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Biochemistry 2300 > Lectures 27/28: Amino Acid Metabolism > Flashcards

Lectures 27/28: Amino Acid Metabolism Flashcards

1
Q

Nitrogen

A

Essential element found in amino acids, nitrogenous bases and many other molecules
Biologically available nitrogen is scarce

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2
Q

Nitrogen Fixation

A

Reduction of N2 by prokaryotic microorganisms to form NH3
Often rate limiting factor in plant growth
High energy requirement
Nitrogen often rate limiting factor in plant growth
Conversion into amide group of glutamine
Catalyzed by nitrogenase complex

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3
Q

Free-living cyanobacteria

A

Most prominent nitrogen-fixing species

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4
Q

Symbiotic bacteria

A

Most prominent nitrogen-fixing species

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5
Q

Nitrogen assimilation

A

Incorporation of inorganic nitrogen compounds into organic molecules
Roots in plants
NH4+ or NO3- incorporated into amino acids

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6
Q

NO3

A

As nitrogen source, two step reaction is used to convert it to NH4+ by nitrite reductase

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7
Q

Glutamine synthetase

A

Catalyzes ATP-dependent reaction of glutamate with NH4+ to form glutamate
Found in all organisms
Entry point in microorganisms for fixed nitrogen
Uses ATP
Glutamate + ammonium to glutamine: formation of irreversible amide bond

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8
Q

Phytoplankton bloom

A

Can trigger dead zone formation
Decomposition carried out by aerobic bacteria: increased oxygen use by bacteria, O2 levels drop, hypoxic conditions for fish

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9
Q

Glutamate synthase

A

Produces glutamate from glutamine and alpha-ketoglutarate
Only bacteria and plants
Together with glutamine synthase leads to assimilation
Does not use ATP
2 Glutamate yield: Can enter glutamine synthetase reaction
Only in plants and microorganisms

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10
Q

Glutamine

A

Acts as amino group carrier

Synthesis in peripheral tissues and transport to liver also transports amino groups

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11
Q

Amino acids

A

Protein monomeric units
Energy metabolites: can be converted into pyruvate, oxaloacetate, or TCA intermediates
Some can only be converted into acetyl CoA, ketone bodies or fatty acids
Precursors for many biologically active nitrogen-containing compounds
Signalling molecules
Essential and non-essential

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12
Q

Essential amino acids

A

Must be taken up with diet

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13
Q

Non-essential amino acids

A

Can be synthesized by body

Plants and microorganisms have enzymes for the synthesis of all 20 amino acids

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14
Q

Transamination

A

Catalyzed by aminotransferase (transaminase)

Reaction with alpha-ketoacid to yield another amino acid and alpha-ketoglutarate

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15
Q

Transaminase

A

All have pyridoxal phosphates as prothetic group

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16
Q

Pyritical phosphate

A

Derived from pyridoxine VitB6

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17
Q

Aspartate aminotransferase

A

alpha-ketoglutarate + aspartate = glutamate + oxaloacetate

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18
Q

Malate-Asparate shuttle

A

Relies on transamination of aspartate and oxaloacetate
Indirectly transfers NADH into mitochondrial matrix
Malate in exchange for KG, Asp in exchange for Glu

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19
Q

Amination/deamination

A

Catalyzed by glutamate dehydrogenase in mitochondrial matrix
Degradation of amino acid to give KG: reversible
Direction determined by reactant concentrations

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20
Q

Amidation

A

Formation of amide bond: irreversible
Glutamine synthetase converts glutamate + NH4+ to glutamine
Costs ATP

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21
Q

Deamidation

A

Catalyzed by glutaminase
Conversion of glutamine to glutamate
Reverse of glutamine syntheses reaction

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22
Q

Amino acid synthesis

A

Animals synthesize from intermediates of glycolysis and citric acid cycle
Bacteria and plants synthesize with sulfur, branched chains, aromatic groups, histidine, lysine and threonine

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23
Q

Cysteine synthesis

A

Can be made from methionine

Not sufficient: essential aa

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24
Q

Glutamate formation

A

From KG by reductive lamination or transamination

Neurotransmitter in brain: conversion to glutamine prevents overstimulation and neurotoxicity

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25
Q

Glutamine-glutamate shuttle

A

In brain
Neurons secrete glutamate as NT: too much extracellular is toxic
Astrocytes (surrounding neutrons) take up glutamate and convert it to glutamine
Glutamine is secreted and taken up by neurons and converted back

