Moore section post midterm Flashcards

1
Q

is there a protein whose sole job is to act as a storage depot for amino acids?

A

nope.

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2
Q

What is the main source for amino acid input to the pool?

A

Cellular protein turnover

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3
Q

What is the weight of proteins recycled in a day due to cellular turnover?

A

300/400g of protein in a day

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4
Q

What are some examples of protein halflife being variable?

A

regulatory proteins degrade in minutes to hours
- collagens or eye lens proteins take months or years

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5
Q

What is the major protein degradation pathway?

A

ubiquitin-proteasome pathway

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6
Q

Give an overview of the ubiquitin proteasome pathway

A

Ubiquitin molecules are linked to a specific lysine residue in the target protein
- protein becomes polyubiquinated which is recognized by the proteosome
- protein is processed into peptides , ubiquitin is cleaved and re utilized.

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7
Q

What links the ubiquitin to the target protein? type of linkage?

A

isopeptide bond - to lysine not amino terminus

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8
Q

Why do we have to degrade proteins to peptides?

A

because they fat as fuck

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9
Q

What is proteolysis?

A

breakdown of protein by hydrolysis, cleavage of proteins by digestive proteinases - enzymes are secreted into stomach and small intestine

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10
Q

What is the benefit of the gastric environment for proteolysis?

A

gastric acid environment denatures proteins and thus enhances proteolysis - due to low pH
- gastric acid also acts as an antiseptic, killing bacteria and viruses

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11
Q

what is the important pump in the stomach?

A

K/H pump in membrane of specialized stomach cells pump protons into the stomach in exchange for K at the expense of ATP hydrolysis - generates acidic environment

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12
Q

What is GERD?

A

gastroesophageal reflux disease
- K/H pump is overactive which results in reflux

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13
Q

what are proteinase zymogens?

A

inactive proteolytic enzymes - activated by proteolysis
- proteinases are synthesized and stored as zymogens so they dont break down proteins in the cells where they are made stored and dont digest themselves prior to secretion

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14
Q

What can pepsin cleave?

A

preferentially cleaves peptide bonds between hydrophobic amino acids or aromatic amino acids

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15
Q

What can trypsin cleave?

A

cleaves bonds following an Arg or Lys residue

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16
Q

What can chymotrypsin cleave?

A

preferentially cleaves peptide bonds after an aromatic amino acid

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17
Q

What can elastase cleave?

A

not as specific - cuts amino acids with smaller hydrophobic side chains such as glycine, alanine or valine

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18
Q

Proteases eventually self _____

A

inactivate - digest themselves

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19
Q

What are endopeptidases?

A

proteolytic enzymes that cleave internal peptide bonds in a substrate

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20
Q

What are aminopeptidases and carboxypeptidases?

A

can only cleave amino or carboxy residue of a peptide - works further down in the intestine - chew up one by one until only amino acids are left

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21
Q

What happens to excess amino acids?

A

not excreted or stored, must be converted to other molecules that can be excreted or repurposed

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22
Q

What is the transamination reaction?

A
  • transfers amino group to aKG
    — donor - L amino acids
    — acceptor - a KG
  • funnels amino groups to glutamate
  • obligatory step in degradation of amino acids except for Lys and Thr
  • Reversible reaction
  • Enzymes - aminotransferases - specific amino group donor and acceptor
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23
Q

What are the two different aminotransferases? And what tissues / cell locations

A

Aspartate aminotransferase - liver mitochondria - see urea cycle
- Alanine aminotransferase - muscle cytosol - muscle amino groups converted to alanine which is transported to liver via blood

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24
Q

What is the ultimate acceptor of donated amino groups - what does this lead to?

A

alpha ketoglutarate - glutamate

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25
Q

what converts glutamate into alphaketoglutarate?

A

mitochondrial glutamate dehydrogenase

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26
Q

What is PLP?

A

Pyridoxal Phosphate - cofactor for transaminases
- amino group acceptor

Pyridoxamine phosphate is an aketo group acceptor

  • bound by default in active site to lys side chain NH3 group
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27
Q

What does the amino group of incoming amino acids do with PLP?

A

forms covalent linkage with aldehyde group - a-keto group leaves

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28
Q

What does the ketone group of incoming a-keto acids do with pyridoxamine phosphate?

A

forms covalent linkage with amino group
- amino group displaves by active site lysine amino group
- glutamate leaves

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29
Q

What is a Schiff base / aldimine?

A

chemical term that defines an imine C—N group derived from an aldehyde

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30
Q

Aminotransferases are important molecules for what?

A

liver or heart damage

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31
Q

What are the fates of glutamate when it enters the mitochondria in the liver/

A

Enters liver - acted on by glutamate dehydrogenase
- some is converted to NH4 and goes to urea cycle
- some is converted back to aKG and goes into TCA cycle

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32
Q

Is NH3 or NH4 odorless?

