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Book > Principles of Biochemistry > Flashcards

Principles of Biochemistry Flashcards

1
Q
  • `What happens during the two phases of glycolysis?
A
  1. One moleculse of glucose is converted to two glyceraldehyde-3-phosphate(GAP) molecules in a series of reactions that consumes 2 ATP.
  2. In the second stage of glycolysis, the two glyceraldehyde-3-phosphate molecules are converted to two pyruvate molecules, generating 4ATP and 2 NADH.
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2
Q
  • How many ATP are invested and how many are recovered from each molecule of glucose that follows the glycolytic pathway?
A
  • This process consumes 2 ATP. And Produces 4 ATP.
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3
Q
  • Compare the oxidation states of glucose and pyruvate.
  • Explain why glycolysis generates NADH.
A
  • To keep the pathway supplied with its primary oxidizing agent, NAD+.
  • To generate the active enzyme.
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4
Q
  • Write the reactions of glycolysis, showing the structure formulas of the intermediates and the names of the enzymes that catalyze the reactions.
A
  • There are 10 steps.
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5
Q
  • Summarize the types of catalytic mechanisms involved.
  • Do any glycolytic enzymes require cofactors?
A
  • There is one between Glu-Pyr. And There are three between Pyr and 3 products.
  • Yes, Glucokinase, which catalyzes the same reaction but which is primarily involed in maintaining blood glucose level.
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6
Q
  • Explain the chemical logic of converting glucose to fructose before aldolase splits the sugar in two.
A
  1. Glucose to G6P (Hexokinase).
  2. G6P to F6P (Phosphoglucose Isomerase).
  3. F6P to FBP (Phosphofructosekinase).
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7
Q
  • Why is triose phosphate isomerase considered to be catalytically perfect?
A
  • The rate of the bimolecular reaction between enzyme and substrate is diffusion controlled, so product formation occurs as rapidly as enzyme and subsgtrate can collide in solution.
  • Any increase in TIM’s catalytic efficiency therefore would not increase its reaction rate.
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8
Q
  • How does phosphorylation differ differ between the kinase-catalyzed reactions and the reaction catalyzed by GAPDH?
A
  • This production of ATP, which does not involve oxygen, is an example of substrate level phosphorylation.
  • The subsequent oxidation of the NADH produced in this reaction by oxygen generates additional ATP by oxidative phosphorylation.
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9
Q
  • What compounds with high phosphate group-transfer potential are synthesized during glycolysis?
A
  • 2-Phosphoglycerate.
  • 2PG is dehydrated to phosphoenolpyruvate(PEP) in a reaction catalyzed by enolase.
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10
Q
  • Explain the chemical logic of dehydrating 2-Phosphoglycerate before its phosphoryl group is transferred.
A
  • There are 2-PG, enolase, Phosphoenolpyruvate and water.
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11
Q
  • Explain how chemical coupling of endergonic and exergonic reactions is used to generate ATP during glycolysis.
A
  • ENERGONIC :The energy investment of the first stage of glycolysis (2ATP consumed) is doubly repaid in
  • EXERGONIC : The second stage of glycolysis because two phosphorylated C3units are transformed to two pyruvates with the coupled synthesis of 4 ATP.
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12
Q
  • Which products of glycolysis are reduced molecules that the cell can oxidize to recover free energy?
A
  • Pyruvate.
  • The two pyruvate molecules produced through the partial oxidation of each glucose are still relatively reduced molecules.
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13
Q
  • Describe the three possible fates of pyruvate.
A
  1. Citric acid cycle
  2. Homolactic fermentation
  3. alcoholic fermentation.
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14
Q
  • Compare homolactic and alcoholic fermentation in terms of the products and the cofactors required.
A
  • Under anaerobic conditions in muscle, pyruvate is reversibly converted to lactate.
  • But in yeast, it is converted to Carbondioxide and ethanol.
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15
Q
  • What is the role of TPP in decarboxylation?
A
  • Thiamine pyrophosphate (TPP) is an essential cofactor of pyruvate decarboxylase.
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16
Q
  • Compare the ATP yields and rates of ATP production for anaerobic and aerobic degradation of glucose.
A
  • The rate of ATP production by anaerobic glycolysis can be up to 100 times faster than that of oxidative phosphorylation.
17
Q
  • Describe how fructose, galactose, and mannose enter the glycolytic pathway.
A
  1. Hexokinase recognizes mannose and convers it to mannose-6-phosphate.
  2. Phosphomannose isomerase then converts this aldose to the glycolytic intermediate F6P in a reaction whose mechanism resembles that of phosphoglucose isomerase.
18
Q
  • Which glycolytic enzymes are used by these tributary pathways.
A
  • Hexokinase
  • Phosphomannose isomerase.
19
Q
  • Write the net equation for the pentose phosphate pathway.
A

