Amino Acid Anabolism Flashcards
1
Q
describe characteristics of N2 (2)
A
- compromises 78.08% of the atmosphere but is inaccessible to most living organisms
- must be “fixed” by soil bacteria living in association with roots of particular plants (legumes, peanuts, soybeans, beans, etc)
2
Q
how do soil bacteria “fix” N2 and what are products used for (2)
A
- living in nodules around roots of legumes, bacteria chemically combine nitrogen in air to form nitrates (NO3-) and ammonia (NH4+)
- these nitrogen products are made available to plants
3
Q
the nitrogen cycle (4)
A
- abundant N2 in environment is fixed by soil bacteria and made into products for plants
- organisms feed on plants and ingest the nitrogen
- organisms release nitrogen in organic wastes
- denitrifying bacteria frees the nitrogen from the wastes, returning it to the atmosphere
4
Q
difficulties with nitrogen fixation (4)
A
- N2 triple bond requires large amount of energy to break
- biological systems have to achieve N2 -> NH4+ at physiological temperature and 1 atm
- only occurs in bacteria
- present O2 would interfere with reducing reactions
5
Q
how has nitrogen fixation been down industrially? (2)
A
- Haber process: converts N2 -> NH4+ with 500ºC and several 100 atmospheres of pressure
- breakdown of sewage products for nitrogen
6
Q
nitrogenase complex (3)
A
- consists of 2 pairs of identical subunits (dinitrogenase, dinitrogenase reductase)
- dinitrogenase reductase: containes 4Fe-4S redox centre which carries e-
- dinitrogenase: contain Fe, Mo, S redox centres
7
Q
what is the chemical formula for the rxn of N2 -> NH4+
A
- N2 + 10H- + 8e- + 16ATP -> 2 NH4+ + 16ADP + 16Pi + H2
8
Q
how is the N2 reduced in the N2 into NH4+ reaction
A
- e- transferred from dinitrogenase (reduced form) one at a time to N2, 8 e- altogether
9
Q
how is the oxidized dinitrogenase reduced in the N2 -> NH4+ reaction?
A
- each time oxidized dinitrogenase is regenerated by interaction with dinitrogenase reductase (reduced form)
10
Q
how is oxidized dinitrogenase reductase reduced in N2 -> NH4+ reaction?
A
- oxidized dinitrogenase reductase is reduced by interaction with ferrodoxin/flavodoxin
11
Q
where does ferrdoxin/flavodoxin obtain its electrons
A
- from oxidation of pyruvate to acetyl-CoA by pyruvate dehydrogenase
12
Q
what are the critical entry points of the incorporation of NH4+ into organic molecules (biomolecules) (2)
A
- glutamate
- glutamine
13
Q
how do plants/bacteria incorporate NH4+ into organic molecules? (3)
A
- alpha-KG + NH4+ -> glutamate
- net incorporation of new NH4+ into biomolecules
- mediated by sequential action of glutamine synthetase and glutamate synthase
14
Q
how do mammals incorporate NH4+ into organic molecules (2)
A
- NH4+ is transferred among biomolecules; no new inorganic NH4+ from outside environment is incorporated
- transaminase reactions can incorporate NH4+ into glutamate (other minor reaction performs same reaction, but it is not covered)
15
Q
net reaction of glutamate synthesis in plants/animals (2)
A
- combination of glutamine synthetase (all organisms) and glutamate synthase (only plants/bacteria)
- alpha-KG + NH4+ + NADPH + ATP -> Glutamate + NADP+ + ADP + Pi
16
Q
what is the significance of glutamine synthetase
A
- key entry point for reduced nitrogen into metabolic pathways
17
Q
how is glutamine synthetase regulated? (3)
A
- allosteric inhibition
- covalent modification (adenylation, addition of AMP to Tyr residue near active site) which enhances sensitivity to allosteric inhibitors
- transcriptional control: high glutamine -> decreased transcription
18
Q
how is glutamine synthetase regulated? (3)
A
- allosteric inhibition: activity depends on MANY inhibitors present, not just a simple ON and OFF switch
- covalent modification (adenylation, addition of AMP to Tyr residue near active site) which enhances sensitivity to allosteric inhibitors
- transcriptional control: high glutamine -> decreased transcription
19
Q
non-essential amino acids in humans (2)
A
- not required in diet
- can be formed from alpha-ketoacids by transamination and subsequent reactions
20
Q
what are the non-essential amino acids (8)
A
- alanine
- asparagine
- aspartate
- glutamate
- glutamine
- glycine
- proline
- serine
21
Q
what are the semi-essential amino acids (2)
A
- cysteine (if we eat enough methionine)
- tyrosine (if we eat enough phenylalanine)
22
Q
essential amino acids (2)
A
- required in the diet
- humans incapable of forming requisite carbon skeletons
23
Q
what are the essential amino acids (8)
A
- isoleucine
- leucine
- valine
- lysine
- methionine
- threonine
- phenylalanine
- tryptophan
24
Q
which amino acids are considered essential in some cases (2)
A
- arginine and histidine
- essential in children or during severe infection, but not essential in adults
25
sources of nitrogen
- from glutamine or glutamate
26
where are intermediates that can build amino acids derived from? (3)
- glycolysis, citric acid cycle, pentose phosphate pathway
27
what is arginine required for? (3)
- protein synthesis
- intermediate precursor of NO and ornithine
- necessary for creatine synthesis
28
why is arginine a semi-essential amino acid? (2)
- biosynthetic pathway (argininosuccinate synthetase and argininosuccinate lyase enzymes of the urea cycle) does not produce sufficient arginine, and so some must still be consumed through diet
- synthesis of arginine is second function of the urea cycle
29
when is arginine supplementation needed?
