Bio 311C Exam II Review - October 2024 PDF

Bio 311C Exam II Review Sunday, October 20, 2024  Review Session Test Information recording will be uploaded to Canvas...

Bio 311C Exam II Review Sunday, October 20, 2024  Review Session Test Information recording will be uploaded to Canvas Exam Date: Tuesday, October 22nd DURING CLASS ○ PLEASE ARRIVE ON TIME (9:30) under “Zoom” tab! ○ Confirm that your RESPONDUS is working This is one of your 3 midterms ○ 50 pts total- Worth 11% your total grade ○ 24 pts - 16 MCQ ○ 26 pts - 4 FRQ Proctoring via RESPONDUS ○ Make sure to have RESPONDUS extension downloaded and running Available from 9:30 am to 11:00 am, only during class! Study Tips TA Review Sources ○ Genna’s Study Materials ○ Ridhas Study Materials PRACTICE, PRACTICE, PRACTICE!!! ○ Use P&P questions for review ○ Square Cap questions available (PDF under TA Exam Review Materials) ○ Pearson Study Guides (has quizzes, chapter exams, an excellent source) ○ Google!! Make flashcards, know diagrams ○ Practice drawing out the pathways from start to finish on a whiteboard ○ Quiz yourself ○ Play teacher! Explain concepts to others Membrane Structure and Function Week 5 The Plasma Membrane Selective permeability: allows some substances to cross more easily than others ○ Lipid-soluble molecules, small nonpolar molecules, and small/uncharged polar molecules CAN DIFFUSE across ○ Larger polar molecules and charged molecules CANNOT DIFFUSE across so require other forms of transport Molecular Structure of the Plasma Membrane Phospholipid bilayer (amphipathic) ○ Hydrophilic head and hydrophobic tail Fluid mosaic model The Fluidity of Membranes Membranes are FLUID structures, not static! ○ Held together by hydrophobic interactions Temperature: ○ Decrease in temperature: phospholipids are more closely packed ○ Increase in temperature: phospholipids are more fluid Saturation: ○ Unsaturated hydrocarbons: more fluidity ○ Saturated hydrocarbons: less fluidity Cholesterol: ○ Low temperatures: more fluidity ○ High temperatures: less fluidity How do molecules move through the membrane? Passive transport: no ATP required; particle moves DOWN a concentration gradient ○ Simple diffusion: through lipid bilayer ○ Facilitated diffusion: aided by a protein Aquaporins: channel proteins that transport water across the membrane Diffusion is crucial in our body! Active transport: requires ATP ○ Against a concentration gradient Diffusion vs. Osmosis Diffusion: movement of a substance so that they spread evenly into a space Solutes move by diffusion ○ Spontaneous process ○ Rate of diffusion depends on: Size of molecule Temperature of the solution Concentration gradient Osmosis: diffusion of water Tonicity Tonicity: the ability of the surrounding solution determines whether a cell gains or loses water Hypertonic: more solute outside the cell ○ Cell will lose water and shrivel ○ Plant cells: plasmolyzed Isotonic: equal amount of solute on both sides of the cell ○ Cell maintains equilibrium, no net movement ○ Plant cell: flaccid Hypotonic: less solute outside the cell ○ Cell gains water (hyppo) ○ Plant cell: turgid Functions of Membrane Proteins ( JETRAT) Junction/Joinings : connect cells Enzymes : increases rates of reactions Transport : facilitated diffusion and active transport Recognition : cell markers / identification Anchorage : cytoskeleton / extracellular matrix Transduction : receptors for signaling 12  Transport Proteins Passive transport: ○ Channel proteins: Opens pathway when solutes need to pass through; usually closed, but can be activated to open Ex) Ion channels ○ Carrier proteins: When molecules bind, protein changes shape A little slower Active transport: Requires energy, moves against the concentration gradient ○ Uses carrier proteins ○ Ex) Na+/K+ pump (3 Na+ out, 2 K+ in) Membrane Potential and the Nervous System Membrane potential: the separation of opposite charges across a membrane ○ Inside of cell is more negative than the environment ○ Membrane potential causes anions (-) to move out of the cell, and cations (+) to move into the cell electrochemical gradient Neuron signaling: ○ Changes in electronegativity across neuron ○ Inside becomes + ○ This change signals the next area to do the same ○ Impulse moves down the neuron Energy Transformation, ATP, & Enzymes Week 6 Energy of Life Organism’s metabolism transforms matter and energy ○ Metabolic: starts with a molecule and ends with a product–catalyzed by a specific enzyme at each step ○ Anabolic: building of molecules; requires energy ○ Catabolic: breaking down of molecules; releases energy Forms of energy: ○ Potential: energy of state or position, or stored energy (ex. Chemical bonds, concentration gradients, electrical charge differences) ○ Kinetic: energy of movement–type that DOES work (ex. Membrane transport, chemical reactions, and mechanical motion) MORE kinetic energy = MORE movement = MORE collisions/heat = HIGHER temperature Laws of Energy Transformation Thermodynamics: ○ Isolated system: unable to exchange energy or matter with its surroundings ○ Open system: energy and matter transferred between the system and its surroundings 1st Law of Thermodynamics: ○ Energy can be transferred and transformed, but it CANNOT be created nor destroyed 2nd Law of Thermodynamics: ○ During every energy transfer/transformation, some energy is usable and is often lost as HEAT ○ Every energy transfer/transformation INCREASES ENTROPY of the universe Entropy (S) Entropy: measurement of randomness of energy in a system ○ High entropy = less order ○ Low entropy = more order ○ Organisms create ORDERED structures from less organized forms of energy and matter, and vice versa ○ Order can be produced with an expenditure of energy Spontaneous processes: occur WITHOUT energy input but must INCREASE entropy Non-spontaneous processes: REQUIRE energy and DECREASES entropy Gibb’s Free Energy and Equilibrium Gibb’s free energy: usable energy or energy that is available to do work; (ΔG°) = ΔH° - TΔS° ○ Enthalpy (ΔH°): how much heat and work was added or removed ○ Exergonic reaction: reaction will occur spontaneously if ΔG0 Equilibrium (ΔG=0): ○ System is not doing work ○ Open systems are never in equilibrium ATP and Work Most energy coupling in cells is mediated by ATP ○ Energy coupling: cells can drive endergonic reactions by supplying them with free energy released by exergonic reactions to do cellular work Chemical work: pushing endergonic reactions ○ ATP hydrolysis: remove 1 phosphate group (ATP → ADP) and release energy Transport work: pumping substances against the direction of spontaneous movement Mechanical work: flagella rotation and muscle cell contraction Enzymes Catalyst: chemical agent that speeds up a reaction without being consumed by the reaction (ex. enzymes) Enzymes: speed up metabolic reactions by decreasing activation energy ○ Active site orients substrates correctly ○ Promotes formation and breaking of covalent bonds ○ Sites are extremely specific to substrate and chemical reaction Activation energy (Eₐ): initial energy needed to start chemical reaction Reaction rates: can be sped by increasing substrates ○ Saturation: when all enzyme active sites are occupied Enzyme-Substrate Interactions Lock-and-key: shape of substrate and conformation of active site are complementary to one another Induced-fit: enzyme undergoes conformational change upon binding to substrate ○ Shape of active site becomes complementary to shape of substrate AFTER binding ○ Substrate held in active site by hydrogen bonding, electrical attraction, and hydrophobic interactions More Enzymes Enzyme Functionality: ○ Each enzyme has its optimum temperature and pH ○ Chemicals that specifically influence its function Non-protein enzyme helpers: ○ Cofactors: inorganic ions that bind to enzymes and initiate transition state ○ Coenzymes: organic molecules that add or remove chemical groups from enzymes ○ Prosthetic groups: covalently bound non-amino acid components of enzymes Enzyme Inhibitors Normal binding Competitive inhibitor: mimics substrate and competes for active site ○ Usually reversible Noncompetitive inhibitor: binds to a site away from the active site and alters the enzyme so that it is no longer fully functional ○ Substrate can still bind, but reaction is blocked--irreversible Allosteric inhibitor: a substance that binds to the allosteric site and induces the enzyme's inactive form ○ Generally acts by switching the enzyme between two alternative states: an active form and an inactive form Enzymes and Pathways Feedback inhibition: prevents cell from wasting chemical resources by synthesizing more products than needed (ex. isoleucine) Gene expression: regulation of genes that encode for specific enzymes or the activity of enzymes help maintain stability in metabolic pathways ○ Altered amino acids, specifically at their active sites, can result in novel enzyme activity or altered substrate specificity Protein modification: ○ Kinase: binds phosphate group ○ Phosphatase: removes phosphate group Practice Question In general, the hydrolysis of