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Biochem 2 > Exam 2 > Flashcards

Exam 2 Flashcards

1
Q

Glycolysis strategy

A
  • Add phosphoryl groups to glucose
  • Form high phosphate group transfer potential intermediates
  • Couple to ATP synthesis
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2
Q

Major fates of glucose

A
  • Structural: extracellular matrix
  • Storage: glycogen
  • ribose-5-phosphate: oxidation via pentose phosphate pathway
  • oxidation via glycolysis: pyruvate
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3
Q

Two phases of glycolysis

A

energy investment phase

  • prepare glucose to be cleaved
  • yields two trioses
  • costs 2ATP/glucose

energy production phase

  • oxidation/phosphorylation
  • 2 substrate-level phosphorylations
  • 2x2 ATP reactions = 4ATP
  • conversion of 2 NAD+ molecules to 2 NADH
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4
Q

Do living systems maintain equilibrium?

A

NO! They maintain steady state

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5
Q

Catabolism

A

Breaking down larger molecules into smaller molecules for energy production

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6
Q

Anabolism

A

Using energy to build larger molecules out of smaller ones.

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7
Q

Principal characteristics of metabolic pathways

A
  • irreversible
  • committed step
  • regulation
  • cellular location
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8
Q

Common biological nucleophiles

A
  • negatively charged oxygen
    • Alkoxides, hydroxides, carboxylates
  • negatively charged sulfhydryl groups
  • carbanion
  • uncharged amine group
  • imidazole
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9
Q

Common biological electrophiles

A
  • carbon atom of carbonyl
  • protonated imine group
  • phosphorous of phosphate group
  • Proton
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10
Q

Electron sink

A
  • a group that can pull electrons from a reactive centre and thus stabilize an electron-deficient intermediate or transition state
  • carbonyl carbons are electrophilic, so they can stabilize adjacent carbanion intermediates.
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11
Q

coupling reactions/intermediates

A

The key to coupling exergonic reactions with endergonic ones is the formation of a phosphorylated intermediate which is more reactive than the original molecule

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12
Q

oxidation-reduction reactions in metabolism

A
  • involve loss or gain of electrons

- the oxidation state of carbon varies depending on the elements with which it shares electrons

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13
Q

Structure and hydrolysis of ATP

A

The sugar ribose, an adenine nucleotide, and three phosphate groups which can be hydrolyzed. Exergonic reactions.

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14
Q

Nucleophilic substitution reactions

A
  • An sp3 hybridized carbon with a good leaving group
  • Good leaving groups are stable anions (often weak bases)
  • Sn1 carbocation intermediate is formed, retention or inversion
  • Sn2 transient pentavalent intermediate, inversion
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15
Q

Nucleophilic acyl substitution

A
  • carbonyl carbon
    • bonded to electronegative or highly polarizable atom
      • O, N, S most common in biological systems
  • tetrahedral oxyanion intermediate
  • product is substituted carbonyl
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16
Q

Group transfer reactions

A
  • proton transfer
  • Methyl transfer acyl transfer
  • glycosyl transfer
  • phosphoryl transfer
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17
Q

Nucleophilic additions

A
  • carbonyl carbon of aldehydes and ketones
  • Carbon and hydrogen are not good leaving groups
  • tetrahedral oxyanion intermediates
  • addition instead of substitution
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18
Q

carbonyl condensation

A
  • two carbonyl carbon compounds react
  • one carbonyl becomes carbanion
  • enolate intermediate
    • resonance stabilized
  • form new C-C bond
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19
Q

Elimination reactions

A
  • formation of double bonds
  • simple dehydration
  • alpha, beta elimination
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20
Q

oxidations and reductions

A
  • redox reactions involve loss or gain of electrons

- The oxidation state of carbon varies depending on the elements with which it shares electrons

