BIO 311C Final Exam Review PDF

Final Exam Review Sunday, Dec 8th 2024 Review is recorded! Slides will also be posted! Exam Information When: Friday December 13th at 10:30 AM CST ○ You are allotted 75 minutes for completion! But exam will ofﬁcially close at 3pm ○ Make sure you start PROMPTLY! Where: On Canvas under the “Quizzes” tab as like all exams before ○ HonorLock system ○ Take the exam as you normally would for all the other midterms. Format: ALL multiple choice questions–NO FRQs ○ 50% of content from Weeks 12, 13, and 14 ○ 50% of content from Weeks 1-11 ○ Final Exam is worth 106 points (21.2 % of your total grade) ○ 53 questions. Each worth 2pt. Content Review by Weeks “Unit 4”: WKs 12, 13, 14 Unit 1: WKs 1-4 Unit 2: WKs 5-8 Unit 3: WKs 9-11 Week 12: Cell Communication and Signalling Cellular Messaging Cell signaling: communication between cells ○ Simplest explanation: ligand binding to a receptor, which causes a response ○ Seen in prokaryotes and eukaryotes Signal transduction: how the signal is transmitted within the cell Local Signaling Autocrine signaling: cell targets itself ○ Often related to negative feedback systems Direct contact: through cell junctions ○ Cell junctions allow communication between the cytoplasm of neighboring cells ○ Gap junctions: animals ○ Plasmodesmata: plants/algae Paracrine signaling: a signaling molecule targets nearby cells ○ Only works with cells in close proximity because signal is spread via diffusion. Long Distance Signaling Endocrine Signaling: animals use hormones that move through bloodstream ○ Bloodstream carries message to target cell in a remote part of the body ○ The message (hormone) will only bind to the cell with the correct receptor in the body Synaptic Signaling Synaptic signaling: neurotransmitter (chemical message) is converted into electrical signal in neurons; allows for responses (i.e. pulling hand away from hot burner) ○ Outside the cell: high Na+ and Cl-; inside the cell: high K+ At rest, inside of the cell is NEGATIVE; outside of the cell is POSITIVE ○ Charges shift during signal transmission → as signal moves across, inside temporarily becomes more positive ○ At end of signal transduction, inﬂux of Ca2+ allows for the release of neurotransmitter to pass signal onto next neuron Signal released: Neurotransmitter Signal received by: neurons; creates a response 3 Stages of Cell Signaling 1. Reception: binding of signal molecule to receptor → conformational change of receptor 2. Transduction: message is being relayed through the cell via the activation of enzymes a. Transduction is any steps in between the reception and response b. Passed along in a cascade that causes each protein to change shape 3. Response: activation of cellular response G-protein coupled receptors 1. Reception ○ When ligand binds, it converts GDP → GTP ○ GTP activates an enzyme that starts the cascade Receptors to know: G-protein Receptor tyrosine kinases coupled receptors, receptor tyrosine ○ Dimerization: 2 signaling molecules bind to 2 receptors, kinases, ligand-gated ion channels, causing the receptors to bind to each other, forming a dimer and steroid receptors ○ Cytoplasmic regions become phosphorylated, activating Q: Which of the major categories of relay proteins transmembrane receptors involves GDP Ion channel receptors being converted to GTP as part of the ○ Signaling molecule binds to receptor and opens channel signal? ○ Ions move across, which causes the cellular response A: G-Protein Coupled Receptor (GPCR) Steroid receptors (intracellular) ○ Steroid hormones freely cross membrane to reach intracellular receptors Non-polar/lipid-soluble messengers ○ Some can bind directly to DNA without ○ Ex: estrogen is a hormone that can bind to different receptors in different kinds of cells to enact various responses Transduction: Phosphorylation/Dephosphorylation When you phosphorylate (add a phosphate group using a kinase) → changes conformation/becomes active When you dephosphorylate (w/ a phosphatase) → restore the protein to its inactive form Phosphorylation cascade: multiple relays of phosphorylation Transduction: Second Messengers