Protein Anabolism

In what form do mammals primarily excrete nitrogenous waste compared to aquatic animals and other organisms (like birds/reptiles)?

Mammals excrete nitrogen as urea; aquatic animals excrete nitrogen as ammonia (NH3); and other organisms (such as birds and reptiles) excrete uric acid.

What is the difference between an essential and a non-essential amino acid?

Essential amino acids cannot be synthesized by the body in sufficient amounts and must be obtained from the diet (synthesized by plants/microbes). Non-essential amino acids can be synthesized in sufficient amounts by the body.

List the 10 essential amino acids for humans.

Histidine, Isoleucine, Leucine, Lysine, Methionine, Phenylalanine, Threonine, Tryptophan, Valine, and Arginine (often conditionally essential).

List the non-essential amino acids.

Alanine, Asparagine, Aspartate, Cysteine, Glutamate, Glutamine, Glycine, Proline, Serine, and Tyrosine.

Under what conditions do Tyrosine and Cysteine become essential amino acids in the diet?

Tyrosine becomes essential if Phenylalanine is deficient (Phe is its precursor). Cysteine becomes essential if Methionine is deficient (Met donates the sulfur precursor).

Why is the synthesis or dietary availability of all required amino acids crucial for protein translation?

If a required amino acid is unavailable

Which major biological macromolecules contain nitrogen?

Proteins (in the amino acid backbone/side chains) and Nucleic Acids (in nitrogenous bases: purines and pyrimidines).

What are the core metabolic pathway sources for amino acid carbon skeletons?

1. Glycolysis (Pyruvate, 3-Phosphoglycerate)
2. Citric Acid Cycle / TCA (α-Ketoglutarate, Oxaloacetate)
3. Pentose Phosphate Pathway (Ribose-5-Phosphate, Erythrose-4-Phosphate)

Which amino acids belong to the Glutamate family and what is their metabolic precursor?

Precursor: α-Ketoglutarate (TCA cycle).
Amino acids: Glutamate, Glutamine, Proline, and Arginine.

Which amino acids belong to the Aspartate family and what is their metabolic precursor?

Precursor: Oxaloacetate (TCA cycle).
Amino acids: Aspartate, Asparagine, Methionine, Threonine, Lysine, and Isoleucine.

Which amino acids belong to the Serine family and what is their glycolytic precursor?

Precursor: 3-Phosphoglycerate (from glycolysis).
Amino acids: Serine, Glycine, and Cysteine.

Which amino acids belong to the Pyruvate family and what is their glycolytic precursor?

Precursor: Pyruvate (from glycolysis).
Amino acids: Alanine, Valine, and Leucine.

Which amino acids belong to the Aromatic family and what are their precursors?

Precursors: Phosphoenolpyruvate (PEP from glycolysis) + Erythrose-4-phosphate (from Pentose Phosphate Pathway).
Amino acids: Phenylalanine, Tyrosine, and Tryptophan.

Which amino acid belongs to the Histidine family and what is its precursor?

Precursor: Ribose-5-phosphate (from Pentose Phosphate Pathway).
Amino acid: Histidine.

How is Glutamate synthesized directly from free ammonium (NH4+) and which enzyme catalyzes it?

α-Ketoglutarate + NH4+ + NADH ⇌ Glutamate + NAD+ + H2O.
Catalyzed by Glutamate Dehydrogenase (rare assimilation route).

How is Glutamine synthesized from Glutamate and ammonium and does it require energy?

Glutamate + NH4+ + ATP → Glutamine + ADP + Pi + H2O.
Catalyzed by Glutamine Synthetase (common assimilation route; consumes 1 ATP).

What is a transamination reaction and where does it occur?

A reversible reaction where a transaminase (aminotransferase) transfers an amino group (-NH2) from an amino acid to an α-keto acid, creating a new amino acid and a new α-keto acid. It occurs in both the cytosol and mitochondria and does NOT require ATP.

What reaction does Aspartate Aminotransferase (AST) catalyze?

Glutamate (Amino Acid 1) + Oxaloacetate (α-Keto Acid 2) ⇌ α-Ketoglutarate (α-Keto Acid 1) + Aspartate (Amino Acid 2).

What reaction does Alanine Aminotransferase (ALT) catalyze?

Glutamate (Amino Acid 1) + Pyruvate (α-Keto Acid 2) ⇌ α-Ketoglutarate (α-Keto Acid 1) + Alanine (Amino Acid 2).

Why are elevated blood levels of AST and ALT used as clinical markers for liver damage?

The liver highly expresses AST and ALT to manage amino acid metabolism and transamination when hepatocytes are damaged or lysed

What are the 3 sequential reaction steps and intermediates in synthesizing Serine from 3-Phosphoglycerate?

1. Dehydrogenation (Oxidation): 3-Phosphoglycerate + NAD+ → 3-Phosphohydroxypyruvate + NADH + H+

2. Transamination: 3-Phosphohydroxypyruvate + Glutamate → 3-Phosphoserine + α-Ketoglutarate

3. Hydrolysis (Dephosphorylation): 3-Phosphoserine + H2O → Serine + Pi"

What is S-adenosylmethionine (SAM) and how is it formed?

SAM is the principal biological methyl (-CH3) donor for transmethylation reactions. It is formed by activating the essential amino acid Methionine with ATP (Methionine + ATP → SAM).

Outline the steps of Cysteine synthesis starting from SAM.

1. SAM donates its methyl group (-CH3) to an acceptor via transmethylation → S adenosylhomocysteine (SAH).

2. Hydrolysis of SAH releases adenosine → Homocysteine.

3. Homocysteine condenses with Serine → Cystathionine.

4. Cleavage of Cystathionine yields Cysteine

Which amino acids donate the carbon skeleton and the sulfur atom in the synthesized Cysteine molecule?

The carbon skeleton and amino group come from Serine; the sulfur (-SH) group comes from Methionine (via Homocysteine).