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Study Guide for Midterm 2--Chp 8-11

by: Aliya Amin

Study Guide for Midterm 2--Chp 8-11 Biol 5A

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Aliya Amin

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These notes cover information from Chapters 8-11
Intro: Cell and Molecular Biology
Eugene Nothnagel
Study Guide
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This 32 page Study Guide was uploaded by Aliya Amin on Wednesday February 24, 2016. The Study Guide belongs to Biol 5A at University of California Riverside taught by Eugene Nothnagel in Winter 2016. Since its upload, it has received 183 views. For similar materials see Intro: Cell and Molecular Biology in Biology at University of California Riverside.


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Date Created: 02/24/16
CHAPTER 8: AN INTRODUCTION TO METBOLISM  Metabolism: the totality of an organism’s chemical reactions; manages material and energy resources of the cell  Metabolic pathway: o Begins with a specific molecule that is altered in steps, resulting in a product (can have multiple starting molecules and products) o Each step is catalyzed by enzymes o Some release energy (exergonic) to break down complex molecules—catabolic pathways (breakdown pathways)  ex: cellular respiration—glucose is broken down in the presence of oxygen gas to carbon dioxide gas and water o Some consume energy (endergonic) to build complex molecules—anabolic pathways (biosynthetic pathways)  Ex: photosynthesis, synthesis of amino acids and proteins o Energy released from downhill catabolic pathways is stored and used to drive uphill reactions of anabolic pathways Forms of Energy  Energy: capacity to cause change o Move matter against opposing forces (gravity and forces) o Rearrange a collection of matter  Kinetic energy: relative motion of objects o heat or thermal energy  kinetic energy associated with the random movement of atoms or molecules  Potential energy: o the energy matter possesses because of its location or structure o arrangement of electrons in bonds between atoms o chemical energy  potential energy available for release in chemical reactions  complex molecules have high chemical energy The Laws of Energy Transformation  Thermodynamics: study of energy transformations that occur in a collection of matter o System: the particular matter under study o Surroundings: everything outside of the system o Isolated system: unable to exchange energy or matter with its surroundings o Open system: energy and matter can be transferred between the system and surroundings o Determines whether a reaction will or will not occur  First Law of Thermodynamics o The energy of the universe is constant—energy can be transformed and transferred but not created or destroyed o Principle of conservation of energy  Second Law of Thermodynamics o Entropy: measure of disorder or randomness o Every energy transfer or transformation increases the entropy of the universe o Spontaneous process: process that can occur without an input of energy  It must increase the entropy of the universe Kinetics  The speed or rates of reactions  Reaction rates are affected by: o Nature of what is undergoing the reaction—reactions involving acids/salts are faster than those involving the breaking or forming of covalent bonds o Physical state o Concentration (the higher the concentration, the higher the rate of particle collisions) o Temperature o Catalyst: substance that accelerates the forward and the reverse reactions by lowering the activation energy Free Energy  ∆G = energy available to do work  ∆H = the total energy of the system  T = temperature  ∆S = change in entropy  T∆S represents heat or unusable energy  Free energy: the portion of the system’s energy that can perform work when temperature and pressure are uniform throughout the system o The measure of a system’s inability/tendency to change to a more stable state o It will predict if a process will be spontaneous—G and H need to be negative, while T and S will be positive o Every spontaneous process decreases the system’s free energy, and processes with a positive or 0 G-value are non-spontaneous o The higher the G-value, the more unstable the system. The system will tend to change in order to have a lower G-value o As a reaction proceeds to equilibrium, the free energy of the mixture of reactants and products decreases  G is at its lowest value  Process is spontaneous and can perform work only when it is moving towards equilibrium Exergonic and Endergonic Reactions in Metabolism  Exergonic reactions: proceeds with a net release of free energy o Free energy is lost o Occur spontaneously o Negative ∆G and ∆H o Positive ∆S o Increase in entropy and temperature o G = -686J; cellular respiration, hydrolysis  Endergonic reactions: one that absorbs free energy from its surroundings o Stores free energy in molecules o Occurs non-spontaneously o Positive ∆G and ∆H o Negative ∆S o Decrease in entropy and temperature o G = +686J; photosynthesis, protein/DNA synthesis Equilibrium and Metabolism  Reactions in isolated systems can reach equilibrium  Chemical reactions of metabolism are reversible  Cells that have reached metabolic equilibrium are dead (living cells are never in equilibrium)  Cells are NOT isolated systems  To create more order, heat is released and causes disorder in the surroundings  Order is maintained by the constant input of energy (loss of order = death) Types of Work Performed by Cells  Chemical work o Pushing of endergonic reactions that would not occur spontaneously (synthesis of polymers from monomers)  Transport work o Pumping of substances across membranes against direction of spontaneous movement  Mechanical work o Beating of cilia, contraction of muscle cells, movement of chromosomes during cellular respiration  Energy coupling: the use of exergonic processes to drive energonic ones o Links +∆G with --∆G (spontaneous/exergonic with non-spontaneous/endergonic) o Uses ATP as an immediate source of energy that powers cellular work Structure and Hydrolysis of ATP  ATP is used for energy coupling and to make RNA  Bonds between the phosphate groups of ATP can be broken by hydrolysis o When the terminal phosphate bond is broken, molecule of inorganic phosphate leaves ATP, becomes adenosine diphosphate (ADP)  Exergonic reaction How the Hydrolysis of ATP