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Biochemistry > Module 4 > Flashcards

Module 4 Flashcards

1
Q

Aerobicity: Glycolysis

A

Anaerobic

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2
Q

How does Glycolysis generate energy?

A

Catabolism of Glucose

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3
Q

Location: Glycolysis

A

Cytoplasm

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4
Q

How does Glycolysis obtain free energy from Glucose without Oxygen being present?

A

Glycolysis involves two sequential stages:

  1. Activation of Glucose via Phosphorylation (“ATP Investment”)
  2. Collection of Energy from High-Energy Intermediates (“ATP Earnings”)
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5
Q

Glycolysis: Stage 1

“ATP Investment”

A

ATP is used to produce activated 3-Carbon sugar compounds.

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6
Q

Glycolysis: Stage 2

“ATP Earnings”

A

ATP is derived from the oxidation of 3-Carbon sugar compounds.

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7
Q

Glycolysis Stage 1: Net Macromolecule Reaction

A

1 Glucose → 2 Glyceraldehyde-3-P

Overall Reaction: 1 Glucose + 2 ATP → 2 Glyceraldehyde-3-P + 2 ADP + 2 Pi

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8
Q

Glycolysis Stage 2: Net Macromolecule Reaction

A

2 Glyceraldehyde-3-P → 2 Pyruvate

Overall Reaction: 2 G3P + 4 ADP + 4 Pi + 2 NAD+ + 2 H+ → 2 Pyruvate + 4 ATP + 2 NADH + 2 H2O

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9
Q

How does Hexokinase-facilitated Glucose phosphorylation trap the former Glucose molecule within the cell?

A

The GLUT4 membrane transport protein cannot bind/recognize Glucose-6-P, so it only transports Glucose across the cell membrane.

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10
Q

How does the phosphorylation of Glucose alter the compound’s free energy?

A

Phosphorylation increases the free energy of Glucose.

Glucose phorphorylation is highly thermodynamically favorable (i.e. irreversible).

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11
Q

Glycolysis 1: Hexokinase Phosphorylation

A

Hexokinase/Glucokinase catalyzes the phosphorylation of Glucose to generate Glucose-6-P (via coupling to an ATP hydrolysis reaction).

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12
Q

Glycolysis 2: Phosphoglucoisomerase Conversion

A

Phosphoglucoisomerase catalyzes the isomerization of Glucose-6-P (6-Carbon ring) to generate Fructose-6-P (5-Carbon ring).

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13
Q

Thermodynamics: Glycolysis 1

Hexokinase Phosphorylation

A

Highly Thermodynamically Favorable

Irreversible

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14
Q

Thermodynamics: Glycolysis 2

Phosphoglucoisomerase Conversion

A

Slightly Thermodynamically Favorable

Reversible

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15
Q

Thermodynamics: Glycolysis 3

Phosphofructokinase-1 Phosphorylation

A

Highly Thermodynamically Favorable

Irreversible

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16
Q

Glycolysis 3: Phosphofructokinase-1 Phosphorylation

A

Phosphofructokinase-1 catalyzes the phosphorylation of Fructose-6-P to generate Fructose-1,6-BP.

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17
Q

Which step of Glycolysis is the major regulatory/commitment step?

A

Glycolysis 3: Phosphofructokinase-1 Phosphorylation

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18
Q

Thermodynamics: Glycolysis 4

Aldolase Cleavage

A

Slightly Thermodynamically Favorable

Reversible

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19
Q

Why does the Aldose Cleavage reaction readily occur in the cell despite being highly thermodynamically unfavorable under standard conditions?

A

The products of the Aldose Cleavage reaction are continuously being used/consumed in other processes, so this reaction is constantly shifted toward the products (per Le Chatelier’s Principle).

The concentrations of the Aldose Cleavage reaction metabolites in the cell results in a mass action ratio that favors the cleavage reaction.

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20
Q

Glycolysis 4: Aldolase Cleavage

A

Aldolase cleaves Fructose-1,6-BP (between C-3 and C-4) to form Glyceraldehyde-3-P (3-Carbon) and Dihydroxyacetone-P (3-Carbon).

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21
Q

Glycolysis 5: Triose Phosphate Isomerase Isomerization

A

Triose Phosphate Isomerase catalyzes the reversible isomerization of Dihydroxyacetone-P to Glyceraldehyde-3-P (via the Enediol intermediate).

