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Biochem 2 > Lectures 15-16 - Amino acids > Flashcards

Lectures 15-16 - Amino acids Flashcards

1
Q

5 circumstances for amino acid catabolism

A
  1. carnivores vs herbivores
    - carnivores consume primarily protein and obtain most of their energy from aa vs only small fraction of E needs of herbivores are met by aa –> plants rarely use aa as fuel source but can degrade aa to form other metabolites
  2. normal protein synthesis and degradation
  3. surplus aa ingested –> dietary aa that excess body’s protein synthesis needs
  4. starvation
  5. uncontrolled diabetes, tumor, etc –> proteins in body can be broken down to supply aa for E when carbs are unavailable or not properly utilized
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2
Q

can aa be stored?

A

no!

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3
Q

protein digestion in humans
1. mouth
2. stomach (4)
3. small intestine (3)
4. absorption

A
  1. mouth: no digestion
  2. stomach: stimulates gastric mucosa to secrete gastrin hormone –> gastrin stimulates secretion of HCl and pepsinogen –> HCl converts pepsinogen to pepsin –> pepsin cleaves protein into peptides in stomach
  3. small intestine:
    - low acid triggers release of secretin –> secretin released in blood: stimulates pancreas to secrete HCO3- –> bicarbonate neutralizes acidic content
    - duodenum: arrival of aa will cause cholecystokinin (CCK) to stimulate secretion of trypsinogen –> converted to trypsin –> trypsin + chymotrypsin cut proteins and larger peptides into smaller peptides
    - aminopeptidase and carboxypeptidase A and B degrade peptides into aa
  4. absorption of aa –> through epithelial cells –> travel through blood to get to liver
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4
Q

most aa are metabolized where?

A

in liver!

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5
Q

main source of aa? other source?

A
  • main source = dietary protein
  • intracellular proteins
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6
Q

fate of amino acid (2) –> each go through what cycle?
(schéma)

A

aa –> NH4+ and carbon skeleton
1. NH4+ –> reused in biosynthesis of aa, nucleotides and biological amines OR become carbamoyl phosphate –> into urea cycle –> urea (nitrogen excretion product)
2. carbon skeletons –> a-keto acids –> citric acid cycle –> oxidize to become CO2 + H2O + ATP OR become oxaloacetate –> glucose (gluconeogenesis or ketogenesis) OR into aspartate-arginino-succinate shunt cycle of citric acid cycle (connected to urea cycle)

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7
Q

describe transamination reaction of aa

A

NH3+ of L-amino acid added to a-ketoglutarate by amino transferase with pyridoxal phosphate (vit B6) as cofactor –> results in L-glutamate and a-keto acid

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8
Q

4 important aa that play role in recycling of nitrogen/ammonia

A
  • glutamate
  • glutamine
  • alanine
  • aspartate
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9
Q

what molecule is the general amino acceptor?

A

a-ketoglutarate

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10
Q

aminotransferases are specific to what?

A

specific to each amino acids
- ie: alanine aminotransferase

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11
Q

where is the transamination reaction of aa?

A

cytosol of liver

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12
Q

describe deamination reaction
- where does it occur?

A

NH3+ group removed from glutamate by glutamate dehydrogenase, using NAD+ OR NADP+ as cofactor –> results in a-ketoglutarate + NH4+
- NH4+ enters urea cycle
- in mitochondria of liver

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13
Q

a-ketoglutarate used for (3)

A
  • transamination
  • TCA cycle
  • gluconeogenesis
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14
Q

how is glutamate dehydrogenase regulated?

