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Life 102 Exam 2 Study Guide

by: Elise Benton

Life 102 Exam 2 Study Guide LIFE 102

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Typed study guide that covers chapters 8-11 from lecture notes. Outline form. Key terms, ideas, specific molecules and proteins we need to know are highlighted in different colors.
Attributes of Living Systems
Louis B Bjostad
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This 12 page Study Guide was uploaded by Elise Benton on Wednesday March 9, 2016. The Study Guide belongs to LIFE 102 at Colorado State University taught by Louis B Bjostad in Spring 2016. Since its upload, it has received 201 views. For similar materials see Attributes of Living Systems in Life Science at Colorado State University.

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Date Created: 03/09/16
Exam 2 Study Guide  Life 102  Prof. Lou Bjostad By Elise Benton  KEY TERMS        KEY IDEAS      KEY MOLECULES      KEY PROTEINS CHAPTER 8 CHEMICAL REACTIONS ● bonds breaking and forming ● Activation energy: initial energy needed to start reaction (energy barrier)  ○ often supplied as heat from surroundings  ● METABOLISM: totality of an organism chemical reactions  ● metabolism is an emergent property of life: emerges from interactions between molecules within the cell  ● metabolic pathways: series of steps that begins with a specific molecule and ends with a  product  ○ each enzyme and molecule different from last ○ catabolic pathways: release energy by breaking down complex molecules into simpler one ■ uses hydrolysis ■ cellular respiration­ breaks down glucose with oxygen ○ anabolic pathways: consume energy to build complex molecules from simpler ones ■ synthesis of proteins from amino acids PHYSICS ● kinetic energy: energy of motion ● heat: or thermal energy, kinetic energy associated with random movement of atoms or  molecules ● potential energy: energy due to location or structure  ● chemical energy: potential energy available for release in a chemical reaction  ● thermodynamics: study of energy  transformations ○ First Law of Thermodynamics:  energy can be transferred or transformed, but not created or  destroyed ○ 2nd law of thermodynamics: energy transfer/transformation increases entropy: disorder of  universe  ■ some energy is unusable some is lost as heat  ■ cells create ordered structure from less ordered materials ■ universes total entropy is increased  ● free energy change: ΔG, living systems free energy can do work  ○ negative free energy change processes are spontaneous  ■ no energy input, occur on their own ■ can be used to do work  ■ start: more free energy, less stable, greater work capacity  ■ change: spontaneous change, free energy decreases, system becomes more stable, free  energy is released and used for work  ■ end: less free energy, more stable, less work capacity ○ exergonic reaction: releases free energy into its surroundings ■ spontaneous, often gravitational  ○ endergonic reactions: absorbs free energy from its surroundings  ■ non spontaneous ATP ● ATP does work by energy coupling  ● overall exergonic reaction ○ energy is released when terminal phosphate bond is broken  ■ ATP­ phosphate group= ADP ■ release of energy powers cellular work ○ energy is consumed to add phosphate to ADP to make ATP= phosphorylation ■ molecules that gain phosphate are phosphorylated ■ energy to phosphorylate comes from catabolic reactions ● ATP used to change shape of carrier proteins, propel motor proteins through cytoskeleton ENZYMES: catalytic, speed up metabolic reaction without being consumed by it ● speed up reaction by lowering activation energy  ● don’t affect total free energy change, only speed up reaction that was going to happen anyways ● specificity ○ each enzyme only works with specific molecules ○ substrate: reactant that enzyme works with  ○ active site: region on enzyme where substrate binds ■ lowers activation energy ● orients substrate correctly ● strains substrate bonds ● provides favorable microenvironment ● covalent bonds to substrate ○ induced fit: active site slightly changes shape to better fit substrate, enhances ability to