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BIOCHEM 2 > Chapter 11 Glycolysis and Gluconeogenesis > Flashcards

Chapter 11 Glycolysis and Gluconeogenesis Flashcards

1
Q

How does galactose enter into the glycolytic pathway?

A

The Leloir Pathway

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2
Q

What are the main steps of the Leloir Pathway?

A

Galactose to Galactose 1- phosphate (reaction catalyzed by galactokinase)

Galactose 1- phosphate to UDP-Galactose catalyzed by uridylyl transferase. In this step we also get Glucose 1-phosphate which is converted to Glucose 6-phosphate (reaction catalyzed by phosphoglucomutase) KEY REACTION FOR ENTERING GLYCOLYSIS!!

UDP-Galactose is oxidized to the carbonyl by UDP Glucose 4-epimerase.

NADH reduces the C-4 carbon, this generates UDP-Glucose.

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3
Q

Explain the significance of the Leloir pathway?

A

The significance of the Leloir Pathway is it gives a way for lactose to be converted to galactose. This galactose can be converted to UDP-glucose and in the process Glucose-1-phosphate is converted to Glucose-6-phosphate which is a key metabolic intermediate for glycolysis.

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4
Q

What is the first step of glycolysis?

A

Glucose is converted to Glucose-6-phosphate by hexokinase.

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5
Q

What is the importance of converting Glucose to Glucose-6-phosphate?

A

This allows to capture glucose-6-phosphate in the cell because there are no transporters for phosphorylated glucose and the negative charge make it impossible for passive diffusion.

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6
Q

What is the relationship between glucose-6-phosphate and hexokinase?

A

Glucose-6-phosphate is an allosteric inhibitor of hexokinase.

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7
Q

How is the first step of glycolysis made energetically favorable?

A

By coupling the reaction to the hydrolysis of ATP.

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8
Q

How is the induced fit property of hexokinase used to prevent unfavorable reactions from happening?

A

Hexokinase is active once glucose is bound, this prevents ATP from transferring a phosphate to water.

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9
Q

What is the second step of glycolysis?

A

Isomerization of glucose-6-phosphate to fructose 6-phosphate by phosphohexose isomerase.

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10
Q

What is the reaction mechanism of the isomerization of glucose-6-phosphate to fructose-6-phosphate?

A

Refer to slides, proton is abstracted from one place and put back in another place which results in isomerization.

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11
Q

In the first step of the phosphohexose isomerase reaction the enzyme abstracts a proton from glucose. Aliphatic protons are in general not acidic, why can the enzyme abstract this particular proton?

A

Electron withdrawal effects by adjacent carbonyl and nearby hydroxyl group.

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12
Q

Why is the isomerization of glucose-6-phosphate to fructose-6-phosphate favorable for the subsequent steps of glycolysis?

A

The reverse aldol in subsequent steps would give a 2 carbon molecule and a 3 carbon molecule instead of two structurally similar 3 carbon molecules.

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13
Q

What is the third step of glycolysis?

A

Reaction of fructose-6-phosphate to fructose 1,6-bisphosphate. Catalyzed by phosphofructokinase 1. THIS IS THE FIRST COMMITTED STEP OF GLYCOLYSIS.

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14
Q

What is the fourth step of glycolysis?

A

Reaction of fructose 1,6-bisphosphate to dihydroxyacetone phosphate and glyceraldehyde phosphate catalyzed by an aldolase.

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15
Q

What is the reaction that is taking place for fructose-1,6-bisphosphate to glyceraldehyde 3-phosphate and dihydroxyacetone phosphate

A

Reverse Aldol reaction

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16
Q

What is the fifth reaction step of glycolysis?

A

Dihydroxyacetone is converted to glyceraldehyde 3-phosphate by the enzyme triose phosphate isomerase.

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17
Q

What is the fifth reaction step of glycolysis?

A

Dihydroxyacetone is converted to glyceraldehyde 3-phosphate by the enzyme triose phosphate isomerase.

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18
Q

What is the relationship of ATP and PFK-1?

A

ATP is both acting as a substrate and allosteric inhibitor of PFK-1

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19
Q

How does triose phosphate isomerase prevent unfavorable side reactions?

A

with the endiol intermediate, stabilizing endiol intermediate prevents intermediate from undergoing dehydration.

Loop closes over the active site functioning like a lid that prevents the intermediate from detaching from the enzyme and participating in unfavorable side chemistry.

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20
Q

The TIM NUMBERS

A

GAP 123: 435261

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21
Q

What is the first energy recovering step reaction of glycolysis?

A

Reaction 6 the GAPDH reaction.

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22
Q

What is the sixth reaction of glycolysis?

A

Glyceraldehyde 3-phosphate to 1,3-bisphosphoglycerate.

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23
Q

What is the sixth reaction of glycolysis?

A

Glyceraldehyde 3-phosphate to 1,3-bisphosphoglycerate using the enzyme glyceraldehyde 3-phosphate dehydrogenase.

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24
Q

The addition of a phosphate group to a carboxylic acid to form a mixed ester is unfavorable. How does this reaction proceed in the GADPH reaction?