A
  • GTP = negative inhibitor
  • ADP = positive activator
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15
Q

why is there a specific way to transport ammonia transported from other tissues to the liver?
- how? (4 steps)

A
  • free ammonia = toxic –> has to be converted to other compound to travel in body
    1. L glutamate becomes a-glutamyl-phosphate (or y-glutamyl-phosphate) through glutamine synthetase + ATP
    2. a-glutamyl-phosphate (or y-glutamyl-phosphate) becomes L-glutamine through glutamine synthetase and NH4+ –> in all tissues!
    3. L-glutamine is exported to liver! = non toxic transport form of ammonia from extrahepatic tissues
    4. in liver, ammonia is released when L-glutamine is converted to L-glutamate in mitochondria by glutaminase –> forming glutamate again
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16
Q

how is ammonia transported from muscle to liver? (4 steps)

A
  1. glutamate transfers its amino group to pyruvate using alanine aminotransferase –> produces alanine + a-ketoglutarate
  2. alanine goes to liver through blood
  3. alanine aminotransferase transfers amino group from alanine to a-ketoglutarate to form pyruvate and glutamate
  4. glutamate enters mitochondria for deamination by glutamate dehydrogenase
    4.2 pyruvate used in gluconeogenesis to make glucose
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17
Q

what is the glucose alanine cycle? (6 steps ish)

A
  • in muscle: glucose –> glycolysis to form pyruvate –> pyruvate –> alanine –> blood alanine –> enters liver –> alanine –> pyruvate –> gluconeogenesis to form glucose –> blood glucose –> enters muscle –> glucose –> repeat
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18
Q

where do the 4 steps of urea cycle occur?

A

step 1 in mitochondria of liver cell
- all other 3 steps in cytosol of liver cell

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19
Q

initial + 4 steps of urea cycle

A

initial step (in mitochondria): NH4+ + HCO3- (source of Co2) + 2 ATP –> carbamoyl phosphate, through carbamoyl phosphate synthetase I
1. carbamoyl phosphate enters urea cycle and merges with ornithine, through ornithine transcarbamoylase –> forming citrulline
(other amino group can enter through aspartate –> aspartate formed in mitochondria through transamination of oxaloacetate and glutamate by aspartate aminotransferase)
2. citrulline enters cytosol –> reacts with ATP through arginosuccinate synthetase to form citrullyl-AMP intermediate –> merges with aspartate (source of 2nd amino group) to form argino succinate using arginosuccinate synthetase (or in simpler way: condensation of aspartate and citrulline to form argininosuccinate)
3. argininosuccinate cleaved by argininosuccinase to form arginine and fumarate
4. arginine cleaved to form urea (goes through to kidney and urine) and ornithine (transported to mitochondria to reenter cycle)
4.1 fumarate converted to malate to enter TCA cycle in mitochondria

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20
Q

what are the 2 sources of amino groups in the urea cycle?

A
  1. carbomoyl phosphate
  2. aspartate
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21
Q

expression of urea cycle enzymes increases during (4)

A
  • high protein diet
  • starvation
  • uncontrolled diabetes
  • tumor
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22
Q

how to regulate urea cycle?

A
  • regulation of rate of synthesis of the 4 main enzymes
  • regulation of carbamoyl phosphate synthetase I
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23
Q

what regulates carbamoyl phosphate synthetase I?

A

N-acetylglutamate = activator of carbomoyl phospahte synthetase I
- N-acetylglutamate is formed from acetyl-CoA and glutamate by N-acetylglutamate synthase

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24
Q

urea cycle is activated when (2) are high

A

acetyl-CoA and glutamate

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25
Q

which 2 enzymes have both cytosolic and mitochondrial isoforms? (For malate aspartate shuttle)

A

fumarase and malate dehydrogenase

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26
Q

how are urea cycle and TCA cycle interconnected?

A

-arginosuccinate from urea cycle is cleaved to form fumarate and arginine
- fumarate can then be converted to malate in cytosol –> malate moved to mitochondria through malate-aspartate shuttle and used in citric acid cycle
- called aspartate-arginino-succinate shunt of citric acid cycle

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27
Q

what percentage range of human E produced through aa catabolism?

A

10-15%

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28
Q

which 5 aa are both keto and glucogenic?