Performs Work  When ATP is hydrolyzed, the release of free energy produces heat  Cells are able to use the energy released by ATP to drive endergonic chemical reactions with enzymes  Phosphorylated intermediate: recipient with the phosphate group covalently bonded to o The key to coupling exergonic and endergonic reactions, more reactive than an un-phosphorylated molecule  Hydrolysis of ATP is also used in transport and mechanical work o Leads to a change in protein’s shape and its ability to bind to another molecule o Sometimes involves phosphorylated intermediate o ATP is bonded non-covalently to motor protein, ATP is hydrolyzed releasing ADP and Pi, then another ATP molecule can bind—at each stage the motor protein changes shape and its ability to bind to the cytoskeleton Regeneration of ATP  ATP is renewable, can be regenerated by the addition of P to ADP  The energy required to phosphorylate ADP comes from exergonic breakdown reactions (catabolism) o ATP cycle o Formation of ATP is not spontaneous; requires the use of free energy o Catabolic pathways, light energy The Activation Energy Barrier  Enzyme: molecule that acts like a catalyst, a chemical agent that speeds up a reaction without becoming consumed by the reaction  Activation energy: initial investment of energy for starting a reaction, energy required to contort the reactant molecules so bonds can break o Amount of energy needed to push reactants uphill so the downhill portion can begin o Supplied as thermal energy that reactants absorb from the surroundings o When enough energy is absorbed, reactants are in the transition state (unstable) o As atoms settle into their new, more stable bonding arrangements, energy is released to the surroundings o Provides a barrier that determines the rate of the reaction How Enzymes Lower the Activation Energy Barrier  Heat speeds up a reaction by allowing reactants to attain the transition state more often o Not a good method for biological molecules:  High temperature denatures proteins and kills cells  Heat would speed up all reactions, not just those that are needed  Enzyme lowers activation energy by enabling reactant molecules to absorb enough energy to reach transition state at even moderate temperatures o Cannot change G (make endergonic into exergonic) o Hasten reactions that would eventually occur  Allow for dynamic metabolism, determine which chemical processes will be going on in a cell at any particular time because they are so specific o Brings reactants closer to each other, requires less energy Substrate Specificity of Enzymes  Substrate: reactant an enzyme acts upon o Enzyme forms an enzymatic substrate complex when it binds to substrate  Enzyme’s specificity arises from its shape, which is a consequence of its amino acid sequence  Active site: restricted region of the enzyme molecule that binds to the substrate o Formed by only a few of an enzyme’s amino acids  Enzymes don’t have stiff structures; change between subtle different shapes in dynamic equilibrium with slight differences in free energy  As substrate enters active site, enzyme changes shape slightly due to interactions between substrate’s chemical groups on the side chains of the amino acids that form the active site o Shape change makes active site fit more snuggly around the substrate—induced fit  Brings chemical groups of active site into positions that enhance their ability to catalyze chemical reactions Catalysis in the Enzyme’s Active Site  Substrate held in active site by weak interactions, H bonds and ionic bonds  R groups of a few amino acids of the active site catalyze conversion of substrate to product  Lower activation energy and speed up a reaction o In reactions involving two or more reactants, the active site provides a template on which substrates can come together in proper orientation for reaction to occur between them o As the active site clutches its bound substrates, the enzyme may stretch the substrate molecules toward their transition state form, stressing and bending chemical bonds that must be broken o Active site may provide a microenvironment that is more conductive to a particular type of reaction than the solution itself would be without the enzyme o Direct participation of the active site in the chemical reaction  Rate at which enzyme converts substrate to product depends on initial concentration of substrate o More substrate molecules, more frequently they access active sites of enzyme molecules o There is a limit as to how fast a reaction can be pushed by adding more substrate o When enzyme population is saturated, the only way to increase its rate of product formation is to add more of the enzyme Effects of Temperature and pH  Rate of enzymatic reaction increases with increasing temperatures (optimal temperature) o Too high temperature disrupts hydrogen bonds that stabilize the active shape of an enzyme and it denatures as a result  Optimal pH around 6-8 Cofactors  Cofactors: non-protein helpers used by enzymes, may be bound tightly to an enzyme as a permanent resident or they may bind loosely and reversibly along with a substrate o Some are inorganic o If it is organic it is called a coenzyme  Most vitamins are important because they act as coenzymes or raw materials from which coenzymes are made Enzyme Inhibitors  Most enzyme inhibitors bind to the enzyme by weak interactions  Competitive inhibitors: reduce productivity of enzymes by blocking substrates from entering active sites o can be overcome by increasing concentration of substrate so active sites become available  Noncompetitive inhibitors: impede enzymatic reactions by binding to another part of the enzyme o Cause enzyme molecule to change its shape in a way that the active site becomes less effective at catalyzing conversion of substrate to product Allosteric Activation and Inhibition  Allosteric regulation: protein’s function at one site is affected by a regulatory molecule to a separate site, may result in inhibition or stimulation of an enzyme’s activity  Most allosterically regulated enzymes are composed from 2 or more subunits, each composed of polypeptide chain with its own active site  Two different shapes: o Catalytically active o Inactive  Activating or inhibiting regularly molecule binds to regulatory site where subunits join ( allosteric site)  Binding of an activator to a regulatory site stabilizes the shape that has active sites  