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26
Q

Aspartate

A

Synthesized from oxaloacetate by transamination

Asparagine, methionine, threonine, lysine and isoleucine are synthesized from aspartate

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27
Q

Asparagine synthetase

A

Synthesizes aspartate into asparagine

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28
Q

Serine

A

Derives carbon skeleton from glycolytic intermediate 3-phosphoglycerate
Served from 3-phosphoglycerate via dehydration, transamination and hydrolysis
Precursor for sphingolipids and phospatidylserine
Enantiomer D-serine is neuromodulator

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29
Q

Glycine

A

Hydromethyl group transfer reaction from serine

Neurotransmitter

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30
Q

Cysteine

A

Serine plus sulphur group from another amino acid
Thiol group is redox active
Precursor for glutathione

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31
Q

Glutathione

A

Antioxidant
Tripeptide of glutamate of cysteine and glycine
Cysteine is lease abundant: supply is rate limiting
reacts with peroxide to give non-reactive thiols
GSSG in oxidized form

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32
Q

One-Carbon metabolism

A

Describes metabolic pathways that are connected to reactions involving the transfer of single carbons: methyl groups of different oxygen states equivalent of methanol, formaldehyde and formate
Includes folate metabolism, methylation cycle and transsulfuration
Most important carriers of 1-C groups: folic acid and S-adenosylmethionine

33
Q

Folic Acid

A 
B vitamin (B9)
Once absorbed by the body, converted to tetrahydrofolate (THF)
One of most important carriers of 1-C groups
Very important during development
Decreased prevalence of neural tube defects following folate fortification of flour
34
Q

S-adenosylmethionine

A

Derivative methionine

One of most important carriers of 1-C groups

35
Q

Tetrahydrofolate

A

Synthesized from folic acid/folate/vitamin B9, requires NADPH
Carrier of 1-C units in several reactions of amino acids and nucleotide metabolism: carrier of methyl groups in different oxidation states
Accepts methyl group from serine to convert serine to glycine

36
Q

Serine hydroxymethyltransferase

A

Catalyzes transfer of methyl-group from serine to tetrahydrofolate to convert serine to glycine

37
Q

Folate metabolism

A

Required for serine to indirectly supply methyl groups for methionine synthesis, B6 and B12 are also required
Methylation requires 3 phosphates

38
Q

Methionine synthase

A

Works with B12

Synthesizes methionine from homocysteine by taking methyl group from 5-methyl-THF to convert it to THF

39
Q

Methionine

A

Converted from homocysteine by accepting methyl group from 5-methyl-THF
Converted into S-adenosyl-methionine by using 3 phosphates

40
Q

S-adenosyl-methionine

A

Converted from methionine

Methylated into S-adenosyl-homocysteine

41
Q

S-adenosyl-homocysteine

A

Addition of H2O and release of adenosine to give homocysteine

42
Q

DNA methylation

A

Methylation of cytosine to 5-methyl cytosine
Catalyzed by DNA transferases
Regulates transcription without changes in DNA sequence

43
Q

Epigenetics

A

DNA methylation

44
Q

Importance of methylation reactions

A

DNA methylation (epigenetic)
Phosphatidylcholine synthesis (from phosphatidylethanolamine)
Thymidine synthesis (dTMP from dUMP)
Purine synthesis
Synthesis of carnitine, creatine, epinephrine and other products

45
Q

Amino acids and signalling molecules

A

Glutamate and glycine as neurotransmitters
Other neurotransmittedrs/neuromodulators derived form amino acids
Catecholamines
Nitric oxide

46
Q

GABA

A

NT derived from glutamate

47
Q

Dopamine

A

From tyrosine

48
Q

Serotonin

A

From tryptophan

49
Q

Melatonin

A

From tryptophan

50
Q

D-Serine

A

NT

By racemizaton of L-serine

51
Q

D-aspartate

A

NT

By racemizaton of L-aspartate

52
Q

Catecholamines

A

Epinephrine, norepinephrine, dopamine

Derivatives of tyrosine

53
Q

Nitric Oxide

A

From precursor arginine

54
Q

Nitric oxide synthase

A

Reacts with arginine and NADPH and oxygen to citrulline, NO, NADP+ and water

55
Q

Purine synthesis

A

AMP and GMP
Requires glutamine, glycine, aspartate, bicarbonate and methyl groups
ATP promotes GMP synthesis
GTP promotes AMP synthesis: two purine will be present in roughly equal amounts

