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MC Biochem 2 > Amino Acid Synthesis > Flashcards

Amino Acid Synthesis Flashcards

1
Q

What is the source of nitrogen for amino acid synthesis?

A

Atmospheric Nitrogen (N2)

  • abundant- 80%
  • Triple Bond is very strong-extrememly unreactive
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2
Q

Sources of Nitrogen Fixation

A

1) 60% Diazotrophic (nitrogen fixing) microorganisms
- Rhizobium Bacteria
2) 15% lighting and UV light
3) 25% commercial process
- habers process
- N2 + 3H2-> 2NH3
- requires 300 atm, 500 Degrees F, Iron Catalyst

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3
Q

Nitrogen Fixation by Rhizobium Bacteria

-Nitrogenase complex

A

Nitrogenase complex

1) reductase
- Provides 8e- from reduced ferredoxin with high reducing potential
- ATP hydrolysis used to transfer e- to nitrogenase (2ATP/ e-)
2) Nitrogenase
- uses electrons provided by reductase to reduce N2 to NH3+

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4
Q

Rhizobium Bacteria: Reductase structure

A

AKA

  • iron proteins
  • Fe protein

Dimer of identical subunits

1) 4Fe-4S cluster
- bridges subunits
- transfers E- ONE AT A TIME to Nitrogenase
2) each subunit contains ATP Binding domain (Ploop)

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5
Q

Rhizobium Bacteria: Nitrogenase Structure

A

AKA:

  • Molybdenum-iron protein
  • MoFe protein
A2B2 Tetramer
1)FeMe Cofactor
-uses electrons from P cluster to reduce N2 to NH3
-2 M-3Fe-3S custers
M=Mo in one cluter
M= Fe in other cluster
*organization unique to nitrogenase
2) P cluster
-stores e- before transfer and use by FeMo

This ENYZME STILL A SUBJECT OF ACTIVE RESEARCH

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6
Q

Source Of Component for Amino Acid Synthesis?

A

Nitrogen:
-Glutamate from Ammonia

Carbon Skeleton:

  • Pyruvate
  • Acetoacetyl CoA
  • Acetyl CoA
  • OAA
  • Fumurate
  • Succinyl CoA
  • A-ketogluterate
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7
Q

Humans can synthesize the 11 nonessential amino acids. What are they?

A

Alanine, Arginine, Asparagine, Aspartate
Glutamate, Glycine, Glutamine
Cysteine, Serine, Tyrosine
Proline

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8
Q

Glutamate Dehydrogenase

A

Assimilates Ammonium Ion (NH4+) into Glutamate (two step process)
-Transamination of alpha amino group nitrogen of glutamate provides (most) amino acids with alpha amino group

Mechanism:

1) Schiff Base between ammonia and carbonyl of a-ketogluterate
- replace C=O with C=NH2+, and releases H2O
2) Protonated Schiff Base is reduced by transfer of hydride from NADPH

Estabilishes stereochemistry

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9
Q

Common Feature of amino acid synthesis

A

Formation of Schiff Base followed by protonation and reduction

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10
Q

Synthesis of Glutamine

A

Glutamine Synthetase
Amidation of R group of glutamate produces glutamine

Precursor-Glutamate
Activated by:Phosphorylation-Phosphate added to R group carboxylic acid
-Phosphate is displaced by NH3+ to form Glutamine

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11
Q

Synthesis of Aspartate

A

Aspartate Transaminase
-synthesized from a-ketoacids in one step by PYRIDOXAL PHOSPHATE-dependent transaminases

Precursor-OAA
OAA + Glutamate -> Aspartate + a-ketogluterate

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12
Q

Synthesis of Alanine

A

Alanine Transaminase
-synthesizes from a-ketoacids in one step by Pyridoxal Phosphate-dependent transmaminases

Precursor: Pyruvate
Pyruvate + Glutamate -> Alanine + a-ketogluterate

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13
Q

Synthesis of Asparagine

A

Asparagine Synthetase

Precursor: Aspartate
Activation- Adenylation
-Asparate adenylated to form Acyl Adenylate intermediate
-Glutamine provides NH3+ which displaces AMP to form Asparagine