Binding of an inhibitor to a regulatory site stabilizes inactive form  Allosteric activation methods: o Fluctuating concentrations of regulators can cause a sophisticated pattern of responses in activity of cellular enzymes o Substrate molecule binding to one active site in a multi-subunit enzyme triggers a shape change in all of the subunits, increasing catalytic activity at other active sites  Cooperativity: amplifies the response of enzyme to substrates  One substrate molecule primers an enzyme to act on additional substrates more readily  Allosteric because binding of substrate to one active site affects catalysis in another active site Identification of Allosteric Regulators  Hard to categorize allosteric molecules because they bind to enzymes at low affinity, therefore hard to isolate  Allosteric regulators exhibit higher specificity for particular enzymes than do inhibitors that bind to the active site  Studies designed to find allosteric inhibitors of caspases (protein digesting enzymes) o By targeting caspases, better able to manage inappropriate inflammatory responses Feedback Inhibition  Metabolic pathway is switched off by inhibitory binding of its end product to an enzyme that acts early on in the pathway  Synthesizing amino acid isoleucine from threonine o As isoleucine accumulates, slows down synthesis by allosterically inhibiting the enzyme from the first step of the pathway  Prevents cell from wasting chemical resources Specific Localization of Enzymes within the Cell  Some enzymes/enzyme complexes have fixed locations within the cell and act as structural components of membranes  Others are in solution within membrane enclosed organelles o Ex: Mitochondria Chapter 9: Cellular Respiration and Fermentation Catabolic Pathways and Production of ATP  Organic compounds possess potential energy that can be broken down by a cell system and enzymes to simpler waste products that have less energy. Some of it can be used to do work, most is lost as heat  Fermentation: catabolic process; partial degradation of sugars and other organic fuels that occurs without the use of oxygen  Aerobic respiration: most prevalent/efficient catabolic pathway; oxygen is consumed as a react along with the organic fuel o cells of most eukaryotes and many prokaryotes o some prokaryotes use substances other than oxygen as a reactant to harvest chemical energy—anaerobic respiration  cellular respiration: includes aerobic and anaerobic processes; but mainly for aerobic processes o organic compounds + oxygen = carbon dioxide + water + energy  breakdown of glucose is exergonic, products store less energy than the reactants and reaction can occur spontaneously (without input of energy)  catabolic processes don’t directly perform cellular work—linked to ATP o cell must regenerate its supply of ATP from ADP and Pi The Principle of Redox  redox reactions: transfer of one or more electrons from one reactant to another o oxidation: loss of electrons o reduction: addition of electrons  energy must be added to pull an electron away from an atom  the more electronegative the atom, the more energy is required to take an electron away from it  electron loses potential energy when it shifts from a less electronegative atom toward a more electronegative one, and energy is released Oxidation of Organic Fuel Molecules During Cellular Respiration  cellular respiration is the oxidation of glucose and other molecules in food  hydrogen is transferred from glucose to oxygen  the oxidation of glucose transfers electrons to a lower energy state, liberating energy that becomes available for ATP synthesis  main energy-yielding foods, carbohydrates and fats, are reservoirs of electrons associated with hydrogen  enzymes in cell will lower the barrier of activation energy, allowing the sugar to be oxidized in steps Stepwise Energy Harvest via NAD+ and the Electron Transport Chain  Each electron travels with a proton (H atom)  H atoms are not transferred directly to oxygen, but instead are passed to an electron carrier, a coenzyme called NAD+ o Can easily cycle between oxidized (NAD+) and reduced (NADH) states o Functions as oxidizing agent  Enzymes called dehydrogenases remove a pair of hydrogen atoms (2 protons and 2 electrons) from glucose, thereby oxidizing it o Enzyme delivers 2 electrons and 1 proton to NAD+ o Other proton released as H+ ion in solution  Each NADH molecule formed during respiration represents stored energy that can be tapped to make ATP when the electrons complete their fall down an energy gradient from NADH to oxygen  Electron transport chain: number of molecules, mostly proteins, built in inner membrane of mitochondria of eukaryotic cells and the plasma membrane of aerobically respiring prokaryotes o Electrons removed from glucose are shuttled by NADH to the top (high E) of chain, at the bottom of chain the O2 captures the electrons along with hydrogen nuclei, forming water o Electrons cascade down chain from one molecule to next in series of redox reactions, losing small amount of energy until they reach oxygen o Oxygen pulls electrons down the chain (because of its electronegativity The Stages of Cellular Respiration: A Preview  Harvesting of energy from glucose by cellular respiration: o Glycolysis o Pyruvate oxidation and the citric acid cycle o Oxidative phosphorylation: electron transport chain and chemiosmosis  Glycolysis: occurs in cytosol, begins degradation process by breaking glucose into two molecules of pyruvate  Pyruvate enters mitochondrion and is oxidized to acetyl CoA, which enters citric acid cycle and carbon dioxide is given off  ETC accepts electrons from breakdown products of first two stages via NADH and passes electrons from one molecule to another  At the end of chain, electrons combined with molecular oxygen and H+ ions to form water  Energy released at each step of chain is stored in mitochondria and can be used to make ATP from ADP  Oxidative phosphorylation: mode of ATP synthesis, powered by redox reactions of ETC  ETC and chemiosmosis occurs in inner membrane of mitochondrion  Oxidative phosphorylation accounts for 90% of ATP generated  Smaller amount of ATP is formed directly during glycolysis and citric acid cycle by substrate level phosphorylation o Occurs when enzyme transfers phosphate group from substrate molecule (organic molecule generated as an intermediate during catabolism of glucose) to