3 G6P + 6 NADP+ + 3 H2O ⇔ 6 NADPH + 6 H+ + 3CO2 + 2 F6P + GAP

20
Q
  • Summarize the reactions of each stage of the pathway.
A
  1. Oxidative reactions produce NADPH.
  2. Isomerization and epimerization Ribulose-5-Phosphate occur.
  3. Involves C-C bond cleavage and formation reactions.
21
Q
  • Compare the trasketolase and transaldolase reactions in terms of substrates, products, mechanism, and cofactor requirement.
A
  • Transaldolase Catalyzes the transfer of C3 units to yielding erythrose-4-phosphate (E4P) and F6P. The reaction occurs by aldol cleavage, which begins with the formation of Schiff base between and amino group of an essential Lys residue and the carbonyl group of S7P.
  • In a second transketolase reaction, a C2 unit is transferred from a second molecule of Xu5P to E4P to form GAP and another molecule F6P. The third stage of the pentose phosphate pathway thus transforms two molecules of Xu5P and one of R5P to two molecules of F6P and one molecule of GAP. To summarize, a series of carbon-carbon bond formations and cleavages convert three C5 sugars to two C6 sugars and one C3 sugar.
22
Q
  • How does flux through the pentose phosphate pathway change in response to the need for NADPH or ribose-5-phosphate?
A
  • The pentose phosphate pathway thus transforms two molecules of Xu5P and one of R5P to two molecules of F6P and one molecule of GAP.
23
Q
  • List the metabolic sources
  • Fates of G6P
A
  • Sources
  1. Free glucose through the action of hexokinase
  2. The product of glycogen breakdown or gluconeogenesis.
  • Fate
  1. It can be used to synthesize glycogen
  2. It can be catabolized cia glycolysis to yield ATP and carbon atoms (as acetyl-CoA) that are further oxidized by the citric acid cycle
  3. It can be shunted through the pentose phosphate pathway to generate NADPH and/or ribose-5-phosphate.
  4. In the live and kidney, G6P can be converted to blucose for export to other tissues via the bloodstream.
24
Q
  • Describe the structure of a glycogen molecule.
  • What is the advantage of its branched structure?
A
  • Glycogen is a polymer of σ(1→4)-linked d-glucose with σ(1→6)-linked branches every 8-14 residues.
  • Glycogen’s highly branched structure therefore permits rapid glucose mobilization through the simultaneous release of the glucose units at the end of every branch.
25
Q
  • List the three enzymes involved in glycogen degradation
  • Describe the type of reactions they catalyze.
A
  • Enzymes
  1. Glycogen phosphorylase (Phosphorylase)
  2. Glycogen debranching enzyme
  3. Phosphoglucomutase.
  • Type of reactions
  1. Release to yield glucose-1-phosphate(G1P)
  2. Remove glycogen’s branches thereby making additional glucose residues accessible to glycogen phosphorylase
  3. Converts G1P to G6P
26
Q
  • List the activators and inhibitors of glycogen phosphorylase.
  • How does phosphorylation affect its activity?
A
  • Activator : AMP
  • Inhibitor : ATP , G6P , Glucose
  • Alter enztmatic activity in manner reminiscent of allosteric regulation
27
Q
  • Why must opposing biosynthetic and degradative pathways differ in at least one enzyme?
A
  • This recurrent metabolic strategy - that biosynthetic and degradative ways of metabolism are different - is particularly importan when both pathways must operate under similar physiological conditions.
  • This situation is thermodynamically impossible if onem pathway is just the reverse of the other.
28
Q
  • List the three enzymes involved in glycogen synthesis.
  • Describe the types of reactions they catalyze.
A
  • Three enzymes
  1. UDP-glucose pyrophosphorylase
  2. Glycogen synthase enzyme
  3. Glycogen branching enzyme
  • Types of reactions
  1. UDP-glucose pyrophosphorylase : combining reaction
  2. Glycogen synthase enzyme : synthase reaction
  3. Glycogen branching enzyme : transfer reaction
29
Q
  • What is the free energy source for glycogen synthesis?
A
  • Under physiological conditions, glycogen breakdown is exergonic.
  • The synthesis of glycogen from G1P under physiological conditions is therefore thermodynamically unfavorable withour free energy input.