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22
Q

Thermodynamics: Glycolysis 6

Glyceraldehyde-3-P Dehydrogenase Oxidation-Phosphorylation

A

Slightly Thermodynamically Favorable

Reversible

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23
Q

Thermodynamics: Glycolysis 5

Triose Phosphate Isomerase Isomerization

A

Slightly Thermodynamically Unfavorable

Reversible

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24
Q

Thermodynamics: Glycolysis 7

Phosphoglyercerate Kinase Phosphorylation

A

Slightly Thermodynamically Favorable

Reversible

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25
Q

Thermodynamics: Glycolysis 8

Phosphoglycerate Mutase Isomerization

A

Slightly Thermodynamically Unfavorable

Reversible

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26
Q

Thermodynamics: Glycolysis 9

Enolase Dehydration

A

Slightly Thermodynamically Favorable

Reversible

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27
Q

Thermodynamics: Glycolysis 10

Pyruvate Kinase Phosphorylation

A

Highly Thermodynamically Favorable

Irreversible

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28
Q

At which steps of Glycolysis does substrate-level phosphorylation occur?

A
  • Step 7: Phosphoglycerate Kinase Phosphorylation
  • Step 10: Pyruvate Kinase Phosphorylation
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29
Q

Glycolysis 6: Glyceraldehyde-3-P Dehydrogenase Oxidation-Phosphorylation

A

Glyceraldehyde-3-P Dehydrogenase catalyzes the coupled oxidation-phorylation reaction that converts Glyceraldehyde-3-P to 1,3-Biphosphoglycerate.

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30
Q

Glycolysis 7: Phosphoglycerate Kinase Phosphorylation

A

Phosphoglycerate Kinase catalyzes the dephosphorylation of 1,3-Biphosphoglycerate to generate ATP (via substrate-level phosphorylation) and 3-Phosphoglycerate.

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31
Q

Glycolysis 8: Phosphoglycerate Mutase Isomerization

A

Phosphoglycerate Mutase catalyzes the isomerization of 3-Phosphoglycerate to generate 2-Phosphoglycerate (via phosphoryl transfer).

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32
Q

Glycolysis 9: Enolase Dehydration

A

Enolase catalyzes the dehydration/condensation of 2-Phosphoglycerate to generate the higher-energy Phosphoenolpyruvate.

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33
Q

Glycolysis 10: Pyruvate Kinase Phosphorylation

A

Pyruvate Kinase catalyzes the dephosophorylation of Phosphenolpyruvate to generate ATP (via substrate-level phosphorylation) and Pyruvate.

34
Q

Which steps of Glycolysis are thermodynamically unfavorable?

A
  • Step 5: Triose Phosphate Isomerase Isomerization
  • Step 8: Phosphoglycerate Mutase Isomerization
35
Q

Glycolysis: Net Reaction

A

1 Glucose + 2 NAD+ + 2 ADP + 2 Pi → 2 Pyruvate + 2 NADH + 2 ATP + 2 H+ + 2 H2O

36
Q

Glycolysis: 10 Steps

A
  1. Hexokinase Phosphorylation
  2. Phosphoglucoisomerase Isomerization
  3. Phosphofructokinase-1 Phosphorylation
  4. Aldolase Cleavage
  5. Triose Phosphate Isomerase Isomerization
  6. Glyceraldehye-3-P Dehydrogenase Oxidation-Phosphorylation
  7. Phosphoglycerate Kinase Phosphorylation
  8. Phosphoglycerate Mutase Isomerization
  9. Enolase Dehydration
  10. Pyruvate Kinase Phosphorylation
37
Q

Glycolysis: Sugar Compounds in Sequence

A
  1. Glucose
  2. Glucose-6-P
  3. Fructose-6-P
  4. Fructose-1,6-BP
  5. Dihydroxyacetone-P
  6. Glyceraldehyde-3-P
  7. 1,3-Biphosphoglycerate
  8. 3-Phosphoglycerate
  9. 2-Phosphoglycerate
  10. Phosphoenolpyruvate
  11. Pyruvate
38
Q

What process regenerates NAD+ under anaerobic conditions?

A

Fermentation

39
Q

Fermentation: Animals vs. Microorganisms

A
  • Animals: Fermentation converts Pyruvate to Lactate
  • Microorganisms: Fermentation converts Pyruvate to Ethanol.
40
Q

Mechanism: Glyceraldehyde-3-P Dehydrogenase Oxidation-Phosphorylation

A
41
Q

What is the regulation of Glycolysis dependent on?

