation (2 CO2 released) 3. Regeneration of oxaloacetate) Krebs cycle summary For each acetyl-CoA entering: Release 2 molecules of CO2 Reduce 3 NAD+ to 3 NADH Reduce 1 FAD (electron carrier) to FADH2 Produce 1 ATP Regenerate oxaloacetate Cycle always happens twice, true end products: ○ 4 CO2, 6 NADH, 2 FADH, 2 ATP After the ﬁrst 3 stages of aerobic respiration One glucose molecule has been oxidized to: ○ 6 CO2 ○ 4 ATP ○ 10 NADH ○ 2 FADH2 Electron transport chain Numbers are collective totals Oxidative phosphorylation- produces most Of ATP derived from glucose oxidation Electron transport chain Three transmembrane enzyme complexes harvest some energy from electrons and pass lower energy electrons onward Complexes use energy harvested from electrons to pump protons (H+) from matrix to intermembrane space ○ Creates concentration gradient- higher proton concentration in intermembrane space compared to matrix Low [H+] ph 8 High [H+] ph 7 Explaining the image NADH delivers electrons to NADH dehydrogenase enzyme ○ Extracts energy to power proton movement across membrane Carrier Q gives to bc1 complex ○ Extracts energy to power proton movement across membrane Cytochrome c ○ Catalyzes reduction of molecular oxygen FADH2 electrons bypass first step Chemiosmosis The proton gradient represents potential energy ○ Only way for protons to move into matrix is thru proton transporter ATP synthase uses energy released by movement of protons to synthesize ATP from ADP and Pi Movement of 4 H+ thru ATP synthase powers the synthesis of 1 ATP molecule from ADP and Pi Calculating the energy yield of respiration Number of ATP molecules produced by ATP synthase depends on ○ Number of protons transported across inner membrane ○ Number of protons needed for ATP synthesis Final electron acceptors For aerobic organisms: With o2 (respiration) ○ o2 Without 02 (fermentation) ○ Organic molecules (pyruvate) Incomplete oxidation For anaerobic organisms: Respiration ○ S or CO2 or inorganic metal ○ Inorganic molecules: sulfate and nitrate Fermentation differences Lactic acid fermentation produced from electron transfer from NADH to pyruvate Ethanol fermentation produces ethyl alcohol and carbon dioxide Extraction of energy from macromolecules Key intermediates *glucose is not the only source of energy* Catabolism of proteins Proteins are broken down into individual amino acids subunits Amino groups removed thru deamination reaction Remainder is converted into molecule ready for glycolysis or krebs cycle Catabolism of fats Fats are first broken down to fatty acid and glycerol Fatty acids are converted to two carbon acetyl groups by beta oxidation ○ Each acetyl group is combined with coenzyme A to form acetyl- CoA ○ Acetyl- CoA enters krebs cycle Photosynthesis overview Energy for almost all life on earth comes from photosynthesis Carbon dioxide is reduced to glucose using electrons gained from oxidation of water driven by sun's energy Photosynthesis and respiration use the products of each other as starting substrates Chloroplasts and mitochondria form an energy cycle Photosynthesis uses products of respiration as starting substrates Respiration uses products of photosynthesis as starting substrates Evolutionary related Photosynthesis occurs in chloroplasts Triple membrane structure ○ Outer membrane with interacts with cytosol ○ Inner membrane that encloses internal compartment Matrix- stroma ○ Thylakoid disks Stacked in columns (garna) Contains chlorophyll and protein complexes Convert light energy to chemical energy Two stages of photosynthesis Light dependent reactions ○ Require light ○ Occur in the thylakoid ○ Capture energy from sunlight ○ Make ATP and reduce NAD+ to NADPH ○ Product O2 as a byproduct Light independent reactions (carbon fixation) ○ Does not require light ○ Occur in the stroma (matrix) ○ Use ATP and NADPH to synthesize organic molecules from CO2 Pigments absorb photons of visible light Photons: particle of light that acts as discrete bundle of energy Energy is inversely proportional to the wavelength of the light ○ Shorter wavelength= more energy ○ Blue (shorter, more energy) than red (longer, less energy) Photoelectric effect When a photon strikes a molecule with the correct amount of energy, the molecule will absorb the photon and raise an electron to a higher energy level ○ Excited electron ○ Chloroplasts in photosynthesis Pigments have characteristic absorption spectra Chlorophyll a ○ Main pigment in plants ○ Absorbs violet-blue and red light ○ Only pigment that can directly convert light energy to chemical energy Chlorophyll b ○ Accessory pigment ○ Absorbs blue and red-orange light ○ Adds to range of absorbed light Carotenoids ○ Accessory pigments ○ Absorbs blue and green light ○ Adds to range of absorbed light ○ Also function as antioxidants Chlorophyll reflects green Carotenoids reflect orange and red Chloroplasts have two linked photosystems Oxygenic photosynthesis: oxygen generating Photophosphorylation: production of NADPH from NADP+ and ATP