catalyze  reaction ● enzymes have specific temp and pressure in which they operate ● Regulating enzyme activity ○ all cells regulate metabolic pathways  ■ switching: on/off genes that encode enzymes ■ regulation ○ allosteric regulation: inhibits or stimulates enzyme activity ■ regulatory molecules bind to protein at ONE site and affects protein function at ANOTHER site ■ polypeptide subunits ■ enzymes have active and inactive forms ● activator: stabilizes active form ● inhibitor: stabilizes inactive form ○ cooperativity: amplifies enzyme activity ■ binding of substrate stabilizes changes in shape to all other subunits, makes each loading faster ○ enzyme inhibitors ■ competitive: bind to active site of enzyme, competing with substrate ■ noncompetitive: bind to another part of enzyme, causes enzyme to change shape  ● active site less effective ○ feedback inhibition: end product of metabolic pathway shuts down the pathway ■ prevents waste of cell resources, no more product synthesized than necessary  ● localization of enzymes in cells ○ structures in cells bring order to metabolic pathways ○ enzyme acts as structural component of cell membrane ■ cristae in mitochondria line up with cell membranes   CHAPTER NINE ENERGY ● 2,000 food Calories a day is reasonable daily diet ● 2,000 food Calories= 2 million calories (lower case c) ● 1 calorie raises 1 gram of H2O by 1 degree C ○ 2 million calories raises 100 kg of H2O by 20 degree C ■ 8.36 mega joules per day, 100 joules per second  ● energy enters systems as light, leaves as heat ● cells use chemical energy from organic molecules to regenerate ATP, which powers work  ○ release CO2 and H2O TYPES OF CATABOLIC PATHWAYS  ● all catabolic pathways yield energy by oxidizing organic molecules (exergonic reaction) to make  ATP  ● fermentation: partial degradation of sugar, 2 ATP produced, no O2 used  ● aerobic respiration: consumes organic molecules and O2 to make ATP  ● anaerobic respiration: like aerobic except uses compounds other than O2 ● cellular respiration: technically includes both aerobic and anaerobic, but used to refer to aerobic ○ trace cellular respiration with glucose, but it can use carbs, fat, and proteins for fuel  ○ 34­38 ATP produced  ○ C6H12O6 + 6 CO2   6 CO2 + 6 H2O + energy (ATP and heat) REDOX REACTIONS ● transfer of electrons, and energy from those electrons, during chemical reactions ○ released energy used for synthesis of ATP ● oxidation: losing and electron, overall charge is more + ● reduction: gaining and electron, reducing (making more negative) overall charge  ● reducing agent: electron donor, becomes oxidized  ● oxidizing agent: electron acceptor, becomes reduced ● most redox reactions just transfer electrons, some change electron sharing in covalent bonds ● in cellular respiration, fuel is oxidized and O2 is reduced  ELECTRON TRANSPORT CHAIN ● NAD+: a coenzyme, or piece of enzyme that allows larger enzyme to function ○ energy from organic molecules is transferred to NAD+ as electrons, becomes NADH ○ NAD+= oxidizing agent ○ NADH stores energy for synthesis of ATP, passes electrons down electron transport chain ■ NADH= car battery ■ ATP= AA battery  ○ NADH and FADH2 alternate between oxidized/reduced states that accept/donate electrons ● electron transport chain breaks down energy from fuel into small, manageable energy pieces  rather than one big explosive reaction ● O2 is the most electronegative, pulls electrons down the chain ○ electrons drop in free energy with each fall down the chain ○ form H2O at the end ● takes place in cristae of mitochondria ● made up of proteins ○ cytochromes: protein with iron atom STAGES OF CELLULAR RESPIRATION ● in first two stages of cellular respiration, ATP is made by substrate level phosphorylation:  enzyme phosphorylates ADP  ● Glycolysis: breaks down glucose into 2 molecules of pyruvate: “splitting sugar”  ○ diagram on page 169  ○ takes place in cytoplasm  ○ 2 ATP is made total ○ 2 phases ■ energy investment: 2 ATP used ■  energy payoff: 4 ATP, 2 NADH, 2 pyruvate, 2 H2O ○ 10 steps  1) glucose   glucose 6 phosphate  a)  hexokinase enzyme transfers phosphate from ATP to glucose 2) glucose 6 phosphate   fructose 6 phosphate