A

Energy Charge Within the Cell

42
Q

During which reactions does the regulation of Glycolysis within muscle tissue occur?

A
  1. Hexokinase Phosphorylation
  2. Phosphofructokinase-1 Phosphorylation
  3. Pyruvate Kinase Phosphorylation

These three reactions are highly exergonic (i.e. irreversible).

43
Q

How does Hexokinase regulation in muscle occur?

A

Allosteric Inhibition via Glucose-6-P

The binding of Glucose-6-P to Hexokinase’s regulatory binding site causes an enzymatic conformational change that inhibits ATP-Hexokinase binding.

44
Q

Detailed Mechanism: Glyceraldehyde-3-P Dehydrogenase Oxidation-Phosphorylation

A
  1. The Sulfhydryl group of G3PD’s active site undergoes nucleophilic attack on G3P’s carbonyl Carbon to generate a thiohemiacetal intermediate.
  2. π-electron rearrangement at the thiohemiacetal Oxygen creates a Hydride ion that undergoes nucleophilic attack on NAD+’s benzene ring to generate NADH. (The thiohemiacetal intermediate is converted to a acyl thioester intermedicate.)
  3. NADH and H+ leave the G3PD active site.
  4. NAD+ and Pi enter the G3PD active site.
  5. The Pi group’s anionic Oxygen undergoes nucleophilic attack on the acyl thioester Carbon to cleave the S—C bond and generate 1,3-Bisphosphoglycerate.
45
Q

4-Step Mechanism: Glyceraldehyde-3-P Dehydrogenase Oxidation-Phosphorylation

A
  1. Nucleophilic attack by G3PD’s Sulfhydril group on G3P’s carbonyl Carbon generates a thiohemiacetal intermediate.
  2. π-electron rearrangement creates a Hydride ion that nucleophilically attacks NAD+’s to generate NADH and an acyl thioester intermedicate.
  3. NADH and H+ leave the G3PD active site; NAD+ and Pi enter the G3PD active site.
  4. The Pi nucleophilically attacks the acyl thioester Carbon to cleave the S—C bond and generate 1,3-Bisphophoglycerate.
46
Q

How does Phosphofructokinase-1 regulation in muscle occur?

A
  • Allosteric Inhibition via ATP
  • Allosteric Stimulation via ADP/AMP

  • When there is high energy charge in the cell, ATP binds to Phosphofructokinase-1’s allosteric site to inhibit (reduce F6P binding) the enzyme’s activity.
  • When there is low energy charge in the cell, AMP/ADP binds to Phosphofructokinase-1’s allosteric site to stimulate (increase F6P binding) the enzyme’s activity.
47
Q

Which reactions of Glycolysis generate ATP?

A
  • Glycolysis 7: Phosphoglycerate Kinase Phosphorylation
  • Glycolysis 10: Pyruvate Kinase Phosphorylation
48
Q

Which reaction of Glycolysis generates NADH?

A

Glycolysis 6: Glyceraldehyde-3-P Dehydrogenase Oxidation-Reduction

49
Q

Which reaction of Glycolysis requires/consumes ATP?

A

Glycolysis 3: Phosphofructokinase-1 Phosphorylation

50
Q

Conformations: Phosphofructokinase-1

A
  • T-State: Inactive (ATP Bound)
  • R-State: Active (AMP/ADP Bound)
51
Q

How does regulation of Pyruvate Kinase in muscle occur?

A
  • Allosteric Inhibition via ATP/Alanine/Acetyl-CoA/LCFA
  • Allosteric Stimulation via F16BP
52
Q

What process generates Alanine from Pyruvate?

A

Transamination

53
Q

How does the Liver function to maintain blood Glucose levels?

A
  • When blood Glucose levels are high, Glucose is stored as Glycogen or converted into fatty acids (for eventual delivery into adipose tissue).
  • When blood Glucose levels are low, Glucose is produced de novo (via Gluconeogenesis) or mobilized from Glycogen stores.
54
Q

Which type of Hexokinase functions in the Liver?

A

Glucokinase

Hexokinase IV

55
Q

How does Glucokinase differ from Hexokinase?

A
  • Glucokinase has lower affinity for Glucose than Hexokinase.
  • Glucokinase is not inhibited by G6P binding (unlike Hexokinase).
56
Q

How does Phosphofructokinase-1 regulation in the Liver occur?

A
  • Allosteric Inhibition via ATP/Citrate
  • Allosteric Stimulation via ADP/AMP/F26BP
57
Q

Which compound is the most important activator of Phosphofructokinase-1 activity in the Liver?

