Biochemistry Exam 3 (CHEM 3420) – Comprehensive Review Flashcards

A set of 100 question-and-answer flashcards covering thermodynamics, glycolysis, gluconeogenesis, the pentose phosphate pathway, electron transport chain, TCA cycle, and glycogen metabolism for CHEM 3420 Exam 3.

What is free energy (ΔG) and what does a negative ΔG indicate?

Free energy is the energy available to do work; a negative ΔG means the reaction is spontaneous.

Define internal energy (U) in biological systems.

Internal energy is the total kinetic and potential energy of a system’s components; it is essentially constant in cells.

What does entropy (S) measure in a system?

Entropy measures the degree of randomness or disorder.

Write the relationship that links ΔG, ΔH, and ΔS.

ΔG = ΔH – TΔS.

State the First Law of Thermodynamics.

Energy cannot be created or destroyed, only transformed.

State the Second Law of Thermodynamics.

The total entropy of the universe increases in a spontaneous process.

Give an example of kinetic energy in cells.

Thermal motion of molecules is cellular kinetic energy.

Give an example of potential energy in metabolism.

The high-energy phosphoanhydride bonds of ATP store potential energy.

What type of energy is released from breaking chemical bonds?

Chemical energy.

Proton gradients across membranes are an example of what energy type?

Electrochemical energy.

What is chemiosmotic coupling?

The process linking electron transport–driven proton pumping to ATP synthesis via ATP synthase.

Where does glycolysis take place?

In the cytoplasm.

How many net ATP molecules are produced per glucose in glycolysis?

Two ATP (net).

How many NADH molecules are produced per glucose in glycolysis?

Two NADH.

Which enzyme catalyzes the first step of glycolysis and how many ATP does it use?

Hexokinase (or glucokinase) uses one ATP to convert glucose to glucose-6-phosphate.

What is the rate-limiting enzyme of glycolysis?

Phosphofructokinase-1 (PFK-1).

Name two activators of PFK-1.

AMP and fructose-2,6-bisphosphate (F2,6BP).

Name two inhibitors of PFK-1.

ATP and citrate.

Which enzyme splits fructose-1,6-bisphosphate into DHAP and G3P?

Aldolase.

Which enzyme interconverts DHAP and G3P?

Triose phosphate isomerase.

Which glycolytic step produces NADH, and what enzyme catalyzes it?

Glyceraldehyde-3-phosphate dehydrogenase converts G3P to 1,3-BPG, producing NADH.

What enzyme catalyzes the first substrate-level phosphorylation in glycolysis?

Phosphoglycerate kinase (1,3-BPG to 3-PG).

Which enzyme converts 2-phosphoglycerate to phosphoenolpyruvate (PEP)?

Enolase.

Which enzyme catalyzes the final step of glycolysis and is it reversible?

Pyruvate kinase; the reaction is irreversible.

List the net products of glycolysis from one glucose.

2 pyruvate, 2 ATP, 2 NADH, and 2 H₂O.

What is the main physiological purpose of gluconeogenesis?

To maintain blood glucose during fasting.

Which organs perform most gluconeogenesis?

Primarily the liver, with some in kidney and small intestine.

Which two enzymes carry out the first bypass of gluconeogenesis from pyruvate to PEP?

Pyruvate carboxylase (to oxaloacetate) and PEP carboxykinase (to PEP).

Which gluconeogenic enzyme requires biotin?

Pyruvate carboxylase.

Which enzyme converts fructose-1,6-bisphosphate to fructose-6-phosphate in gluconeogenesis?

Fructose-1,6-bisphosphatase.

Which enzyme hydrolyzes glucose-6-phosphate to free glucose and where is it located?

Glucose-6-phosphatase in the endoplasmic reticulum of liver and kidney cells.

Does gluconeogenesis consume or produce ATP/GTP overall?

It consumes ATP and GTP.

What two major products are generated in the oxidative phase of the pentose phosphate pathway (PPP)?

Ribulose-5-phosphate and 2 NADPH.

Which enzyme is rate-limiting for the PPP?

Glucose-6-phosphate dehydrogenase (G6PD).

Which cofactor does transketolase require?

Thiamine pyrophosphate (TPP).

Give two major cellular uses of NADPH produced by the PPP.

Fatty-acid biosynthesis and regeneration of reduced glutathione for detoxification.

Name the two phases of the PPP and state their reversibility.

Oxidative (irreversible) and non-oxidative (reversible).

At which complex does NADH enter the electron-transport chain?

Complex I (NADH dehydrogenase).

At which complex does FADH₂ (from succinate) enter the ETC?

Complex II (succinate dehydrogenase).

How many protons are pumped across the inner mitochondrial membrane per NADH oxidized?

Ten protons.

How many protons are pumped per FADH₂ oxidized?

Six protons.

Approximately how many ATP are produced per mitochondrial NADH?

About 2.5 ATP.

Approximately how many ATP are produced per mitochondrial FADH₂?

About 1.5 ATP.

What is the primary function of ETC Complex I?

It transfers electrons from NADH to FMN and then to CoQ while pumping protons.

What is the primary function of ETC Complex II?

It oxidizes succinate to fumarate, passing electrons from FADH₂ to CoQ without pumping protons.

What is the primary function of ETC Complex III?

It transfers electrons from reduced CoQ to cytochrome c via the Q cycle and pumps protons.

What is the primary function of ETC Complex IV?

It transfers electrons from cytochrome c to O₂, forming water and pumping protons.

Which enzyme harnesses the proton gradient to make ATP?

ATP synthase (Complex V).

How many ATP equivalents are generated from one acetyl-CoA via the TCA cycle and oxidative phosphorylation?