- special conditions like burn recovery, sepsis, protein malnutrition, urea cycle disorders, excess ammonia production, infection, peritoneal dialysis
30
what are the 4 families of essential amino acids?
- pyruvate family
- aromatic family
- aspartate family
- histidine
31
aromatic family of aromatic amino acids
- phenylalanine, tyrosine, tryptophan
| - begins with synthesis of chorismate, an important intermediate for many biosynthetic pathways
32
what are the beginning substrates and what is consumed in synthesis of aromatic amino acids? (2)
- substrates: erythrose 4-phosphate and phosphoenol pyruvate
| - consumed: NADPH, H+, 1 ATP for every chorismate formed
33
glyphosphate (2)
- acts as a potent, competitive inhibitor by competing with PEP for binding to EPSPS
- binding to EPSPS results in no chorismate formation and death of the plant/bacteria
34
how is amino acid synthesis regulated? (4)
- feedback negative, allosteric inhibition
- sequential feedback inhibition
- interlocking regulatory systems
- concerted inhibition
35
allosteric inhibitor
- binds to a distinct site on the enzyme that is independent of the substrate-binding domain to inhibit the reaction
36
concerted inhibition
- multiple products of certain molecule inhibit the enzyme that produces the certain molecule
37
sequential feedback inhibition
- inhibition of multiple steps in synthesis by product
38
interlocking regulatory system
- combinations of both sequential feedback system and concerted inhibition interlocking with one another
39
biomolecules derived from amino acids
- GABA, nitric oxide, histamine, catecholamine, melanin, serotonin, and nicotinic acid
40
alanine synthesis
- aminotransferase catalyzes reaction of pyruvate to alanine
41
aspartate synthesis
- aminotransferase catalyzes reaction of oxaloacetate to aspartate
42
asparagine synthesis
- asparagine synthetase synthesizes reaction of aspartate to asparagine
- needs ATP and glutamine
- produces glutamate, AMP and PPi
43
glutamate synthesis
- aminotransferase catalyzes reaction of alpha-KG to glutamate
44
glutamine synthesis (4)
- glutamine synthetase catalyzes reaction of glutamate to glutamine
- intermediate: gamma-glutamylphosphate
- consumed: ATP + NH3
- produced: ADP + Pi
45
what is the first reaction in ornithine synthesis? (2)
- glutamate kinase catalyzes reaction of glutamate to gamma-glutamylphosphate
- 1 ATP consumed and 1 ADP produced
46
what is the second reaction in ornithine synthesis? (3)
- glutamate dehydrogenase catalyzes reaction of gamma-glutamylphosphase to glutamate gamma-semialdehyde
- uses NAD(P)H and H+
- produces NAD(P)+ and Pi
47
what is the third reaction in ornithine synthesis? (3)
- ornithine delta-aminotransferase catalyzes reaction of glutamate gamme-semialdehyde to ornithine
- uses glutamate and produces alpha-KG
- transaminase involves amino carbon of delta group
48
ornithine synthesis (enzymes, intermediates, full reaction) (3)
- enzymes: glutamate kinase, glutamate dehydrogenase, and ornithine delta-aminotransferase
- intermediates: gamma-glutamylphosphate and glutamate gamme-semialdehyde
- 2 glutamate + ATP + NAD(P)H + H+ -> ornithine + ADP + NAD(P)+ + Pi + alpha-KG
49
arginine synthesis (3)
- enzymes: ornithine carbamoyl-transferase, argininosuccinate synthetase, argininosuccinate
- intermediates: citrulline, argininosuccinate
- ornithine + carbamoylphosphate + aspartate + ATP -> arginine + Pi + AMP + PPi + fumerate
50
serine synthesis (general formula and reaction types) (2)
- 3-phosphoglycerate + NAD+ + glutamate -> serine + NADH + alpha-KG + Pi
- 3 reactions: oxidation, transamination, loss of phosphate group
51
what is the net energy used for serine/glycine metabolic pathways
- exergonic pathway: energy is produced in form of reduced NADH and does not require energy input
52
glycine synthesis (2)
- serine hydroxymethyl-transferase catalyzes reaction of serine to glycine
- produces H2O
53
cystein synthesis (2)
- serine + homocysteine -> cystathionine + H2O -> alpha-KG + cysteine + NH3
- sulfur donor: S-Adenosylmethionine (SAM)
54
tyrosine synthesis (3)
- phenylalanine hydroxylase catalyzes reaction of phenylalanine to tyrosine
- uses O2, NADH, H+
- produces NAD+ and H2O
55
chorismate synthesis (3)
- 2 PEP + erythrose 4-phosphate -> chorismate
- uses NADPH, H+ and ATP
- produces NADP+, ADP, H2O, 2 Pi
56
tyrosine synthesis (from chorismate) (2)
- chorismate -> prephenate -> 4-hydroxyphenyl-pyruvate -> tyrosine
- last reaction: aminotransferase with glutmate -> alpha-KG
57
phenylalanine synthesis (2)
- chorismate -> prephenate -> phenypyruvate -> phenylalanine
| - last reaction: aminotransferase with glutmate -> alpha-KG