from ADP Light dependent reactions Overall goal: creation of proton gradient across the thylakoid membrane where the concentration is greater in thylakoid space than stroma Water is electron donor- replaces electrons pairs that reaction center donated to electron acceptor Low [H+] High [H+] ATP is produced via chemiosmosis ATP synthase uses proton gradient to produce energy for ATP synthesis Low protons (high pH) High protons (low pH) Stroma Low [H+] Thylakoid membrane High [H+] Thylakoid space Noncyclic photophosphorylation Noncyclic photophosphorylation generates NADPH and ATP but building organic molecules requires more energy ○ Occurs in both photosystems cyclic photophosphorylation Cyclic photophosphorylation allows cells to produce additional ATP by “short-circuiting” photosystem I to create larger proton gradient ○ High energy electrons leave photosystem I are used to make ATP instead of NADPH ○ Cycle between photosystem I and- b6f complex (infinite loop) 2e Light independent reactions: the calvin cycle Biochemical pathway that allows for carbon fixation ○ Uses ATP as energy source ○ Uses NADPH as source of protons and electrons ○ Converts inorganic CO2 into organic carbohydrates ○ Also called C3 photosynthesis ○ Occur in the stroma The calvin cycle has three phases Occurs in stroma of chloroplasts 1. Carbon fixation a. Key step: RuBP+CO2= 2 PGA b. Uses enzyme ribulose bisphosphate carboxylase/oxygenase (Rubisco) 2. Reduction a. PGA is reduced to G3P 3. Regeneration of RuBP a. G3P is used to regenerate RuBP 3 turns (3 CO2) to make enough carbon to make new G3P 6 turns to incorporate enough carbon for 1 glucose molecule photorespiration CO2 O2 Rubisco has 2 enzymatic activities RUBISCO Carboxylation Carboxylation Oxidation ○ Leads to carbon fixation ○ Addition of CO2 to RuBP RuBP ○ Favored under normal conditions Oxidation Carbon fixation Photorespiration ○ Leads to photorespiration (Calvin cycle) ○ Addition of O2 to RuBP leads to CO2 release ○ Favored in hot and dry conditions Reverse processes/ compete with each other Results: ○ CO2 and O2 compete for active site on Rubisco ○ Problems for C3 plants C4 and cam pathways minimize photorespiration Some plants have evolved to capture CO2 by another mechanism C4 and CAM Add CO2 to PEP to form a 4-carbon molecule ○ Use PEP carboxylase instead or rubisco ○ Has greater affinity for CO2 and no use for oxidase activity Minimizing impact of photorespiration C4 plants use a spatial solution CAM plants use a time-based solution Nucleic acids are assembled from nucleotides DNA is a nucleic acid composed of nucleotides Nucleotides consist of: ○ 5-carbon sugar (deoxyribose) Each carbon is bound to different functional group ○ Nitrogenous base Adenine, thymanine, cytosine, guanine Determines identity of nucleotide Attached by covalent bond ○ Phosphate group (PH4) Attached to a 5’ carbon of the sugar ○ Free hydroxyl group (-OH) attached at the 3’ carbon of the sugar Attached to daughter during replication Dna and rna differences DNA: Deoxyribose sugar Thymine base pairs with adenine Double strand RNA: Ribose sugar Uracil base pairs with adenine Single strand Phosphodiester bonds link nucleotides Phosphodiester bonds ○ Formed between the phosphate group of one nucleotide and the 3’ (-OH) of another nucleotide ○ Form long chains of DNA thru dehydration synthesis reactions ○ Phosphate group is linked to two sugars by ester bonds ○ Will always have free 5’ and 3’ at different ends ○ The chain of nucleotides has intrinsic polarity (5’-3’ orientation) Chargaff’s rules Amounts: ○ Amount of adenine= amount of thymine ○ Amount of cytosine= amount of guanine Proportion of purines (A and G)= the proportion of pyrimidines (C and T) ○ Or add to 50 The watson-crick model of dna Proposed a double helix structure Two nucleotide strands ○ Backbone made of repeating phosphate and sugar units joined by phosphodiester bonds ○ nitrogenous bases on each nucleotide pair with nitrogenous bases in the opposing strand thru hydrogen bonds Strands are antiparallel ○ Can deduce sequence of one strand from the other Complementary base pairs G forms 3 H bonds with C A forms 2 H bonds with T Gives consistent diameter An introduction to dna replication Semi-conservative: one strand from parent model remains intact DNA replication requires: Something to copy: parental DNA molecule (template) Something to do the copying: enzymes (DNA polymerase) Building blocks to make new copy: nucleoside triphosphates ○ Only pentose sugar and nitrogenous base DNA replication occurs in 3 stages: Initiation: the process of replication starts Elongation: new DNA strands are synthesized Termination: the process of replication ends DNA polymerase Matches template base with complementary nucleotides and link incoming nucleotide to daughter strand Several types: all have several common features ○ Add new bases to 3’ end of existing strands ○ synthesize in 5’ to 3’ direction ○ Require a primer of RNA Reading in 3’ to 5’ Writing in 5’ to 3’ Prokaryotic