56
Q

Pyrimidine synthesis

A

UMP and CMP
Requires glutamine, aspartate, bicarbonate
dUMP is methylated to generate dTMP
CTP inhibits pyrimidine synthesis (negative feedback)
ATP is feedforward activator for pyrimidine synthesis

57
Q

Deoxyribonucleotide synthesis

A

ATP, GTP, CTP and UTP are dephosphorylated, then reduced to deoxyribonucleotides by ribonucleotide reductase and phosphorylated again: requires NADPH

58
Q

Ribonucleotide reductase

A

Reduces dephosphorylated ATP, GTP, CTP and UTP to deoxyribonuceotides
Two regulatory sites: 1 to regulate overall activity, and one to regulate substrate specificity (overall synthesis and relative amount of the different dNTP)
Activated by ATP
dATP decreases activity
Binding of purine ATP: reductase prefers pyrimidines
Binding of pyrimidine dTTP: reductase prefers purine GDP

59
Q

Protein degradation

A

By proteasome or lysosomal proteases
Each protein has a biological half-life
Most amino acids are degraded to precursors for gluconeogenesis: carbon skeleton of amino acids resemble energy metabolites and can be oxidized for energy

60
Q

Lysosomes

A

Internal vesicular organelles that have very low pH
Contain many different proteases
Usually takes place after endocytosis of extracellular and membrane material
Intracellular material and whole organelles can also be packaged into large double-membrane vesicles which fuse with lysosomes for degradation: autophagy

61
Q

Autophagy

A

Intracellular material and whole organelles can be packaged into large double-membrane vesicles which fuse with lysosomes for degradation

62
Q

Proteasomal degradation

A

Breaks down single proteins
Proteins are tagged with small 76aa protein ubiquitin and degraded by large multi protein complex proteasome
Important quality control mechanism: breaks down misfiled and damaged proteins

63
Q

Both glycogenic and ketogenic amino aicds

A 
Isoleucine
Phenylalanine
Threonine
Tryptophan
Tyrosine
64
Q

Ketogenic amino acids

A

Leucine

Lysine

65
Q

Branched chain amino acids catabolism

A

First two steps for all are transamination and decarboxylation
BCKD

66
Q

Maple Urine Syrup Disease

A

Caused by defects in BCKD

67
Q

Degradation of aa carbon skeleton

A

Carbon skeleton of glycogenic amino acids are used for pyruvate of TCA cycle intermediates: useful for anaplerosis and glucogneogenesis
Of ketogenic amino acids: converted to acetyl-CoA energy substrate but not for gluconeogenesis or anapldrotic reactions

68
Q

Negative N balance

A

Nin less than Nout
Starvation
Serious illness
Insufficient essential amino acids

69
Q

Postitive N balance

A

Nin less than Nout
Growth
Pregnancy
Recovery illness or starvation

70
Q

Excretion of excess nitrogen

A

Amino acid transamination does not eliminate nitrogen form the body
Some reactions set free ammonium, which can be directly eliminated form the body
High ammonium concentrations are cytotoxic (especially for the brain)
Terrestrial animal secrete nearly 80% excess N as urea
Some eliminated as ammonium salts or uric acid
Purines are broken down to uric acid

71
Q

Lysine

A

Only amino acid that cannot be transaminated

72
Q

Urea

A

Highly water soluble
Non-Toxic
pH neutral
Eliminates two amino groups per molecule urea
Highly efficient nitrogen disposal
Terrestrial animal secrete nearly 80% excess N as urea
Direct precursor is arginine

73
Q

Arginine

A

Direct precursor of urea

Intermediate in urea cycle

74
Q

Direct substrates of urea cycle

A

Aspartate and carbamoyl phosphate

75
Q

Products of urea cycle

A

Urea and fumarate

Fumarate is covered to oxaloacetate through TCA cycle reactions

76
Q

Carbamoyl phosphate synthesis

A

Investment of energy to generate a transferable amino group

Controls urea production

77
Q

Carbamoyl phosphate synthetase

A

Controls the urea cycle and is activated by N-acetylglutamate: controls urea production

78
Q

N-acetylglutamate

A

Allosteric activator

Formed when degradation of amino acids lead to high concentration of acetyl-CoA and glutamate

79
Q

Urea

A

Formed from cyclic pathway in liver
Intermediates are not used up
One amino group stamps from ammonia, one from aspartate, carbon comes from bicarbonate
Enters blood stream and is filtered out by kidney into urine: requires large quantities of water to be excreted

Biochemistry 2300 (10 decks)

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