Biochemistry Chapter 5 (Exam 3) – Flashcards
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Why are catalysts necessary for reactions in living systems to proceed at a useful rate?
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Speeds up the rate of reaction by lowering the activation energy.
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What affects the reaction equilibrium between substrate and product? which aspect of a reaction can an enzyme alter?
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-The free energy of the ground state of Product is lower than that of Substrate, so G for the reaction is negative and the equilibrium favors Product. - Catalysts enhance reaction rates by lowering the activation energy.
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What does a large positive Keq "e.g Keq=1000" mean in terms of final concentration of products and reactants?
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Final product concentration of product is a 1000x more then substrate.
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-What does K`eq mean in terms of the standard free-energy change of the reaction? -How does it relate to the speed at which equilibrium is reached?
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G= -RT*ln*keq A large negative value for G reflects a favorable reaction equilibrium-but as already noted, this does not mean the reaction will proceed at a rapid rate.
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Why is it important for an enzyme to be complementary to the reaction transition state rather then to the substrate?
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Optimal interactions between substrate and enzyme occur during the transition state.
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What is the Lock and Key hypothesis?
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Substrate binds to the portion off the enzyme with a complementary shape.
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What is the Induced fit model?
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Binding of the substrate induces a change in the conformation of the enzyme that results in a complementary fit.
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Explain the effects of saturating levels of substrate on enzyme-catalyzed reactions.
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The saturation effect is a distinguishing characteristic of enzymatic catalysts and is responsible for the plateau observed in Figure 6-11. The pattern seen in Figure 6-11 is sometimes referred to as saturation kinetics.
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Why is there no K-2 in the equation describing the reaction from E+S to E+P?
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Early in the reaction, the concentration of the product, [P], is negligible, and we make the simplifying assumption that the reverse reaction, P---->S (described by K-2), can be ignored.
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What is the steady state assumption?
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The rate of formation of ES is constant- That is that the rate of formation of ES is equal to the rate of its breakdown.
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What does the Michaelis-Menten equation describe?
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For a one-substrate enzyme-catalyzed reaction. It is a statement of the quantitative relationship between the initial velocity, the maximum velocity, and the initial substrate concentration [S], all related through the Michaelis constant Km.
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What are two definitions of Km?
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-It is the substrate concentration at initial velocity that equals half of the Vmax. - (K-1+K2)/(K1)
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What are the units of Km?
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moles/liter or molarity or M
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Under what conditions does Km (in this case called Kd) represent a measure of affinity of the enzyme for the substrate?
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Revisit page 204 or 198
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What does a high Kcat value mean?
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High catalytic turnover number. Which means the number of substrate molecules converted to product in a given unit of time on a single enzyme molecule when the enzyme is saturated with substrate.
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What does a high Km value mean for velocity?
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Km has an inverse relationship to velocity- Thus it will have a low velocity.
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Why are inhibitors necessary as enzymatic control mechanisms in biological systems?
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It is biologically efficient to turn enzymes on or off instead of wasting resources to build new enzymes.
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How does a competitive inhibitor effect Km and Vmax?
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-Km is increases (decreases apparent affinity) -Vmax = Unchanged
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How does uncompetitive inhibition effect Km and Vmax
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-Km = Decreases -Vmax = Decreases
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How does noncompetitve (mixed inhibition) effect Km and Vmax?
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-Km = remains constant -Vmax = decreases
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How do the serine, histidine, and aspartate residues in chymotrypsin act together to stabilize the transition state during catalysis?
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See page 214 or 207.
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Are enzymes always proteins, consisting of only amino acids?
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NO ex. RNA, co-factors, co-enzymes
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Why must the covalent bond formed between enzyme and substrate and covalent catalysis be transient?
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The enzymes must be regenerated in free form (the covalent bond to the substrate / product must be undone) to be able to catalyze the reaction again. Enzymes are catalysts and must be recycled many times.
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Review Question 8-12 on page 79
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Do YOU know the FACTS? Chapter 6..
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Quick equation for finding Kcat?