replication E. coli contains a singular circular molecule of DNA (chromosome) Replication ○ Begins at one origin of replication- particula genome where replication is initiated ○ Catalyzed by replisomes (contains DNA polymerase) ○ Proceed in both directions around the chromosome The e.coli replication fork Helicase and primase (replisome) : unwinds DNA and synthesizes new primer for lagging strand DNA gyrase: relieve torsional strain in DNA SSBs: maintains template DNA as single strand DNA polymerase III (2): keep strand separate ○ Use clamp molecule to keep DNA on track ○ Carry out simultaneous synthesis of both leading and lagging strands Looping in lagging strand: polymerases can move together in direction of replication fork Fork moves in direction of parent DNA Replication is semi-discontinuous DNA is composed of two antiparallel strands DNA polymerase can only synthesize in 5’ to 3’ direction ○ Problem: how can both standards be synthesized simultaneously? ○ Solution: replication is semi-discontinuous Synthesis occurs continuously on one strand and discontinually on the other Leading strand is synthesized continuously from an initial primer Lagging strand synthesized discontinuously with multiple priming and synthesis events ○ Creates Okazaki fragments Synthesized in opposite direction of fork movement Eukaryotic replication Basic components/ mechanisms similar to prokaryotic situation Complicated by: ○ Larger amounts of DNA Multiple origins of ○ Multiple chromosomes replication Can occur simultaneously or genome is replicated within reasonable time ○ Linear chromosomes: must deal with replications of ends Needs special mechanisms to ensure ends are copied Telomeres Specialized structures found at the ends of eukaryotic chromosomes Composed of short repeated DNA sequences Protect ends from nucleases and maintains chromosome integrity telomerase Allows for replication of lagging strand ends Contains RNA template (matches repeating sequence) Synthesizes last segment of DNA ○ Can base pair to telomere DNA and synthesizes short stretches of DNA at the end Connection between senescence (cell aging) and telomere length ○ Expressed in embryos and childhood ○ Not expressed in adults (only stem cells) ○ Stop dividing when lose telomerase activity Cancer cells generally show activation of telomerase Cells contain multiple dna repair mechanisms Mistakes may occur during replication ○ DNA polymerase has “proofreading” ability to fix mistakes ○ Some mistakes remain and maintain genetic variation Mutagens (radiation and chemicals) ○ Increase the number of mutations above the background level Two general categories for DNA repair systems: ○ Specific repair: targets a single type of DNA damage and repairs only that damage ○ Nonspecific repair: use a single mechanics, to repair multiple types of DNA Photorepair removes thymine dimers Specific repair mechanism: ○ UV light induces thymine dimers Covalent link of adjacent thymine bases ○ Photorepair by photolyase Absorbs light in visible range ○ Uses energy to cleave thymine dimer Excision repair Nonspecific repair mechanism: Steps: ○ Recognition of damage ○ Removal of damaged region ○ Re-synthesized using the info on the undamaged strand as template Gene expression and the central dogma Transcription- RNA synthesis Translation- protein synthesis DNA to RNA to protein Gene: discrete nucleotide sequence on a chromosome that codes for an RNA or protein Types of rna All types of RNA are synthesized from DNA template by transpicton ○ Messenger RNA (mRNA)- codes for proteins ○ Ribosomal RNA (rRNA)- components of ribosome, catalyze protein synthesis ○ Transfer RNA (tRNA)- adaptors between mRNA and amino acids ○ Small nuclear RNA (snRNA)- pre-mRNA splicing Noncoding sequences are removed ○ micro-RNA (miRNA)- regulates of gene expression rna polymerase Enzyme of synthesis- catalyzed phosphodiester bond formation Makes a single stranded RNA copy of template DNA strand Made of multiple subunits which form the core enzyme Synthesizes in 5’ to 3’ direction ○ Needs single strand DNA template Does not need primer Must be position on promoter sequence upstream of the gene to be transcribed ○ Key regions: -35 (AACTGT) and -10 (ATATTA) ○ Starts at and follows green arrow AACTGT ATATTA -35 -10 +1 Sequence process review of initiation (step 1) 5’ 3’ Coding strand A G T C A G T C A G T C A G T C A G T C 3’ 5’ Template strand +1 RNA pol opens DNA and inserts 1st subunit 5’ 3’ A G T C A G T C A G 5’ 3’ U T C A G T C A G T C 3’ 5’ Initiation of transcription Sigma subunit DNA unwound ahead Sigma subunit recognizes promoter of start site released after around 10 subunits Termination of transcription Terminator sequence: RNA base pairs with itself to create hairpin ○ Disrupts DNA/RNA/RNA polymerase interaction Eukaryotic transcription Occurs in the nucleus Three different types of RNA polymerase ○ Prokaryotes only have one ○ RNA polymerase II transcribes mRNA Promoter position and sequence differs from prokaryotes A series