study tips for exam 2

What B vitamin is used to make TPP (thiamine pyrophosphate)?

Vitamin B1 (thiamine)

What major metabolic enzyme complexes require TPP (B1)?

• Pyruvate dehydrogenase

• Alpha-ketoglutarate dehydrogenase

• Branched-chain alpha-keto acid dehydrogenase

• Transketolase

What B vitamin is used to make FAD and FMN?

Vitamin B2 (riboflavin)

Which enzymes/pathways commonly use FAD/FMN?

• Succinate dehydrogenase

• ETC complexes

• oxidative metabolism reactions

What B vitamin is used to make NAD+ / NADP+?

Vitamin B3 (niacin)

Which pathways depend heavily on niacin-derived cofactors?

• Glycolysis

• Pyruvate dehydrogenase

• Citric acid cycle

• Electron transport chain

• Pentose phosphate pathway

What B vitamin is used to make CoA (coenzyme A)?

Vitamin B5 (pantothenic acid)

What is the main metabolic role of CoA?

Acyl group transfer

What B vitamin is used to make PLP (pyridoxal phosphate)?

Vitamin B6 (pyridoxine)

What major metabolic process commonly uses PLP (B6)?

Amino acid metabolism / transamination

What B vitamin is used to make biotin-dependent coenzymes?

Vitamin B7 (biotin)

What type of reactions does biotin help with?

Carboxylation reactions

What B vitamin is involved in one-carbon transfer and folate metabolism?

Vitamin B9 (folate)

What B vitamin is involved in methyl transfer and works with folate?

Vitamin B12 (cobalamin)

What are the 3 irreversible enzymes of glycolysis?

• Hexokinase

• PFK-1

• Pyruvate kinase

What enzyme is the rate-limiting / committed step of glycolysis?

PFK-1

What are the allosteric activators of PFK-1?

• AMP

• ADP

• Fructose-2,6-bisphosphate (F2,6BP)

What are the allosteric inhibitors of PFK-1?

• ATP

• citrate

What does an allosteric activator do to enzyme affinity?

It increases affinity for substrate → enzyme works better at lower substrate concentration.

What does an allosteric inhibitor do to enzyme affinity?

It decreases affinity for substrate → more substrate is needed for activity.

How does an activator usually affect the velocity vs substrate curve?

It shifts the curve left and often makes it less sigmoidal

How does an inhibitor usually affect the velocity vs substrate curve?

It shifts the curve right and may increase sigmoidicity

What is an example of feedforward activation in glycolysis?

Fructose-1,6-bisphosphate activates pyruvate kinase

What is an example of feedback inhibition in metabolism?

ATP inhibits PFK-1

What is an example of product inhibition?

Glucose-6-phosphate inhibits hexokinase

What does anaerobic glycolysis produce from 1 glucose?

• 2 lactate

• 2 ATP net

What does aerobic glycolysis produce from 1 glucose?

• 2 pyruvate

• 2 ATP net

• 2 NADH

Why is lactate dehydrogenase (LDH) essential in anaerobic glycolysis?

It regenerates NAD+ from NADH, allowing glycolysis to continue.

It regenerates NAD+ from NADH, allowing glycolysis to continue.

It is used by LDH to reduce pyruvate to lactate and regenerate NAD+

What happens to the NADH made in aerobic glycolysis?

It can be used for oxidative phosphorylation (via shuttles)

How much ATP is made from glycolysis alone under anaerobic conditions?

2 ATP per glucose

How does blocked blood flow / low oxygen affect metabolism?

• shifts toward anaerobic glycolysis

• increases lactate

• decreases oxidative phosphorylation

• decreases total ATP production

What drives ATP synthesis in substrate-level phosphorylation?

Transfer of phosphate directly from a high-energy metabolic intermediate to ADP

What drives ATP synthesis in oxidative phosphorylation?

The proton gradient across the inner mitochondrial membrane

What are the two substrate-level phosphorylation steps in glycolysis?

• Phosphoglycerate kinase

• Pyruvate kinase

What is the substrate-level phosphorylation step in the citric acid cycle?

Succinyl-CoA synthetase

Approximately how much ATP can be produced under aerobic conditions from 1 glucose?

About 30–32 ATP

Approximately how much ATP can be produced under anaerobic conditions from 1 glucose?

2 ATP

What is the Cori cycle?

The cycle in which muscle (or RBCs) produce lactate, and the liver converts lactate back to glucose

What does the Cori cycle allow?

It allows anaerobic tissues to keep making ATP while the liver recycles lactate into glucose.

What pathways are involved in the Cori cycle?

• Anaerobic glycolysis

• Gluconeogenesis

What enzyme removes glucose residues from glycogen by phosphorolysis?

Glycogen phosphorylase

What product is released by glycogen phosphorylase?

Glucose-1-phosphate

What enzyme converts glucose-1-phosphate → glucose-6-phosphate?

Phosphoglucomutase

What are the two activities of the debranching enzyme?

1. Transferase activity

2. Alpha-1,6-glucosidase activity

What does the transferase activity of the debranching enzyme do?

Moves a small block of glucose residues to another chain.

What does the alpha-1,6-glucosidase activity of the debranching enzyme do?

Removes the branch-point glucose as free glucose

How does fructose enter glycolysis in the liver?

Fructose → fructose-1-phosphate → DHAP + glyceraldehyde → glycolytic intermediates

What important regulatory step is bypassed by liver fructose metabolism?