A

Fructose-2,6-Biphosphate

F26BP binding to Phosphofructokinase-1 increases PFK affinity for F6P and decreases ATP inhibition of PFK (to increase rates of Glycolysis when Glucose is abundant).

58
Q

How does regulation of Pyruvate Kinase in the Liver occur?

A
  • Allosteric Inhibition via ATP/Alanine/Acetyl-CoA/LCFA
  • Allosteric Stimulation via F16BP
  • Covalent Inhibition via Phosphorylation
  • Covalent Stimulation via Dephosphorylation
59
Q

Which enzyme catalyzes the phosphorylation of Pyruvate Kinase in the Liver?

A

Protein Kinase A

PKA

60
Q

Fate of Pyruvate: Anaerobic vs. Aerobic

A
  • Anaerobic: Converted to Lactate/Ethanol (in Cytoplasm)
  • Aerobic: Used to Generate Acetyl-CoA (in Mitochondria)
61
Q

What is the function of the Pyruvate Dehydrogenase Complex?

A

Formation of Acetyl-CoA from Pyruvate

The PDH Complex catalyzes the irreversible conversion of Pyruvate to Acetyl-CoA (and the formation of NADH).

62
Q

Subunits: Pyruvate Dehydrogenase Complex

A
  • E1: Pyruvate Dehydrogenase
  • E2: Dihydrolipoyl Transacetylase
  • E3: Dihydrolopoyl Dehydrogenase
63
Q

E1: Pyruvate Dehydrogenase

A

A tetrameric protein that decarboxylates Pyruvate (to generate Hydroxyethyl-TPP and CO2) and transfers a Hydroxyethly group to the E2 Lipoamide (to generate TPP).

64
Q

E2: Dihydrolipoyl Transacetylase

A

A trimeric protein that oxidizes a Hydroxyethyl group (to generate Acetate) and transfers Acetate to Coenzyme A (to generate Acetyl-CoA).

65
Q

E3: Dihydrolipoyl Dehydrogenase

A

A dimeric protein that oxidizes the E2 Dihydrolipoamide (to generate Lipoamide), catalyzes the reduction of FAD (to generate FADH2), and catalyzes the reduction of NAD+ (to generate NADH).

66
Q

Drugs for Increasing Insulin Sensitivity

Treatments for Diabetes

A
  • α-Glucosidase Inhibitors (Miglitol)
  • Sulfonylurea Drugs (Glipizide)
  • AMPK-Activating Drugs (MetFormin)
  • PPaRγ Agonists (Thiazolidinedione)
67
Q

MetFormin

A

An AMPK-activating drug that stimulates increased Glucose uptake and utilization.

68
Q

Glipizide

A

A Sulfonylurea drug that stimulates increased Insulin secretions by inhibiting K+ leak channels (in the plasma membranes).

69
Q

Miglitol

A

An α-Glucosidase inhibitor that blocks carbohydrate degredation in the small intestine (to lower blood Glucose levels).

70
Q

Thiazolidinedione

A

A PPaRγ agonist that improves Insulin sensitivity (in liver/muscle cells)

71
Q

Steady State

A

A condition of metabolic stability in which the rate of catabolism, the rate of anabolism, and the concentration of substrates are maintained at constant levels.

Not Equilibrium: The rate of catabolism and the rate of anabolism are NOT equal.

72
Q

Which reactions of a metabolic pathway give the pathway its directionality?

A

Exergonic Reactions

73
Q

Equilibrium: Committed Step

A

Far from Equilibrium

Exergonic

74
Q

How can a reaction have a positive/unfavorable ∆G, but a negative/favorable ∆G°’?

A
  • ∆G takes into consideration the concentration of reactant and products, which shift the reaction away from standard conditions.
  • ∆G°’ is a measure of free energy at standard conditions, which does not consider differing concentrations of reactants and products.
75
Q

Why is ADP + Pi more stable than ATP?

A
  • Greater Charge Separation (Less Charge Repulsion)
  • More Stable Resonance Structures
  • Greater Solvation of Compounds
76
Q

What molecules is the Inner Mitochondrial Membrane permeable to?

A
77
Q

What molecules can pass through the Outer Mitochondrial Membrane?

A
78
Q

Equation: Standard Reduction Potential

A
79
Q

Equation: ∆G (Concentrations)

A
80
Q
A

Biochemistry (7 decks)

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