of transposition factors are needed that recruit and activate RNA pol II Termination sites are not well defined Primary transcripts are processed to produce mature mRNA Processing of eukaryotic MRNA Primary transcript is modified to mature mRNA by: ○ Addition of a 5’ cap- protects mRNA from degradation; helps align mRNA for translation ○ Addition of 3’ poly-A tail- protects mRNA from degradation ○ Removal of non-coding regions (introns) by spliceosome Alternative splicing Exons- coding regions that specify amino acids Introns- non-coding regions that don't need to be translated Single primary transcript may be spliced into different mRNAs by the inclusion of exons Translation Process of protein synthesis ○ Convert RNA sequence into polypeptide sequence Basics are the same in prokaryotes and eukaryotes Occurs in three stages: initiation, elongation, and termination mRNA provides template tRNAs read template and deliver specific amino acids rRNAs and proteins from translation machinery (ribosome) Protein synthesis is N-terminus to C-terminus Translation In translation, what is the importance of polymer directionality for mRNA and polypeptides mRNA is read 5' to 3', and polypeptide is synthesized N-terminus to C-terminus For "What is the major difference in mRNA organization between prokaryotes and eukaryotes?" Prokaryotic mRNA can code for multiple different proteins because one mRNA transcript contains coding sequences for all of the genes included in an operon. Because eukaryotes don't organize genes as operons, each eukaryotic mRNA only codes for one protein. Prokaryotic vs eukaryotic mrna mRNA sequence is always read 5’ to 3’ Prokaryotic mRNA (orange) often contains multiple coding sequences (due to operons) ○ Single RNA strand for coding info for 2 different proteins Eukaryotic mRNA (green) contains a single coding sequence ○ Not organized into operons Start Start Protein 1 Protein 2 5’ UTR UTR 3’ Start Protein 1 5’cap UTR UTR AAAAA-3’ Genetic code Each amino acid is specified by a sequence of 3 nucleotides, the codon 64 possible codons, but only 20 code for amino acids ○ Genetic code is redundant Genetic code is practically universal ○ Common evolutionary ancestry amongst all living things Anticodon- 3 nucleotide sequence located at the end of a tRNA molecule The ribosome Consists of two subunits ○ Small subunit- ‘decode’ the mRNA ○ Large subunit- catalyzes peptide bond formation link the appropriate amino acids to the prescribed protein The ribosome has 3 tRNA binding sites ○ Formed when large and small subunits come together with mRNA molecule ○ E-site (exit): binds tRNA of previous amino acid Just added to c terminus of growing peptide ○ P-site (peptidyl): binds tRNA attached to growing peptide chain ○ A-site (aminoacyl): holds tRNA attached to next amino acid Trna- mrna base pairing Some tRNAs can recognize more than one codon ○ Possible through wobble Wobble wobble pairing involves less stringent base pairing between 3’ base of codon and 5’base of the anticodon Redundancy- multiple sequences for the same type of amino acid Initiation: recognition of the translation start site Initiation tRNA is tRNA-met Small subunit binds to 5’ cap to determine translation start site Large subunit binds A site open to accept next tRNA amino acid Switch to elongation Elongation cycle adds successive amino acids Termination of translation Elongation continues until stop codon (UAA, UAG, UGA) is reached Release factor recognizes stop codon ○ Triggers release of new polypeptide from P-site tRNA ○ Last c terminal amino acid in ribosome Ribosome shifts one ‘codon’ and disassembles Point mutations Point mutations alter a single base ○ Base substitution: one base is substituted for another ○ Silent mutation: change in DNA nucleotide does not alter amino acid ○ Missense mutation- change to DNA nucleotide changes encoded amino acid ○ Nonsense mutation- change to DNA nucleotide that leads to a stop codon Gene expression changes over time Levels of RNA and protein for a particular gene change over time, showing gene expression is regulated Prokaryotes regulate gene expression in response to environment changes ○ Can change rapidly in response to the environment Eukaryotes regulate gene expression for development and to maintain homeostasis Maintains in all organisms using at least one of three mechanisms: ○ Transcriptional regulation, post-transpictual regulation, or post-translational regulation Gene expression 1: Transcriptional regulation Depends on the ability of RNA polymerase to interact with the DNA and thus its ability to initiate transcription Most common form of regulation of gene expression in both pro- and eukaryotic cells Dna binding proteins control transposition initiation Promoter- contains binding sites for regulatory proteins that affect the ability of a cell to begin the transcription of a gene Promoter region- regulatory DNA sequence upstream from transcription start site RNA polymerase binds to core promoter Regulatory proteins