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21
Q

isomerization

A

glucose-6-phosphate to fructose-6-phosphate

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22
Q

stabilization of carbanion

A
  • resonance stabilization
  • enzymes can add to stabilization
    • h-bonding or protonation
    • Formation of Schiff base
    • coordination to metal ion
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23
Q

Ways of controlling metabolic pathways

A
  • Control amount of enzyme
    • Rate of synthesis and degradation
  • Control enzyme activity
    • substrate/product
    • allosteric effectors
    • Covalent modification
      • phosphorylation is most common
  • Compartmentation
    • Pathways may be localized to specific locations in the cell
  • Hormones
    • second messengers
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24
Q

Flux generating step

A

Two opposing metabolic pathways are both thermodynamically favored

  • Regulation occurs at reactions that are far from equilibrium
  • coordinated kinetic control of opposing enzymes
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25
Q

The enzyme ____ is NOT involved in gluconeogenesis

A

pyruvate kinase*
PEP carboxykinase
glucose-6-phosphatase
pyruvate carboxylase

26
Q

Under which metabolic condition is gluconeogenesis activated?

A
  • Increased fructose 2,6-bisphosphate levels
  • increased insulin in the bloodstream
  • low cellular atp
  • none of the above*
27
Q

Which is the proper order or events for glycolysis?

A

I. formation of fructose 6-phosphate
II. Formation of NADH
III. Production of ATP
IV. a reaction catalyzed by aldolase

I, IV, II, III

28
Q

Which of the following reactions would you expect to proceed in the direction shown, under standard conditions, in the presence of the appropriate enzyme?

A

A) Malate + NAD+ –> OAA + NADH + H+
B) Acetoacetate + NADH + H+ –> beta-hydroxybutarate + NAD+
C) pyruvate + NADH + H+ –> lactate + NAD+ **
D) malate + pyruvate –> oxaloacetate + lactate

29
Q

Which of the following is not considered a “high energy” compound?

A

A) 1,3-bisphosphoglycerate
B) ATP
C) glucose-6-phosphate*
D) Phosphoenol pyruvate

30
Q

Which of the following would you expect to act as an electrophile?

A

A) Phosphorous of a phosphate group*
B) imidazole of a histidine
C) carbanion
D) both b and c

31
Q

Glycolysis occurs in the

A

A) mitochondrial matrix
B) cytosol*
C) lipid bilayer
D) A and B

32
Q

NAD+/NADH is considered a

A

A) one electron carrier
B) two electron carrier*
C) one or two electron carrier
D) “high energy” compound

33
Q

How much does it “cost” the cell to produce phosphoenolpyruvate (PEP) from pyruvate in gluconeogenesis?

A

A) 1 ATP
B) 2 ATPs*
C) 3 ATPs
D) 4 ATPs

34
Q

Gluconeogenesis occurs in the

A

A) mitochondrial matrix
B) cytosol
C) lipid bilayer
D) A and B*

35
Q

Formation of ATP is increased by

A

A) a high ratio of ATP to ADP
B) a high ratio of ADP to ATP*
C) a high ratio of ATP to AMP
D) a high ratio of NADH to NAD+

36
Q

If we consider a mole of NADH to be equivalent in energy to 2.5 ATP and a mole of FADH2 to be equivalent in energy to 1.5 ATP, what is the total number of moles of ATP that could be generated by oxidation of one mole of pyruvate via the citric acid cycle?

A

A) 46
B) 30
C) 12.5 *
D) 9

37
Q

The reduced coenzymes of the citric acid cycle, such as FADH2 and NADH, must pass their electrons into the ETC to produce ATP, but one step of the cycle yields a compound with high transfer potential that can provide energy for phosphorylation of ADP at the substrate level. What is this high-energy compound?

A

A) citrate
B) isocitrate
C) fumarate
D) succinyl CoA *

38
Q

Which of the reactions are involved in regulation of the citric acid cycle?

