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Amino Acid Metabolism

1. Proteins are degraded to amino acids

2. Removal of nitrogen is first step in degradation

3. Ammonium is converted into urea

4. C-skeleton enters known pathways

5. Nitrogen fixation -> ammonia production

6. Amino acids are made from intermediates of other pathways

7. Amino acids are precursors

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Amino Acid Metabolism

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Amino Acid Metabolism

Protein Turn Over

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Ubiquitin (8.5 kDa) marks proteins (in eukaryotes) for destruction -> tag

Ubiquitin-Activating Enzyme (E1)

Ubiquitin-Conjugating Enzyme (E2)

Ubiquitin-Protein Ligase (E3)

Protein Turn Over

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What determines if protein ubiquitinated?

-> n-terminal amino acid (N-rule)

-> proteins containing PEST sequence Phosphorylation of PEST domains activates ubiquitinationGlycosylation of some PEST proteins with N-acetylglucosamine (GlcNAc) has the opposite effect, prolonging the half-life of these proteins.

-> Some proteins (e.g., mitotic cyclins involved in regulation of the cell cycle) have a sequence called a destruction box that is recognized by a domain of the corresponding Ubiquitin Ligase. 

A chain of four or more ubiquitins targets proteins for degradation in proteasomes.

Protein Turn Over

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Proteasome digests Ub-tagged proteins

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Amino Acid Metabolism

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Fate of Nitrogen in Different Organism

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Amino Acid Degradation

1st Step -> Removal of Nitrogen

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Amino Acid Degradation

Removal of Nitrogen by aminotransferase

Prosthetic group involved in amino transfer

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Serine and Threonine can be Directly Deaminated

Threonine

Urea

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Ammonium Ion is Converted into Urea

Urea cycle

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The Urea Cycle is Linked to the Citric Acid Cycle

NH4+

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Fate of the C-Skeleton of Amino Acids

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Fate of the C-Skeleton of Amino Acids

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Fate of the C-Skeleton of Amino Acids

Aromatic amino acids need oxygenases + O2

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Biosynthesis of Amino Acids

The nitrogen cycle

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Biosynthesis of Amino Acids

Nitrogen Fixation -> Microorganism

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Major Ammonium ion carrier

Ammonium Ion Is Assimilated into Amino Acids Through Glutamate and Glutamine

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Biosynthesis of Amino Acids

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Biosynthesis of Amino Acids in Bacteria and Plants

Essential ones are in bold letters

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Biosynthesis of Amino Acids in Bacteria and Plants

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In Mammals

Plants and bacteria can produce all

of them

Feedback inhibition regulates amino acid biosynthesis

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Amino acids are precursors

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Amino acids are precursors

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Amino acids are precursors

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Heme degradation:

-> bilirubin responsible for color of bruises