affect the ability of RNA polymerase to bind to the promoter or to initiate transcription ○ Influence ability of RNA polymerase to bind to core promoter Regulatory RNA Transcription Protein Polymerase Start Site DNA Gene Coding Protein Binding Core Sequence Site Sequence Promoter Promoter Region Transcriptional control can be positive or negative RNA Polymerase II Transcriptional Activator Positive Protein control Promoter DNA Gene Coding DNA RNA Polymerase II Transcriptional Repressor Negative Protein control Promoter DNA Gene Coding DNA Many prokaryotic genes are organized into operons Operon- a cluster of genes which have related functions which are all controlled by a single promoter ○ Allows prokaryotes to changing environmental changes due being able to make all proteins needed from a single promoter ○ Whole thing in picture Operons always have a promoter, but may have any number/combo of activator binding sites and operators Operator Transcription or Start Site Activator Binding Site DNA Activator binding site Core Promoter Region Genes Examples of transcriptional regulation in prokaryotes The lac operon produces the proteins required for lactose metabolism ○ Lactose can be used as food source if it is present and there are no preferred food sources available Negative control- lac repressor protein inhibits transcription when lactose is absent ○ Only produce proteins for lactose metabolism when lactose is present Positive control- the CAP activator protein promotes transcription when glucose is absent ○ When glucose is a more convenient food source for bacteria Transcription Operator Start Site DNA CAP binding site Core Promoter Region Operon Genes Summary of some transcriptional control mechanisms Induction- molecule in environment stimulates transcription Repression- molecule in environment prevents transcription Positive control- transcription regulated by activator protein ○ Activator protein binds to activator binding site Negative control- transcription regulated by repressor protein ○ Repressor protein binds to operator Regulation by general and speciﬁc transcription Transcription factors- regulatory proteins involved in transcription factors General transcription factors- assemble at the core promoter and recruit RNA polymerase to enable basal transcription Changing the availability of binding ability of these transposition factors can be one way to regulate transcription in eukaryotes ○ To bind DNA or interact with RNA polymerase Speciﬁc transcription factors increase gene expression May only affect one gene or a small subset of genes Found in both prokaryotic and eukaryotic cells May not always bind at or near the core promoter (eukaryotes more) Some bind to DNA regulatory regions- DNA enhancer elements ○ Increase transcription Can work together to give fine control of gene expression Chromatin structure inﬂuences gene expression In eukaryotes, DNA and histone proteins are organized into nucleosomes, assembled into a chromatin structure Changes in chromatin structure occurs by chemical modification of histones Or by ATP dependent movement of nucleosomes ○ Sliding, moving DNA, or remodeling Both affect the accessibility of the DNA for transcription Gene expression 2: post-transcriptional gene regulation Occurs during mRNA processing, mRNA transport, and translation Only occurs in eukaryotes mRNA alternative splicing, inhibition of transcript exports from the nucleus, inhibition of translation, mRNA regulation by small RNAs Alternative splicing: different proteins from one mRNA Primary mRNA transcript is spliced to remove introns from the sequence ○ Introns- DNA segment that does not code for proteins Ultimately uses same base to produce to two different proteins with different functions Export inhibition and regulation of translation initiation Export of mRNA from nucleus can be regulated ○ Prevents translation of mRNA ○ Mechanisms unknown ○ Only about 5% of mRNA is exported to cytoplasm for translation Regulation of translation initiation ○ Limit availability of proteins necessary for translation ○ Proteins bind to mRNA to prevent translation Small rnas regulate mrna to knock down gene expression Two types of small RNAs microRNA (miRNA)- single stranded RNA folds to form a small segment of double stranded RNA ○ Typically encoded in the organism's genome Small interfering RNA (siRNA)- derived from long segments of double stranded RNA ○ Can be endogenously produced by various mechanisms or introduced exogenously ○ Pairing two mRNAs RNA interference: small rnas in research RNA interference (RNAi)- the intro of double stranded RNA into an organism to selectively knock-down gene expression ○ Signals cells to produce interfering RNAs which will reduce the expression of the complementary gene Commonly used in: Nematodes, Mice, Fruit flies, Mouse ear cress Allows researchers to analyze effects of gene loss Gene expression 3: post translational gene regulation Protein modification: Primarily associated with protein modifications