A
  • isoleucine
  • phenylalanine
  • threonine
  • tryptophan
  • tyrosine
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29
Q

how do you define aa that are ketogenic vs glugogenic?
- what do the aa yield?

A
  • ketogenic: aa yielding acetyl-coa
  • glucogenic: aa yielding other end products like glutamate, succinyl-coa, fumarate, oxaloacetate and pyruvate
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30
Q

which 6 aa can yield pyruvate?

A
  • alanine
  • tryptophan
  • cysteine
  • serine
  • glycine
  • threonine
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31
Q

which 7 aa can yield acetyl-coa?

A
  • isoleucine
  • phenylalanine
  • threonine
  • tryptophan
  • tyrosine
  • lysine (only ketogenic)
  • leucine (only ketogenic)
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32
Q

which 2 aa are only ketogenic?

A

lysine and leucine

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33
Q

which 5 aa yield a-ketoglutarate?

A
  • proline
  • histidine
  • arginine
  • glutamate
  • glutamine
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34
Q

which 4 aa yield succinyl-CoA?

A
  • methionine
  • isoleucine
  • threonine
  • valine
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35
Q

which 2 aa yield oxaloacetate?

A
  • asparagine
  • aspartate
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36
Q

which 2 aa yield fumarate?

A
  • phenylalanine
  • tyrosine
37
Q

which 3 aa are used as fuel in muscle, adipose, brain?
- why?

A
  • leucine
  • isoleucine
  • valine
  • because branched-chain aminotransferase (produce a-keto-acid) is only expressed in extra-hepatic tissues –> absent in liver
38
Q

all 4 enzymes of urea cycle and carbamoyl phosphate synthase I are regulated by what?

A

nutritional status (diet and starvation)

39
Q

how is high energy (ATP) used by urea cycle offset?

A

by NADH malate-oxaloacetate conversion reaction (1 NADH = 2.5 ATP) in TCA cycle

40
Q

which steps in complete/general urea cycle need ATP? how many?

A
  • carbamoyl phosphate synthetase I uses 2 ATP
  • argininosuccinate synthetase uses 1 ATP
41
Q

can all aa be derived from intermediates of metabolic pathways?
- which metabolic pathways (3) through which intermediates?

A

yes!
- glycolysis: 3-phosphoglycerate + phosphoenolpyruvate + pyruvate
- citric acid cycle: a-ketoglutarate + oxaloacetate
- pentose phosphate: ribose-5-phosphate + erythrose 4-phosphate

42
Q

how many aa can bacteria, plants and mammals synthesize?

A
  • bacteria and plants: all 20 aa
  • mammals: only 10 aa (non-essential aa)
43
Q

which 2 aa are the source of most amino groups?

A

glutamate and glutamine

44
Q

which 9 aa are essential?

A
  • Valine
  • Phenlyalanine
  • Histidine
  • Leucine
  • Methionine
  • Threonine
  • Isoleucine
  • Tryptophan
  • Lysine
45
Q

what are the 3 non-coding aa?
1. _________ (2 ex)
2. _________ (2 characteristics + present in ?)
3._________ (found in ?)

A
  1. non protein coding (ie: GABA + homocystein)
  2. 21st aa: selenocysteine: it is synthesized on its tRNA + only aa encoded by uGA codon + present in glutathione peroxidase
  3. 22nd aa: pyrrolysine: only found in bacteria
46
Q

what does conditionally essential means?

A

required to some degree in young, growing animals and/or sometimes during illness

47
Q

what are the 6 conditionally essential aa?

A
  • arginine
  • cysteine
  • glutamine
    -glycine
  • proline
  • tyrosine
48
Q

what are the 5 non-essential aa?