A

NH4

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33
Q

Go back and look at second lecture of stan

A

yes maam

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34
Q

What are the three ways of removing nitrogen / ammonia?

A

NH4+ - ammonium in aquatic vertebrates and fish
Urea - most terrestrial vertebrates
Uric acid - reptiles and birds

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35
Q

What happens in the urea cycle?

A

converts NH4 to urea
- occurs in liver
- urea is secreted into blood, filtered by kidney and excreted in urine

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36
Q

What are the three precursors of urea?

A

NH4, CO2, Aspartate

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37
Q

What is a major regulation point of urea cycle?

A

Carbamoyl Phosphate Synthetase I
(not actually part of the cycle)

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38
Q

What occurs in step 1 of the urea cycle? forming carbamoyl phosphate?

A
  • Bicarbonate turns into carboxyphosphate using ATP
    -Carboxyphosphate turns into carbamic acid
  • carbamic acid goes to carbamoyl phosphate using ATP
  • effectively NH2, Co2 and phosphate
  • occurs in mito matrix
  • enzyme is CPS1
  • Allostericaly regulated
    -uses 2 ATP
  • N-acetylglutamate is a required allosteric activator
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39
Q

What is N-Acetyl-Glutamate and how is it formed?

A

Required allosteric activator of CPSI
- Acetyl coa plus glutamate
- forms amide bond
- only occurs with excess amino acids in liver

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40
Q

What occurs in step 2 - forming citrulline in the urea cycle?

A
  • formed in mito
  • Ornithine (basically Lys) amide bonds with Carbamoyl phosphate using ornitihine transcarbamoylase
  • makes citrulline
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41
Q

What occurs in step 3 - forming argininosuccinate in the urea cycle?

A

occurs in cytosol so citrulline has to exit mito
- citrulline and aspartate - aspartate is thedonor of the second NH3 group to urea
- uses 1 ATP
- forms arginosuccinate via arginosuccinate synthetase
- also forms L-citrulline intermediate

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42
Q

What happens in step 4 - forming arginine in the urea cycle?

A

Arginosuccinate gets broken down to arginine and fumarate by arginosuccinase
- fumarate goes to TCA
- arginine continues in urea cycle

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43
Q

Do we need arginine in our diet?

A

No, we make enough in the urea cyc;e

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44
Q

What happens in the 5th step, hydrolysis or arginine in the urea cycle?

A

Arginine is converted into ornithine and urea via arginase
- ornithine is regenerated and goes back to the start

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45
Q

How many ATP are used in the urea cycle?

A

3 - 2ATP, one AMP (whatever the activated form is)

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46
Q

What is a common treatment for deficiencies in Urea cycle enzymes?

A

supplement diet with benzoate phenybutyrate
- these molecules can form enzyme catalyzed amide linkages with glycine or glutamine
- can help deplete liver nitrogen eventually lowering ammonia levels in blood

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47
Q

Give a summary of the major sources of free NH4+? 4

A
  1. Major source is dietary and body protein
    - glutamate dehydrogenase activity in liver leads to free NH4 - urea
    - Ser and Thr dehydratase in liver generates NH4- urea
    -glutaminase in liver releases NH4+ - urea
    - Amino groups from other tissues come to liver in the form of alanine and glutamine- nh4 is released by transanimation/glutamate dehydrogenase and glutaminase
  2. Kidney
  3. Amines
  4. purines in pyrimidines
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48
Q

In the liver, free ammonium can also be produced from the breakdown of what two amino acids?

A

Serine and threonine by respective dehydratases
- serine turns to pyruvate + NH4
- threonine turns to aketobutyrate + NH4

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49
Q

Ammonia can be secreted ___ by the kidney

A

Directly - ammonia is generated by the metabolism of glutamate by enzymes glutamate dehydrogenase and glutaminase - secreted in the urine as free ammonium

50
Q

What are the ketogenic amino acids and what do ketogenic amino acids become?

A
  • Iso, Leu, Thr, Trp, Lys, Phe, Tyr
  • becomes acetylCoA or AcetoacetylCoA
51
Q

What do glucogenic aminoacids become?

A

pyruvate
oxaloacetate
aketoglutarate
succinyl coa
fumarate

52
Q

Which two amino acids are ONLY ketogenic?

A

Leucine Lysine

53
Q

What does ketogenic mean?

A

Can make ketone bodies - metabolites its broken down into

54
Q

What are glucogenic amino acids used for?

A

Glucogenic metabolites - will be used to make molecules for glycolysis or atp synthesis

55
Q

Phenylalanine breakdown generates products that are ____ and ____

A

ketogenic and glucogenic
- acetoacetate is ketogenic
- fumarate is glucogenic via gluconeogenesis

56
Q

What are the fates of B branched amino acids + methionine? Why is isoleucine special?