ADP, rather than adding inorganic phosphate to ADP as in oxidative phosphorylation Glycolysis harvests chemical energy by oxidizing glucose to pyruvate  “sugar splitting”  Glucose (6 carbon sugar) is split into two 3- carbon sugars and then oxidized to form pyruvate  Two phases: o Energy investment: cell spends ATP o Energy payoff: ATP is produced by substrate level phosphorylation and NAD+ is reduced to NADH by electrons released from oxidation of glucose  Net energy yield from glycolysis per glucose molecule: 2 ATP and 2 NADH  All of the carbon originally present in glucose is accounted for in pyruvate, no carbon dioxide is released  Occurs whether or not oxygen is present o If oxygen is present, chemical energy stored in pyruvate and NADH can be extracted by pyruvate oxidation, citric acid cycle, and oxidative phosphorylation After pyruvate is oxidized, the citric acid cycle completes the energy- yielding oxidation of organic molecules  Glycolysis requires less than a quarter of the chemical energy in glucose than can be released by cells; most of the energy remains in the two molecules of pyruvate  If oxygen is present, pyruvate enters mitochondrion where oxidation of glucose is completed (in cytosol for prokaryotes) Oxidation of Pyruvate to Acetyl CoA  Pyruvate is converted to acetyl CoA upon entering mitochondrion via active transport  Process carried out by a multi-enzyme complex that catalyzes three reactions: o Pyruvate’s carboxyl group is removed and given off as a molecule of carbon dioxide o Remaining two carbon fragment is oxidized, forming acetate. Extracted electrons are transferred to NAD+, storing energy in form of NADH o CoA is attached via its sulfur atom to the acetate, forming acetyl CoA (has a high potential energy) The Citric Acid Cycle  Cycle functions to oxidize fuel derived from pyruvate  Pyruvate is broken down to three carbon dioxide molecules (including the one released during conversion of pyruvate to acetyl CoA)  Cycle generates 1 ATP per turn by substrate level phosphorylation but most chemical energy is transferred to NAD+ and coenzyme FAD during redox reactions  Reduced coenzymes, NADH and FADH2, shuttle their high energy electrons into the ETC  8 steps, each catalyzed by a specific enzyme o Acetyl group of acetyl CoA joins cycle by combining with oxaloacetate, from citrate  Next 7 steps decompose citrate back to oxaloacetate (regeneration) o for each acetyl group entering cycle, 3 NAD+ are reduced to NADH o in step 6, electrons transferred to FAD which accepts 2 electrons and 2 protons to become FADH2 o step 5 produces GTP by substrate level phosphorylation in animals  can be used to make ATP molecule or directly be used to power work in a cell  in plants/bacteria, step 5 forms ATP molecule directly by substrate level phosphorylation  output from step 5 represents only ATP generated directly from cycle  most ATP produced from respiration results from oxidative phosphorylation, when NADH and FADH2 made from citric acid cycle relay electrons extracted from food to ETC o supply energy for phosphorylation of ADP to ATP During oxidative phosphorylation, chemiosmosis couples electron transport to ATP synthesis  substrate level phosphorylation produces 2 net ATP from glycolysis and 2 ATP from citric acid cycle The Pathway of Electron Transport  folding of inner membrane to form cristae increases its surface area, providing for thousands of copies if ETC in each mitochondrion  most components are proteins that exist in protein complexes I to IV  prosthetic groups: non-protein compounds essential for catalytic functions of certain enzymes are bound to protein complexes  electron carriers alternate between reduced and oxidized states as they accept and donate electrons  each component of chain becomes reduced when it accepts electrons from uphill; it then returns to oxidized form as it passes electrons to its downhill (more electronegative) neighbor  electrons removed from glucose by NAD+ are transferred from NADH to first molecule of ETC in complex I o the molecule is a flavoprotein, FMN  in the next redox reaction, flavoprotein returns to oxidized form as it passes electrons to an iron-sulfur protein Fe-S in complex I  Fe-S passes electrons to ubiquinone, Q o Only member of ETC that isn’t a protein  most of the remaining electron carriers between Q and oxygen are proteins called cytochromes o their prosthetic group (heme group) has an iron atom that accepts and donates electrons o several type in ETC each with a different protein and slightly different heme group o last cytochrome of chain, cyt a3, passes electrons to oxygen o each oxygen atom also picks up a pair of H+ from aq solution, forming water  Another source of electrons for ETC is FADH2 o Adds its electrons to ETC from complex II, at a lower energy level than NADH does o ETC provides about 1/3 less energy for ATP synthesis when electron donor is FADH2  ETC doesn’t make an ATP directly, it simply eases the fall of electrons from food to oxygen Chemiosmosis: The Energy- Coupling Mechanism  ATP synthase: enzyme that makes ATP from ADP and inorganic phosphate, inside of inner membrane of mitochondrion or prokaryotic plasma membrane o Uses the energy of an existing ion gradient to power ATP synthesis o Power source is the difference in concentration of H+ on opposite sides of inner mitochondrial membrane  Chemiosmosis: energy stored in the form of a hydrogen ion gradient across a membrane used to drive cellular work such as the synthesis of ATP  Flow of H+ through synthase powers ATP generation o Synthase is made of four parts, each made of multiple polypeptides  Establishing H+ gradient is a major function of ETC o Uses exergonic flow of electrons from NADH and FADH2 to pump H+ across the membrane, from mitochondrial matrix into intermembrane space o Energy stored in an H+ gradient across a membrane couples redox reactions of ETC to ATP synthesis o At certain steps of ETC, electron transfers cause H+ to be taken up and released into the surrounding solution o H+ gradient that results is referred to as a proton motive force; force drives H+ back across the membrane through H+ channels provided by ATP synthases  Chemiosmosis is an energy coupling mechanism that uses energy stored in the form of an H+ gradient across a membrane to drive cellular work o Chloroplasts use chemiosmosis to generate ATP during photosynthesis An