Small, non-protein molecules that diffuse freely through the cell Participate in GPCRs and RTKs Ex: Ca2+ ○ Normally at very low levels inside the cell ○ When Ca2+ enters cell, a small amount Ca2+ can act as 2nd messenger Signal Regulation 1. Speciﬁcity: ligand-receptor speciﬁcity a. Same signaling molecule and location, different responses from cell’s particular collection of proteins b. Branching and cross talk 2. Ampliﬁcation: make a signal bigger than it is a. Analogy: speaking into a megaphone 3. Diversity: same molecule binds to different receptors enacting different responses a. Helps with tissue specialization 4. Overall efﬁciency of response a. Response enhanced by scaffolding proteins that group proteins in the pathway together 5. Termination/control of signal a. Resetting the system by removing the stimuli or degrading components Week 13: Mitosis and Meiosis DNA/Chromosomal Structure ★ Chromatin ○ Loose form of DNA and proteins ○ Present when cell is NOT dividing ★ Chromosomes ○ Condensed/tightly packed form of DNA ○ Found ONLY during cell division ★ Chromatid ○ Describes a singular copy of a chromosome ○ Sister chromatids are two copies of a chromosome (formed via duplication) and connected at the centromere The Cell Cycle Two Key Stages 1. INTERPHASE: cell spends most time here ○ G1 phase: growth, protein synthesis, cell functions ○ S phase: “synthesis” - DNA replication Amount of DNA doubles ○ G2 phase: growth pt.2, organelles replicate 2. M PHASE: mitosis & cytokinesis ★ What about prokaryotes? ○ Binary Fission ○ DNA replication → chromosome segregation → cytokinesis = 2 EXACT copies of parent Mitosis - Exact Copy of Cells Eukaryotic nuclear division. Conserves chromosome number by allocating replicated chromosomes equally to each of the daughter nuclei. Prophase ○ Chromatin condenses into discrete chromosomes, mitotic spindle form, nucleolus dissolves (Prometaphase) ○ Nuclear envelope fragments to permit mitotic spindle “grabbing” chromosomes at kinetochores Metaphase ○ Spindle is complete and chromosomes align on metaphase plate/equator: “Meet in the Middle” Anaphase: chromatids separate Apart ○ Pulled toward opposite ends of cell (poles) Telophase ○ Daughter nuclei form, mitotic spindle disappears Cytokinesis: division of cytoplasm ○ Cleavage furrow (animal cells) or cell plate (plant cells) splits daughter cells into 2 Mitosis Diagram Human Ploidy How many sets/copies of chromosomes in a cell? Somatic cells: diploid (2n) - two copies of genetic material subdivided into chromosomes ○ Any cell that is not a reproductive cell Human somatic cell: 22 pairs of autosomes and 2 sex chromosomes ○ Autosome meaning anything that isn't a sex chromosome Gamete cells: haploid (n) - one copy of each chromosome (unpaired). Allele: any alternative version of a gene that *may* produce different phenotypes Diploid vs. Haploid Q: In a diploid cell with 3 chromosome pairs (2n = 6), how many sister chromatids will be found in metaphase of mitosis? Q: What will the daughter A. 12 cells look like after mitotic division? Indicate ploidy. A. Q: Meiosis results in _ _ cells a. 2 haploid c. 2 diploid b. 4 haploid d. 4 diploid A. Meiosis results in 4 haploid cells (from 1 diploid cell) Homologous Chromosomes ★ Homologous Chromosomes ○ “Homologous” refers to the similarity between structures ○ SET of chromosomes, where each chromosome comes from mom and the other comes from dad ○ NOT genetically identical ★ What makes homologous chromosomes? ○ Must be similar in size and shape ○ Have the same genes in the same order, but can be different in variation, resulting in different alleles ★ KEY CONCEPT IN MEIOSIS!! Homologous Chromosomes Example This set of chromosomes are NOT homologous because they are a different size and shape. Meiosis Cell division that occurs in SEXUALLY reproducing organisms. Consists of 1 replication and 2 divisions. Results in half the number of chromosomes, product is known as gametes! Meiosis I separates homologous chromosomes. Meiosis II separates sister chromatids. 