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14
Q

Synthesis of Proline

A

Multiple Steps
Precursor: Glutamate
Activated- Phosphorylation
-Acyl-Phosphate Int is reduced to Glutamic Y-semialdehyde at the expense of NADPH to NADP+
-Glutamic Y-Semialdehyde dehydrated(No enzymatic reaction-spontaneous) then reduced to Proline at the expense of NADPH to NADP+

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15
Q

Synthesis of Arginine

A

Multiple Steps
Precursor: Glutamate
Activated- Phosphorylation
-Acyl Phosphorylate Intermediate is reduced to Glutamic y-semialdehyde at the expense of NADPH to NADP+\
-Glutamate transfers amino group to Glutamic Y-semialdehyde to form Ornithine
-Ornithine enters Urea Cycle-> Arginine

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16
Q

Synthesis of Serine

A

Multiple steps
Precursor: 3-Phosphoglycerate
-3-PG oxidized to 3-phosphohydroxypyruvate at the expense of NAD+ to NADH
-Glutamate transfers Amino group to 3-phosphohydroxylpyruvate forming a-ketogluterate + 3-Phosphoserine
-3-phosphoserine is hydrolyzed displacing the Phosphate with OH to produce Serine

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17
Q

Synthesis of Glycine

A

2 Pathways

1)Serine hydroxymethyl transferase
-reversing this enzyme can be used to produce serine from glycine
-allows one carbon units to be synthesized from carbohydrates
Precursor- Serine

Serine + THF -> glycine + methylenetetrahydrofolate + H2O

2)Serine Synthase (glycine cleavage enzyme)
Precursor: NH4 + CO2
NH4 + CO2 + N5,N10methyleneTHF + NADH-> GLYCINE + THF + NAD+

18
Q

THF

A

tetrahydrofolate=COFACTOR
Carries activated one carbon units
-one carbon units attach to N5 or N10 or both
-one carbon units are interconvertible while attached to THF

Humans unable to synthesize
-obtained from diet or intestinal microorganisms

19
Q

SAM

A

S-Adenosylmethionine

Methyl Group donor as part of activated methyl Cycle

  • Synthesized from Met and ATP
  • Methyl group is activated due to + charge on sulfur

ALL 3 phosphates are lost
-hydrolyzed into Pi (orthophosphate) and PPi (pyrophosphate)-> further hydrolyzed to 2Pi

20
Q

Activated Methyl Cycle

A

Regenerates Methionine from homocysteine

1) Methionine + ATP-> S-adenoysl Methionine (SAM)
2) SAM releases Activated CH3 to form S-adenosyl Homocysteine
3) S-Adenosyl Homocysteine is hydrolyzed to form homocysteine+ adenosine
4) Homocysteine is methylated (-CH3)-> Methionine
- catalyzed by Methionine synthase (aka homocysteine methyl transferase)
- N5-methyl THF-> THF
- requires Methylcobalamin derived from Vit B12

21
Q

Synthesis of Cysteine

A

2 steps:
Precursor: Serine and Homocysteine
1)Cystathionine B-Synthase
Homocysteine + Serine-> Cystathionine + H2O
-Ser R group attaches to Sulfur and loses O

2)Cystathioninase
Cystathionine hydrolyzed to NH4+ + a-ketobutyrate + CYSTEINE

22
Q

Synthesis of Tyrosine

A

Phenylalanine Hydroxylase (monooxygenase)
Precursor: Phenylalanine
Phe + O2+ tetrahydrobiopterin-> Tyr + H2O + quinoid dihydrobiopterin
-Hydroxylates

-in humans Phe is essential if Phe is not present then tyrosine becomes essential

23
Q

Synthesis of Amino Acids that are essential in humans are found in?

A

Plants and bacteria

24
Q

Plant and Bacteria:

-Phenylalanine, tryptophan, Tyrosine synthesis

A

Bacteria: substrates

  • Phophoenolpyruvate from glycolysis
  • erythrose 4-Phosphate from Pentose phosphate pathway

Intermediates

  • Shikimate after phosphorylation can be inhibited by Glyphosate (round up)
  • Chorismate-common intermediate for aromatic aa **
25
Q

Substrate channeling

A

Indole is hydrophobic and would diffuse out of cell thus use Substrate channeling:

  • Substrate goes through channel and is passed from active site to active site until released
  • speeds up rate of synthesis
26
Q

Chirality of Amino Acids

-all aminotransferases contain 2 conserved amino acids?

