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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
**Thermodynamics:** Glycolysis 8 | Phosphoglycerate Mutase Isomerization
*Slightly* Thermodynamically **Unfavorable** | Reversible
26
**Thermodynamics:** Glycolysis 9 | Enolase Dehydration
*Slightly* Thermodynamically **Favorable** | Reversible
27
**Thermodynamics:** Glycolysis 10 | Pyruvate Kinase Phosphorylation
*Highly* Thermodynamically **Favorable** | Irreversible
28
At which steps of Glycolysis does **substrate-level phosphorylation** occur?
* **Step 7:** Phosphoglycerate Kinase Phosphorylation * **Step 10:** Pyruvate Kinase Phosphorylation
29
**Glycolysis 6:** Glyceraldehyde-3-P Dehydrogenase Oxidation-Phosphorylation
Glyceraldehyde-3-P Dehydrogenase catalyzes the **coupled oxidation-phorylation** reaction that converts Glyceraldehyde-3-P to 1,3-Biphosphoglycerate.
30
**Glycolysis 7:** Phosphoglycerate Kinase Phosphorylation
Phosphoglycerate Kinase catalyzes the **dephosphorylation of 1,3-Biphosphoglycerate** to generate ATP (via substrate-level phosphorylation) and 3-Phosphoglycerate.
31
**Glycolysis 8:** Phosphoglycerate Mutase Isomerization
Phosphoglycerate Mutase catalyzes the **isomerization of 3-Phosphoglycerate** to generate 2-Phosphoglycerate (via phosphoryl transfer).
32
**Glycolysis 9:** Enolase Dehydration
Enolase catalyzes the **dehydration/condensation of 2-Phosphoglycerate** to generate the higher-energy Phosphoenolpyruvate.
33
**Glycolysis 10:** Pyruvate Kinase Phosphorylation
Pyruvate Kinase catalyzes the **dephosophorylation of Phosphenolpyruvate** to generate ATP (via substrate-level phosphorylation) and Pyruvate.
34
Which steps of Glycolysis are thermodynamically **unfavorable**?
* **Step 5:** Triose Phosphate Isomerase Isomerization * **Step 8:** Phosphoglycerate Mutase Isomerization
35
**Glycolysis:** Net Reaction
1 Glucose + 2 NAD+ + 2 ADP + 2 Pi → 2 Pyruvate + 2 NADH + 2 ATP + 2 H+ + 2 H2O
36
**Glycolysis:** 10 Steps
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
**Glycolysis:** Sugar Compounds in Sequence
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
What process *regenerates* NAD+ under anaerobic conditions?
Fermentation
39
**Fermentation:** Animals vs. Microorganisms
* **Animals:** Fermentation converts Pyruvate to *Lactate* * **Microorganisms:** Fermentation converts Pyruvate to *Ethanol*.
40
**Mechanism:** Glyceraldehyde-3-P Dehydrogenase Oxidation-Phosphorylation
41
What is the *regulation* of Glycolysis dependent on?
Energy Charge Within the Cell
42
During which reactions does the *regulation* of Glycolysis within **muscle tissue** occur?
1. Hexokinase Phosphorylation 2. Phosphofructokinase-1 Phosphorylation 3. Pyruvate Kinase Phosphorylation ## Footnote These three reactions are highly exergonic (i.e. irreversible).
43
How does Hexokinase regulation in *muscle* occur?
Allosteric Inhibition via Glucose-6-P ## Footnote The binding of Glucose-6-P to Hexokinase's regulatory binding site causes an enzymatic conformational change that inhibits ATP-Hexokinase binding.
44
**Detailed Mechanism:** Glyceraldehyde-3-P Dehydrogenase Oxidation-Phosphorylation
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
**4-Step Mechanism:** Glyceraldehyde-3-P Dehydrogenase Oxidation-Phosphorylation
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
How does Phosphofructokinase-1 regulation in *muscle* occur?
* Allosteric **Inhibition** via ATP * Allosteric **Stimulation** via ADP/AMP ## Footnote * 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
Which reactions of Glycolysis generate ATP?
* **Glycolysis 7:** Phosphoglycerate Kinase Phosphorylation * **Glycolysis 10:** Pyruvate Kinase Phosphorylation
48
Which reaction of Glycolysis generates NADH?
**Glycolysis 6:** Glyceraldehyde-3-P Dehydrogenase Oxidation-Reduction
49
Which reaction of Glycolysis requires/consumes ATP?
