Biochemistry - Metabolic Pathways & Regulation Flashcards

Question 1

What is the rate-limiting enzyme of glycolysis, and how is it regulated?

Accepted Answer

The rate-limiting enzyme is **Phosphofructokinase-1 (PFK-1)**, which converts Fructose-6-phosphate to Fructose-1,6-bisphosphate.

* **Allosteric Activators:** AMP, Fructose-2,6-bisphosphate (F-2,6-BP)
* **Allosteric Inhibitors:** ATP, Citrate

Question 2

What is the net energy yield per glucose molecule during glycolysis under aerobic conditions?

Accepted Answer

Per 1 molecule of glucose ($C_6H_{12}O_6$):

* **Net ATP:** $2	ext{ ATP}$ ($4	ext{ produced} - 2	ext{ invested}$)
* **NADH:** $2	ext{ NADH}$ (yields $\approx 3-5	ext{ ATP}$ via oxidative phosphorylation)
* **Pyruvate:** $2	ext{ Pyruvate}$

Question 3

Which cofactors are required by the Pyruvate Dehydrogenase Complex (PDC)?

Accepted Answer

The PDC converts Pyruvate to Acetyl-CoA using **5 essential cofactors**:

1. **T**hiamine pyrophosphate (TPP / Vitamin $B_1$)
2. **F**AD (Vitamin $B_2$)
3. **N**AD+ (Vitamin $B_3$)
4. **C**oenzyme A (Pantothenate / Vitamin $B_5$)
5. **L**ipoic acid

*Mnemonic: **T**ender **F**or **N**ice **C**ouples **L**oving*

Question 4

What is the rate-limiting enzyme of the Citric Acid (Krebs) Cycle, and what regulates it?

Accepted Answer

The rate-limiting enzyme is **Isocitrate Dehydrogenase**, catalyzing:  
$	ext{Isocitrate} + 	ext{NAD}^+ ightarrow \alpha	ext{-Ketoglutarate} + 	ext{NADH} + 	ext{CO}_2$

* **Activators:** ADP, $	ext{Ca}^{2+}$
* **Inhibitors:** ATP, NADH

Question 5

What is the net yield of one turn of the Citric Acid Cycle per Acetyl-CoA?

Accepted Answer

For every $1	ext{ Acetyl-CoA}$ oxidized:

* $3	ext{ NADH}$
* $1	ext{ FADH}_2$
* $1	ext{ GTP}$ (or ATP)
* $2	ext{ CO}_2$

*(Note: Double these values per initial glucose molecule, as glucose yields 2 Acetyl-CoA).*

Question 6

Which 4 enzymes bypass the 3 irreversible steps of glycolysis in Gluconeogenesis?

Accepted Answer

1. **Pyruvate Carboxylase:** Pyruvate $\rightarrow$ Oxaloacetate (requires Biotin, ATP)
2. **PEP Carboxykinase (PEPCK):** Oxaloacetate $\rightarrow$ Phosphoenolpyruvate (requires GTP)
3. **Fructose-1,6-Bisphosphatase:** Fructose-1,6-BP $\rightarrow$ Fructose-6-P (*Rate-limiting step*)
4. **Glucose-6-Phosphatase:** Glucose-6-P $\rightarrow$ Glucose (in ER of liver/kidneys)

Question 7

How does Fructose-2,6-Bisphosphate (F-2,6-BP) reciprocally regulate Glycolysis and Gluconeogenesis?

Accepted Answer

F-2,6-BP acts as an intracellular metabolic switch controlled by the bifunctional enzyme **PFK-2/FBPase-2**:

* **High F-2,6-BP (fed state / Insulin):** Stimulates **PFK-1** ($\uparrow$ Glycolysis), inhibits **FBPase-1** ($\downarrow$ Gluconeogenesis).
* **Low F-2,6-BP (fasted state / Glucagon):** Deactivates PFK-1, activates FBPase-1 ($\uparrow$ Gluconeogenesis).

Question 8

What is the chemical structure and mechanism of ATP in energy transfer?

Accepted Answer

ATP (**Adenosine Triphosphate**) consists of an adenine base, a ribose sugar, and three phosphate groups.

* High-energy phosphate transfer occurs via cleavage of **phosphoanhydride bonds**.
* Standard free energy of hydrolysis: $\Delta G^{\circ'} \approx -30.5	ext{ kJ/mol}$ ($	ext{ATP} + 	ext{H}_2	ext{O} ightarrow 	ext{ADP} + 	ext{P}_i$).

Question 9

How do NADH and FADH2 differ in structure and electron insertion into the Electron Transport Chain?

Accepted Answer

* **NADH:** Derived from Niacin ($B_3$). Transfers $2 e^-$ and $1 H^+$ to **Complex I** (NADH Dehydrogenase). Yields $\approx 2.5	ext{ ATP}$.
* **FADH2:** Derived from Riboflavin ($B_2$). Transfers $2 e^-$ and $2 H^+$ to **Complex II** (Succinate Dehydrogenase). Yields $\approx 1.5	ext{ ATP}$ because it bypasses Complex I.

Question 10

List the four complexes of the Electron Transport Chain (ETC) and their functions.

Accepted Answer

* **Complex I (NADH-Q oxidoreductase):** Accepts $e^-$ from NADH, pumps $4 H^+$.
* **Complex II (Succinate-Q reductase):** Accepts $e^-$ from $	ext{FADH}_2$, pumps $0 H^+$.
* **Complex III (Q-cytochrome c oxidoreductase):** Passes $e^-$ from Ubiquinone to Cytochrome c, pumps $4 H^+$.
* **Complex IV (Cytochrome c oxidase):** Passes $e^-$ to $	ext{O}_2$ (forming $	ext{H}_2	ext{O}$), pumps $2 H^+$.