Accounting of ATP Production by Cellular Respiration  Most energy flows in this sequence: o Glucose – NADH – ETC – proton-motive force – ATP  Glycolysis: +2 ATP, +2 NADH/FADH2  Pyruvate oxidation: +2 NADH  Citric acid cycle: +2 ATP, +6 NADH, +2 FADH2  Oxidative phosphorylation: +26/28 ATP (depending on if NADH or FADH2 shuttled the electrons from glycolysis) Fermentation and anaerobic respiration enable cells to produce ATP without the use of oxygen  An electron transport chain is used in anaerobic respiration but not in fermentation  Anaerobic respiration: o Takes place in certain prokaryotic organisms that live in environments without oxygen o Final electron acceptor is not oxygen, but some other electronegative substance  Ex: marine bacteria use sulfate ion at the end of their respiratory chain  Operation of chain builds up proton-motive force used to produce ATP, but hydrogen sulfide is made as a by-product instead of water  Fermentation: o Way of harvesting chemical energy without using oxygen or electron transport chain (without cellular respiration) o An extension of glycolysis that allows continuous generation of ATP by substrate level phosphorylation of glycolysis  Requires a sufficient supply of NAD+ to accept electrons during the oxidation step of glycolysis  Under aerobic conditions NAD+ is recycled from NADH by the transfer of electrons to the electron transport chain but under anaerobic conditions electrons are transferred from NADH to pyruvate, the end product of glycolysis Types of Fermentation  Alcohol fermentation o Pyruvate is converted to ethanol in two steps:  Carbon dioxide is released from pyruvate, which is converted to the two-carbon compound acetaldehyde  Acetaldehyde is reduced by NADH to ethanol which regenerates supply of NAD+ needed for continuation of glycolysis o Many bacteria carry out this fermentation under anaerobic conditions o Yeast (fungus) also carries out alcohol fermentation—used in brewing, winemaking, and baking  Lactic acid fermentation o Pyruvate is reduced directly by NADH to form lactate as an end product, with no release of Co2 (lactate is the ionized form of lactic acid) o This fermentation by certain fungi and bacteria is used in the dairy industry to make cheese and yogurt o Human muscle cells make ATP by this fermentation when oxygen is scarce  Occurs during strenuous exercise  Cells switch from aerobic respiration to fermentation  The excess lactate is gradually carried away by the blood to the liver, where it is converted back to pyruvate by liver cells Comparing Fermentation with Anaerobic and Aerobic Respiration  Three alternative cellular pathways for producing ATP by harvesting chemical energy for food  All use glycolysis to oxidize glucose and other organic fuels to pyruvate, with net production of 2 ATP by substrate level phosphorylation  NAD+ is oxidizing agent that accepts electrons from food during glycolysis  Process of oxidizing NADH back to NAD+: o Fermentation—final electron acceptor is an organic molecule such as pyruvate or acetaldehyde o Cellular respiration—electrons carried by NADH are transferred to an ETC, which regenerates NAD+  Amount of ATP produced: o Fermentation—2 molecules of ATP from substrate level phosphorylation o Cellular respiration—pyruvate is completely oxidized in the mitochondrion, thereby harvesting more energy from each sugar molecule, about 32 molecules of ATP per glucose molecule  Obligate anaerobes: only carry out fermentation or anaerobic respiration o Cannot survive in the presence of oxygen  Facultative anaerobes: can make ATP to survive using either fermentation or respiration o Our muscles behave as such The Versatility of Catabolism  Aside from glucose, other organic molecules such as fats, proteins, sucrose, starch, etc can be used by cellular respiration to make ATP Biosynthesis (Anabolic Pathways)  Not all of the organic molecules of food are destined to be oxidized as fuel to make ATP  Food must also provide the carbon skeletons that cells require to make their own molecules  Compounds formed as intermediates of glycolysis and the citric acid cycle can be diverted into anabolic pathways as precursors from which the cell can synthesize the molecules it requires  Glycolysis and the citric acid cycle function as metabolic interchanges that enable our cells to convert some kinds of molecules to others as we need them Regulation of Cellular Respiration via Feedback Mechanisms  Feedback inhibition: the end product of the anabolic pathway inhibits the enzyme that catalyzes an early step in the pathway—prevents the needless diversion of key metabolic intermediates from uses that are more urgent  The cell also controls its catabolism—the control is based mainly on regulating the activity of enzymes at strategic points in the catabolic pathway  One important switch is phosphofructokinase, the enzyme that catalyzes a step of glycolysis o It’s the first step that commits the substrate irreversibly to the glycolytic pathway o By controlling the rate of this step, the cell can speed up or slow down the entire catabolic process  Phosphofructokinase is the “pacemaker” of respiration o Also an allosteric enzyme with receptor sites for specific inhibitors and activators  It’s inhibited by ATP and stimulated by AMP, which the cell derives from ADP  As ATP accumulates, inhibition of enzyme slows down glycolysis  Enzyme becomes active again as cellular work converts ATP to ADP (and AMP) faster than ATP is being regenerated  The energy that keeps us alive is released, not produced, by cellular respiration Chapter 10: Photosynthesis The Process That Feeds the Biosphere  Organism acquires organic compounds it uses for energy and carbon skeletons by: o Autotrophic nutrition o Heterotrophic nutrition  Autotrophs: “self-feeders,” sustain themselves without eating anything derived from other living beings o Produce their organic molecules from CO2 and other inorganic raw materials from the environment o Known as the producers of the biosphere because they are the ultimate source of organic compounds for all non-autotrophic organisms o Plants are photoautotrophs—organisms that use light as a source of energy to synthesize organic substances o Also common in algae, unicellular eukaryotes, and some prokaryotes  Heterotrophs: obtain organic material by living on compounds produced by other organisms; unable to make their own food o The