Lecture 8 - Amino Acid catabolism

Question 1

How is amino acid catabolism different in plants, fungi and bacteria in comparison to animals.

Answer 1

Plants, fungi and bacteria are deficient in nitrogen and devote energy to ensure they take up as much as possible. They do not excrete nitrogen. These organisms have mechanisms for the storage of protein.

Animals take in nitrogen as protein and normally have excess nitrogen. They do not store nitrogen in any form and therefore need to excrete it.
Following ingestion, proteins are hydrolysed to amino acids after which they are primarily used for growth and repair. However, amino acids in excess of immediate requirements, the amino groups are removed and excreted and the carbon skeletons are metabolised to a fuel source or are stored.

Question 2

Where do amino acids in the cell originate from?

Answer 2

Cellular amino acid catabolism
1. Digestion and absorption of dietary protein - proteases such as pepsin, chymotrypsin and trypsin
2. Turnover of own cellular proteins - Mis-folding, regulation and damaged proteins. (Ubiquitin signals death)
Ubiquitin ligase selects its target by the N-terminal rule - depending on the residue on the N terminus the half-life of the protein.

Question 3

What is the fate of ammino acids released on protein degradation?

Answer 3

If not needed the amino groups of most amino acids are removed by an amino transferase to form a keto acid and a glutamate.

Amino acid (NH3) + α-ketoglutarate (keto group) —> Keto acid (NH3) + glutamate

The amino acid has the amino group remove and it is replaced with a ketone group
The α-ketoglutarate loses its ketone group to the amino acid and it is replaced with the amino group from the amino acid
This forms a keto group and a glutamate.
The reaction is catalysed by and aminotransferase (Transaminase)

Amino acids are termed Glucogenic when their carbon skeletons (keto acid) can be used in the citric acid cycle and be converted to glucose via gluconeogenesis.
There are 3 key keto acids through which glucogenic acids ultimately donate their carbon skeletons to the citric acid cycle
* Pyruvate - 3 chain glucogenic amino acids
* Oxaloacetate - 4 chain glucogenic amino acids
* α-ketoglutarate - 5 chain glucogenic amino acids
* They can join through other routes but the above are the most common

Amino acids that can’t be metabolised to citric acid cycle components are termed Ketogenic amino acids. These amino acids are metabolised to acetyl CoA or acetoacetyl CoA and therefore can’t be converted to glucose. They can then contribute to the synthesis of fatty acids or ketone bodies.

Some amino acids are both ketogenic and glucogenic (Tryptophan)

Question 4

Give examples of glucogenic amino acids using pyruvate as an entry point.

Answer 4

Glycine
Glycine is first converted into serine by serine hydroxymethyl transferase. The serine is then deaminated by serine dehydratase into pyruvate

Tryptophan
Tryptophan’s indole ring is first opened by oxygenases converting it either into acetoacetate which is then used in fatty acid synthesis or to alanine which is transaminated directly to form pyruvate and glutamate (from α-ketoglutarate)

Threonine
Threonine is first transferred to aminoacetone by threonine dehydrogenase. The aminoacetone is deaminated directly to pyruvate.

Question 5

Give examples of glucgenic amino acids using oxaloacetate as an entry point.

Answer 5

Aspartate
Aspartate is directly transaminated to form oxaloacetate and glutamate.

Asparagine
Asparagine is first converted to aspartate through the removal of the additional amino group by asparaginase. The Aspartate is then directly transaminated to form oxaloacetate and glutamate.

Question 6

Give examples of glucogenic amino acids using a-ketoglutarate as an entry point.

Answer 6

Glutamine
Glutamine is hydrolysed by glutaminase to glutamate. Glutamate is then deaminated to form α-ketoglutarate.

Proline and Arginine
Proline and arginine are both first converted to glutamate-γ-semialdehyde. The glutamate-γ-semialdehyde is then oxidated to glutamate. Glutamate is then deaminated to form α-ketoglutarate.

Histidine
Histidine is deaminated, the amide bond in its ring is hydrolysed and the formimino group is converted to tetrahydrofolate by transferase. It can then be converted to glutamate. Glutamate is then deaminated to form α-ketoglutarate.

Question 7

Descrbe the catabolism of teh carbon chains fo ketogenic amino acids.

Answer 7

1. The amino acid is transaminated in the same way as glucogenic amino acids. (α-ketoglutarate loses its ketone group to the amino acid and it is replaced with the amino group from the amino acid to form glutamate and a keto acid)
   
   2. Through oxidative decarboxylation the keto acids COO- is lost and replaced with a S-CoA
   3. Through hydration and carboxylation acetoacetate and acetyl-CoA form

Question 8

What is the fate of the a-amino group and how is the amonia removed.

Answer 8

Whether glucogenic, ketogenic or both, the amino group from most amino acids being broken down ends up on the glutamate via transamination reactions.
The glutamate is subsequently oxidised to yield ammonia (Toxic). This reaction is catalysed by glutamate dehydrogenase
Glutamate —–H2O and NAD - NADH + H+ —-> α-ketoglutarate

The toxic ammonia must be removed
* Aquatic animals release it directly into the water
* Birds and reptiles secrete uric acid in faeces (Conserves water)
Terrestrial vertebrates synthesise urea in the liver and excrete in the urine via the urea cycle

Question 9

Describe the urea cycle.

Answer 9

1. Bicarbonate gains a phosphate group from an ATP molecule to form carboxy phosphate. The Pi is substituted with NH2 to form carbamic acid. A phosphate group is added from a second ATP molecule which leads to the formation of carbamoyl phosphate.
2. Ornithine and carbamoyl phosphate react with the help of ornithine transcarbamoylase to form citrulline
3. A second amino group is added from aspartate forming arginosuccinate
4. Fumarate is formed as a side product (removes the carbon skeleton) as arginosuccinate is converted to arginine
5. With the addition of water arginine is converted to urea and ornithine
6. Orthenine reacts with carbamoyl phosphate to form citrulline.

Regeneration of aspartate - fumarate produced as a side product as arginosuccinate is formed is converted by a second cycle into aspartate.

Overall the urea cycle is very efficient using only 1C in the excretion of 2N

Question 10

Describe some diseases of amino acid metabolism.

Answer 10

Phenylketonuria - Phenylalanine builds up due to the lack of function of the phenylalanine hydroxylase. In order to compensate transamination to phenylpyruvate which can then be excreted is carried out. The down side of this is that lots of calcium is also lost. As treatment phenylalanine intake should be restricted/
Arginosuccinate deficiency - Usually results in NH4+elevation and death if untreated. Treatment involves surplus arginine and restricting protein levels in diet. The deficiency is due to arginino-succinate not being able to be converted into arginine