A
  • alanine
  • asparagine
  • aspartate
  • glutamate
  • serine
49
Q

which aa can be derived from a-ketogluterate?
- bacteria vs mammals

A

glutamate!
- bacteria: glutamate can form glutamine, proline and arginine
- mammals: glutamine, proline and arginine are conditionally essential bc glutamate can’t form them

50
Q

which aa can be derived from 3-phosphoglycerate?
- bacteria vs mammals

A

serine!
- bacteria: serine can form glycine and cysteine
- mammals: glycine and cysteine are conditionally essential bc serine can’t form them

51
Q

which aa can be derived from oxaloacetate?
- bacteria vs mammals

A

aspartate!
- bacteria: aspartate can form methionine, asparagine, lysine and threonine
- mammals: aspartate can form asparagine! but cannot form methionine, lysine and threonine = essential

52
Q

which aa can be derived from pyruvate?
- bacteria vs mammals

A

alanine = non essential for both bacteria and mammals
- bacteria: also valine, leucine and isoleucine
- mammals: valine, leucine and isoleucine are essential

53
Q

which aa can be derived from phosphoenolpyruvate and erythrose 4-P?
- bacteria vs mammals

A
  • bacteria: phenylalanine, tyrosine and tryptophan
  • mammals: phenylalanine and tryptophan are essential BUT tyrosine can be produced by phenylalanine (conditionally essential)
54
Q

which aa can be derived from ribose 5-P?
- bacteria vs mammals?

A
  • bacteria: histidine!
  • mammals: histidine is essential
55
Q

4 amino acid derivatives

A
  1. phorphyrin rings (heme)
  2. creatine and phosphocreatine
  3. glutathione
  4. neurotransmitters and signaling molecules
56
Q
  • porphyrin makes up what of what?
A
  • heme of hemoglobin
57
Q

which aa can generate heme?
- bacteria/plants vs mammals?

A
  • mammals: glycine
  • plants and bacteria: glutamate
58
Q

4 steps to make heme from glycine/glutamate

A
  1. glycine reacts with succinyl-coA to yield a-amino-b-ketoadipate –> then decarboxylated to d-aminolevulinate
  2. 2 d-aminolevulinate condense to form phorphobilinogen
  3. through series of enzymatic reactions, 4 porphobilinogen come together to form protoporphrin
  4. iron will be incorporated to protoporphyrin to form heme
59
Q

what are the 3 important intermediates in synthesis of porphyrins?

A
  • d-aminolevulinate
  • porphobilinogen
  • protoporphyrin
60
Q

what happens when there is a genetic defect in biosynthesis of porphyrin?

A

accumulation of porphyrin intermediates –> porphyria diseases

61
Q

what is the inhibitor of synthesis of heme?

A

heme acts as negative feedback inhibitor

62
Q

heme from degradation of erythrocytes is degraded to _______ in 2 steps
- 3 colors?

A
  • bilirubin!
  • blue: color of hemoglobin
    1. heme oxygenase linearizes heme to create biliverdin = green compound –> produces CO and Fe2_
    2. biliverdin reductase converts biliverdin (along with NADPH and H+) to bilirubin = yellow compound
63
Q

what are the 2 ways bilirubin (in blood) travels to intestine/bile?

A
  1. travels bound to serum albumin in bloodstream
  2. glucuronyl-bilirubin transferase converts bilirubin to bilirubin diglucuronide –>secreted/transported into small intestine –> becomes bilirubin again
64
Q

what are the 2 fates of bilirubin?

A
  • bacteria in small intestine converts bilirubin to urobilinogen
    1. some urobilinogen transported to kidney –> converted to urobilin = yellow color of urine
    2. if urobilinogen stays in intestine, bacteria converts it to stercobilin = red-brown color of feces
65
Q

what is jaundice?
- results from pathological reason (2)
- and physiological reason?
- treated how?

A
  • jaundice = yellowish pigmentation of skin, whites of eyes, etc.
    pathological reason (usually in adults):
    1. impaired liver (liver cancer, hepatitis)
    2. blocked bile secretion (gallstones, pancreatic cancer)
    physiological reason (usually in newborn):
    1. insufficient glucuronyl bilirubin transferase to process bilirubin (occurs in infants)
  • treated with UV to cause photochemical breakdown of bilirubin into other soluble compounds that can be excreted
66
Q

which 3 aa can synthesize creatine?