A
  • All can be broken down into propionyl coa which is eventually turned into succinyl coa which is a glucogenic precursor
  • Iso is special because it can also become acetyl coa
57
Q

What does maple syrup urine disease cause?

A

mental deficits and death

58
Q

What are the most common results of amino acid breakdown?

A

aketoglutarate and pyruvate

59
Q

What is phenylketonuria?

A

genetic disorder of phenylalanine metabolism
- caused by defect in phenylalanine hydroxylase that does not work so phenylalanine builds up in the blood
- if not caught early can cause sever mental defects.

60
Q

What is the only way we can synthesize argenine?

A

urea cycle

61
Q

Where does the majority of earths fixed nitrogen come from>

A

60% comes from nitrogen fixing microorganisms like rhizobium

62
Q

Give a brief overview of the biotic nitrogen cycle

A
  • nitrogen is assimilated to biomolecules
  • nitrates are reduced to ammonium
63
Q

what is indirectly required for nitrogen fixation?

A

oxygen - for ATP formation in oxidative phosphorylation

64
Q

Why must nitrogen fixation be done in relatively anoxic conditions?

A

because nitrogenase is very sensitive to inactivation by O2

65
Q

Reductase and nitrogenase are both what kind of proteins?

A

iron sulfur cluster proteins

66
Q

What can glutamate and glutamine both donate in other biosynthetic pathways?

A

can both donate amino groups
- Glutamate - amino for other amino acids through aminotransferase
- Glutamine - source of amino group in many biosynthetic processes

67
Q

What is the primary control point in nitrogen metabolism?

A

glutamine synthetase
- allosteric dodecamer
- controlled by 8 allosteric inhibitors
- can also be covalently modified by adenylating glutamine synthetase which makes the enzyme more responsive to allosteric inhibitors

68
Q

What are some known allosteric regulators of glutamine synthetase?

A

carbamoyl phosphate
alanine
CTP

69
Q

Adenylation of glutamine synthetase occurs on ___

A

a tyr residue
- leads to inactivation

70
Q

What is an example of an amino group transfer reaction?

A

asparagine synthesis - glutamine and asparagine synthetase move the amino group from glutamine onto aspartate to make asparagine

71
Q

All amino acids are built from intermediates of what three pathways?

A
  • glycolysis
  • TCA
  • PPP
72
Q

What are the nonessential amino acids?

A

Alanine
Asparagine
Aspartate
Glutamate
Serine

73
Q

What three amino acids are conditionally essential and why?

A

Arginine, Glutamine and Tyrosine
Why? unsure - go review pg 90 ish in set 3

74
Q

How do we synthesize serine (go check slides)

A

3 phosphoglycerate to 3 phosphohydroxypyruvate to 3 phosphoserine to serine

75
Q

Why is arginine conditionally essential?

A

in newborns, urea cycle cannot compensate for arginine so it is needed in diet

76
Q

Why do we get some amino acids from diet as opposed to synthesizing them?

A

because it is energetically expensive to do so - cheaper to get from diet

77
Q

What is an important reaction in amino acid and nucleotide synthesis?

A

1 carbon transfer reactions using tetrahydrofolate (TH4)

78
Q

What is tetrahydrofolate?

A

single carbon carrier

79
Q

What is serine a precursor for?

A

glycine and cystine

80
Q

What 2 nitrogens do 1 carbon tranfers occur on?

A

N5 and/or N10

81
Q

What is used as the reduction agent for TH4 reactions?

A

NADPH

82
Q

What modification occurs on both N5 and N10?

A

methylene modification

83
Q

What modification only occurs on N5?

A

methyl modification

84
Q

What does TH4 do for amino acid synthesis?

A

acts as a single carbon donor for making certain amino acids?

85
Q

How is methionine synthesized and how is TH4 involved?

A

methionine is synthesized from homocysteine using methionine synthase, it gains a methyl group from N5 methylTH4 and turns the N5 TH4 to just TH4 (coenzyme b12)

86
Q

What does the adenylation of methionine form?

A

S- adenosylmethionine (SAM)

87
Q

What is important about S -adenosylmethionine?

A

methyl donor in many reacitions
- can eventually form homocysteine - which can then be turned back into methionine

88
Q

What type of inhibition regulates amino acid biosynthesis?

A

feedback inhibition
- 3 phosphate dehydrogenase is the first step in serine biosynthesis
- enzyme is allosterically regulated
- domain binds the end product serine
- binding serine lowers vmax and inhibits enzyme
-

89
Q

What amino acid is a precursor for epinephrine?

A

tyrosine but go check

90
Q

What amino acid is a orecursor for serotonin?

