Amino acid Metabolism

Question 1

Give an overview of amino acid breakdown?

Answer 1

10-15% of metabolic energy in animals comes from breakdown of amino acids

Amino acids can be degraded into one of seven common metabolic intermediates
Some are compounds that can be metabolised to CO2 and H2O
Some are compounds that can be used in gluconeogenesis

Question 2

What are the two types of amino acids that can be broken down?

Answer 2

Glucogenic - amino acids that can be degraded to glucose precursors
E.g. Pyruvate, a-Ketoglutarate, Succinyl-CoA, Fumarate and Oxaloacetate
Ketogenic - amino acids that can be degraded to precursors of fatty acids and ketone bodies
E.g. Acetyl-CoA and Acetoacetate

Question 3

Which amino acids are special in their break down?

Answer 3

Only lysine and leucine is exclusively ketogenic as acetyl-CoA cannot be converted to oxaloacetate or pyruvate so can yield no net synthesis of carbohydrates
Therefore they can’t convert fats to glucose, as all Cs are lost as CO2

Question 4

Which amino acids are broken down into pyruvate?

Answer 4

Alanine - is transaminated and catalysed by alanine transferase
Serine - catalysed by serine dehydratase (PLP enzyme) and releases NH3
Glycine - is 1st converted to serine using serine hydroxymethyltransferase (PLP enzyme)
Theronine - converted to glycine using SHMT as above
Cysteine - the sulfhydryl group is released as either H2S, SO3 2- or SCN-

Question 5

How does serine dehydratase work?

Answer 5

It breaks the α-carbon-H bond
Then a carbanion breaks down, leading to the loss of sidechain OH on the serine R-group
Aminoacrylate is formed and released, spontaneously hydrolyses to pyruvate and ammonia

Question 6

Which amino acids are broken down in oxaloacetate?

Answer 6

Asparagine - using l-asparaginase and water this releases ammonium

Aspartate - using aminotransferase in a transamination reaction

Question 7

Which amino acids are broken down into a-ketoglutarate?

Answer 7

Arginine, glutamine, histidine and proline are all degraded into glutamate

Glutamate is then deaminated to a-ketoglutarate using GDH, releasing NH3

Question 8

Which amino acids are broken down into succinyl Co-A?

Answer 8

Methionine, Threonine, Isoleucine and Valine

They are all degraded to propionyl-CoA, which is then conveted into succinyl-CoA (using biotin and coenzyme B12)

Question 9

What other molecule can be used as C1 carriers to transfer to another molecule (cofactors)?

Answer 9

Tetrahydrofolates (THF)
It is a 6-methylpterin derivative, linked to a p-aminobenzoic acid and a glutamate residue

Structurally similar to flavins (e.g. FAD)

Question 10

What can be used as an inhibitor to THF?

Answer 10

Sulfonamindes - antibiotics that are structural analogs of the p-aminobenzoic acid

Question 11

What is phenylalanine degraded to?

Answer 11

Fumarate and Acetoacetate

This uses 6 enzymes including the cofactor tetrahydrobiopterin (a THF)

Question 12

What is a disease related to the breakdown of phenylalanine?

Answer 12

Phenylketonuria - PKU, deficiency of phenylalanine hydroxylase
Known as an inborn error - inherited disease that causes mental retardation
PKU leads to a build up of phenylalanine in the blood
Excess phenylalanine is converted into phenylpyruvate via transamination

People with PKU have lighter hair and skin than their siblings for example
This is due to having excess phenylalanine, it inhibits tyrosine hydroxylation and dihydroxyphenylalanine (L-DOPA) is a precursor for synthesis of melanin

Question 13

How can PKU be helped?

Answer 13

Follow a low-phenylalanine diet (low protein)
Supplements can be taken to provide the necessary amino acids
However this is hard as for example some sweeteners e.g. Aspartame = aspartylphenylalanine methyl ester, which contains phenylalanine

Kuvan treats PKU
Sapropterin – synthetic form of tetrahydrobiopterin can be used to maximise remaining PH activity in these patients, allowing phenylalanine to be turned into tyrosine

Question 14

How many essential amino acids? What are they?

Answer 14

Only 9/20 are essential - they must be obtained in the diet

Methionine, Valine, Histidine, Leucine, Phenylalanine, Threonine, Isoleucine, Lysine and Tryptophan

Pneumonic - Many Very Happy Little Pigs Take Iced Lemon Tea

Question 15

What may be considered as an essentail amino acid?