A

A) citrate synthase reaction and succinyl CoA synthase reaction
B) fumarase reaction and aconitase reaction
C) isocitrate dehydrogenase reaction and alpha-ketoglutarate dehydrogenase reaction*
D) succinate dehydrogenase reaction and malate dehydrogenase reaction

39
Q

Which of the following amino acids participates in the transfer of a phosphate group in the reaction catalyzed by succinyl-CoA synthetase?

A

A) serine
B) glutamate
C) histidine *
D) lysine

40
Q

The citric acid cycle is said to be both catabolic and anabolic. Which of the following terms is used to describe this property?

A

A) amphibolic *
B) amphipathic
C) anaplerotic
D) cataplerotic

41
Q

The effect of ATP on phosphofructokinase-1 (PFK-1) is shown below. For a given concentration of fructose-6-phosphate, the PFK-1 activity increases with increasing concentration of ATP, but a point is reached beyond which increasing concentrations of ATP cause inhibition of the enzyme. Explain how ATP can be both a substrate and an inhibitor of PFK-1. How is the enzyme regulated by ATP?

A

Due to two binding sites present on PFK-1, ATP can be both a substrate and an inhibitor. When [ATP] is low, it will only bind in the substrate binding site and deinhibit PFK-1. When [ATP] is high it will bind not only in the substrate binding site but also in the allosteric site and inhibit PFK-1.

42
Q

The effect of ATP on phosphofructokinase-1 (PFK-1) is shown below. For a given concentration of fructose-6-phosphate, the PFK-1 activity increases with increasing concentration of ATP, but a point is reached beyond which increasing concentrations of ATP cause inhibition of the enzyme. The inhibition of PFK-1 by ATP is diminished when the AMP concentration is high. How can this observation be explained?

A

Inhibition of PFK-1 by ATP is diminished when there is high [AMP] because AMP has a high affinity for the allosteric site, which causes the enzyme to adopt the relaxed (R) state, and so ATP is only able to bind to the substrate binding site.

43
Q

The effect of ATP on phosphofructokinase-1 (PFK-1) is shown below. For a given concentration of fructose-6-phosphate, the PFK-1 activity increases with increasing concentration of ATP, but a point is reached beyond which increasing concentrations of ATP cause inhibition of the enzyme. How do AMP levels affect the binding of fructose-6-phosphate? Which amino acid residues in the enzyme active site are involved with fructose-6-phosphate binding? Explain their roles.

A

low [AMP] indicates the tense (T) state of the enzyme, in which ATP binds to both the substrate binding and allosteric sites. This decreases the binding of frc-6-p. High [AMP] indicates that is in the relaxed (R) state, and frc-6-p binding is favored. Arginine and glutamate are involved w/ frc-6-p binding. Arginine is present during the relaxed state to stabilize the enzyme and lead to gluconeogenesis. Glutamate is present in the T-state to stabilize the enzyme and lead to glycolysis.

44
Q

Most enzymes in metabolic pathways catalyze near-equilibrium reactions. How is flow of metabolites (flux) controlled in these reactions? How is flux controlled for enzyme-catalyzed reactions that are metabolically reversible?

A

In near-equilibrium reactions, flux is controlled by simple equilibrium, or control of the concentration of metabolites that are moved through the pathway. In irreversible metabolic reactions, the enzymes that are responsible for converting metabolic species from one metabolite to another are subject to allosteric or covalent modification in order to control their catalytic efficiency

45
Q

Which reactions in a metabolic pathway are likely to be regulatory steps?

A

Reactions far from equilibrium are likely to be regulatory steps because they are irreversible.

46
Q

Glycolysis is divided into two phases. The preparatory phase and the payoff phase. Describe the preparatory phase of glycolysis

A

The preparatory phase of glycolysis involves preparing glucose to be cleaved into two trioses. Glc is phosphorylated into glc-6-p which traps it in the cytosol where it can then be converted into frc-6-p and then cleared.

47
Q

Describe the payoff phase of glycolysis.