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Kcat = ( Vmax / Total Enzyme )
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Why is the term K-2 not included in the Michealis-Menten equation?
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The Michealis-Menten equation only describes initial reaction rates!
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T or F? Km has the dimensions per second?
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FALSE
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T or F? Km= (K2+K-1)/K1
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TRUE
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T or F? Km is equal to the substrate concentration that will bring the reaction to maximal velocity?
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FALSE
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T or F? At very high substrate concentration the velocity of the reaction is independent of substrate concentration.
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TRUE
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T or F? The concentration of the enzyme substrate complex stays constant throughout the reaction.
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TRUE *Steady State Assumption
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T or F? Enzyme concentration is much lower then substrate concentration.
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True
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T or F? The velocity of the reaction is equal to the mathematical product of concentration of enzyme substrate complex and the rate constant. Vo=[ES]k2
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True
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T or F? To be effective enzymes must be present at the same concentration as their substrate.
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False
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T or F? Enzymes increase the rate in which substrate is converted to product
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True
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T or F? Enzymes insure all substrate is converted to product.
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False
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T or F? Enzymes insure that the product is more thermodynamically stable then the substrate.
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FALSE
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What is an epimer?
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epimer refers to one of a pair of stereoisomers. The two isomers differ in configuration at only one stereogenic center. All other stereocenters in the molecules, if any, are the same in each.
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T or F? Is glucose an epimer of mannose?
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True
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T or F? Is galactose an epimer of mannose?
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False
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T or F? is Glucose an epimer of Galactose?
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True
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T or F? Is allose a epimer of glucose?
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True
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How many isomers of glucopyranose are possible?
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32!
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Describe glucopyranose with four chemical terms.
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-Hexose -Aldose -Pyranose -Reducing Sugar
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How many isomers of fructofuranose
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16
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Describe fructofurnanose in four chemical terms
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-hexose -ketose -furanose -Reducing Sugar
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T or F? what other compounds aside from monosaccarides have enantiomers?
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Amino Acids
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What Amino Acids compose collegen?
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Glycine-proline-hydroxyproline
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what is the structure of collegen
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-The secondary structure of each peptide is a left handed alpha chain.
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What does vitamin C do for collagen
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it hydroxylates the proline to form hydroxyproline
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What is the Fc region
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crystalizable fragment
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What is the Fab region?
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antigen binding fragment
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+Delta G
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endergonic
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-Delta G
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exergonic
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What type of fit does Hexokinase have?
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Induced Fit
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What is an example of irreversible enzyme inhibition using asprin?
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Asprin will acetylate cycloxygenase, thus it cannot produce prostoglandins.
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How are fibers of collagen connected?
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-They are covalently bonded between the R-groups of lysine on the N-terminus of one strand, to the C-terminus of another strand. -Lysyl oxidase----> aldehyde derivatives----> dehydration and binding.
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kcat
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Catalytic constant (turnover number); represents the number of catalytic events per enzyme molecule
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Kcat/Km
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Specificity constant; since the rate of the reaction varies directly with how often enzymes and substrate encounter with one another, kcat/km is a measure of an enzyme's catalytic efficiency.
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Delta Gb
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The difference in activation energy between a catalyzed and catalyzed reaction.
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Kcat/kn
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Rate acceleration; ratio of the rate constant in the presence of enzyme divided by the rate constant in the absence of enzyme.
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Three ways to control enzyme activity
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-Enzyme inhibition -Covalent modification -Allosteric regulation
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Three types of reversible enzyme inhibition?
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-Competitive -Uncompetitive -Noncepetitive
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Enzyme classification according to reaction type (OTHLIL)
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1. Oxidoreductase 2. Tranferase 3. Hydrolases 4. Lyases 5. Isomerases 6. Ligases
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Enzyme Commission Numbers?
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1.Classname 2.Subclass 3.Acceptor Group 4.Acceptor Substrate
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What is the only aldose that commonly occurs in nature as a monosaccharide?
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D-Glucose
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T or F? Glyceraldehyde is an aldotriose?
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True
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T or F? Dihydroxyacetone is a ketotriose?
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True