1. Prophase I: duplicated chromosomes pair with homologs (synapsis). *CROSSING OVER* 2. Metaphase I: homologous pairs line up facing the pole, microtubules attached 3. Anaphase I: pairs of homologs separate to poles 4. Telophase I: each half cell is now haploid 5. Prophase II: spindle app forms 6. Metaphase II: sister chromatids at plate not necessary identical 7. Anaphase II: sister chromatids separate and cohesin separates 8. Telophase II: nuclei form, chromosomes decondense Meiosis Diagrams Crossing Over - Meiosis The reciprocal exchange of genetic material between two nonsister chromatids during prophase I of meiosis. Non-sister chromatids are broken at corresponding positions DNA breaks are repaired, joining DNA from one non-sister chromatid to the corresponding position of another Independent Assortment - Meiosis Random arrangement of pairs of homologous chromosomes at the center of a cell during metaphase I Meiosis allows for novel combinations of traits that were not observed in the previous generation - genetic variation! Animal Life Cycle Haploid gametes (egg and sperm) are produced by meiosis Two gametes fuse during fertilization and form a diploid zygote Zygote goes through mitosis → multicellular body Other Eukaryotic Life Cycles: Plants/algae have alternation of generations Fungi/protists have spores. Most of their life is spent as haploid. Week 14: Genomes and Biotechnology Recombinant DNA Plasmids: vehicles of recombinant DNA ○ Non-chromosomal DNA ○ Easy to isolate and manipulate Ways to introduce recombinant DNA: ○ Once inside the cell, the DNA is incorporated into the cell’s DNA by natural genetic recombination ○ Can add methyl groups to nucleotides to prevent insertion Retroviruses: Can also be used to deliver a gene ○ RNA virus that replicates by inserting DNA into a cellular chromosome (reverse transcriptase) Polymerase Chain Reaction (PCR) Use PCR to amplify DNA (make copies) for use in DNA cloning ○ Exponential generation of target DNA sequence ○ Cycle 1 consists of 3 steps, each with a very speciﬁc temperature: 1) Denaturation, 2) Annealing, 3) Extending DNA Technology Probes/FISH: single-stranded sequence of RNA or DNA used to search for its complementary sequence in a sample genome Fluorescence allows binding to be visualized Identiﬁes presence or location of speciﬁc mRNAs Reverse-Transcriptase-Polymerase Chain Reaction (RT-PCR): used RNA as template to help reverse transcribe RNA into complementary DNA (cDNA) using reverse transcriptase Standard PCR procedure used to amplify cDNA and detection (i.e. COVID tests!) Gel Electrophoresis Use gel electrophoresis for separating and visualizing DNA according to molecular size ○ DNA is negatively charged (phosphate group), so the sequences will travel down towards the anode (positive-end). ○ Smaller fragments will travel further Larger fragments will be closer to cathode–travel least distance DNA Technology DNA microarrays: This gene is expressed by which cells? ○ Used to study the expression of ALL genes ○ Compare patterns of gene expression across genome in different tissues at different times or under different conditions ○ Microarray consists of tiny amounts of many single-stranded genes ﬁxed to a glass slide CRISPR-Cas9 system: Gene-editing technology ○ Cas9 enzyme will cut both strands of DNA complementary to the guide RNA After the cut, the DNA is repaired and nucleotides may be introduced to modify it Also used to disable/knock out the target gene to study it Small Nucleotide Polymorphism (SNPs) Each SNP represents a difference in a nucleotide 3 million SNPs in human genome ○ The majority of variation in human genomes Frequently associated with inherited disorders, but they are rarely directly involved in the disease because they’re in the noncoding regions Stem Cells Q: ___ cells can give rise to any type of cell, but ___ cells can only give rise to a limited subset of cells. A: embryonic stem cells; adult stem cells Embryonic (pluripotent) stem cells: ○ Undifferentiated and can become ANY kind of cell ○ Obtained from embryos Adult stem cells: ○ Can only become a LIMITED number of cell types Induced pluripotent stem cells: ○ Generally skin or bloods (differentiated) cells that have been reprogrammed