A

The reaction can be viewed as two separate steps:
1. the oxidation of glyceraldehyde to the carboxylic acid. (FAVORABLE)

  1. the phosphorylation of the carboxylic acid (unfavorable)
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25
Q

The addition of a phosphate group to a carboxylic acid to form a mixed ester is unfavorable. How does this reaction proceed in the GADPH reaction?

A

The reaction can be viewed as two separate steps:
1. the oxidation of glyceraldehyde to the carboxylic acid. (FAVORABLE)

  1. the phosphorylation of the carboxylic acid (unfavorable)
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26
Q

What is the role of the thiohemiacetal in the GADPH reaction?

A

We bring in a cysteine, form a thiohemiacetal and we oxidize the thiohemiacetal since it can undergo any resonance.

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27
Q

What is the leaving group of the GADPH reaction?

A

The protein is the leaving group, nucleophile: inorganic phosphate. Electrophile: thioester.

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28
Q

What is the seventh step of glycolysis?

A

1,3-bisphosphoglycerate to 3-phosphoglycerate by the enzyme phosphoglycerate kinase.

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29
Q

What is the first energy recovering step in glycolysis?

A

glyceraldehyde 3-phosphate to 1,3-bisphosphoglycerate

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30
Q

What is the meaning of the term substrate level phosphorylation?

A

phosphate group is transferred from a substrate molecule directly to ADP forming ATP.

31
Q

Why do we say that phosphoglycerate kinase participates in super-coupling?

A

there is coupling between two distinct steps to drive the reaction forward.
1. using free energy of hydrolysis of 1,3-bisphosphoglycerate to drive synthesis of ATP.

  1. 1,3-bisphosphoglycerate was synthesized using free energy of oxidation of glyceraldehyde 3-phosphate.
32
Q

How is glycolysis directly linked to oxygen transport?

A

2,3-BPG is a molecule that is produced as an intermediate in the glycolytic pathway from 1,3-bisphosphoglycerate.

33
Q

What enzyme catalyzes the critical connection between 1,3-BPG and 2,3-BPG?

A

bisphosphoglycerate mutase.

34
Q

What is the role of 2,3-BPG?

A

binds to hemoglobin in red blood cells and reduces its affinity for oxygen.

35
Q

What is the 8th step of glycolysis?

A

3-phosphoglycerate to 2-phosphoglycerate by the enzyme phosphoglycerate mutase.

36
Q

What is the unusual chemical bond that is present in the mutase mechanism?

A

the direct nitrogen to phosphorous bond.

37
Q

Is the phosphate group moved directly between the oxygens on carbon-2 and on carbon-3?

A

No the OH on carbon two picks up phosphate from the direct nitrogen to phosphorous bond in the enzyme. The reaction goes through 2,3-BPG intermediate. The phosphate on carbon 3 is taken by the enzyme.

Pre-existing phosphate group in enzyme attached to histidine is used.

38
Q

What is the 9th step of glycolysis?

A

2-phosphoglycerate to phosphoenolpyruvate by the enzyme enolase.

39
Q

Which mechanism uses three distinct types of catalysis?

A

the enolase mechanism in ninth step of glycolysis:
1. acid base catalysis
2. metal ion catalysis
3. isomerization catalysis

40
Q

What is the 10th step of glycolysis?

A

phosphoenolpyruvate to pyruvate by enzyme pyruvate kinase.

41
Q

What is the second substrate level phosphorylation in glycolysis?

A

phosphoenolpyruvate to pyruvate by enzyme pyruvate kinase.

42
Q

Which reactions of glycolysis have large negative free energies?

A
  1. glucose to glucose-6-phosphate
  2. fructose-6-phosphate to fructose-1,6-bisphosphate
  3. phosphoenolpyruvate to pyruvate

These are the regulated steps because they are committed steps that drive the reaction forward.

43
Q

What are the two fates of pyruvate?

A

Anaerobic: fermentation takes pyruvate to other small molecule metabolites such as ethanol or lactate.

Aerobic: pyruvate is routed into the citric acid cycle.

44
Q

What is the purpose of the fermentation steps in anaerobic organisms?

A

Get rid of NADH, so that we have continual supply of NAD+ to undergo glycolysis.

45
Q

What does lactic acid fermentation involve?

A

Putting the electrons of NADH onto pyruvate to generate L-Lactate using enzyme lactate dehydrogenase.

46
Q

What does ethanol fermentation involve?

A

pyruvate to acetaldehye using cofactor TPP and enzyme pyruvate decarboxylase . Then acetaldehyde is converted to ethanol by enzyme alcohol dehydrogenase.

47
Q

What is the role of the TPP cofactor in ethanol fermentation?

A

acts as a temporary place to store the electrons from the loss of CO2.

48
Q

Draw the chemical mechanism of pyruvate carboxylase.

A
49
Q

What are the two major regulatory points for glycolysis?

A

pyruvate kinase and phosphofructokinase-1.

50
Q

How is pyruvate kinase regulated?