PFK-1

Why is bypassing PFK-1 important?

Because fructose metabolism in the liver can avoid the major rate-limiting regulation step of glycolysis.

How does galactose enter glycolysis?

It is converted into intermediates that eventually become glucose-1-phosphate / glucose-6-phosphate

What is the main function of the electron transport chain (ETC)?

To transfer electrons and pump protons to create the proton gradient used to make ATP.

Why does electron flow through the ETC occur spontaneously?

Because electrons move toward molecules with higher reduction potential / greater electron affinity

What is the final electron acceptor in the ETC?

Oxygen

What happens if oxygen is not available?

The ETC stops, oxidative phosphorylation stops, and metabolism shifts toward anaerobic pathways.

What enzyme makes fructose-2,6-bisphosphate (F2,6BP)?

PFK-2

What enzyme is activated by F2,6BP?

PFK-1

What enzyme is inhibited by F2,6BP?

Fructose-1,6-bisphosphatase (FBPase-1)

What pathways are affected by F2,6BP?

• Glycolysis increases

• Gluconeogenesis decreases

What does a left shift mean when F2,6BP activates PFK-1?

Higher affinity of PFK-1 for fructose-6-phosphate

Can lipids be metabolized into the central metabolic pathway?

yes

How do lipids feed into central metabolism?

Fatty acids are broken into acetyl-CoA by beta-oxidation

Can proteins be metabolized into the central metabolic pathway?

yes

How do proteins feed into central metabolism?

Amino acids can be converted into:

• pyruvate

• acetyl-CoA

• TCA intermediates

What does Gibbs free energy (ΔG) describe?

Whether a process is thermodynamically favorable / spontaneous

What equation relates ΔG, ΔH, and ΔS?

ΔG = ΔH − TΔS

What does a negative ΔG mean?

The reaction is spontaneous / exergonic

What does a positive ΔG mean?

The reaction is nonspontaneous / endergonic

What contributes to ΔG?

• ΔH (enthalpy)

• ΔS (entropy

What is enthalpy (ΔH) related to?

Heat / bond energy

What is entropy (ΔS) related to?

Disorder / randomness

What are the major contributors to internal energy?

• kinetic energy

• potential energy

• bond energy / molecular motion concepts

What is an exergonic reaction?

A reaction with negative ΔG that releases usable energy.

What is an endergonic reaction?

A reaction with positive ΔG that requires energy input.

What is energy coupling?v

Using an exergonic reaction to drive an endergonic reaction

How does epinephrine raise blood glucose?

It stimulates:

• glycogen breakdown

• increased fuel mobilization

• glucose release (especially via liver pathways)

How is regulation of glycogen breakdown different in liver vs muscle?

• Liver: maintains blood glucose

• Muscle: uses glycogen for its own ATP needs

What activates glycogen breakdown in muscle during activity?

• AMP

• Ca²⁺

• epinephrine signaling

What is the main goal of glycogen breakdown in the liver?

To maintain blood glucose

What are the major control points of the citric acid cycle?

• Citrate synthase

• Isocitrate dehydrogenase

• Alpha-ketoglutarate dehydrogenase

Which citric acid cycle enzyme is often considered the most important regulatory step?

Isocitrate dehydrogenase

Which TCA enzymes are redox reactions?

• Isocitrate dehydrogenase

• Alpha-ketoglutarate dehydrogenase

• Succinate dehydrogenase

• Malate dehydrogenase

Which TCA step is a dehydration / hydration / isomerization-type step?

Aconitase (citrate ↔ isocitrate via cis-aconitate)

What is the oxidative half reaction?

The part where a molecule loses electrons

What is the reductive half reaction?

The part where a molecule gains electrons

How would niacin deficiency affect metabolism overall?

It would impair pathways that require NAD+ / NADP+, reducing energy production and redox metabolism.

What’s the difference between an oxidized and reduced coenzyme?

• Oxidized = can accept electrons

• Reduced = has already gained electrons

Which is oxidized and which is reduced: NAD+ vs NADH?

• NAD+ = oxidized

• NADH = reduced

Which is oxidized and which is reduced: FAD vs FADH2?

• FAD = oxidized

• FADH2 = reduced

What does PEPCK do?

It converts oxaloacetate → phosphoenolpyruvate (PEP) in gluconeogenesis.

What would happen with PEPCK deficiency?

Gluconeogenesis would be impaired, reducing the ability to make glucose from non-carbohydrate sources.

What is PP1 (protein phosphatase 1)?

A phosphatase that removes phosphate groups from regulatory enzymes.

What is the general metabolic effect of PP1 in the fed state?

It promotes:

• glycogen synthesis

• decreased glycogen breakdown

• storage metabolism

How is NADPH mainly produced?

Mostly by the pentose phosphate pathway (PPP)

What reactions/pathways require NADPH?

• ROS defense

• fatty acid synthesis

• reductive biosynthesis

Why is NADPH different from NADH metabolically?

• NADH is mainly used for ATP production

• NADPH is mainly used for biosynthesis and antioxidant defense

What are ROS (reactive oxygen species)?

Reactive oxygen-containing molecules that can damage cells.

What reducing power is required for many ROS defense systems?

NADPH

What is the Second Law of Thermodynamics?

The entropy of the universe tends to increase

How is protein folding related to thermodynamics?

Folding is favored when the overall free energy decreases, even if local ordering occurs.