A

tryptophan

91
Q

What percent of nucleosides are absorbed for nucleic acid synthesis?

A

only 5%

92
Q

What do 25% of the nucleosides we consume in our diet go towards?

A

rapidly regenerating enterocytes which are specialized intestinal cells

93
Q

What are the three main uses for raw nucleotides?

A
  • precursors of DNA and RNA
    -ATP - energy currency
  • Adenine nucleotides - components of 3 major coenzymes
94
Q

What 3 coenzymes are Adenine nucleotides components of?

A

NAD, FAD, CoA

95
Q

What are four more uses for nucleotides - specific examples

A
  • activated intermediates for many pathways - UDP glucose
  • metabolic and physiologic regulators - cAMP
  • GTP is used by G proteins in signal transduction pathways
  • CTP is used in the biosynthesis of glycerophospholipids
96
Q

Give an overview of the de novo pathway for pyrimidine synthesis

A

bicarbonate and nh3 and 2 atp are used to make carbamoyl phosphate
- joins with aspartate to make the pyrimidine ring
- pyrimidine ring and PRPP (activated ribose) join to make UTP or CTP

97
Q

What is the rate limiting step in pyrimidine synthesis?

A

the synthesis of carbamoyl phosphate

98
Q

What are the differences between carbamoyl phosphate synthetase I and II? Which is used in pyrimidine synthesis?

A

CPS I is used in urea synthesis and is located in the mito matrix
- the N donor is NH4+

CPS II is used in pyrimidine synthesis and is located in the cytosol
- the N donor is Glutamine

99
Q

What is ATCase?

A
  • Aspartate transcarbamoylase
  • allosterically regulated control point in nucleotide synthesis
  • enzyme that changes carbamoyl phosphate into carbamoylaspartate which leads to the end product of CTP
  • allosterically inhibited by CTP (product) and activated y ATP
100
Q

How is the ring closed in carbamoyl aspartate to form ?

A
  • dihydroorotate synthetase forms an amide bond on carbamoylaspartate to close the ring, creating dihydroorotate
  • dihydroorotate loses to H to FMN via dihydroorotate dehydrogenase to form orotate, forming a double bond in the ring
101
Q

you missed nov 29 lecture?

A

yes go back

102
Q

What two chemicals are effective competitive inhibitors of dihydrofolate reductase?

A

methotrexate and aminopterin

103
Q

methotrexate can be used to treat what disorders?

A

arthritis and eczema

104
Q

What does trimethoprim do to dihydrofolate reductase?

A

competitive inhibitor of DHFR, but not in humans, mainly in bacteria and protozoa meaning it can target bacterial infection without damaging humans

105
Q

What does acyclovir do?

A

inhibits biosynthesis of deoxynucleotides in viruses, can be used to treat herpes, chicken pox and shingles
- effectively terminates viral DNA synthesis

106
Q

What does zidovudine do?

A

reverse transcriptase inhibitor which is a nucleoside analog
- used in HIV medication
- cellular enzymes will convert it to the 5’ triphosphate but the azido group on C3 prevents further DNA elongation

107
Q

what happens when a nucleoside monophosphate is added to ATP?

A

will become the nucleoside diphosphate of the specific base and ADP

108
Q

What happens when a nucleoside diphosphate is added to ATP?

A

Will become the nucleotide triphosphate of the specific base and then ADP

109
Q

What are the precursors needed for the de novo pathway of purine synthesis?

A

Ribose 5p. Asp, CO2, Gly, Gln, Formate

110
Q

What molecule acts as the backbone for purine synthesis?

A

ribose 5 phosphate

111
Q

Which N atom is the starting point for purine synthesis?

A

N 9

112
Q

What is the first step in purine synthesis?

A

Adding ammonia to C1 of ribose 5p
- glutamate is the origin of the amino group
- does not require ATP bc good leaving group
- product is very unstable so next reaction must happen quickly

113
Q

What is the second step in denovo synthesis of purines?

A

glycine comes in and tons of complicated shit happens

114
Q

turning inosinate (IMP) to AMP and GMP requires what?

A

GMP - requires ATP and aspartate
AMP - requires GTP and Gln

115
Q

What inhibitors are used in the split pathway after making IMP in purine synthesis?

A

AMP inhibits AMP synthesis
IMP inhibits IMP synthesis

116
Q

Purine degradation results in _____

A

uric acid

117
Q

Most purines from diet are converted to uric acid which is ____

A

excreted

118
Q

What can purine synthesis be salvaged from?

A
  • PRPP + Adenine to AMP via APRT
  • PRPP + guanine to GMP via HGPRT
  • PRPP + Hypoxanthine to IMP via HGPRT
119
Q

Gout is caused by what?

A

high blood levels of uric acid or urate due to overproduction of uric acid

120
Q
A