a) phosphogluco­isomerase 3) fructose 6 phosphate  fructose­1,6­bisphosphate a)  phosphofructokinase takes phosphate from ATP  4) fructose­1, 6­bisphosphate dihydroxyacetone phosphate (DHAP) and glyceraldehyde 3­ phosphate (G3P) a) aldolase: splits fructose­1,6­bisphosphate into two different carbon sugars  5) two sugars are converted between forms, never reaching equilibrium so G3P can be used for  next step as fast as it is made a) isomerase 6) G3P 1,3­bisphosphoglycerate and 2 NADH a) triose phosphate dehydrogenase 7) 1,3­bisphosphoglycerate 3­phosphoglycerate and 2 ATP a) phosphoglycerokinase 8) 3­phosphoglycerate 2­phosphoglycerate a) phosphoglyceromutase 9) 2­phosphoglycerate phosphoenolpyruvate(PEP) and 2 H2O a) enolase 10)PEP pyruvate and 2 ATP a) pyruvate kinase ● Citric Acid Cycle ○ diagram page 171  ○ pyruvate enters mitochondria, has to be converted to acetyl coenzyme A (CoA) before it can be  sued by citric acid cycle  ■ 3 reactions via a multi­enzyme complex: release of CO2, reduction of NAD+ to NADH and H+,  addition of CoA   acetyl CoA ○ generates 1 ATP, 3 NADH, and 1 FADH2 per turn ○ 8 steps 1) acetyl CoA joins with oxaloacetate citrate 2) citrate isocitrate  3) isocitrate ­ketoglutarate and 1 NADH 4) ?­ketoglutarate succinyl CoA and 1 NADH 5) succinyl CoA succinate and 1 ATP 6) succinate fumarate and 1 FADH2 7) fumarate malate 8) malate oxaloacetate and 1 NADH ● oxidative phosphorylation ○ after citric acid cycle, NADH and FADH2 make up most of energy from food ○ electron transport chain= first part ○ electron transfer in transport chain causes proteins to pump H+ from mitochondrial matrix to  intermembrane space ■ H+ moves across membrane ○ chemiosmosis: second part, the use of proton motor force (energy in H+ gradient) to drive  cellular work ■ energy coupling: energy stores in H+ gradients couples redox reactions of electron transport  chain to ATP synthesis ■ ATP Synthase: uses flow of H+ to drive phosphorylation of ATP ■ 32 to 34 ATP made ENERGY OF CELLULAR RESPIRATION ● energy flow: glucose NADH electron transport chain proton motive force ATP ● 40% of energy in glucose transfers to ATP= 38 ATP ○ 2(glycolysis) + 2(citric acid cycle) + 32/34(oxidative phosphorylation) FERMENTATION & ANAEROBIC RESPIRATION ● when O2 sources are low or non­existent  ● glycolysis can make ATP with or without O2 : absence of O2, use glycolysis and  fermentation/anaerobic respiration  ● fermentation: uses phosphorylation not electron transport to generate ATP ○ consists of glycolysis and reactions that regenerate NAD+ to be re­used for glycolysis  ○ fermentation vs. aerobic respiration: ■ both use glycolysis  ● oxidize glucose/organic molecules to make pyruvate ■ final electron acceptors: ● fermentation: organic molecule ● respiration: O2 ■ 38 ATP per glucose in respiration, only 2 ATP per glucose in fermentation ○ alcohol fermentation: pyruvate converted to ethanol in 2 steps, first of which releases CO2 ■ baking and brewing ○ lactic acid fermentation: pyruvate reduced to NADH, makes lactate ■ no release of CO2 or H2O ■ bacteria and fungi ■ muscle cells ○ obligate anaerobes: cannot live in O2 environments, only fermentation ○ facultative anaerobes: can use aerobic  respiration or fermentation ■ yeast/bacteria ■ pyruvate acts as fork in road: leads to 2 different catabolic routes ● anaerobic respiration: use compounds other than O2 in electron transport chain as final electron acceptor (like sulfate)  VERSATILITY OF CATABOLISM ● glycolysis accepts more than just glucose: amino acids, glycerol, fatty acids ○ amino acids can be used in glycolysis or citric acid cycle ○ glycerol + fatty acids generate acetyl CoA ■ fatty acids broken down by beta oxidation ■ 1g of fat produces more than twice as much ATP a 1g of carb BIOSYNTHESIS: body uses small molecules to build other substances ● anabolic FEEDBACK MECHANISMS ● feedback inhibition controls respiration ○ if ATP concentration drops, respiration speeds up and vice versa ● catabolism controlled by regulatory activity of phosphofructokinase at specific points ○ allosteric site on enzyme recognizes signals  ○ ATP from citric acid cycle inhibits ○ AMP (ATP­ 2 phosphate groups) stimulates