biosphere’s consumers o Some consume the remains of dead organisms by decomposing and feeding on organic litter, known as decomposers  most fungi and many prokaryotes get their nourishment this way Photosynthesis converts light energy to the chemical energy of food  photosynthetic enzymes and other molecules are grouped together in biological membrane, enabling the necessary series of chemical reactions to be carried out efficiently  plants store light energy in the form of sugar and starch and derive it when needed in the dark Chloroplasts: The Sites of Photosynthesis in Plants  chlorophyll is located in thylakoids which are in chloroplasts that are found mainly in cells of the mesophyll: tissue in the interior of the leaf  carbon dioxide enters leaf, and oxygen exits through microscopic pores called stomata  electrons become excited when chloroplast pigments absorb light  the granum has photosynthetic pigments  there exists an electrochemical gradient across thylakoid molecules The Splitting of Water  chloroplast splits water into hydrogen and oxygen  hydrogen is incorporated into the sugar and is a source for electrons and the oxygen gas is given off as a waste product The Two Stages of Photosynthesis: A Preview  the two stages of photosynthesis: o Light reactions o Calvin cycle  Light Reactions o Convert solar energy to chemical energy o Water is split, providing a source of electrons and protons, and oxygen gas is given off as a by product o Light is absorbed by the chlorophyll and it drives a transfer of electrons and hydrogen ions from water to a temporary electron acceptor, NADP+ o Solar energy is used to reduce NADP+ to NADPH by adding a pair of electrons and a proton o Also generate ATP using chemiosmosis (movement of H+ across membrane) to power the addition of a phosphate group to ADP, photophosphorylation o Light energy is initially converted to chemical energy in the form of two compounds: NADPH and ATP o Occurs in the thylakoids  Calvin Cycle o CO2 from the air is incorporated into organic molecules present in the chloroplast—known as carbon fixation o Fixed carbon is reduced to carbohydrate by addition of electrons from NADPH o CO2 is combined with a 5-Carbon compound to produce a 6-carbon molecule that is broken down into 2, 3-carbon compounds o The cycle also uses ATP as chemical energy o None of the steps require direct light o Occurs mainly during the daylight because it’s dependent on the products of the light reactions o ATP is hydrolyzed and NADPH is oxidized o Occurs in the stroma The light reactions convert solar energy to the chemical energy of ATP and NADPH  The light that is absorbed is the same light that is used in photosynthesis  Chlorophylls have a larger input than do carotenoids  Similarity of action spectrum of photosynthesis and the absorption spectra of chlorophyll tells us that chlorophylls are the most important pigments in the process  Action spectrum shows the wavelength of light that is most effective in photosynthesis  A photon of blue light carries the most energy Figure 1: Absorption Spectra  Figure 2: Action Spectrum T h e conversion of solar energy to chemical energy occurs within the photosystems  Reaction center complex: after receiving electrons in their excited states from the light harvesting complex, two chlorophyll molecules donate them to the primary electron acceptor so they can undergo the electron transport chain  Light harvesting complex: gathers light to raise an electron to an excited state so they can travel to the reaction center complex  Primary electron acceptor: accepts electrons and functions in shuttling electrons from photosystem to the electron transport chain to product ATP  Photosystem 1 is referred to by the wavelength at which its reaction center best absorbs light, or P700; photosystem 2 is known as P 680 Linear Electron Flow  the source of electrons for linear electron flow come from water, it’s also the source of oxygen gas in the atmosphere  as electrons fall between the two photosystems, the cytochrome complex uses the energy to pump H+ ions. This builds a proton gradient that is used in chemiosmosis to produce ATP  in photosystem 2, the excited electron is eventually used by NADP+ reductase to join NADP+ and a H+ ion to form NADPH Cyclic Electron Flow  Product of cyclic electron flow is ATP  No water is split and there is no production of NADPH and no release of oxygen gas  Only photosystem is used, therefore, increasing the production of ATP  More ATP is required to complete photosynthesis than is generated relative to NADPH production by linear flow alone A Comparison of Chemiosmosis in Photosynthesis and Cellular Respiration Photosynthesis Similarities Cellular Respiration -Photophosphorylation -ETC pumps H+ across a -oxidative phosphorylation -source of e- from water protein from an area of low -high energy e- dropped -don't need food to make ATP concentration to high down ETC are extracted from (uses light) -protons diffuse back acrossorganic molecules (food) -transfer light energy into membrane through ATP -transfer chemical energy chemical energy synthase, driving synthesis from food molecules to ATP of ATP Chemiosmosis in Light Reactions Stores electrons in NADPH Photophosphorylation —uses light energy to pump H+ (vs. oxidative phos.)  Light reactions store chemical energy in NADPH and ATP, which shuttle the energy to the carbohydrate- producing Calvin cycle The Calvin Cycle Uses ATP and NADPH to Convert CO2 to Sugar  The Calvin cycle is a metabolic pathway in which each step is governed by an enzyme, much like the citric acid cycle from cellular respiration  Calvin cycle uses energy and is therefore, anabolic; in contrast, cellular respiration is catabolic and releases energy that is used to generate ATP and NADH  The carbohydrate produced directly from the Calvin cycle is not glucose, but the 3-carbon compound G3P  Each turn of the Calvin cycle fixes one molecule of CO2; therefore it will take 3 turns of the Calvin cycle to net one G3P  Carbon fixation stage: o CO2 is attached to a 5-carbon sugar, catalyzed by rubisco o The product is a very unstable 6 carbon sugar that is split into 2 G3P  Reduction stage: o Reducing power of NADPH will donate electrons to the low energy acid 1, 3-bisphosphoglycerate form the 3-carbon sugar Need more ATP than NADPH (cyclic flow) Increase in potential energy; reverse of glycolysis