Question 11

What is the difference between ETC Inhibitors and Uncoupling Agents?

Accepted Answer

* **ETC Inhibitors** (e.g., Cyanide, CO, Rotenone): Block electron flow, stopping proton pumping, ATP synthesis, and oxygen consumption.
* **Uncouplers** (e.g., 2,4-DNP, Thermogenin): Increase inner mitochondrial membrane permeability to $H^+$. Protons leak back into matrix without driving ATP Synthase; energy dissipates as **heat**, while $O_2$ consumption increases.

Question 12

How are fatty acids transported into the mitochondrial matrix for beta-oxidation?

Accepted Answer

1. **Activation:** Fatty acyl-CoA synthetase attaches CoA to fatty acid in the cytosol ($1	ext{ ATP} ightarrow 1	ext{ AMP}$).  
2. **Carnitine Shuttle:** **Carnitine Palmitoyltransferase-I (CPT-I)** replaces CoA with carnitine to transport acyl-carnitine across the inner membrane.

*CPT-I is the rate-limiting enzyme and is inhibited by **Malonyl-CoA** during fatty acid synthesis.*

Question 13

What are the four repeating steps of Fatty Acid Beta-Oxidation?

Accepted Answer

Each cycle removes a 2-carbon unit as Acetyl-CoA via:

1. **Oxidation:** Catalyzed by Acyl-CoA dehydrogenase (produces $1	ext{ FADH}_2$)
2. **Hydration:** Enoyl-CoA hydratase
3. **Oxidation:** Hydroxyacyl-CoA dehydrogenase (produces $1	ext{ NADH}$)
4. **Thiolysis:** Thiolase (cleaves $1	ext{ Acetyl-CoA}$)

Question 14

How does Insulin regulate metabolic pathways at a hormonal level?

Accepted Answer

Insulin is an **anabolic hormone** secreted by pancreatic $\beta$-cells during high blood glucose states (fed state).

* Activates **protein phosphatases** (dephosphorylates target enzymes).
* **Promotes:** Glycolysis, Glycogen synthesis, Fatty Acid synthesis, Protein synthesis.
* **Inhibits:** Gluconeogenesis, Glycogenolysis, Lipolysis.

Question 15

How does Glucagon regulate metabolic pathways at a hormonal level?

Accepted Answer

Glucagon is a **catabolic hormone** secreted by pancreatic $\alpha$-cells during low blood glucose states (fasted state).

* Binds G-protein coupled receptors $ightarrow$ $\uparrow	ext{ cAMP}$ $ightarrow$ activates **Protein Kinase A (PKA)** (phosphorylates target enzymes).
* **Promotes:** Gluconeogenesis, Glycogenolysis, Lipolysis, Ketogenesis.
* **Inhibits:** Glycolysis, Glycogen synthesis.

Question 16

What is the function and physiological significance of the Cori Cycle?

Accepted Answer

The Cori Cycle prevents lactic acidosis during anaerobic muscle exertion:

1. **Muscle:** Converts Glucose $\rightarrow$ Pyruvate $\rightarrow$ **Lactate** via anaerobic glycolysis.
2. **Blood:** Transports lactate to the liver.
3. **Liver:** Converts Lactate $\rightarrow$ Pyruvate $\rightarrow$ **Glucose** via gluconeogenesis, releasing glucose back into the blood.

Question 17

What is the rate-limiting enzyme of the Pentose Phosphate Pathway (PPP) and its products?

Accepted Answer

The rate-limiting enzyme is **Glucose-6-Phosphate Dehydrogenase (G6PD)**.

* **Non-ATP Yielding Products:**
  1. **NADPH:** Used for reductive biosynthesis (fatty acids, steroids) and detoxifying reactive oxygen species (ROS) via glutathione maintenance.
  2. **Ribose-5-Phosphate:** Used for nucleotide and nucleic acid synthesis.

Question 18

What are the key rate-limiting enzymes for Glycogenesis and Glycogenolysis?

Accepted Answer

* **Glycogenesis (Synthesis):** **Glycogen Synthase**
  * Activated by: Insulin, Glucose-6-phosphate
  * Inhibited by: Glucagon, Epinephrine
* **Glycogenolysis (Breakdown):** **Glycogen Phosphorylase**
  * Activated by: Glucagon, Epinephrine, AMP
  * Inhibited by: Insulin, ATP, Glucose-6-phosphate

Question 19

What causes Ketogenesis, where does it occur, and what are the main ketone bodies?

Accepted Answer

Occurs in **liver mitochondria** during prolonged fasting, starvation, or uncontrolled type 1 diabetes when oxaloacetate is depleted by gluconeogenesis, causing an excess accumulation of Acetyl-CoA.

* **Ketone Bodies:** Acetoacetate, $\beta$-Hydroxybutyrate, Acetone.
* **Rate-limiting enzyme:** **HMG-CoA Synthase**.

Question 20

How does Citrate regulate carbohydrate and lipid metabolism simultaneously?

Accepted Answer

Citrate signals high mitochondrial energy charge:

* Translocates from mitochondria to cytosol.
* **Inhibits PFK-1** $\rightarrow$ slows down Glycolysis.
* **Activates Acetyl-CoA Carboxylase (ACC)** $ightarrow$ rate-limiting step of Fatty Acid Synthesis (converts Acetyl-CoA to Malonyl-CoA).

Biochemistry - Metabolic Pathways & Regulation

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