30
Q
  • Describe the role of glycogenin.
A
  • Acting as glycosyltransferase
  • Attatches a glucose residue donated by UDPG to the OH group of its Tyr 194.
  • Glycogenin then extends the glucose chain by up to senven additional UDPG-donated glucose residues to form a glycogen “primer”.
31
Q
  • Summarize the effects of AMP and G6P on glycogen phosphorylase and glycogen synthase.
A
  • Both glycogen phosphorylase and glycogen synthase are under allosteric control by effectors that include ATP, G6P, and AMP.
32
Q
  • Summarize the effects of phosphorylation and dephosphorylation on glycogen phosphorylase and glycogen synthase.
A
  • The interconversion of the a and b forms of glycogen synthase and glycogen phosphorylase is accomplished through enzyme-catalyzed phosphorylation and dephosphorylation, a process that is under hormal control.
33
Q
  • Why does a phosphorylation/dephosphorylation system allow more sensitive regulation of a metabolic process than a simple allosteric system?
A
  • That modulates the responsiveness of the enzymes to their allosteric effectors.
34
Q
  • ?Draw a simple diagram, similar to Fig.16-13, showing how a kinase and phosphatase can regulate the activities of two enzymes that catalyze opposing processes.
A
35
Q
  • How does regulation of glycogen metabolism differ between liver and muscle?
A
  1. Glycogen metabolism in the liver is largely controlled by the polypeptide hormones insulin and glucagon acting in opposition.
  2. In muscle and various tissues, control is exerted by insulin and by adrenal hormoes epinephrine and norepinephrine.
  • Glucagon, like insulin, is synthesized by the pancreas in response to the concentration of glucose in the blood.
36
Q
  • Summarize the effects of insulin, glucagon, and epinephrine on glycogen metabolism.
A
  • These hormones affect metabolism in their target tissues by ultimately stimulating covalent modification (phosphorylation) of regulatory enzymes.
37
Q
  • What are the intracellular effects of cAMP and Ca2+?
A
  • cAMP
  1. When hormonal stimulation increases the intracellular cAMP concentration, PKA activity increases, increasing the rates of phosphorylation of many proteins and decreasing their dephosphorylation rates as well.
  2. When cAMP concentration decreases, phosphorylation rates decrease, dephosphorylation rates increase, and the fraction of enzymes in their dephospho forms increases.
  • Ca2+​
    1. Ephinephrine binding to the alpha-adrenergic receptor stimulates an increase in intracellular concentration of Ca2+, which reinforces the cells’ response to cAMP (recall that phosphorylase kinase, which activates glycogen phosphorylase and inactivates glycogen synthase, is fully active only when phosphorylates and in the presence of increased concentration of Ca2+.
38
Q
  • Which four elements occur in virtually all biological molecules?
  • Summarize the major stages of chemical evoulution.
  • Practice drawing a simple condensation and hydrolysis reaction.
  • Explain why complemetarity would have been necessary for the development of self-replicating molecules.
A
  • Carbon , Hydrogen , Oxygen , Nitrogen
  • Biological molecules arose from in organic material. Complex self-replicating systems evolved from simple molecules.
  • Need Picture
  • Specific pairing between complementary fuctional groups permits one member of a pair to determine the identity and orientation of the other member.
39
Q
  • Explain the selective advatages of compartmentation and metabolic pathways.
  • Discuss the differences between prokaryotes and eukaryotes.
  • Make a list of the major eukaryotic organelles and their functions.
  • Explain why a taxonomy based on molecular sequences is more accurate than one based on morphology.
  • Which of the three domains are prokaryotic? Which domain is most similar to eukaryotes?
  • Explain how individual variations allow evolution to occur.
  • Why is evolutionarty change constrained by its past but impossible to predict?
A

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