back into an embryonic-like pluripotent state that allows for development into a variety of cell types ○ Used for therapeutic treatments Cloning Therapeutic cloning: ○ the use of cloned embryos as a source of stem cells to treat disease Cloning plants using single-cell cultures ○ Easy to clone/genetically engineer because there are more ways to transfer recombinant DNA into plants Cloning animals using nuclear transplantation ○ Fuse nucleus of a differentiated body cell to an un-nucleated egg cell Only a small percentage of cloned embryos develop normally to birth–many show defects ○ Epigenetic changes in adulthood may conﬂict with developmental needs of an embryo ○ Flaws with mtDNA Genomics and Bioinformatics Forensic applications: ○ Every individual’s genetic proﬁle is unique because of their highly repetitive and individually distinctive short tandem repeats (STRs) STRs help us crack cold cases and release those falsely imprisoned by determining how many sets of repeats a individual has Bioinformatics: genome analysis ○ The use of computer programs/ mathematical models to organize and study the vast amount of biological data Transposable Elements Transposable elements: prokaryotes and eukaryotes have stretches of DNA that can move from one location to another within a genome ○ Makes up ~75% of human repetitive DNA Helps facilitate recombination or crossing over, may carry gene(s) to a new position, may create new sites for RNA splicing → genome evolution Comparing Genomes Chromosome sets contribute to diversity ○ Chromosomal mutations introduced by chromosomal duplication ○ Some genes diverged so much that they have a new protein function ○ Multigene families: collections of 2+ identical or very similar genes Very Similar ex: different genes for globins expressed at different times in development allowing hemoglobin to be most effective depending on the environmental condition. Comparing genome sequences provides us clues to evolution and development ○ Compare highly conserved genes, genes in closely related species or genes within a species ○ Branch points on phylogenetic tree represent divergence from a common ancestor. Genome size ≠ Organism complexity Covalent bonds: sharing pair of valence electrons ○ Non-polar covalent: equal sharing of electrons ○ Polar covalent: more electronegative atoms have greater pull on electrons Ionic bonds: based on charge; transfer of electrons to make ions ○ Makes a cation (+) and anion (-) Intermolecular forces/Chemical Interactions: ○ Van der Waals: due to instantaneous dipoles (+/- charges) between molecules - super important in our bodies! Week 1-2 ○ Ex: Geckos can climb on walls due to VDW Hydrogen bonds: H covalently bound to an electronegative molecule (F, O, N) can interact with F, O, N Intro to Biology on another molecule & H bonds give water its unique properties! Chemical Bonds, Water, and Carbon Ex: cohesion, adhesion, high speciﬁc heat, evaporative cooling, expansion upon freezing, great solvent Water dissociates to form hydroxide (OH-) and hydronium (H3O+) ions Isomers: carbon-based molecules with the same molecular formula, but different structure and properties Water’s ability to create intermolecular hydrogen bonds results in its inability to break up which of the following compounds? a) Sugars b) Ions c) Amino acids d) Lipids Water’s ability to create intermolecular hydrogen bonds results in its inability to break up which of the following compounds? a) Sugars Nonpolar compounds will not be adequately dissolved b) Ions in aqueous solutions. Lipids are nonpolar compounds c) Amino acids that are mainly insoluble in water. This causes lipids to congregate together, rather than be broken apart in d) Lipids aqueous solutions. Lipids will generally come together to form globs or balls called micelles. Ions, amino acids, and sugars (carbohydrates) are all polar, and will be adequately dissolved and ionized by water. Carbohydrates: ○ Disaccharides: dehydration of 2 monosaccharides Forms a glycosidic linkage b/t 2 monomers ○ Alpha: -OH group attached to BOTTOM ○ Beta: -OH group attaches to TOP Indigestible to humans (ex: cellulose) ○ Polysaccharides: complex carbs Storage: starch (plants) + glycogen (animals) Structural: cellulose (plants) + chitin (exoskeleton and fungi cell wall) Lipid: not a true polymer b/c not made of monomers ○ Fats/triglyceride: ester bond of OH of glycerol to the carboxyl group of the fatty acids Week 3 ○ Phospholipid: 2 fatty acid heads + 1 glycerol ○ Steroids: 4-carbon ring lipids ○ Saturated: SOLID at room temp, linear structure ○ Unsaturated: LIQUID at room temp, cis bonds cause kinks in fatty acids Monomers and Macromolecules: Protein: amino acids joined by peptide bond; each AA has unique R group/side chain with unique properties (polar, nonpolar, basic, etc.) Carbohydrates, Nucleic Acids, ○ 4 levels of structure (1°, 2°, 3°, 4° - know these!) Proteins, and Lipids ○ Shape determines function; pH, temp, salt [ ] can affect shape Nucleic Acids: nucleotides joined by phosphodiester bonds ○ DNA: double stranded; A-T & C-G; deoxyribose ○ RNA: single stranded; A-U & C-G; ribose 3 types: mRNA, rRNA, tRNA Aquaporins are proteins embedded in the plasma membrane that allow water molecules to move between the extracellular matrix and the intracellular space. Based on its function and location, describe the key features of the protein’s shape and the chemical characteristics of its amino acids. Aquaporins are proteins embedded in the plasma membrane that allow water molecules to move between the extracellular matrix and the intracellular space. Based on its function and location, describe the key features of the protein’s shape and the chemical characteristics of its amino acids. The protein must form a channel in the plasma membrane that allows water into the cell since water cannot cross the plasma membrane by itself. Since aquaporins are embedded in the plasma membrane and connect with both the intracellular and extracellular spaces, it must be amphipathic like the plasma membrane. The top and bottom of the protein must contain charged or polar amino acids (hydrophilic) to interact with the aqueous environments. The exterior transmembrane region must contain non-polar amino acids (hydrophobic) that can interact with the phospholipid tails. However, the inside of this channel must contain hydrophilic amino acids since they will interact with the traveling water molecules. Miller-Urey Experiment: stimulated early earth environment (no O2, had gases CH4, NH3, H2, H2O) ○ Proved life originated by abiotic synthesis of small, organic molecules (molecules → macromolecules → protocells → RNA) Order of things on Earth: ○ Prokaryotes → O2 on Earth → single-celled eukaryotes → multicellular eukaryotes → animals Oxygen revolution: signiﬁcant rise in O2 levels due to photosynthetic cyanobacteria releasing O2 Week 4 ○ Opportunity: using oxygen for aerobic respiration (more usable energy) ○ Problem: oxygen and side products react with bonds, inhibit enzymes, damage cells (wiped out many prokaryotic groups) LARGE surface area : volume ratio = GOOD Prokaryotes and Eukaryotes, Origins, and Cell Structure and Function Eukaryotes Plasma membrane structure: ○ Selective permeability ○ Temperature, cholesterol presence, and types of fatty acid affects packing Types of transport: ○ Passive (no ATP) vs. active (ATP needed) Week 5 ○ Osmosis vs. diffusion Tonicity: ○ Compare relative to the environment OUTSIDE of the cell Membrane Structure and ○ ○ Hypertonic (outside has more solute) Hypotonic (outside has less solute) Function, and Gradients ○ Isotonic: equal amount of solute on both sides Membrane proteins: ○ Integral, peripheral, and transmembrane Functions of membrane proteins: ○ JETRAT Selective Permeability Plasma Membrane Diffusion Across the Membrane Molecules allowed to cross easily without Passive diffusion assistance by proteins ○ Along the concentration gradient ○ Small non-polar molecules (ex. gases) ○ No energy involved ○ Steroids ○ Can be unfacilitated (simple) or facilitated ○ Small, uncharged polar molecules (water) ○ Ex. osmosis Factors that affect permeability: Active diffusion ○ Temperature is related to kinetic energy ○ Against the concentration gradient ○ Cholesterol reverses