Answer 15

Arginine may sometimes be listed as an essential amino acid as during pregnancy and childhood it is essential for growth - as at these times the body can’t make enough to maintain an increased growth rate

Question 16

What are some issues for vegetarians?

Answer 16

Vegetarians can struggle to acquire all essential amino acids
Cysteine, methionine and tryptophan are most commonly lacking in plant proteins
Vegetarians needs to eat a range of combinations of protein

Question 17

What are the amino acid precursors and the amino acids they synthesise in amino acid biosynthesis?

Answer 17

Pyruvate - alanine and valine&leucine (these 2 are only produced by this path in plants/bacteria)

A-ketoglutarate -> Glutamate - glutamine, proline and arginine

Oxaloacetate -> aspartate - arginine (in humans); methionine, threonine -> isoleucine and lysine (these 4 are just produced within plants/bacteria)

3-phosphoglycerate -> serine - glycine and cysteine

PEP + erythrose-4-phosphate - tryptophan, phenylalanine and tyrosine

Question 18

How does 3-phosphoglycerate synthesise serine?

Answer 18

The first reaction converts to a ketone, uses transamination and then hydrolysis to get to serine
The enzymes used are phosphoglycerate dehydrogenase, aminotransferase and phosphoserine phosphatase

Question 19

Which biosynthesis of amino acid reactions used transamination?

Answer 19

Alanine, aspartate and glutamate are all synthesised by simple transamination reactions, using an aminoacidtransferase and a coupled reaction with an amino acid going to a-keto acid

We have a taste receptor that recognises glutamate - therefore we add MSG to foods to improve flavour

Question 20

Give an overview of glutmaine synthesis?

Answer 20

Glutamine synthesis is a mechanism for taking up ammonium ions
It can be viewed as a storage form of ammonium

It is a donor of amino groups e.g. Purines and pyrimidines as well as amino sugars
The amino sugars glucosamine and galactosamine have important roles in connective tissue, synovial fluid in joints

Glutamine synthetase is a central control point in nitrogen metabolism

Question 21

What is the difference with bacterial enzymes in glutamine synthesis?

Answer 21

Bacterial enzymes are more complex as this is the point where fixed nitrogen is assimilated into biologically

The ammonia is combined with a-ketoglutarate
E.coli is allosterically controlled by 9 different modulators
Modulators include 6 different end-products of reaction pathways from glutamine

Less adenylated glutamine synthetase is more active

Question 22

Describe tryptophan synthase?

Answer 22

It is a bifunctional enzyme with two subunits and two active sites an α-subunit and a β-subunit
The indole is never released from the enzyme – instead it is channelled directly from the a-subunit to the b-subunit

Question 23

Give an overview of nitrogen?

Answer 23

All of the nitrogen in biological molecules is derived from atmospheric N2
N≡N bond is very stable: 945 kJmol-1
Sources of Nitrogen - fertiliser, lightening and nitrogen fixing bacteria that colonise the root nodules of legume plants

Question 24

What is the nitrogen cycle?

Answer 24

Nitrogen fixation: atmospheric N2 -> ammonia (nitrogenase)
Ammonification: ammonia nitrogen containing biomolecules (saprobiotic bacteria)
Nitrification: ammonium -> nitrite/nitrate (oxidised using nitrate reductase)
Denitrification: nitrates -> atmospheric N2 (de-nitrifying bacteria)

Question 25

Describe the enzyme in nitogen fixing?

Answer 25

Nitrogenase - the nitrogen fixing bacteria (diazotrophs)
It is a complex of 2 proteins – an Fe-S containing protein (a homodimer) and a tetrameric protein containing both Fe and Mo
Fe and Mo are unusual redox cofactors

Each dimer has 2 bound redox centers: the P-cluster and the FeMo-cofactor

Question 26

Is nitrogen fixing - energy requirements?

Answer 26

This is energetically very costly needing 20-30 ATP per N2 fixed
ATP usage is increased by futile cycling in the first step
Nitrogenase reduces water to hydrogen
Hydrogen reacts with the diamine to form nitrogen

This process would have needed 16 ATPs without this stage

Question 27

How are electrons used in nitrogen fixing?

Answer 27

ATP hydrolysis is coupled to electron transfer in nitrogenase

Electrons are generated oxidatively/phosophosynthetically depending on the organism
Electrons are tranferred ti ferredoxin - that transfers electrons to the nitrogenase

Question 28

What is used to prevent degredation of nitrogenase?

Answer 28

Leghemoglobin has a high affinity for O2 within the cyanonacteria, which keeps the pO2 low enough to protect the nitrogenase but maintain O2 for the aerobic bacterium