and degradation ○ Reduce the amount of time a protein can function Can occur in both prokaryotes and eukaryotes Degradation: Can be targeted by the addition of ubiquitin proteins ○ Ubiquitinated proteins are targeted to the proteasome for degradation Protein degradation removed unneeded, damaged, or misfolded proteins Regulation occurs at all stages of gene expression Transcriptional regulation- what is transcribed, if it happens? ○ Regulation by transcription factors, DNA accessibility Post-transcriptional regulation- what is being translated? ○ Regulation by mRNA processing, translation inhibition Post-translational regulation- how does the protein function? ○ Regulation of protein stability, activity Prokaryotic cells reproduce by binary ﬁssion Single cell splits into two cells Mitochondria and chloroplasts also divide by binary fission eukaryotic cells reproduce by mitosis and cytokinesis mitosis= nuclear division ○ Cells genome is passed onto daughter cells cytokinesis= cytoplasmic division ○ Responsible for splitting one cell into two Both rely on temporary cytoskeleton machines ○ Mitotic spindle made of microtubules Mitosis is similar for all, cytokinesis varies ○ Animal cells use contractile ring and plant cells use cell plate Karyotype: the array of chromosomes in a species or individual May be arranged according to size, staining properties, or other features Haploid (1n): the complete set of chromosomes necessary to define the species ○ 23 for humans Diploid (2n): two complete sets of chromosomes ○ 46 for humans (two copies of each in the haploid set) ○ Usually originates thru sexual reproduction ○ Each parent provides one set ○ The two copies are termed “homologous” ○ Each chromosome of a pair is a “homolog” Chromosome replication Kinetochore- where the chromosome will attach to the microtubules of the mitotic spindle Cohesins- let chromosomes line up along middle of cell during replication Each chromosome represents a single DNA molecule Two Xs= one pair Eukaryotic chromosomes Composed of chromatin (a complex of DNA and protein) Each single chromosome is one continuous DNA molecule The typical human chromosome is 140 million nucleotides A human cell contains 6 feet of DNA Two main types of chromatin present in the nucleus: ○ Heterochromatin- tightly packed and not expressed ○ Euchromatin- loosely-packed and able to be expressed DNA packaging Mitotic DNA Nucleosome solenoid chromosome DNA+histones- Compacted 10 nm Further condensed 10 nm fiber to 30 nm into around 10,000 “Beads on a string” fiber, usual fold + Charged interphase state histones attract - charged DNA The eukaryotic cell cycle Duplication of genome, accurate segregation of that genome, and division of cells contents Cell division phases: G1- primary growth stage ○ Duplicating plasma membrane, organelles, and macromolecules S- replication of DNA G2- more growth and prep for M phase M- nuclear division and cytoplasmic division ○ Cell completely rearranges its contents to mitosis and cytokinesis Interphase- G1+S+G2 The stages of the m phase G2 prophase prometaphase metaphase anaphase telophase cytokinesis Prep M Bipolar Chromosomes Chromosomes Sister Chromosomes Animals: phase spindle attach to align at chromatids decondense cleavage assembles MTs, spindle separate Nucleus furrow Centrosome Chromosomes orient, and equator Chromosomes begins to Plants: cel duplicates move to condense congress re-form poles NEDB Poles further separate Control of the eukaryotic cell cycle Basic control mechanisms are conserved: Cell cycle has two irreversible points ○ Replication of genetic material (S phase) ○ Separation of the sister chromatids Cell cycle can be put on hold at certain checkpoints ○ Process can be halted if errors are detected ○ Allows cell to respond to internal and external signals Internal- problem detection External- start or stop cell cycle progression Cell cycle checkpoints G1/S checkpoint Spindle checkpoint Are there enough nutrients? Are all Has the cell grown large chromosomes enough and made enough aligned at the components to pass on? metaphase plate? Are there growth factors? G2/M checkpoint damage repair completion of DNA replication Cell cycle control in multicellular eukaryotes Central control mechanisms same as single-cell prokaryotes Key difference: cell don’t reproduce until “told” to do so ○ Growth factor signal is recognized by receptor protein ○ Activator receptor leads to expression of proteins that cause the cell to move past the G1/S checkpoint Failure of animal cell cycle control leads to cancer Cancer involved uncontrolled cell proliferation and metastasis (inappropriate movement of cells within the animal) When mutated, two kinds of genes can perturb cell cycle control: Proto-oncogenes: ○ Normal genes that have become oncogenes when mutated ○ Oncogene may be overexpressed or stuck in “on” state (creates push) ○ Gain-of-function mutation- only one copy needs to be mutated tumor suppressor genes: ○ Normal genes that code for proteins