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BIOL 302 Part 1 > Amino Acid Anabolism > Flashcards

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)
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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
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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
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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
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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
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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
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7
Q

what is the chemical formula for the rxn of N2 -> NH4+

A
  • N2 + 10H- + 8e- + 16ATP -> 2 NH4+ + 16ADP + 16Pi + H2
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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
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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)
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10
Q

how is oxidized dinitrogenase reductase reduced in N2 -> NH4+ reaction?

A
  • oxidized dinitrogenase reductase is reduced by interaction with ferrodoxin/flavodoxin
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11
Q

where does ferrdoxin/flavodoxin obtain its electrons

A
  • from oxidation of pyruvate to acetyl-CoA by pyruvate dehydrogenase
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12
Q

what are the critical entry points of the incorporation of NH4+ into organic molecules (biomolecules) (2)

A
  • glutamate

- glutamine

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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
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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)
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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
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16
Q

what is the significance of glutamine synthetase

A
  • key entry point for reduced nitrogen into metabolic pathways
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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
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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
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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

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20
Q

what are the non-essential amino acids (8)

A
  • alanine
  • asparagine
  • aspartate
  • glutamate
  • glutamine
  • glycine
  • proline
  • serine
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21
Q

what are the semi-essential amino acids (2)

A
  • cysteine (if we eat enough methionine)

- tyrosine (if we eat enough phenylalanine)

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22
Q

essential amino acids (2)

A
  • required in the diet

- humans incapable of forming requisite carbon skeletons

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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
Q

sources of nitrogen

A
  • from glutamine or glutamate
26
Q

where are intermediates that can build amino acids derived from? (3)

A
  • glycolysis, citric acid cycle, pentose phosphate pathway
27
Q

what is arginine required for? (3)

A
  • protein synthesis
  • intermediate precursor of NO and ornithine
  • necessary for creatine synthesis
28
Q

why is arginine a semi-essential amino acid? (2)

A
  • 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
Q

when is arginine supplementation needed?

A
  • special conditions like burn recovery, sepsis, protein malnutrition, urea cycle disorders, excess ammonia production, infection, peritoneal dialysis
30
Q

what are the 4 families of essential amino acids?

A
  • pyruvate family
  • aromatic family
  • aspartate family
  • histidine
31
Q

aromatic family of aromatic amino acids

A
  • phenylalanine, tyrosine, tryptophan

- begins with synthesis of chorismate, an important intermediate for many biosynthetic pathways

32
Q

what are the beginning substrates and what is consumed in synthesis of aromatic amino acids? (2)

A
  • substrates: erythrose 4-phosphate and phosphoenol pyruvate

- consumed: NADPH, H+, 1 ATP for every chorismate formed

33
Q

glyphosphate (2)

A
  • 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
Q

how is amino acid synthesis regulated? (4)

A
  • feedback negative, allosteric inhibition
  • sequential feedback inhibition
  • interlocking regulatory systems
  • concerted inhibition
35
Q

allosteric inhibitor

A
  • binds to a distinct site on the enzyme that is independent of the substrate-binding domain to inhibit the reaction
36
Q

concerted inhibition

A
  • multiple products of certain molecule inhibit the enzyme that produces the certain molecule
37
Q

sequential feedback inhibition

A
  • inhibition of multiple steps in synthesis by product
38
Q

interlocking regulatory system

A
  • combinations of both sequential feedback system and concerted inhibition interlocking with one another
39
Q

biomolecules derived from amino acids

A
  • GABA, nitric oxide, histamine, catecholamine, melanin, serotonin, and nicotinic acid
40
Q

alanine synthesis

A
  • aminotransferase catalyzes reaction of pyruvate to alanine
41
Q

aspartate synthesis

A
  • aminotransferase catalyzes reaction of oxaloacetate to aspartate
42
Q

asparagine synthesis

A
  • asparagine synthetase synthesizes reaction of aspartate to asparagine
  • needs ATP and glutamine
  • produces glutamate, AMP and PPi
43
Q

glutamate synthesis

A
  • aminotransferase catalyzes reaction of alpha-KG to glutamate
44
Q

glutamine synthesis (4)

A
  • glutamine synthetase catalyzes reaction of glutamate to glutamine
  • intermediate: gamma-glutamylphosphate
  • consumed: ATP + NH3
  • produced: ADP + Pi
45
Q

what is the first reaction in ornithine synthesis? (2)

A
  • glutamate kinase catalyzes reaction of glutamate to gamma-glutamylphosphate
  • 1 ATP consumed and 1 ADP produced
46
Q

what is the second reaction in ornithine synthesis? (3)

A
  • glutamate dehydrogenase catalyzes reaction of gamma-glutamylphosphase to glutamate gamma-semialdehyde
  • uses NAD(P)H and H+
  • produces NAD(P)+ and Pi
47
Q

what is the third reaction in ornithine synthesis? (3)

A
  • 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
Q

ornithine synthesis (enzymes, intermediates, full reaction) (3)

A
  • 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
Q

arginine synthesis (3)

A
  • enzymes: ornithine carbamoyl-transferase, argininosuccinate synthetase, argininosuccinate
  • intermediates: citrulline, argininosuccinate
  • ornithine + carbamoylphosphate + aspartate + ATP -> arginine + Pi + AMP + PPi + fumerate
50
Q

serine synthesis (general formula and reaction types) (2)

A
  • 3-phosphoglycerate + NAD+ + glutamate -> serine + NADH + alpha-KG + Pi
  • 3 reactions: oxidation, transamination, loss of phosphate group
51
Q

what is the net energy used for serine/glycine metabolic pathways

A
  • exergonic pathway: energy is produced in form of reduced NADH and does not require energy input
52
Q

glycine synthesis (2)

A
  • serine hydroxymethyl-transferase catalyzes reaction of serine to glycine
  • produces H2O
53
Q

cystein synthesis (2)

A
  • serine + homocysteine -> cystathionine + H2O -> alpha-KG + cysteine + NH3
  • sulfur donor: S-Adenosylmethionine (SAM)
54
Q

tyrosine synthesis (3)

A
  • phenylalanine hydroxylase catalyzes reaction of phenylalanine to tyrosine
  • uses O2, NADH, H+
  • produces NAD+ and H2O
55
Q

chorismate synthesis (3)

A
  • 2 PEP + erythrose 4-phosphate -> chorismate
  • uses NADPH, H+ and ATP
  • produces NADP+, ADP, H2O, 2 Pi
56
Q

tyrosine synthesis (from chorismate) (2)

A
  • chorismate -> prephenate -> 4-hydroxyphenyl-pyruvate -> tyrosine
  • last reaction: aminotransferase with glutmate -> alpha-KG
57
Q

phenylalanine synthesis (2)

A
  • chorismate -> prephenate -> phenypyruvate -> phenylalanine

- last reaction: aminotransferase with glutmate -> alpha-KG

BIOL 302 Part 1 (4 decks)

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