A

the payoff phase of glycolysis involves converting two g3p molecules produced in the prep phase into 2 pyruvate molecules. This is an energy producing step and is the final step of glycolysis. Oxidation and phosphorylation reactions occur to accomplish this.

48
Q

How many ATPs are used/generated in each phase of glycolysis?

A

2 used and 4 generated

49
Q

What is the net ATP generated per glucose molecule in glycolysis?

A

2 ATP/glucose

50
Q

Discuss the chemical logic of the phosphoisomerase-catalyzed reaction, which converts glucose 6-phosphate into fructose 6-phosphate in the glycolytic pathway.

A

The logic here is to move the carbonyl group from C-1 to C-2 which then makes C-3 and C-4 the alpha and beta carbons which are better positions for cleavage.

51
Q

In glycolysis, phosphoenolpyruvate is converted to pyruvate in a reaction catalyzed by pyruvate kinase. However, in gluconeogenesis pyruvate is converted to phosphoenolpyruvate in two steps rather than one. Why is it important that gluconeogenesis is not the exact reversal of glycolysis?

A

If it were the exact reversal of glycolysis, it would be too easy to enter a futile cycle where both metabolites were being produced at a high rate. This would result in no energy being stored from the reactions.

52
Q

What is the role of the biotin prosthetic group of pyruvate carboxylase?

A

To move CO2 from active site to a 2nd site allowing for pyruvate to bind more readily to it.

53
Q

Explain what is meant by a substrate cycle

A

Coupling through substrate/product pairs of an energy requiring reaction with an energy-producing reaction that regenerates one of the products of the first reaction. The result is a net consumption of ATP and heat production.

54
Q

explain how PFK-1 and FBPase-1 are involved in the reciprocal regulation of glycolysis and gluconeogenesis

A

PFK-1 and FBPase-1 are allosteric enzymes that participate in substrate cycling between metabolites fructose-6-phosphate and fructose-1,6-bisphosphate. When the concentration of one of the metabolites in the cycle builds up, it can act as an allosteric inhibitor or agonist for each of the enzymes.

55
Q

PDC is a multienzyme complex responsible for catalyzing the conversion of pyruvate into acetyl CoA. E2 of the complex contains a “swinging arm”. What is the cofactor that makes up this “swinging arm”? How is it attached to the enzyme, E2?

A

Lipoic acid is the cofactor that makes up the “swinging arm”. It is attached to E2 by an amide bond from a lysine residue.

56
Q

What is the function of the “swinging arm” of the E2 complex?

A

The function of the swinging arm is to move the acetyl group from E1 to the next site on E1 or E2 to form acetyl CoA.

57
Q

What are the roles of E1 and E3 in the complex?

A

The role of E1 in the complex is to catalyze the decarboxylation of pyruvate into the acetal group that will be moved to the E2 complex as acetyl-TPP. The role of E3 is to regenerate the disulfide bonds in the lipoate, and return it to its original state.

58
Q

Jones et al looked at the structure of the swinging arm and concluded there was restricted motion of the arm as opposed to a freely moving arm. They suggested increased the efficiency of the reaction. Explain how this may increase efficiency.

A

If the swinging arm was not limited in the degree of which it can swing, then it is not guided to the correct catalytic sites on each of the enzyme components, which would make for inefficiency. Since the swinging arm has a fairly rigid motion of action, the arm can only swing back and forth from catalytic site to catalytic site, increasing the enzyme complex’s efficiency.

59
Q

What is the logic behind the aconitase reaction?

A

The logic behind the aconitase reaction is that the 3’ alcohol present on citrate cannot be oxidized and therefore cannot reduce NAD+ –> NADH. It must be converted to a 2’ alcohol for this reaction to occur.

60
Q

glycogen phosphorylase

A

releases glc-1-p from nonreducing end of the polymer

61
Q

glycogen debranching enzyme

A

removes branches allowing for glycogen phosphorylase to complete reaction

62
Q

phosphoglucomutase

A

converts glc-1-p to glc-6-p

Biochem 2 (1 decks)

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