Protein and AA Metabolism FOR KLE- no audio

Course Information

Course Title: Protein & Amino Acid Metabolism
Instructor: Dr. David Watson
Location: Room 303b
Email: d.watson@keele.ac.uk

Learning Outcomes

Understand catabolic processes for producing amino acids from dietary proteins.
Outline the degradation of amino acids and the urea cycle.
Describe the integration of amino acid catabolism products into central metabolic pathways.
Further Reading:
- Biochemistry by Berg et al., Chapter 23.
- Garret and Grisham, Module e-book, Chapter 25.

Amino Acid Sources & Protein Turnover

Cellular Protein Recycling

Constant recycling of proteins:
- Damaged/unwanted proteins tagged for degradation through ubiquitin attachment.
- Proteins with polyubiquitin chains are degraded by the proteasome, an ATP-dependent complex.

Main Sources of Amino Acids

Dietary Protein Digestion:
- Occurs in the gut, involving the breakdown of proteins.
Intracellular Degradation:
- Recycling of amino acids from damaged proteins.
Non-Essential Amino Acids:
- Synthesized in the liver.

Protein Digestion

Stomach: begins in an acidic environment.
- Proteins denatured for breakdown.
- Primary protease: Pepsin (optimum pH 2).
Intestinal Lumen:
- Continuing degradation by pancreatic proteases.
- Completed by aminopeptidases in the intestinal membrane, absorbing amino acids, di-, and tri-peptides into blood.

Protein Turnover Mechanisms

Cellular Degradation Rates

Varying rates of protein degradation depending on protein and location in the cell.
Ubiquitin System:
- Tags proteins for degradation.
- Process involves three enzymes:
  - Ubiquitin activating enzyme (E1)
  - Ubiquitin conjugating enzyme (E2)
  - Ubiquitin protein-ligase (E3)

Ubiquitin Activation Process

Activation: Terminal carboxylate of ubiquitin converts to acyl-phosphate.
Conjugation: Activated ubiquitin is transferred to E2.
Ligation: E3 catalyzes the transfer of ubiquitin to the target protein's amino group.
Formation of a polyubiquitin chain through isopeptide bonds.

Protein Degradation via the Proteasome

20S Proteasome Structure: Comprises 28 units in four rings.
Regulatory Complex: 19S complex controls access to the catalytic core and cleaves off intact ubiquitin for recycling.
Degraded peptides result in free amino acids for further metabolic processing.

Uses of Amino Acids

Primary Functions:
- Synthesis of proteins and peptides.
- Source of nitrogen for:
  - Other amino acids (synthesis).
  - Nitrogenous compounds (nucleotide bases).
Excess Amino Acids: Not stored; processed for metabolic fuel.
- Removal of the alpha-amino group; resulting carbon skeletons converted into metabolic intermediates.
- Alpha-amino groups converted to urea via urea cycle.

Examples of Amino Acid Transfer

Aspartate Aminotransferase:
- Transfers aspartate's amino group to alpha-ketoglutarate:
  - Aspartate + alpha-ketoglutarate → Oxaloacetate + Glutamate
Alanine Aminotransferase:
- Transfers alanine's amino group to alpha-ketoglutarate:
  - Alanine + alpha-ketoglutarate → Pyruvate + Glutamate
Coenzyme Involvement:
- Pyridoxal phosphate (derived from vitamin B6) acts as a coenzyme.

Glutamate Dehydrogenase

Converts glutamate (amino group) to ammonium ion (NH4+).
Ammonia Conversion:
- NH4+ is usually converted to urea for excretion in terrestrial vertebrates.

Urea Cycle

Steps of the Urea Cycle

Formation of carbamoyl phosphate.
Transfer to ornithine creates citrulline.
Citrulline condenses with aspartate in cytosol.
Cleaved to fumarate and arginine.
Arginine hydrolyzed to generate urea and ornithine.

Metabolic Fate of Amino Acids

Differentiation of amino acids into gluconeogenic and ketogenic pathways.
- Examples:
  - Gluconeogenic Amino Acids: Alanine, Glycine, Serine.
  - Ketogenic Amino Acids: Leucine, Lysine, Tryptophan.
Various amino acids convert into specific metabolic intermediates like pyruvate, acetyl CoA, or intermediates of the TCA cycle.