Biochem Definitions

definitions

what is glycolysis

• A metabolic pathway that converts 1 glucose into 2 pyruvate in the cytoplasm, producing ATP and NADH.

• It is an anaerobic process that provides quick energy and is the first step in cellular respiration.

GLUT/GLUT2

• GLUT proteins are membrane transporters that move glucose across cell membranes by facilitated diffusion.

• GLUT2 is found in the liver and pancreas and allows glucose to move in or out of cells depending on blood glucose levels.

Gluconeogenesis

• A metabolic pathway that synthesizes glucose from non-carbohydrate sources such as lactate, glycerol, and amino acids.

• It occurs mainly in the liver and requires energy (ATP and GTP).

Hexokinase

• An enzyme that catalyzes the phosphorylation of glucose to glucose-6-phosphate in the first step of glycolysis.

• It uses ATP and traps glucose inside the cell.

Kinase

• Enzymes that transfer a phosphate group from ATP to a substrate.

• They play key roles in metabolism and regulation of cellular processes.

GAP dehydrogenase

• (Glyceraldehyde-3-phosphate dehydrogenase)

• An enzyme in glycolysis that converts glyceraldehyde-3-phosphate into 1,3-bisphosphoglycerate.

• This reaction produces NADH through oxidation.

• GAP = end of stage 1 of glycolysis

Fermentation pathway

• A metabolic process that regenerates NAD⁺ from NADH when oxygen is not available.

• It allows glycolysis to continue producing ATP under anaerobic conditions.

ethanol fermentation

• A type of fermentation in which pyruvate is converted into ethanol and CO₂.

• It occurs in yeast and some microorganisms under anaerobic conditions.

Acetyl CoA

• A molecule formed from pyruvate by the pyruvate dehydrogenase complex before entering the TCA cycle.

• It carries a two-carbon acetyl group into the citric acid cycle for energy production.

fructokinase

• An enzyme that phosphorylates fructose to fructose-1-phosphate in fructose metabolism.

• It is primarily found in the liver.

phosphofructokinase

• PFK-1

• A key regulatory enzyme in glycolysis that converts fructose-6-phosphate into fructose-1,6-bisphosphate using ATP.

• It is the rate-limiting and highly regulated step of glycolysis.

Insulin

• A hormone released from the pancreas that lowers blood glucose levels.

• It promotes glucose uptake, glycogen synthesis, and fat storage.

Explain the basic steps of glycolysis

Stage 1

• trap and prep phase

• no ATP generated

• 3 steps

  • trap glucose in cell

  • form compound that’s readily made into phosphorylated 3-C units (fructose 1,6-bisphosphate

  • makes 2-C units readily convertible into DHAP and GAP

Stage 2

• 3-C fragments oxidized to pyruvate

• ATP harvested

Net rxn of Glucose to pyruvate

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

• 2 ATP in

• 4 ATP out

• Net 2 ATP

How is NAD+ regenerated from pyruvate?

“NAD⁺ must be regenerated from NADH through fermentation or aerobic respiration so that glycolysis can continue producing ATP.”

1) Glycolysis requires regeneration of NAD⁺ to continue

• NAD⁺ is reduced to NADH during the GAP dehydrogenase step, and cells have limited NAD⁺ supplies.

• NAD⁺ must be regenerated to maintain redox balance and allow glycolysis to keep producing ATP.

2) In the absence of oxygen, pyruvate is metabolized by fermentation

• Pyruvate is converted into lactate or ethanol, which regenerates NAD⁺ from NADH.

• Fermentation is a redox-neutral process that allows ATP production without oxygen.

3) In the presence of oxygen, pyruvate is fully oxidized for maximum energy

• Pyruvate is converted into carbon dioxide and water through the TCA cycle and electron transport chain.

• Oxygen acts as the final electron acceptor, producing more ATP than fermentation.

Briefly explain the pathway for glucose to ethanol

• Glucose is converted to pyruvate by glycolysis, producing ATP and NADH. In anaerobic conditions, pyruvate is converted to ethanol and CO₂. This regenerates NAD⁺ so glycolysis can continue.

• 1) Glucose is broken down into pyruvate through glycolysis

  • Glycolysis converts glucose into 2 pyruvate, producing 2 ATP and 2 NADH in the cytoplasm.

  • This process does not require oxygen.

  2) In the absence of oxygen, pyruvate is converted into ethanol

  • Pyruvate is first converted into acetaldehyde, releasing CO₂, and then reduced to ethanol.

  • This occurs in yeast and some microorganisms during fermentation.

  3) Ethanol fermentation regenerates NAD⁺ so glycolysis can continue

  • NADH is oxidized back to NAD⁺, maintaining redox balance.

  • This allows continued ATP production from glycolysis under anaerobic conditions.

Explain how fructose can enter glycolysis

• Fructokinase converts fructose to fructose 1-phosphate in the liver, producing intermediates that enter glycolysis.