A

Lysine that forms the Schiff base with PLP

-Arginine that interacts with alpha-carboxylate group of the ketoacid

27
Q

Methionine Synthase

A

AKA homocysteine methyltransferase

  • requires methylCobalamin derived from Vit B12
  • this enzyme exists in some organisms that doesn’t require methylcobalamin

Homocysteine is methylated by N5,methyl THF-> methionine + THF

28
Q

PRPP

A

activated form of ribose

29
Q

Negative Nitrogen Balance

A

Deficiency of even one amino acid leads to this

More proteins degraded then synthesized, and more nitrogen is excreted then ingested

30
Q

What do all aminotransferases contain?

A
  • Lysine that forms Schiff base with PLP

- Arginine that interacts with alpha carboxylate group of the ketoacid

31
Q

Glutathione

A

Sulfhydryl Buffer and Antioxidant that protects us from Reactive Oxygen Species (ROS)

Structure- Tripeptide w/Sulfhydryl ECG
-Glutamate R group attaches to Cysteins N displace O-

GSH-> GSSG
Glutathione reductase
-Uses NADPH to reduce GSSG to GSH
-Prosthetic group-FAD

Glutathione Peroxidase
Reduces hydrogen peroxide to water
Selenium (Se) replaces Sulfur in R group of cysteine active site
-E-Se-(selenolate) reduces peroxide to hydroxyl while being oxidized to to an acid E-S-OH (Seleninic acid)
-E-S-OH is then reduced by GSH which is oxidized to GSSG
-GSSG then reduced by NADPH to NADP+

32
Q

Nitric Oxide

A

Second messenger in signal transduction pathway

  • synthesized from Arginine, NADPH, and O2
  • enzyme is another reason why animals must inhale O2

Nitric Oxide Synthase

1) Arginine ->N-w-hydroxyarginine
- O2 (monooxygenase)-> H2O
- NADPH to NADP+
2) N-w-Hydroxyarginine-> Citrulline + NO
- O2-> H2O (monooxygenase)
- NADPH- to NADP+

33
Q

Porphyrins

-no mechanism just general info

A

used to synthesize heme

  • synthesized from Succinyl CoA and glycine
  • cyclic compounds that readily bind iron
34
Q

Where does Heme Synthesis occur?

-Compartmentalization?

A

Cellular Localization

  • Mitochondria
  • Cytoplasm

Organ Localization

  • Liver=variable rate
  • Erythrocytes producing cells of bone marrow: constant rate
35
Q

S-aminolevulinate Synthase

A

1) S-aminolevulinate Synthase
Gly + Succinyl CoA -> S-aminolevulinate (ALA or S-aminlevulinic acid)
-Amino Group of Glycine attaches to Carbonyl of Succinyl CoA
-releases CoA and CO2
-occurs in matrix of mitochondria

8 S-aminoleveulinate is required to synthesize one heme

36
Q

S-aminolevulinic dehydratase

A

S-aminolevulinic (x8)-> (x4) Porphobilinogen

  • occurs in cytosol
  • two molecule are joined to form porphobilinogen

*Lead inhibits causing the anemia associated with lead poisoning

37
Q

Hydroxymethylbilane synthase

A

-links 4 porphobilinogen molecules to form linear tetrapyrole

38
Q

What are the last 3 steps in Porphyrin synthesis

A

Uroporphyrinogen III synthase

  • cytosol
  • cyclized linear tetra pyrrole to form ring

Uroporphyrinogen carboxylase

  • cytosol
  • produce coproporphyrinogen III has methyl instead of A group

Coproporphyrinogen-> Protoporphyrin IX

  • matrix of mitochondria via multiple steps
  • Fe added is final step to form HEME
39
Q

Ferritin

A

Iron storage protein

40
Q

Transferrin

A

Iron transport protein

41
Q

Ferrochelatase

A

enhances rate of addition of iron (Fe2+) to protoporphyrin IX
-this may occur without enzyme as well

42
Q

Degradation of Heme

A

1) Heme-> Biliverdin
- O2-> H2O (monooxygnease)
- releases Fe3+
- NADPH-> NADP+

2) Biliverdin-> Bilirubin
- Biliverdin reductase
- NADPH to NADP+

MC Biochem 2 (31 decks)

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