that detect problems.stop cycle ○ Loss of “safety net” when inactivated or deleted ○ Loss-of-function mutation: both copy needs to be mutated and inactivated Sexual reproduction transmits genetic information thru cycles of meiosis and fertilization Involved alterations between diploid and haploid states ○ Diploid state dominates in most animals Diploid adults mitosis Germ-line cells carry Diploid adult out meiosis to make haploid gametes or Haploid Zygote gametes inherits fuse to genetic make info from 2 diploid parents zygote Meiosis has key features that distinguish it from mitosis Includes two rounds of division (meiosis I and meiosis II) Only includes one round of DNA replication Replication Meiosis I Meiosis II 2n, 2c 2n, 4c 1n, 2c 1n, 1c Synapsis- association between homologous chromosome pairs in meiosis I Crossing over- homologous exchange DNA segments Synapsis Occurs early during prophase I The homologous chromosomes become closely associated Involves formation of synaptonemal complex ○ Pairs homologous chromosomes along their length with a matrix of connecting proteins ○ Also called a tetrad or bivalent Crossing over Occurs during prophase I Genetic recombination between non-sister chromatids Allele of genes that were formerly on separate homologues can now be found on the same homologue Sister chromatids are no longer identical Sites of crossing over are termed chiasmata Contacted maintained until anaphase I Meiosis i Orientation of Different combos of homologues maternal and paternal is random homologues= independent assortment Sister chromatids are no longer identical because of crossing over (prophase I) Cells are haploid Meiosis II Occurs after an internal or variable length DNA replication is suppressed between meiosis I and meiosis II Resembles a mitotic division ○ Separation of sister chromatids Each daughter cell receives a complete set of chromosomes, consisting one member of each homologous pair In plants, fungi, protists- reproduce mitotically to increase number In animals- develop directly into gametes Errors during meiosis Nondisjunction leads to aneuploid gametes ○ Have either missing or extra chromosome ○ Most common cause of spontaneous abortions From the point of view of a species, the benefit of genetic variation produced by meiosis far outweighs the chances and impact of potential errors Monohybrid cross experimental design Parent generation ○ True breeding- self-fertilization, exhibits trait of interest from one generation to the next F1 generation ○ Showed dominant trait F2 generation ○ ¾ dominant phenotype ○ ¼ recessive phenotype 3:1 F2 ratio is actually 1:2:1 (genotype) ○ 1 true breeding dominant plant (homozygous) ○ 2 not-true breeding dominant plants (heterozygous) ○ 1 true breeding recessive plant Principles of segregation Each individual receives one copy of a gene from each parent Chromosomes segregate during meiosis ○ Individual haploid gametes Individuals are diploid ○ One set of chromosomes from each parent Mendel had no knowledge of chromosomes of meiosis Dihybrid cross experimental design Crosses homozygous dominant with homozygous recessive Use FOIL to ensure all possible allele combos are used Gametes are haploid, each possible offspring is diploid Principle of independent assortment In a dihybrid cross, alleles assort independently Segregation of allele pairs is independent Independent alignment of different homologous chromosomes pairs during metaphase I leads to independent segregation of allele pairs Creates haploid gametes Interpreting pedigrees- dominant pedigrees Circle= biological female Square= biology male Horizontal line= mating Bb bb Vertical line= offspring Shaded region= individuals who are bb bb Bb Bb bb affected by the trait ○ Show trait phenotype Bb Bb Bb Dominant pedigrees ○ Affected individuals can be heterozygous ○ Unaffected offspring can be born to affected parents ○ Cannot skip generations Interpreting pedigrees- recessive pedigrees Double horizontal line= mating between related individuals Half-shaded individual= a heterozygous carrier Recessive pedigrees ○ Affected individual must be homozygous ○ Can “skip” generations ○ Affected individuals can be born to unaffected parents ○ Affected offspring more frequent when parents are related ABO blood typing 3 different alleles for expressing antigens on surface of blood cell ○ IA allele (dominant) ○ IB allele (dominant) ○ i allele (recessive) 4 possible phenotypes i is recessive (no surface antigens present) IAIB expresses both surface antigens R allele (dominant) ○ Rh antigen present ○ Positive blood type r allele (recessive) ○ No antigen present ○ Negative blood type Polygenic inheritance vs Pleiotropy Phenotype is accumulation One genes impacts multiple of contribution by multiple phenotypes genes Multiple symptoms can be Traits show continuous traced back to one allele variation: termed Difficult to predict quantitative traits Ex- cystic fibrosis Many genes control one One gene controls all Incomplete dominance vs