ATP drives cellular work by __________. A. acting as a catalyst B. lowering the free energy of the reaction C. releasing free energy that can be coupled to other reactions D. changing to ADP and phosphate E. releasing heat Answer: C. releasing free energy that can be coupled to other reactions With the help of specific enzymes, the cell can couple the energy of ATP hydrolysis directly to endergonic processes. Practice Question If a reaction is spontaneous, what must be true of its entropy and free energy? A. ΔG > 0 and entropy is increasing B. ΔG < 0 and entropy is increasing C. ΔG > 0 and entropy is decreasing D. ΔG < 0 and entropy is decreasing Answer: B. ΔG < 0 and entropy is increasing Spontaneous reactions release free energy (-ΔG) and increase entropy/disorder (2nd Law of Thermodynamics). Cellular Respiration Week 7 Redox reactions Transfer of electrons during chemical reactions releases energy stored in organic molecules Oxidation = losing electrons, losing hydrogens, gaining oxygens Reduction = gaining electrons, gaining hydrogens, losing oxygens OILRIG: Oxidation Is Loss of electrons Reduction Is Gain of electrons Oxidizing agent : electron acceptor (being reduced) Reducing agent : electron donor (being oxidized) If something is an oxidizing agent, then it is being reduced (oxidizing another molecule) Question: If something is being oxidized, is it a reducing agent or oxidizing agent? Cell Respiration -Oxygen dependent process, series of redox reactions -Substrate level (glycolysis and Krebs cycle) vs. Oxidative Phosphorylation (ETC & chemiosmosis) (generates 90% of ATP) -Main players of Cell Respiration: -ATP = Adenosine Triphosphate: high energy release when going from ATP -> ADP +Pi -NAD+/NADH: Intermediate electron acceptor (Brings electrons and H+ ions to ETC) -FAD/FADH2: Intermediate electron acceptor: (Brings electrons and H+ ions to ETC) Aerobic = with oxygen, Anaerobic = without oxygen C6H12O6 + 6O2 -> 6H2O + 6CO2 + ATP Stages of Cellular Respiration 1.Glycolysis : splitting of sugar to get pyruvate (3 C sugar) 2.Pyruvate oxidation : pyruvate oxidized to produce acetyl CoA 3.Citric acid (Krebs) cycle : acetyl CoA oxidized to produce ATP and electron-carriers (NADH + FADH ) 2 4.Oxidative phosphorylation : end product of ATP synthesized 1) Electron transport chain (ETC) 2) Chemiosmosis Step 1: Glycolysis (glyco-sugar, lysis - split) Breaks down 6 C sugar (Glucose) into 3 C sugar (Pyruvate) Harvests chemical energy by oxidizing glucose to pyruvate Occurs in the cytosol with/without oxygen - seen in early prokaryotes that likely used glycolysis to produce ATP before O2 revolution 2 major phases : energy investment phase and energy payoff phase Used in cellular respiration and fermentation 1 glucose (6C) + 2 NAD+ + 2 ADP + 2 Pi → 2 pyruvate (3C) + 2 NADH + 2 H+ + 2 net ATP Step 2: Pyruvate Oxidation 3 different enzyme-catalyzed reactions: 1) oxidation of pyruvate and releases CO2 (3C -> 2C) 2) reduction of NAD+ to NADH 3) combination of remaining 2-carbon fragment + coenzyme A to form acetyl CoA Occurs in the mitochondrial matrix, where oxygen is required to finish out glucose oxidation Will not happen without oxygen Remember: 2 acetyl CoA is made from one glucose molecule! 2 pyruvate + 2 NAD+ + 2 coenzyme A → 2 acetyl CoA + 2 NADH + 2 CO2 + 2 H+ Step 3 Krebs Cycle: Completes breakdown of glucose (Tip: Follow the carbons!) First Step: Acetyl CoA (2C) + oxaloacetate (4C) -> Citrate (6C) Occurs in the mitochondrial matrix, where oxygen is indirectly needed to regenerate NAD+ and FAD+ FADH2 and NADH produced are electron-carriers that will aid in the electron transport chain (ETC) Remember: The Krebs cycle occurs twice for one glucose molecule! Question: How many molecules of FADH2 is made from one glucose molecule? 2 acetyl CoA + 6 NAD+ + 2 FAD + 2 ADP + 2 Pi → 4 CO2 + 6 NADH + 6 H+ + 2 FADH2 + 2 ATP Step 4: Oxidative Phosphorylation -ETC NADH carries hydrogen ions and high-energy electrons to ETC, where they combine with O2 to form H2O and ATP + NADH gets oxidized to NAD Electrons give the energy necessary to pump hydrogen ions from the matrix into the intermembrane space After electrons are done passing through the electron transport chain, oxygen (O2) is the final electron acceptor (Final destination for the electron) Oxygen is reduced to water ETC does not directly generate ATP Step 4: Oxidative Phosphorylation - Chemiosmosis Couples ETC to ATP synthase + Chemiosmosis: H then moves down its concentration gradient back across the inner mitochondrial