1) Fructose is primarily metabolized in the liver through the fructose 1-phosphate pathway

• Fructokinase phosphorylates fructose to fructose 1-phosphate using ATP.

2) Fructose 1-phosphate is split into glycolytic intermediates

• It is cleaved into glyceraldehyde and dihydroxyacetone phosphate (DHAP), which can enter glycolysis.

3) In other tissues, fructose can enter glycolysis by a different route

• Hexokinase can phosphorylate fructose to fructose 6-phosphate, allowing it to enter glycolysis directly.

How does galactose enter glycolysis?

• Galactose is phosphorylated, converted to glucose-1-phosphate via UDP intermediates, and then isomerized to glucose-6-phosphate to enter glycolysis.

1) Galactose is phosphorylated and activated for conversion to glucose

• Galactokinase converts galactose into galactose-1-phosphate using ATP.

• Galactose-1-phosphate then receives a uridyl group from UDP-glucose, forming an activated intermediate.

2) Galactose is converted into a glucose form through epimerization

• UDP-galactose 4-epimerase converts UDP-galactose into UDP-glucose (C4 epimerization).

• This allows galactose to be transformed into a glucose derivative.

3) The final product enters glycolysis as glucose-6-phosphate (G-6-P)

• Glucose-1-phosphate is converted into glucose-6-phosphate by phosphoglucomutase.

• G-6-P can then enter glycolysis or other metabolic pathways.

Explain how the glycolytic pathway is regulated

1) Glycolysis is regulated at irreversible enzyme steps that act as control points

• The three main regulatory enzymes are hexokinase, phosphofructokinase (PFK-1), and pyruvate kinase.

• These enzymes control the rate of conversion of glucose into pyruvate.

2) The primary signal regulating glycolysis in muscle is the ATP/AMP ratio (energy charge)

• Low ATP and high AMP stimulate glycolysis, signaling that the cell needs more energy.

• High ATP inhibits glycolysis, indicating sufficient energy is available.

3) Phosphofructokinase (PFK-1) is the most important regulatory enzyme

• ATP and citrate inhibit PFK-1, while AMP and fructose 2,6-bisphosphate activate it.

• This step is the major control point determining the rate of glycolysis.

4) Hexokinase and pyruvate kinase are regulated by feedback and feedforward mechanisms

• Hexokinase is inhibited by its product, glucose-6-phosphate (G-6P).

• Pyruvate kinase is inhibited by ATP and activated by fructose 1,6-bisphosphate (feedforward activation).

5) Regulation differs between muscle and liver based on function

• Muscle regulates glycolysis mainly to meet energy demands for contraction.

• Liver regulates glycolysis to maintain blood glucose levels, using fructose 2,6-bisphosphate as a key signal when glucose is abundant.

explain how Glycolysis Helps Pancreatic β Cells Sense Glucose

• Insulin is a polypeptide hormone secreted by pancreatic β cells in response to increased blood glucose.

• The function of insulin is to stimulate glucose uptake by tissues and lower blood glucose levels.

• Glucose enters β cells through GLUT2, a transporter with a high KM, allowing glucose entry only when blood glucose is high.

• This ensures insulin is released only when glucose is abundant.

• The pancreas expresses glucokinase, which also has a high KM, allowing phosphorylation of glucose only at high glucose concentrations.

• Glucose is metabolized through glycolysis and cellular respiration, producing ATP.

• The increase in the ATP/ADP ratio causes ATP-sensitive K⁺ channels to close.

• Closure of K⁺ channels leads to membrane depolarization.

• Depolarization opens voltage-gated Ca²⁺ channels, allowing Ca²⁺ influx into the cell.

• Increased Ca²⁺ triggers fusion of insulin-containing vesicles with the cell membrane.

• Insulin is released into the bloodstream, promoting glucose uptake and restoring normal blood glucose levels.

Explain gluconeogenesis

1) Gluconeogenesis is the synthesis of glucose from non-carbohydrate precursors

• These precursors include lactate, glycerol, and amino acids.

2) The primary site of gluconeogenesis is the liver, with smaller amounts in the kidney

• Very little occurs in the brain, skeletal muscle, or heart.

3) The function of gluconeogenesis is to maintain blood glucose levels

• It converts pyruvate into glucose-6-phosphate or glucose to supply energy to tissues such as the brain and muscle.