effects of temp. ○ Energy involved ○ Saturated vs. unsaturated fats Entropy (S), Enthalpy (H), Gibbs Free Energy (G) Spontaneous reactions: ○ Aka exergonic, ΔG0, requires energy, anabolism Enzymes, which are catalysts, have Week 6 speciﬁc temp and pH that they function in, which will affect their ability to lower energy activation barriers to increase reaction rates Energy Transformation, ATP, and Enzyme inhibitors: ○ Competitive inhibitor, non-competitive inhibitor, Enzymes and allosteric inhibitor Enzyme-substrate interactions: ○ Lock-and-key model and induced-ﬁt model ATP aids in energy-coupling reactions in cells, which drives photosynthesis and cellular respiration Thermodynamics Entropy vs. Free Energy Endergonic vs. Exergonic Entropy - The measure of disorder Exergonic - Net release of free energy Free energy - The measure of instability (or ○ Gproducts < Greactants the availability of energy) ○ ∆G < 0 Endergonic - Requires free energy to begin the reaction ○ Gproducts > Greactants ○ ∆G > 0 Enzymes Enzymes Enzyme Regulation Protein catalysts that speed up reactions by Competitive inhibition decreasing activation energy (Ea) ○ The inhibitor attaches to the active site ○ They do NOT change the free energy Non-competitive inhibition Enzyme activity is altered primarily by ○ The inhibitor attaches to a site away from temperature, pH, and pressure the active site changing the shape of it. ○ Can you look at a graph and determine the Feedback inhibition optimal conditions for an enzyme? ○ The product inhibits the enzymes/gene Redox reactions: ○ Oxidation (OIL): losing an electron ○ Reduction (RIG): gaining an electron ○ Track hydrogen atoms to track movement of e⁻ 2 types of phosphorylation: ○ Substrate-level vs. oxidative phosphorylation Week 7 3 types of catabolic pathways: ○ 1) Aerobic respiration (36-38 ATPs), 2) anaerobic respiration (2-36 ATPs), 3) fermentation (2 ATP) Cellular Respiration Stages of Cellular Respiration: ○ 1. Glycolysis ○ 2. Pyruvate oxidation ○ 3. Citric acid (Krebs) cycle ○ 4. Oxidative phosphorylation Lactic acid fermentation vs. alcoholic fermentation First Two Steps of Cell Respiration Glycolysis Pyruvate Oxidation Occurs in the cytoplasm Pyruvate (a 3-carbon mlcl) is transported Two step process - Net 2 ATP from the cytoplasm to within the ○ Investment phase: 2 ATP invested mitochondria ○ Payoff phase: 4 ATP, 2 NADH, and 2 ○ Only in the presence of O2! pyruvate Two key things ATP is generated via substrate ○ Loading NAD+ with hydrogen phosphorylation ○ Pyruvate transforming into acetyl-CoA Final Two Steps of Cell Respiration Krebs Cycle Oxidative Phosphorylation Completely breaks down pyruvate into Two step process within the mitochondria: CO2 within the mitochondria ○ ETC - NADH and FADH2 pass down Creates the following (per acetyl CoA!) electrons to other carriers → release of ○ 1 GTP (functionally equivalent to ATP) via energy ○ The energy is used to pump H+ ions from substrate phosphorylation the matrix to the intermembrane space ○ 3 NADH ○ 1 FADH2 ○ Chemiosmosis - the H+ ions diffuse back in via ATP synthase to create ATP ○ 2 CO2 Fermentation Without O2 the ETC does not function properly → no terminal acceptor! ○ An alternative pathway is fermentation The key purpose is to regenerate NAD+ ○ If NAD+ is not regenerated, then the preceding process of glycolysis will not occur ○ It is also good for producing minimal levels of ATP Stages of photosynthesis: ○ 1. Light reactions (“light” part) PSII → PSI → chemiosmosis ○ 2. Calvin cycle (“synthesis” part) Electron ﬂow pathways: ○ Linear electron ﬂow ○ Cyclic electron ﬂow–used to make Week 8 more ATP or if too much NADPH Calvin cycle stages: ○ 1. Carbon ﬁxation ○ 2. Reduction and sugar formation Photosynthesis ○ 3. Regeneration of RuBP Alternative mechanisms of carbon ﬁxations ○ Photorespiration C3, C4, and CAM plants Light Reactions Photosystems Cyclic vs. Linear The main players in the light reactions Linear Flow Need to funnel photons to the center of the ○ Two ETCs and Two Photosystems used system in order to excite electrons. First ETC responsible for ATP Second ETC responsible for NADPH PSII (680) is unique: Cyclic Flow ○ It is considered the strongest biological ○ One ETC used (via PSI) oxidizing agent ○ Only produces ATP Calvin Cycle and Adaptations The Calvin Cycle Adaptations Requires the products, ATP and NADPH, of Photorespiration → Process of combining linear electron ﬂow to reduce CO2 RuBP with O2 instead of CO2 Produces ADP and NADP+ which will be ○ Sucks because it is a wasteful process that reused in the Light Reactions uses up ATP and no sugar is being formed ○ This means that if there is a fault in the C4 and CAM Photosynthesis Calvin Cycle, the Light Reactions will also ○ Both are energy inefﬁcient suffer ○ Both still maximize photosynthesis Produces G3P, a precursor to glucose Different experiments: ○ T.H. Morgan: genes are on chromosomes ○ Frederick Grifﬁth: DNA is responsible for transformation ○ Avery, McCarthy, MacLeod: DNA is responsible for transformation ○ Hershey and Chase: DNA is the genetic material ○ Chargaff’s rule: A+G = T+C ○ Wilkins and Franklin: DNA is a double-helix Week 9 ○ Watson and Crick: DNA is anti-parallel ○ Meselson and Stahl: Replication follows a semi-conservative model Replication steps and enzymes: DNA Structure, Replication, and ○ DNA grows in 5’ → 3’ direction ○ Leading strand vs lagging strand Hereditary ○ DNA polymerase I vs III ○ Prokaryotes vs. eukaryotes DNA repair: ○ Mismatch repair: DNA polymerase proof-read newly made DNA replacing any incorrect nucleotides ○ Nucleotide excision repair: nuclease cuts out damaged nucleotides Questions What does primase do? a. Synthesizes an RNA primer at 5’ end of the leading strand b. Synthesizes an RNA primer at 5’ end of each Okazaki fragment of the lagging strand c. Synthesizes an RNA primer at 3’ end of each Okazaki fragment of the lagging strand d. Synthesizes an RNA primer at 5’ end of the leading strand and at 5’ end of each Okazaki fragment of the lagging strand Answer What does primase do? a. Synthesizes an RNA primer at 5’ end of the leading strand b. Synthesizes an RNA primer at 5’ end of each Okazaki fragment of the lagging strand c. Synthesizes an RNA primer at 3’ end of each Okazaki fragment of the lagging strand d. Synthesizes an RNA primer at 5’ end of the leading strand and at 5’ end of each Okazaki fragment of the lagging strand Universal genetic code: ○ Redundant but not ambiguous ○ Start codon and 3 stop codons Transcription: ○ DNA → mRNA ○ Enzyme: RNA polymerase ○ Template vs coding strand ○ Initiation, elongation, termination ○ Transcription complex Week 10 Translation: ○ mRNA → protein ○ Initiation, elongation, termination (tRNA, E/P/A sites) ○ Wobble The Genetic Code, Transcription, ○ Signal-recognition particle Prokaryotes vs. eukaryotes: Translation, and Mutations ○ Polyribosome (both) ○ Coupling (only prokaryotes) Mutations: ○ Frameshift mutation ○ Substitution mutation (silent, missense, nonsense) Question What is the difference between the Template and Non-Template strands in Transcription? Answer The template strand provides a template from which the RNA is actually transcribed (5’ to 3’ direction) The non-template strand (coding) strand sequence speciﬁes the AA sequence of the encoded protein Prokaryotic gene regulation - operon (and others): ○ Inducible: lac operon ○ Repressible: trp operon ○ Positive regulation - cAMP and CAP Eukaryotic gene regulation: ○ Regulation of chromatin structure ○ Transcription regulation (ex.promoter, Week 11 transcription factors) ○ RNA processing regulation (ex.alternative splicing) ○ Post-translational modiﬁcation Gene Regulation and Expression (ex.proteolysis) Embryonic development: ○ Cytoplasmic determinant ○ Induction Cancer development: ○ Mutation of proto-oncogene: growth factor ○ Mutation of tumor-suppressor gene: p53 Questions In order to increase chromatin condensation, one would need to (increase/decrease) histone acetylation or (increase/decrease) methylation? Answer In order to increase chromatin condensation, one would need to (increase/decrease) histone acetylation or (increase/decrease) methylation? Q&A Session

BIO 311C Final Exam Review PDF

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