Approximately 10 ATP.

Which TCA enzyme is considered rate-limiting?

Isocitrate dehydrogenase.

Which TCA enzyme is also part of the ETC?

Succinate dehydrogenase (Complex II).

How many NADH are produced per acetyl-CoA in the TCA cycle?

Three NADH.

How many FADH₂ are produced per acetyl-CoA in the TCA cycle?

One FADH₂.

How many GTP are produced per acetyl-CoA in the TCA cycle?

One GTP (equivalent to one ATP).

What is the estimated total ATP yield per glucose in muscle or brain?

About 30 ATP.

Why does the choice of shuttle system affect ATP yield from glycolysis?

Because the glycerol-3-phosphate shuttle yields ~1.5 ATP per NADH, whereas the malate-aspartate shuttle yields ~2.5 ATP per NADH.

What is the primary linkage between glucose residues in glycogen?

α(1→4) glycosidic bonds.

What type of linkage forms glycogen branches and how often do they occur?

α(1→6) linkages approximately every 8–12 residues.

Name the two main tissues that store significant glycogen.

Liver and skeletal muscle.

Which enzyme catalyzes glycogen phosphorolysis and what cofactor does it require?

Glycogen phosphorylase; it requires pyridoxal phosphate (PLP).

Give two allosteric activators of glycogen phosphorylase.

AMP and Ca²⁺ (via phosphorylase kinase activation).

Give two allosteric inhibitors of glycogen phosphorylase.

ATP and glucose-6-phosphate.

What are the two activities of the debranching enzyme in glycogenolysis?

Transferase activity moves a trisaccharide, and α(1→6) glucosidase hydrolyzes the remaining branch glucose.

In liver, what happens to glucose-6-phosphate derived from glycogen?

It is dephosphorylated by glucose-6-phosphatase and released into the bloodstream.

Which enzyme converts glucose-1-phosphate to UDP-glucose during glycogen synthesis?

UDP-glucose pyrophosphorylase.

What reaction does glycogen synthase catalyze?

Addition of UDP-glucose to a growing α(1→4) glycogen chain.

Which hormone activates the cAMP-PKA cascade that stimulates glycogen breakdown?

Glucagon (in liver) or epinephrine (in liver and muscle).

Which hormone promotes glycogen synthesis by activating protein phosphatase 1?

Insulin.

Is glycogen synthase active when phosphorylated or dephosphorylated?

Active when dephosphorylated.

What is the role of glycogenin?

It serves as a self-glycosylating primer that initiates new glycogen granules.

Which enzyme creates α(1→6) branches in glycogen?

Branching enzyme (amylo-(1,4→1,6)-transglycosylase).

How many protons passing through ATP synthase are required to synthesize one ATP?

Four protons (including those for phosphate transport).

PFK-1 is the main control point of which metabolic pathway?

Glycolysis.

Biotin is required by which key gluconeogenic enzyme?

Pyruvate carboxylase.

Oxaloacetate (OAA) connects which two major metabolic pathways?

The TCA cycle and gluconeogenesis.

How many protons are pumped per NADH oxidized by the ETC?

Ten protons.

How many protons are pumped per FADH₂ oxidized by the ETC?

Six protons.

What variables determine the sign and magnitude of ΔG?

Changes in enthalpy (ΔH), temperature (T), and entropy (ΔS).

Which enzyme generates the second ATP in glycolysis?

Pyruvate kinase (PEP to pyruvate).

Which shuttle yields ~1.5 ATP per cytosolic NADH?

Glycerol-3-phosphate shuttle.

Which shuttle yields ~2.5 ATP per cytosolic NADH?

Malate-aspartate shuttle.

How many ATP are produced directly by substrate-level phosphorylation in glycolysis?

Four ATP produced, with a net gain of two after investment.

What is the relationship between ΔG and reaction spontaneity?

Negative ΔG means the reaction is spontaneous; positive ΔG is non-spontaneous.

Which enzyme converts citrate to isocitrate in the TCA cycle?

Aconitase.

Which TCA step generates GTP by substrate-level phosphorylation?

Succinyl-CoA synthetase converting succinyl-CoA to succinate.

Which TCA enzyme produces succinate and is part of the ETC?

Succinate dehydrogenase (Complex II).

The PPP’s non-oxidative phase converts five-carbon sugars into what type of molecules?

Glycolytic intermediates such as fructose-6-phosphate and glyceraldehyde-3-phosphate.

Is the hexokinase reaction reversible in glycolysis?

No, it is irreversible.

G6PD deficiency primarily decreases the production of what molecule?

NADPH, leading to increased oxidative stress.

Which PPP enzyme requires thiamine pyrophosphate?

Transketolase.

What is the cellular function of ribose-5-phosphate produced by the PPP?

It serves as a precursor for nucleotide and nucleic acid synthesis.

The Q cycle operates in which ETC complex?

Complex III (cytochrome bc₁).

What is the final electron acceptor of the mitochondrial ETC?

Molecular oxygen (O₂).

How does high ATP concentration affect PFK-1 activity?

High ATP inhibits PFK-1, slowing glycolysis.

Which glycolytic enzyme releases water during its reaction?

Enolase (2-PG to PEP).

How many ATP are consumed during the preparatory phase of glycolysis?

Two ATP.

Is glycolysis considered a catabolic or anabolic pathway?

Catabolic.

In which cellular compartments does gluconeogenesis occur?

Both the mitochondrial matrix (for pyruvate carboxylase) and the cytosol (for most other steps).

Which gluconeogenic enzyme is located in the endoplasmic reticulum membrane?

Glucose-6-phosphatase.