membrane, passing through ATP synthase + - as H moves through ATP synthase, ADP is converted into ATP (exergonic w/ endergonic reactions!) Don’t get confused with H+ flow! ETC: Matrix to intermembrane space (Low to high concentration) Chemiosmosis: Intermembrane space back to matrix (High to low) Fermentation - Lactic Acid/Alcohol Fermentation will directly follow glycolysis if there is NO oxygen present Main function is to regenerate NAD+ from NADH in order to reuse NAD+ for glycolysis Lactic acid fermentation: - regenerates NAD+ required by glycolysis - in animals’ skeletal muscle - C6H12O6 + 2 ADP + 2 Pi → 2 lactic acid + 2 ATP Alcohol fermentation: - regenerates NAD+ required by glycolysis - done by yeast (eukaryotes) and some plant cells - C6H12O6 + 2 ADP + 2 Pi → 2 CO2 + 2 ethanol + 2 ATP Helpful Links for Studying Cellular Respiration Cheat Sheet (Genna's Doc) Overview of Cellular Respiration (Khan Academy) Article of the Steps of Cellular Respiration (Khan Academy) You got this! :) Photosynthesis (WK 8) Photosynthesis is Redox Photosynthesis is captured by the following formula: 6CO2 + 6H2O → C6H12O6 + 6O2 Why can we say this is redox? ○ Well what is being oxidized? → What is losing H atoms? ○ What is being reduced? → What is gaining H atoms Recall with redox, this is the manipulation of e- which messes with potential energy ○ Loss of e- = Loss of H atoms = Loss of potential energy (oxidation) Chloroplasts The site of photosynthesis ○ Thylakoids: the site of the light reactions Therefore contains chlorophyll ○ Stroma: the site of the Calvin cycle Pigments facilitate light capture ○ Chlorophyll a - the main pigment ○ Chlorophyll b ○ Carotenoids ○ Why are plants green? Photosystems These are the main players in the Light Reactions The Light Harvesting Complex ○ “Antenna” pigments funnel the photons to the centermost chlorophyll a pigments ○ These are known as… The Reaction Center Complex ○ These are specialized chlorophyll a pigments that donate the received photon to an electron acceptor Light Energy = Sunlight Wavelength: distance between crests of electromagnetic waves (determines the type of energy) ○ Wavelengths produce colors we can see from 380nm-750nm. Plants produce different light-absorbing pigments that absorb and reflect specific wavelengths. When pigment absorbs light, it goes from ground state to (unstable) excited state. Linear Electron Flow Key ideas: ○ Uses both photosystems ○ Produces roughly equal amounts of ATP and NADPH ○ Two ETCs traversed One for ATP production One for NADPH production ○ Photophosphorylation The first ETC generates enough Note where the H+ ions are moving! energy to create a H+ gradient In the light reactions, the ETC forces movement from ATP synthase takes up the the stroma to the thylakoid. accumulated H+ Sounds familiar? What about ATP synthase then? Cyclic Electron Flow Key ideas: ○ Uses only PSI ○ Produces only ATP via photophosphorylation ○ One ETC traversed ○ No oxygen produced Why might that be? (Think PSII) ○ Protects cells from light-induced damage Why might this be needed? ○ Usage of ATP > Usage of NADPH  Slides 15-18 The Calvin Cycle Requires the products, ATP and NADPH, of linear electron flow to reduce CO2 Produces ADP and NADP+ which will be reused in the Light Reactions ○ This means that if there is a fault in the Calvin Cycle, the Light Reactions will also suffer Produces G3P, a precursor to glucose ○ For every molecule of G3P, 3 cycles are needed Three Parts of the Calvin Cycle 1) Carbon Fixation a) Each CO2 is combined with a 5-C molecule RuBP via the enzyme rubisco b) Creates a 6-C molecule which is broken down into two 3-C molecules (3P-G) 2) Reduction and Sugar Formation a) Requires ATP and NADPH (consequently creating ADP and NADP+) b) Creates a reduced G3P from 3P-G → can be used for glucose, starch, or… 3) RuBP reformation a) Requires ATP b) Complex and beyond the scope of this course Adaptations Stomatal Closing → stomata is where O2 is released and CO2 is received ○ Ideal in hot and arid conditions in order to limit loss of water ○ Sucks because the ideal process of C3 photosynthesis is halted in favor of… ○ Photorespiration → Process of combining RuBP with O2 instead of CO2 Ideal for using up the products of the Light Reactions and preventing them from accumulating Sucks because it is a wasteful process that uses up ATP and no sugar is being formed Adaptations (cont.) C4 Photosynthesis CAM Photosynthesis At the end of the day both tradeoff the minimized water loss with greater energy consumption