A

The pyruvate kinase in glycolytic tissues are positively allosterically regulated by Fructose-1,6-bisphosphate. Negatively allosterically regulated by ATP, acetyl coA, and alanine

The pyruvate kinase in liver becomes inactivated when phosphorylated by protein kinase A (G alpha stimulatory pathway) and active when dephosphorylated.

51
Q

How is phosphofructokinase-1 (PFK-1) regulated?

A

PFK-1 is positively regulated by ADP and AMP. PFK-1 is negatively regulated by ATP and citrate.

Fructose 2,6-bisphosphate positively regulates PFK-1 which stimulated glycolysis and inhibits gluconeogenesis.

52
Q

What is PFK-2 (phosphofructokinase-2)?

A

converts fructose-6-phosphate to fructose-2,6-bisphosphate.

53
Q

What is FBPase-2?

A

converts fructose-2,6-bisphosphate to fructose-6-phosphate.

54
Q

What is importance of PFK-2?

A

PFK-2 synthesizes some of fructose to fructose-2,6-bisphosphate in order to regulate glycolysis.

55
Q

What is a substrate cycle?

A

when two overlapping pathways run in opposite directions, have some enzymes in common while others differ.

56
Q

Why are bypass reactions necessary in gluconeogenesis?

A

complimentary reactions in glycolysis are extremely exergonic.

57
Q

In the first bypass reaction of gluconeogenesis how is the bicarbonate activated?

A

The bicarbonate is phosphorylated.

58
Q

Explain the mechanism of the first bypass reaction of gluconeogenesis

A

refer to slides

59
Q

Why was CO2 attached to pyruvate to make oxaloacetate only for it to be liberated one step later?

A

The CO2 was jammed onto pyruvate and taken off to provide energy because the chemistry for putting on the CO2 and taking off the CO2 are completely different.

60
Q

Why when starting gluconeogenesis from pyruvate is oxaloacetate exported from the mitochondria in the form of malate?

A

There is no transporter for oxaloacetate out of the mitochondria. Oxaloacetate transported from the mitochondria in the form of malate through the malate shuttle.

61
Q

Oxaloacetate exported from the mitochondria in the form of malate, how is this necessary and advantageous?

A

Electrons in NADH go on malate

We net moved out net reducing equivalents of NADH from mitochondria to cytosol (where it is rare) in the right amount.

62
Q

Why does final bypass reaction take place in ER?

A

Glycolysis takes place in cytoplasm, this prevents glucose-6-phosphate being generated in glycolysis from being stripped off of its phosphate.

63
Q

What is the major regulatory step of glycolysis and gluconeogenesis?

A

The PFK-1/FBPase-1 step

64
Q

What is the special structural property of PFK-2 and FBPase-2?

A

They are both part of a single protein that has two active sites.

65
Q

Explain the regulation of PFK-2/FBPase-2?

A

Single phosphorylation event regulates which enzyme is on or off.

High glucose—> insulin activates another phosphatase which takes off phosphate from PFK-2/FBPase-2

PFK-2 turns on, FBPase-2 turns off.
(GLYCOLYSIS ACTIVATED, INHIBIT GLUCONEOGENESIS).

Low glucose —-> release of glucagon—> activates cAMP dependent protein (protein kinase A) —-> kinase phosphorylates PFK-2/FBPase-2.
PFK-2 turns off, FBPase-2 turns on.
(INHIBIT GLYCOLYSIS, ACTIVATE GLUCONEOGENESIS)

66
Q

What is the Cori cycle?

A

metabolic pathway that occurs between the liver and skeletal muscle.

Allows for recycling of lactate in skeletal muscle back into glucose in the liver.

67
Q

What is the Forkhead box other transcription factor (FOXO1)?

A

stimulates the synthesis of genes for gluconeogenesis and suppresses glycolytic genes. It carries out these functions in the unphosphorylated state.

68
Q

How can FOXO1 be phosphorylated?

A

By protein kinase B through the insulin signaling pathway.

69
Q

Phosphorylated FOXO1 is a substrate for…

A

ubiquitination enzymes

70
Q

What does glucagon do to FOXO1?

A

Inhibits phosphorylation of FOXO1 allowing it to continue as a transcriptional regulator.

71
Q

How do insulin and glucagon regulate the expression of PEPCK?

A

Insulin downregulates PEPCK through insulin signaling.

Glucagon upregulates PEPCK through cAMP signaling.

72
Q

Why does excess gluconeogenesis occur in type II diabetes?

A

Diabetes is not responding to insulin signaling pathway and is therefore not downregulating gluconeogenesis.

73
Q

Why is it probably not a good idea to overexpress PEPCK in your muscles in an attempt to develop superhuman powers?

A

We will become extremely aggressive, uncontrolled aggression.

74
Q

Explain the complete mechanism by which glucose regulates the release of insulin present in a diabetic patient.

A

Glucokinase present at high glucose concentrations.

Glucose enters the pancreas and
is converted to Glucose-6-phosphate.

Glucose-6-Phosphate leads to the
production of ATP through a specific pathway.

ATP causes potassium ions to stay in the cell. Calcium ions enter cell.

The increase in calcium leads to the release of insulin.

BIOCHEM 2 (17 decks)

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