CHAPTER TEN ● autotrophs: “self­feeding,” make their own food rather than consuming other organisms ○ i.e. producers ○ make organic molecules from CO2 and other inorganic molecules ○ photoautotrophs: mostly all plants, use photons from sunlight to make sugar and starch ○ plants, algae, prokaryotes, and protists ● heterotrophs: obtain energy from other organisms ○ i.e. consumers ○ depend on photoautotrophs for food and O2 PHOTOSYNTHESIS: converts solar energy to chemical energy ● 6 CO2+ 12 H2O+ light  C6H12O6+ 6 O2+ 6 H2O ● indirectly or directly nourishes the world ● structural organization of chloroplasts allow for chemical reactions of photosynthesis ○ similar to, or evolved from photosynthetic bacteria  ○ located in leaves ■ chlorophyll: pigment that gives chloroplasts, and leaves green color ● reflects green light ● located in membranous sacs called thylakoids  ○ stacked into granum columns inside chloroplast ○ surrounded by stroma fluid ● absorbs light energy, drives synthesis of organic molecules  ■ CO2 enters/ O2 exists leaf through microscopic pores: stomata ○ chloroplasts found in mesophyll cells: interior tissue of plants ■ 30­40 chloroplasts per mesophyll cell ○ split H2O into H and O, incorporate H+ into sugar molecules ■ H2O oxidizes, CO2 reduces ● two parts ○  light reactions ■ splits H2O ■ releases O2 ■ reduces NADP+ to NADPH ■ generates ATP from ADP­ phosphorylation ○ Calvin cycle ■ uses NADPH and ATP from light reactions to make sugar from CO2 PHOTOSYNTHETIC PIGMENTS ● pigments absorb visible light  ● specific to wavelength  ● wavelengths not absorbed are transmitted/reflected ○ chlorophyll reflects green ● chlorophyll a makes up majority of pigments ○ all others= accessory pigments: chlorophyll b, carotenoids ■ broaden spectrum, absorb excessive light that could damage chlorophyll  ● excitation of chlorophyll  ○ pigment absorbs light ■ electrons go from ground state to unstable excited states ■ electrons fall back down to ground state ● release energy, shown in fluorescence LIGHT REACTIONS ● photosystems ○ consist of reaction center complex (proteins) surrounded by light harvesting complexes: funnel  energy of photons to reaction center ○ primary electron acceptor: reaction center, = 1st step in light reaction ● linear electron flow: both photosystems used to produce ATP and NADPH via light energy ○ Photosystem II ● functions first (#’d in order of discovery)  ● absorbs best at 680 nm: PS680 ● 4 steps 1) photon hits pigment, passed  among pigments until it excited P680 2) excited electron from P680  transferred to primary electron acceptor: accepts excited electrons from chlorophyll a via solar power 3) enzyme splits H2O, electrons transferred from H atoms to P680+ a) P680+=  strong oxidizing agent b) O2 released 4) each electron falls down  electron transport chain from PSII to PSI a) energy  released drives creation of proton gradient across thylakoid membrane b) diffusion of H+ drives ATP synthesis ■ Photosystem I ● functions second ● absorbs best at 700 nm: P700 ● steps 1) transferred light energy excites P700, loses electron to primary electron acceptor 2) P700+ accepts electron passed down from PSII via electron transport chain 3) electron from electron acceptor falls down chain to protein ferredoxin (Fd) 4) electron transferred from NADP+ NADPH ● cyclic electron flow: uses only photosystem I ○ produces ATP but not NADPH ○ generates surplus ATP, satisfying higher demand ○ some organisms have PSI but not PSII ■ purple sulfur bacteria ■ evolved before linear electron flow ■ may protect cells from light induced damage CHEMIOSMOSIS: mitochondria vs. chloroplasts ● mitochondria ○ chemical energy from FOOD to ATP ○ H+ protons pumped to intermembrane space, diffuse back to mitochondrial matrix ● chloroplasts ○ light energy to chemical energy ○ H+ protons pumped to thylakoid space, diffuse back to stroma to generate ATP CALVIN CYCLE ● like citric acid cycle, regenerates starting molecule ● builds sugar from small molecules ○ uses 6 ATP, 6 NADPH ● Carbon enters as CO2, leaves as glyceraldehyde­3 phosphate (G3P) ○ for net synthesis of 1 G3P, cycle must take place 3 times ■ fixes 3 CO2 molecules ● 3 