A

glycine + arginine + methionine

67
Q

how are is phosphocreatine synthesized? role?

A
  • creatine (from glycine, arginine and methionine) phosphorylated by creatine kinase to phosphocreatine
  • phosphocreatine stores phosphate group for ATP synthesis –> energy buffer for muscular ATP = maintains constant level of ATP during exercise ish until other mechanisms come in
68
Q

2 steps for synthesis of glutathione?

A
  1. glutamate activated by ATP to react with cysteine –> form intermediate (y-glu-cys)
  2. intermediate reacts with glycine to form glutathione (reduced form)
69
Q
  • glutathione is a major __________
  • what converts glutathione to its reduced/oxidized form?
  • role of glytathione?
  • oxidized glutathione linked by what?
A
  • anti-oxidant
  • glutathione peroxidase converts reduced glutathione (GSH) to oxidized form (GSSG)
  • prevents oxidative damage
70
Q

4 aa yield different neurotransmitters
1. _________ –> Dopamine, epinephrine and norepinephrine + under/overproduction of 1st one + fct of 2nd and 3rd
2. _______ –> GABA + 2 fcts + underproduction?
3. _______ –> histamine + 4 fcts
4. _________ –> serotonin –> 2 fcts

A
  1. tyrosine –> dopamine + norepinephrine + epinephrine
    - dopamine: underproduction = parkinson’s disease –> treated with L-dopa VS overproduction = schizophrenia
    - norepinephrine + epinephrine –> flight-fight
  2. glutamate –> y-aminobutyrate (GABA)
    - main inhibitory signal in central nervous system
    - needed for muscle tone
    - underproduction = epileptic seizures –> treated with GABA analogs
  3. histidine –> histamine
    - released during allergic rcn
    - stimulates HCl secretion in stomach
    - powerful visodilator
    - histamine receptor antagonist –> treatment of duodenal ulcers
  4. tryptophan –> serotonin
    - regulates intestinal movement
    - feel-good hormone
71
Q

why are nucleotides important (5)

A
  1. precursors of nucleic acids DNA and RNA
  2. carriers of energy (ATP and GTP)
  3. components of cofactors (NAD, FAD, CoA)
  4. initiators of glycogenesis (component of UDP glucose)
  5. second messengers cAMP, cGMP
72
Q

difference btw nucleosides, nucleotides and nucleic acids?

A
  • nucleoside = nitrogenous base + pentose sugar
  • nucleotide = nitrogenous base + pentose sugar + 1 or more phosphate group
  • nucleic acid: sequence of nucleotides
73
Q

what are the 2 types of nitrogenous base?
- characteristic?
- examples

A
  1. purine molecule –> 2 carbon-nitrogen rings
    - guanine and adenine
  2. pyrimidine molecule –> 1 carbon-nitrogen ring
    - cytosine, thymine and uracil
74
Q

how are nucleotides attached to each other in nucleic acids?

A

phosphate group links carbon 3 of pentose sugar with carbon 5 of other pentose sugar

75
Q

2 pathways for nucleotide synthesis? explain

A
  1. de novo pathway: uses metabolic precursors (aa, ribose-5-phosphate, CO2 and NH3)
  2. salvage pathway: purine/pyrimidine bases released from degradation of molecules
76
Q

are purine and pyrimidines synthesized as independent molecules like glucose or FA? explain

A

no!
- purine rings are build up on ribose phosphate
- pyrimidine ring is first synthesized as orotate and then attached to ribose phosphate

77
Q

are nucleotide pools kept high or low? why?

A

low! so cells must continually synthesize them during nucleic acid synthesis

78
Q

what is an important precursor for nucleotide synthesis? this precursor is synthesized from what?

A
  • 5-phosphoribosyl 1-pyrophosphate (PRPP)
  • synthesized from ribose 5-phosphate
79
Q

which 3 aa are important precursors –> for purine vs pyrimidine?

