7. Amino Acid Metabolism (Lect 8)

Question 1

Protein catabolism (breakdown)

What are some purposes of protein degradation?

Answer 1

1. Degrade misfolded proteins (prions) that may cause disease.
2. Provide a source of energy during starvation
3. Eliminate unwanted proteins, as proteins usually have a finite lifespan and need to be continously turned over (e.g. enzymes)

Question 2

Protein catabolism (breakdown)

Which organ does protein degradation usually occur?

Answer 2

Liver

Question 3

Protein catabolism (breakdown)

What are the 2 main steps of protein degradation?

Answer 3

1. Protein ubiquitination
2. Protein degradation in proteosome

Question 4

Protein catabolism (breakdown)

What is the main purpose of ubiquitination (in relation to protein degradation)?

Answer 4

To tag / label proteins before they are degraded.

Question 5

Protein catabolism (breakdown)

What are the 3 main steps of ubiquitination and what enzymes are involved in those steps?

Answer 5

1. Activation : Ubiquitin is conjugated / bonded to Ubiquitin enzyme E1, a process which requires ATP. The purpose is to activate ubiquitin.
2. Conjugation : Ubiquitin is transferred to ubiquitin conjugating enzyme, E2.
3. Transfer : Ubiquitin protein-ligase, E3, transfers the activated ubiquitin from E2 to a lysine residue of the condemned protein via an isopeptide bond.

Question 6

Protein catabolism (breakdown)

A protein can be efficiently degraded, as long as there is 1 ubiquitin molecule binded to the protein. True or false?

Answer 6

False. In degradation, a protein must be linked to a chain of at least 4 tandemly linked ubiquitin molecules (polyubiquitin chain)

In the polyubiquitin chain, the lys 48 residue of one ubiquitin molecule is bonded to the carboxyl group of the next ubiquitin molecule via isopeptide bond.

Question 7

Protein catabolism (breakdown)

What is the function of the polymerised ubiquitin chain?

Answer 7

It acts as a signla that shuttles proteins from the liver into the proteasome.

Question 8

Protein catabolism (breakdown)

What are the 2 main functional components / units of the proteasome?

Answer 8

1. 20S core catalytic complex (with α and β subunits)
2. two 19S regulatory subunits (19S cap)

Question 9

Amino acid catabolism (breakdown)

Why are amino acids degraded?

Answer 9

The body cannot store excess amino acids

Question 10

Amino acid catabolism (breakdown)

What happens to the :
1. amino group
2. carbon skeleton

of amino acids when they are degraded?

Answer 10

1. Converted into ammonia, which undergoes urea acid cycle to form urea
2. Used to generate glucose (glucogenic amino acids), or converted into acetyl-CoA or ketone bodies (ketogenic amino acids)

Question 11

Amino acid catabolism (breakdown)

What is deamination? What are the 2 ways that deamination can occur?

Answer 11

Deamination : removal of amino group from amino acid

2 ways of deamination:
1. Transamination
2. Oxidative deamination

Question 12

Amino acid catabolism (breakdown)

What is the purpose of transamination?

Answer 12

Transfer of an amino group from amino acid to α-ketoglutarate.
- This reaction does not release free ammonia but allows amino acids to be metabolized into keto acids / glucose for energy or biosynthesis.

Question 13

Amino acid catabolism (breakdown)

What is the overall reaction of transamination?

Answer 13

Amino acid + α ketoglutarate → α keto acid + glutamate

Note : α ketoglutarate is an intermediate in the TCA cycle

Question 14

Amino acid catabolism (breakdown)

What is the name of the enzyme that is involved in transamination, and what important cofactor does it require?

Answer 14

Transaminase, which requires Pyridoxal Phosphate (PLP) as a cofactor.

Question 15

Amino acid catabolism (breakdown)

How is the transaminase enzyme conjugated / bonded to the PLP cofactor?

Answer 15

Transaminase is conjugated to PLP through a critical lysine residue, where the NH₂ side chain of the lysine residue in the enzyme binds to the aldehyde group of PLP

Question 16

Amino acid catabolism (breakdown)

** What is the role of PLP in trasamination reactions?

Answer 16

• PLP (Pyridoxal Phosphate) acts as an electron sink, stabilizing reaction intermediates which sre negatively charged
• It forms a Schiff base with the amino acid, facilitating the transfer of the amino group from an amino acid to an α-keto acid, enabling transamination.

Question 17

Amino acid catabolism (breakdown)

What is the purpose of oxidative deamination?

Answer 17

To remove the amino group from glutamate, regenerating α-ketoglutarate for reuse in metabolism
- It is the primary mechanism where free ammonia is generated, which then undergoes the urea acid cycle for excretion.

Question 18

Amino acid catabolism (breakdown)

What enzyme catalyses the oxidative deaminaton reaction?

Answer 18

Glutamate dehydrogenase.

Question 19

Amino acid catabolism (breakdown)

Write the overall reaction of oxidative deamination.

Answer 19

Glutamate + H₂O + NAD(P)⁺ → α-ketoglutarate + NH₃ + NAD(P)H + H⁺

Question 20

Amino acid catabolism (breakdown)

What is so special about the glucose-alanine and cori cycle?

Answer 20

They are metabolic reactions that link glucose production in the liver to energy production in the muscles.

Question 21

Amino acid catabolism (breakdown)

Sketch out the glucose-alanine cycle.

Answer 21

See notes.

In muscle : glucose → pyruvate → alanine (transamination)

In liver : Alanine → pyruvate → glucose