phases 1) carbon fixation a) via enzyme rubisco 2) reduction a) almost backwards process of glycolysis 3) regeneration of CO2 acceptor a) RuBP b) uses 3 ATP ● alternatives to carbon fixation ○ hot, arid climates ■ dehydration bad for plants ■ limits metabolism ○ plants close stomata  ■ conserves H2O ■ limits photosynthesis ○ photorespiration ■ C3 plants ■ rubisco adds O2 instead of CO2 to Calvin cycle ■ consumes O2, releases CO2 ■ no ATP or sugar produced ■ evolutionary background: rubisco evolved when there was less rubisco ■ limits damaging products of light reactions that build up in absence of Calvin cycle ● can drain 50% of CO2 made by Calvin cycle  ○ C4 plants ■ use CO2 to make 4 carbon organic acids ● in mesophyll cells ● requires PEP carboxylase ○ higher affinity for CO2 than rubisco ○ fixes CO2 even when concentrations are low ■ 4C acids exported to bundle sheath cells ● release CO2, then used in Calvin cycle ■ avoids photorespiration ○ CAM Plants ■ succulents use crassulacean acid metabolism ■ open stomata at night, closed during the day ■  incorporates CO2 into organic acids ● used in Calvin cycles CHAPTER ELEVEN CELL SIGNALING ● Signal transduction pathway: signal on cells surface converted into specific cellular responses ○ First evolved in prokaryotes, modified by eukaryotes ○ 3 stages: ■ Reception ● Ligand: binding between signal molecule and receptor protein ○ Signal molecules are highly specific to receptors and water soluble ■ Transduction ● Shape change of receptor initiates transduction ■ Response ● 3 types of receptors:  ○ G protein coupled receptor: in plasma membrane, works with help of G protein ■ G protein acts as on/off switch ■ steps 1. GDP is phosphorylated to make GTP 2. GTP powers G protein, activates receptor and receives response 3. G protein then activates enzyme 4. Enzyme triggers cellular response 5. Left with GDP and phosphate group ○ Receptor tyrosine kinase: in plasma membrane, multi­part system that triggers “fire alarm” ■ Kinase: transports phosphate to other molecules ■ steps 1. 2 signal molecules activate 2 receptors, which combine to form dimer 2. 6 ATP used to phosphorylate tyrosine’s 3. Tyrosine’s activate multiple relay proteins 4. Relay proteins generate cellular response ○ Ligand gated ion channel: act as gate when receptor changes shape ■ Steps 1. Signal molecule binds to receptor, changing shape a. “Opens” gate 2. Specific ions can flood through tunnel ● Messengers ○ First messengers:  extracellular signal molecules ○ Second messengers: small, non­protein, water soluble molecules ■ Ions ■ Spread via diffusion ■ Used in G protein coupled receptors and receptor tyrosine kinases ■ Cyclic AMP: widely used second messenger ● Activated by G protein coupled receptor ● Adenylyl cyclase: in plasma membrane, converts ATP to cAMP in response to extracellular  signal ● Phosphodiesterase: converts cAMP to AMP, shuts down signal ■ Calcium pumps: concentrate Calcium (Ca2+) ions ● Reserves act as secondary messengers in emergencies ● Intracellular receptors ○ Inside the cell rather than inside the plasma membrane ○ Small, hydrophobic molecules can cross membrane and active receptors in cytoplasm/ nucleus ■ steroid/ thyroid hormones of animals ○ Hormone­receptor complex: acts as a transcription factor, can turn on specific genes ■ Synthesis of mRNA PROTEIN PHOSPHORYLATION ● Cascade: waterfall of protein phosphorylation transmits signal ○ Step of transduction ○ Speedy ○ Amplifies cell response ● Molecular switch ○ Protein kinases: transfer phosphate to molecules, phosphorylation ○ Protein phosphatases: take phosphate from molecules, dephosphorylation SCAFFOLDING PROTEINS: “tool belt,” carry groups of protein “tools” ● Large relay proteins, carry other relay proteins APOPTOSIS: regulated cell suicide ● Cell is chopped into vesicles and digested by scavengers ○ Infected, damaged cells; cells that have reached end of life ○ Prevents enzymes from damaging other cells ● Caspases: type of protease, an enzyme that helps cut up proteins ○ Carries out apoptosis ● Ex: growth of fingers ○ Apoptosis cuts away extra tissue between fingers during growth


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