codominance Incomplete dominance ○ heterozygous is intermediate phenotype between homozygotes ○ Red flowers x white flowers= pink flowers Codominance ○ Heterozygous shows aspects of both homozygous phenotypes ○ Ex- type AB blood Epistasis One gene masks or modifies the expression of the other gene If gene products are involved in the same pathway, expected dihybrid cross ratios altered B gene determines coat color E gene determines color extension E gene epistatic to B gene ○ Any lab w the inability to distribute coat color to hair will be yellow Produces phenotypic 9:3:4 ratio Sex chromosomes and sex determination In drosophila, number of X chromosomes determines sex ○ Females have 2 X chromosomes ○ Males have 1 X chromosome and 1 Y chromosome X and Y are common sex chromosomes Structure, number, and terminology of sex chromosomes vary according to species During meiosis: ○ Female gametes= X ○ Male gametes= X or Y X linked and sex linked are the same thing Human sex determination In humans, presence of Y chromosome determines sex Y chromosome is highly condensed ○ Recessive allele on male’s X have no allele counterpart on Y Default setting for humans is female ○ Requires SRY gene on Y for maleness Image of male contains both X and Y chromosomes 22 pairs of non-sex chromosomes (autosomes) Epigenetic mechanism: dosage compensation Ensures equal expression of genes from the sex chromosomes even though females (XX) have twice the number of X chromosomes as males (XY) Levels of proteins expressed in essentially the same Differential regulation of genes on X chromosome between males and females In each human female cell, 1 of the X chromosomes is inactivated and is highly condensed into a Barr body X chromosome inactivation and genetic mosaics Females heterozygous for genes on the X chromosome are genetic mosaics ○ Different cells express different alleles depending on which X chromosome is inactivated Fur color determined by gene present on X chromosome Patchy distribution is due to a second epistatic gene Example of epistasis and X chromosome inactivation Epigenetic mechanism: genomic imprinting Imprinted genes are inactivated Genes are inactivated based on which parental line the gene was inherited ○ Imprinted allele from one parent will be inactivated, allele from other parent is expressed Expectations to mendelian inheritance Not all genes behave according to the mendelian model of inheritance Epigenetic mechanisms: regulators of gene function/expression that do not involve a change in the DNA sequence ○ Epi- (over and above), genetic (inheritance) ○ Often due to change in chromosome structure ○ Examples: Dosage compensation Genomic imprinting DNA for organelle genomes ○ Mitochondria ○ chloroplasts Nondisjunction of sex chromosomes Does not generally produce severe developmental abnormalities May cause somewhat abnormal features, but many reach maturity and in some cases may be fertile X chromosome fails to segregate ○ Triple X syndrome- female born with extra x chromosome ○ Klinefelter syndrome- male born with extra x chromosome ○ Turner syndrome- females born with 1 X chromosome Y chromosome fails to segregate ○ XYY (Jacobs syndrome) ○ Male gets extra y from father Nondisjunction change chromosome number Nondisjunction: failure of homologues or sister chromatids to separate properly during meiosis ○ Leads to aneuploidy- gain or loss of a chromosome monosomy= chromosome loss trisomy= chromosome gain Aneuploid human embryos rarely develop ○ Can survive to adulthood with 3 copies of chromosome 21 or 22 Genetic mapping/crossing over exchanges alleles on homologues Organisms have more genes/traits that assort independently than chromosomes Independent assortment of genes on same chromosomes is due to crossing over ○ Genetic recombination If crossing over occurs, parental allele are recombined producing recombinant chromosomes and thuse recombinant gametes Recombination reﬂects genetic distance TH Morgan suggested frequency of recombinant progeny reflects the relevant location of genes on chromosomes As physical distance between genes increases, so does the probability of recombination (crossover) occurring between the gene loci Measure recombination frequency with a test cross ○ Large # recombinant phenotypes= traits distant to one another ○ Small # recombinant phenotypes= traits nearby one another “Linked” traits Genetic mapping a two-point cross”: linkage analysis Recombinant frequency= # recombinant offspring/ # total offspring X 100 for % Human genome maps str Methods ○ Test crosses: “linkage analysis” ○ Disruption of genes of unknown function ○ Inducing mutant phenotypes ○ Historical pedigrees based on phenotype ○ Determines homo or heterozygous offspring Large number of genetic markers that do not alter phenotype- ○ Landmarks ○ Short tandem repeats (STRs) 2-4 bases repeated in genome ○ Single nucleotide polymorphisms (SNPs) Differences affecting a single base of a gene locus snp

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