Rearrange carbon atoms to regenerate  Cycle must be turned three times for the production of one G3P molecule  Each turn will require a starting molecule of ribulose bisphosphate, a 5-carbon compound  We start with 15 carbons distributed into 3RuBPs  After fixing three CO2 using the enzyme rubisco, Calvin cycle forms 6-G3Ps with a total of 18 carbons—net gain of carbons is 3 (or one net G3P molecule)  Three turns of the calvin cycle nets one G3P because the other 5 must be recycled to RuBP. The last step of the cycle rearranges 5-carbon skeletons of G3P to 3 RuBP molecules; 3 molecules of ATP are needed for this  Net production of G3P requires 9 molecules of ATP and 6 molecules of NADPH  Return ADP, inorganic phosphate, and NADP+ to the light reactions Alternative Mechanism of Carbon Fixation Have Evolved in Hot, Arid Climates  C3 Plant o Plant that uses the calvin cycle for carbon fixation to form G3P o Hot, dry days when the stomata is closed o Encouraged during night-time o Oxygen buildup from light reactions o Undergoes photorespiration: rubisco binds to oxygen, thus no carbohydrate is generated; it consumes organic fuel and releases CO2 without producing ATP or a carbohydrate  Photosynthetic output is decreased—plants cannot make food  C4 Plant o Calvin cycle is preceded by reactions that incorporate CO2 into 4- carbon components whose end products supplies CO2 for the calvin cycle o Minimize the cost of photorespiration by incorporating CO2 into 4- carbon compounds in mesophyll cells o Compounds are exported to bundle-sheath cells where they release CO2 used in the Calvin cycle o The C4 pathway doesn’t replace the Calvin cycle but works as a CO2 pump that prefaces the Calvin cycle o CO2 concentrations are maintained in the bundle sheath so that photosynthesis will be favored over respiration In mesophyll cells, the enzyme PEP carboxylase adds CO2 to PEP A 4-carbon compound conveys the atoms of the CO2 into a bundle-sheath cell via plasmodesmata In bundle sheath cells, CO2 is released and enters the Calvin cycle High CO2, Comparison of C4 plants and CAM plants C4 CAM CO2 Mesoph CO2 Nigh yll t Open stomata at night, incorporating CO2 into Organic Organic organic acids which acid acid are stored in mesophyll cells— Bundle- CO2 during day, stomata sheath CO2 Day close, CO2 is released from organic acids for Calvin Calvin use in the Calvin cycle Cycle Cycle Suga Suga r r  The initial steps of  Both live in arid  2 stages of carbon fixation are environments and use photosynthesis are separated structurally PEP carboxylase to fix separated temporarily from the Calvin cycle CO2 but occur in the same  Fix CO2 in one location cells and it is used  CO2 is fixed at one somewhere else time and it is used at a different time Chapter 11: Cell Communication General Principles of Cell Signaling  Chemical signals can be proteins, amino acids, peptides, nucleotides, steroids, gases  Some signals (proteins, amino acids, peptides) are hydrophilic  Some signals are hydrophobic (steroid hormones)  Signals produced by signal cell and detected by receptor protein on a target cell 1) A wide ranging form of signaling involves a signal produced by the endocrine system called a hormone. Hormones communicate to cells over some distances, produced at one site and act on another. Transported through the bloodstream in animals/sap of plants More localized communication: 2) Paracrine Signaling:  One cell secretes local regulators into the extracellular fluid and it acts on nearby target cells  Ex. Histamines in inflammatory response, nitric oxide 3) Synaptic/Neuronal signaling:  Neuron releases neurotransmitter into a space  Neurotransmitters diffuse across the space into neighboring neuron or muscle and activate it, causes a change in the target cell to affect some change or carry the signal in the form of a nerve impulse  Messages can be delivered over great distances but occur through private lines at a rapid rate Most direct form of communication:  Cell-to-cell communication by plasma membrane o Doesn’t require the release of secreted molecules o Signaling molecules in plasma membrane of one cell bind to receptors embedded in adjacent cells o Also between gap junctions and plasmodesmata General Stages of Cell Signaling  Cells must respond selectively to the different signaling chemicals 1) Reception:  Ligand molecules bind to a specific cellular protein— receptor—that is located on a target cell  Hormones (adrenaline, estradiol, insulin, glucagon), local regulators (PDGF, NO, NGF), and neurotransmitters (acetylcholine)  Receptors usually activated by only one signaling molecule and function to take an extracellular signal and convert it into an intracellular signal  Most signal receptors are plasma membrane proteins (G protein linked receptor, tyrosine kinase receptor, ion channel receptors) 2) Transduction:  Ligand causes a conformation change in receptor protein, causes a series of responses in the cell that convert the original signal into a cellular response 3) Response:  Intracellular signaling molecule can eventually cause an enzyme to become activated or cause the expression of a gene G-Protein Coupled Receptor  Largest family of receptors but they are not enzymes  Signaling molecules can be hydrophilic, water soluble, protein/amino acid derivative  When signal molecule binds to G- protein linked receptor, a change of conformation occurs enabling it to interact with an inactive G protein on the intracellular side of the membrane, GDP is displaced by GTP o G proteins are made of 3 protein subunits that are separated from the receptor complexes o G proteins are activated with GTP bound to them. Activated G proteins are able to diffuse along the membrane to find their target proteins  Activated G proteins bind to other proteins (enzyme that catalyzes reaction, enzyme that adds P, ion channel) that begin signal transduction pathway. The longer they are bound, the stronger and more prolonged the signal  G proteins can be deactivated by the hydrolysis of GTP to GDP. Once GTP is replaced, G protein is inactive and ready to be activated by another signaling molecule  Defects in turning on/off the G protein linked receptors are linked to metabolic disorders and diseases Receptor Tyrosine Kinase (enzyme-linked receptor)  A kinase is an enzyme that catalyzes the transfer of phosphate groups  Tyrosine kinase extends into cytoplasm and