It is NOT a reversal of glycolysis.

explain gluconeogenesis from pyruvate to glucose

1) Pyruvate → Oxaloacetate (OAA)

• Enzyme: Pyruvate carboxylase

• Location: Mitochondria

• Energy: Uses ATP

• Requires: Biotin (vitamin B7)

• Reaction type: Carboxylation (adds CO₂)

• Regulation: Activated by acetyl-CoA

• Purpose: Begins bypass of the irreversible pyruvate kinase step in glycolysis

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2) Oxaloacetate (OAA) → Phosphoenolpyruvate (PEP)

• Transport step:

  • OAA is reduced to malate by malate dehydrogenase

  • Malate crosses mitochondrial membrane

  • Malate is oxidized back to OAA in cytoplasm, producing NADH

• Enzyme: Phosphoenolpyruvate carboxykinase (PEPCK)

• Energy: Uses GTP

• Reaction type: Decarboxylation and phosphorylation

  • CO₂ is removed

  • Phosphate is added

• Result: Formation of phosphoenolpyruvate (PEP)

• Purpose: Completes bypass of the pyruvate kinase step

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(Between Steps 2 and 3)

Glycolysis runs in reverse from PEP to fructose-1,6-bisphosphate (F1,6BP)

Key reversible enzymes in this section:

• Enolase

• Phosphoglycerate mutase

• Phosphoglycerate kinase

• GAP dehydrogenase

• Triose phosphate isomerase

• Aldolase

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3) Fructose-1,6-bisphosphate (F1,6BP) → Fructose-6-phosphate (F6P)

• Enzyme: Fructose-1,6-bisphosphatase (FBPase)

• Reaction type: Hydrolysis (removes phosphate)

• Products: Fructose-6-phosphate + Pi

• Role: Primary regulatory step of gluconeogenesis

• Bypasses: The irreversible glycolysis step catalyzed by phosphofructokinase-1 (PFK-1)

• Regulation:

  • Inhibited by: AMP, fructose-2,6-bisphosphate

  • Activated by: ATP

4) Only the liver and kidney have glucose-6-phosphatase.

Therefore:

• Liver/kidney → can release glucose into the bloodstream

• Most other tissues → gluconeogenesis ends at G6P

• G6P is then:

  • Stored as glycogen, or

  • Used for biosynthesis (e.g., nucleotides)

define reciprocal regulation of gluconeogenesis and glycolysis

• when glucose is abundant —> glycolysis predominates

  • rate of glycolysis is regulated by [glucose]

• when glucose is scarce —> gluconeogenesis takes over

  • gluconeogenesis regulated by [lactate'] and ther glucose precursors

• Key site in gluconeogenesis regulation is at F6P and F1,6BP

• both reciprocally regulated at PEP and pyruvate in liver

how are glycolysis and gluconeogenesis regulated in the liver?

• Fructose-2,6-bisphosphate (F-2,6-BP) determines whether glycolysis or gluconeogenesis predominates in the liver

Control of F-2,6-BP Levels — Bifunctional Enzyme

• The concentration of F-2,6-BP is regulated by a bifunctional enzyme containing both:

  • PFK-2 (kinase activity)

  • FBPase-2 (phosphatase activity)

• These two activities are reciprocally controlled by phosphorylation of a single serine residue.

When Blood Glucose Is Low → Gluconeogenesis Predominates

Hormone: Glucagon

• Glucagon triggers a cAMP signaling cascade.

• Protein kinase A (PKA) phosphorylates the bifunctional enzyme.

• FBPase-2 is activated and PFK-2 is inhibited.

• The concentration of F-2,6-BP decreases.

• PFK activity decreases and FBPase activity increases.

• Gluconeogenesis predominates to raise blood glucose.

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When Blood Glucose Is High → Glycolysis Predominates

Hormone: Insulin

• Insulin activates a protein phosphatase, which dephosphorylates the bifunctional enzyme.

• PFK-2 is activated and FBPase-2 is inhibited.

• The concentration of F-2,6-BP increases.

• PFK activity increases and FBPase activity decreases.

• Glycolysis predominates to lower blood glucose.

what is the Cori cycle?

• Muscle produces lactate during anaerobic glycolysis.

• Lactate travels to the liver and is converted into glucose by gluconeogenesis.

• Glucose returns to muscle to provide energy.

Define the pyruvate dehydrogenase complex

The pyruvate dehydrogenase complex is a multi-enzyme complex in the mitochondrial matrix that converts pyruvate into acetyl-CoA through oxidative decarboxylation.

This irreversible reaction links glycolysis to the citric acid cycle and produces NADH and CO₂.

Contains 3 enzymes and 5 cofactors

How is acetyl CoA formed from pyruvate?

• Converts pyruvate into acetyl-CoA so it can enter the citric acid cycle (TCA cycle).

• Links glycolysis to the TCA cycle.

• Occurs in the mitochondrial matrix under aerobic conditions.

Three Main Steps of the Reaction

1) Decarboxylation

• Pyruvate loses CO₂.

• Catalyzed by pyruvate dehydrogenase (E1).

• Requires TPP.

2) Oxidation

• The remaining 2-carbon fragment is oxidized.

• Electrons are transferred through lipoic acid and FAD.

• Energy is captured.

3) Formation of Acetyl-CoA

• The acetyl group is transferred to CoA.

• Produces acetyl-CoA, ready for the TCA cycle.

• Catalyzed by dihydrolipoyl transacetylase (E2).

• NAD⁺ is reduced to NADH by dihydrolipoyl dehydrogenase (E3)