A
  • glycine for purine
  • aspartate for pyrimidines + source of amino group in purine
  • glutamine = source of amino groups in de novo pathway –> pyrimidine and purine
80
Q

what are adenine and guanine synthesized as?

A
  • as adenosine 5-monophosphate AMP (adenylate)
  • as guanosine 5-monophosphate GMP (Guanylate)
81
Q

de novo synthesis of purines
- 4 steps to form first important intermediate

A
  1. PRPP reacts with glutamine
  2. then purine ring build up from addition of 3 C from glycine
  3. then glutamine donates another amino group
    (2 steps (steps 6 and 7) only in bacteria, not in higher eukaryotes)
  4. then aspartate donates another amino group –> forms inosinate (IMP) = first intermediate with full purine ring
82
Q

how does inosinate form AMP vs GMP?

A
  • insertion of amino group from aspartate to carbon 7 of inosinate –> requires GTP –> forms AMP
    VS
  • inosinate + H2O + NAD+ + glutamine + ATP –> GMP (on 2nd carbon)
83
Q

how is de novo synthesis of purines regulated? (4)

A

overall inhibition:
1. glutamine PRPP amidotransferase is inhibited by IMP, AMP and GMP
2. PRPP synthesis if inhibited by ADP and GDP

Specific inhibition:
1. excess GMP inhibits formation of xanthylate from inosinate by IMP dehydrogenase (blocks formation of GMP)
2. excess AMP inhibits formation of adenylosuccinate from inosinate by adenylosuccinate synthetase (blocks formation of AMP)

84
Q

why is all regulation of de novo synthesis of purines inhibitory?

A

to make sure not too much AMP and GMP are formed –> need to keep at low levels

85
Q

What are pyrimidines C and U synthesized as?

A
  • cytidine 5-monophosphate CMP (cytidylate)
  • uridine 5-monophosphate UMP (Uridylate)
86
Q

Pyrimidines synthesized from what (3)?
how are pyrimidines (UTP and CTP) synthesized? 5 steps

A
  • aspartate + carbamoyl phosphate + PRPP
    1. carbamoyl phosphate reacts with aspartate via cytoplasmic carbamoyl phosphate synthetase II to form 1st intermediate
    2. series of reactions until pyrimidine ring synthesized as orotate (ring part of pyrimidine)
    3. PRPP adds its ribose-5-P side chain to orotate to form orotidylate
    4. orotidylate decarbosylated + phosphorylated to form UTP
    5. glutamine = gives amino group to UTP on carbon 4 to form CTP
87
Q

how are ribonucleotides converted to deoxyribonucleotides?
- what is necessary?
- what action is done?
- 2 pathways?
ENZYMES!!!

A
  • direct reduction of C2 of the ribonucleotide
  • pair of H atoms required for reduction to “deoxy” form are donated by NADPH
  • OH is replaced by H at 2nd carbon of ribose sugar
    1. using glutathione reductase –> NADPH to GSH to glutaredoxin to ribonucleotide reductase –> reduces ribonucleoside to dNDP
    2. using thioredoxin reductase –> NADPH to FADH2 to thioredoxin to ribonucleotide reductase –> reduces ribonucleoside to dNDP
88
Q

how is thymine synthesized?
- only in what form?
(SCHÉMA)
- thymine for DNA or RNA?

A
  • only in deoxynucleotide form
    1. CDP –> dCDP OR UDP –> dUDP by ribonucleotide reductase
    2. dCDP –> dCTP OR dUCP -> dUTP by nucleoside diphosphate kinase
    3. dCTP –> dUTP by deaminase
    4. dUTP –> dUMP by dUTPase
    5. dUMP –> dTMP by thymidylate synthase
  • thymine = for DNA
89
Q

Key step in formation of neurotransmitter from aa?
- requires what cofactor?

A

Amino acid decarboxylation
- requires PLP cofactor!

Biochem 2 (8 decks)

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