catalyzes the transfer of phosphate group from ATP to amino acid tyrosine on substrate protein (attach phosphates to tyrosines)  Important in cell division/cell repair, primarily as a growth factor receptor  The cytoplasmic side of receptor acts as an enzyme  Switched on by the ligand on the extracellular side of the membrane  Ligand causes binding of TK receptor subunits to form a dimer  The cytoplasmic side of the receptor becomes phosphorylated by ATP  Other cellular proteins interact with phosphorylated domain of TK receptor and becomes activated and can initiate numerous transduction systems  Termination of signaling processes occurs when protein phosphates (opposite of kinases) remove phosphate groups off of proteins. Tyrosine domain loses phosphates and is no longer active. Activated receptors can be brought into the cell by endocytosis and destroyed with lysosomes. Ligand Gated Ion Channel  Serve for rapid transmission across synapses in nervous system  Responsible for the conversion of neurotransmitters from outside to an electrical signal inside of the membrane of neurons  Binding of ligands causes conformation change in channel that allows specific ions to flow  Once channels open, the movement of ions is determined by the electrochemical (concentration, charge) gradients  G protein linked receptors and TK receptors function to transmit signals into the cell in form of relay systems formed from intracellular signaling molecules inside of the cell  Signaling molecules generate other signals or receive a signal in one part of the cell and move to another part (signaling proteins act as molecular switches)  Common mechanism to turn on proteins is the addition of a phosphate group from ATP  ATP phosphorylate proteins that are able to begin operation in some pathway, proteins act as switches on the “On” position  To stop transduction pathways, the initial signal molecule must be removed from the receptor. Protein phosphatase removes phosphate group from activated protein, turning it off  Not all of the components of the transduction pathway are proteins. Some signaling systems rely on small, non-protein, water soluble molecules or ions. These molecules act as secondary messengers, taking information from the primary messenger (the initial signal ligand) and relaying it through the pathway 2nd Messengers: Cyclic AMP  Formed from ATP through the removal of 2 phosphate groups using the enzyme adenylyl cyclase  Water soluble so it can move easily throughout the cell  Messengers binds to the G protein linked receptors and activate the G protein complex  Activated G protein activates adenylate cyclase initiating the conversion of ATP to cyclic AMP  Cyclic AMP exerts effects within the cell by activating the enzyme it’s bound to  Activation of protein kinase A causes other phosphorylation events to occur rapidly (activating CAMP production can cause rapid effects): o Glycogen breakdown in skeletal muscles o Fat breakdown in adipose tissue to fatty acids o Increase in heat rate and force of contraction o Fight or flight responses  Other responses are slow, such as the control of gene expression o Hormone—G protein linked receptor—G protein—adenylate cyclase—cAMP —protein kinase A—gene regulatory protein—gene transcription altered nd 2 Messengers: Calcium ions and IP3  Muscle contraction, neurotransmitter released by neurons, growth of cytoskeleton  Stored in high concentration in ER (actively pumped into ER from cytosol) and released by IP3 when the proper signal is detected  Calcium ions enter a cell through gated ion channels o Neurotransmitters bind to channel proteins and the flow of ions occurs. It changes the electrical potential of cells across the membrane  Calcium ions can also be added through the IP3 pathway o Ligand binds to the receptor causing a conformation change o Phospholipase C acts on membrane PIP o PIP is hydrolyzed to form 2 molecules: IP3 and DAG o IP3 leaves the plasma membrane and diffuses into the ER where it binds to calcium channels in the ER membrane o Concentration of calcium increased in the cytosol o DAG helps activate another protein kinase which can be used to phosphorylate other proteins  Signal molecule—G protein receptor—G protein—activation of phospholipase C— breakdown of PIP  IPS—diffuses to ER—opens calcium gated channels—increases calcium concentration in cell—calcium binds to calmodulin (calmodulin has 3 calcium binding sites; it changes its shape and wraps around protein)  DAG and IP3 pathways are used for platelet activation, muscle contraction, insulin and amylase secretion, glycogen breakdown Apoptosis  Essential for normal development of the nervous system  Programmed cell death, when: o DNA damaged/mutated o Caused by a signal o Elimination of cells during development o Does not activate immune system  During: o Nuclear DNA fragmented o Cytoskeleton dismantled o Blebbing—fragments of dead cells make up apoptotic bodies taken up by macrophages and used  Ced-9: in outer mitochondrial membrane, master regulator of apoptosis, promotes apoptosis when signal is received, activates proteases (breaks proteins/enzymes) and nucleases (breaks DNA) o Main proteases are caspases—Ced-3 is the main caspase  Ced-3 and Ced:4 are proteins (activated by death ligand)  As long as Ced-9 is active, apoptosis is inhibited and the cell remains alive  When the cell receives the death signal, Ced-9 is inactivated, reliving it’s inhibition of Ced-3 and Ced-4. Active Ced-3 triggers cascade of reactions leading to the activation of nucleases and other proteases—eventually leading to cell death Neurosis  Swelling destruction of cell after massive injury Signal transduction pathways are a means for a cell to:  relay signals from one cell to the cytoplasm of another cell  amplify a signal by allowing a few extracellular signals to evoke increased production of secondary messengers  diverge the signal by causing pathway to split and be relayed into a number of different targets  control activation and inhibition by interfering with any of the steps through mutations, intercellular signals and extracellular signals  produce a signal that is recognized by only a specific group of cells with the appropriate receptors  rapidly respond to changes (fight or flight, food and smell, photoreceptors in eyes) Figure 3: The Specificity of Cell Signaling


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