**Glycolysis 3:** Phosphofructokinase-1 Phosphorylation
50
**Conformations:** Phosphofructokinase-1
* **T-State:** Inactive (ATP Bound) * **R-State:** Active (AMP/ADP Bound)
51
How does regulation of Pyruvate Kinase in *muscle* occur?
* Allosteric **Inhibition** via ATP/Alanine/Acetyl-CoA/LCFA * Allosteric **Stimulation** via F16BP
52
What process generates Alanine from Pyruvate?
Transamination
53
How does the Liver function to maintain blood Glucose levels?
* 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
Which type of Hexokinase functions in the Liver?
Glucokinase | Hexokinase IV
55
How does *Glucokinase* differ from *Hexokinase*?
* Glucokinase has *lower affinity for Glucose* than Hexokinase. * Glucokinase is *not inhibited by G6P binding* (unlike Hexokinase).
56
How does Phosphofructokinase-1 regulation in the *Liver* occur?
* Allosteric **Inhibition** via ATP/Citrate * Allosteric **Stimulation** via ADP/AMP/F26BP
57
Which compound is the *most important activator* of Phosphofructokinase-1 activity in the Liver?
Fructose-2,6-Biphosphate ## Footnote 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
How does regulation of Pyruvate Kinase in the *Liver* occur?
* Allosteric **Inhibition** via ATP/Alanine/Acetyl-CoA/LCFA * Allosteric **Stimulation** via F16BP * Covalent **Inhibition** via Phosphorylation * Covalent **Stimulation** via Dephosphorylation
59
Which enzyme catalyzes the phosphorylation of Pyruvate Kinase in the Liver?
Protein Kinase A | PKA
60
**Fate of Pyruvate:** Anaerobic vs. Aerobic
* **Anaerobic:** Converted to Lactate/Ethanol (in Cytoplasm) * **Aerobic:** Used to Generate Acetyl-CoA (in Mitochondria)
61
What is the function of the Pyruvate Dehydrogenase Complex?
Formation of **Acetyl-CoA** from Pyruvate ## Footnote The PDH Complex catalyzes the *irreversible* conversion of Pyruvate to Acetyl-CoA (and the formation of NADH).
62
**Subunits:** Pyruvate Dehydrogenase Complex
* **E1:** Pyruvate Dehydrogenase * **E2:** Dihydrolipoyl Transacetylase * **E3:** Dihydrolopoyl Dehydrogenase
63
**E1:** Pyruvate Dehydrogenase
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
**E2:** Dihydrolipoyl Transacetylase
A *trimeric* protein that **oxidizes a Hydroxyethyl group** (to generate Acetate) and **transfers Acetate to Coenzyme A** (to generate Acetyl-CoA).
65
**E3:** Dihydrolipoyl Dehydrogenase
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
Drugs for Increasing Insulin Sensitivity | Treatments for Diabetes
* α-Glucosidase Inhibitors (Miglitol) * Sulfonylurea Drugs (Glipizide) * AMPK-Activating Drugs (MetFormin) * PPaRγ Agonists (Thiazolidinedione)
67
MetFormin
An AMPK-activating drug that stimulates increased Glucose uptake and utilization.
68
Glipizide
A Sulfonylurea drug that stimulates increased Insulin secretions by inhibiting K+ leak channels (in the plasma membranes).
69
Miglitol
An α-Glucosidase inhibitor that blocks carbohydrate degredation in the small intestine (to lower blood Glucose levels).
70
Thiazolidinedione
A PPaRγ agonist that improves Insulin sensitivity (in liver/muscle cells)
71
Steady State
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. ## Footnote **Not Equilibrium:** The rate of catabolism and the rate of anabolism are NOT equal.
72
Which reactions of a metabolic pathway give the pathway its **directionality**?
Exergonic Reactions
73
**Equilibrium:** Committed Step
Far from Equilibrium | Exergonic
74
How can a reaction have a **positive/unfavorable ∆G**, but a **negative/favorable ∆G°'**?
* **∆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
Why is ADP + Pi more stable than ATP?
* Greater Charge Separation (Less Charge Repulsion) * More Stable Resonance Structures * Greater Solvation of Compounds
76
What molecules is the Inner Mitochondrial Membrane permeable to?
77
What molecules can pass through the Outer Mitochondrial Membrane?
78
**Equation:** Standard Reduction Potential
79
**Equation:** ∆G (Concentrations)
80

Biochemistry (7 decks)

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