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BIOL 3421 - molecular biochem > amino acid oxidation II > Flashcards

amino acid oxidation II Flashcards

1
Q

in what form does the amino nitrogen leave the body in aquatic vertebrates

A

as NH4+ (ammonium)

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2
Q

in aquatic vertebrates, amino nitrogen leaves as ammonium, but isn’t this toxic? explain

A

the toxicity is irrelevant, as NH4+ is immediately diluted in surrounding water

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3
Q

in what form does the amino nitrogen leave the body in terrestrial vertebrates (mammals)

A

urea

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4
Q

benefit of nitrogen being excreted as urea?

A

minimizes water loss

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5
Q

in what form does the amino nitrogen leave the body in reptiles and birds

A

uric acid

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6
Q

benefit of nitrogen being excreted as uric acid?

A

minimizes water loss

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7
Q

which organ does the urea cycle occur in

A

liver

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8
Q

where in hepatocytes does the urea cycle occur

A

mito and cytosol

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9
Q

urea cycle: what molecule does the pre-step form

A

carbamoyl-phosphate

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10
Q

urea cycle: what molecule does step 1 form

A

citrulline

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11
Q

urea cycle: what molecule does step 2 form

A

argininosuccinate

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12
Q

urea cycle: what molecule does step 3 form

A

arginine

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13
Q

urea cycle: what molecule does step 4 form

A

urea

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14
Q

pre step: what molecule are we starting with

A

NH4+

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15
Q

pre step: describe what happens to NH4+ in the hepatocyte matrix. What does it convert to and what does this require?

A

NH4+ and bicarbonate join to form carbamoyl phosphate

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16
Q

how many carbons is carbamoyl phosphate

A

1

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17
Q

pre step: T or F: since ammonia and bicarbonate join to form carbamoyl-phosphate, there must be lots of bicarbonate in the mito matrix

A

true

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18
Q

pre step: explain why there’s lots of bicarbonate in the hepatocyte matrix

A

bicarbonate contains hidden CO2, so it’s very easy to make bicarbonate from CO2. There’s lots of CO2 in the matrix due to CAC

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19
Q

pre step: describe what can happen once carbamoyl-phosphate is formed

A

carbamoyl-P can donate it’s carbamoyl to ornithine

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20
Q

T or F: ornithine is proteinogenic

A

false; it’s non-proteinogenic

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21
Q

what amino acid is ornithine derived from

A

glutamate

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22
Q

step 1: what molecule(s) do we start with

A

carbamoyl and ornithine

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23
Q

step 1: describe what reaction occurs

A

carbamoyl and ornithine generate citrulline

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24
Q

step 1: T or F: citrulline is proteinogenic

A

false; it’s non-proteinogenic

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25
Q

step 2: how many carbons is citrulline

A

6

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26
Q

step 2: what happens to citrulline once it’s formed in the matrix

A

it leaves the matrix and enters the cytosol

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27
Q

step 2: what molecule do we start with

A

citrulline

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28
Q

step 2: describe the reaction that occurs

A

citrulline undergoes a 2-step conversion to argininosuccinate

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29
Q

step 2: what is the purpose of argininosuccinate production

A

it introduces the second amino group that’s eventually found in urea

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30
Q

step 2: describe the 2 steps that citrulline undergoes to form argininosuccinate

A

2a: 2 ATP used to make AMP-bound citrulline
2b: displacement of AMP by aspartate, which comes with its own amino group

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31
Q

step 2: how many amino groups does argininosuccinate have

A

4

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32
Q

step 2: aspartate is used in the 2 step conversion of citrulline to argininosuccinate. Where does all this aspartate come from?

A

comes from the hepatocyte mito matrix, where it was transaminated from glutamate (which is plentiful)

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33
Q

step 2: argininosuccinate is a structural combination of which two molecules

A

succinate (CAC intermediate) and arginine (proteinogenic amino acid)

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34
Q

step 3: what molecule do we start with

A

argininosuccinate

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35
Q

step 3: where in the cell are we

A

cytosol

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36
Q

step 3: describe the reaction that occurs

A

argininosuccinate is cleaved to make free arginine and fumarate

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37
Q

step 3: relevance of fumarate? (hint: isn’t argininosuccinate a combo of succinate and arginine?)

A

fumarate is the CAC intermediate following succinate. They are very similar in structure

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38
Q

step 4: what molecule(s) do we start with

A

arginine and fumarate (but fumarate isn’t important)

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39
Q

step 4: describe the reactions that occur

A

water is added to arginine to form ornithine. Urea is displaced

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40
Q

step 4: what happens to the urea that’s formed by the addition of water to arginine

A

it’s displaced. Travels through the blood and to the kidneys to be excreted

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41
Q

step 4: what happens to ornithine once it’s formed

A

it returns to the mito matrix for another round of the cycle

42
Q

what enzyme converts ammonia and bicarbonate to carbamoyl-phosphate

A

carbamoyl-phosphate synthetase I

43
Q

what enzyme converts carbamoyl and ornithine to citrulline

A

ornithine transcarbamoylase

44
Q

what enzyme converts citrulline to argininosuccinate in a two step conversion

A

argininosuccinate synthetase

45
Q

what enzyme cleaves argininosuccinate to arginine and fumarate

A

argininosuccinase

46
Q

what enzyme adds water to arginine to form ornithine

A

arginase

47
Q

what two things is the urea cycle regulated based on

A

amount of protein in the diet + frequency/timing of eating

48
Q

most regulation of the urea cycle is through activity and expression levels of ___________________

A

urea cycle enzymes

49
Q

what happens if one of your urea cycle enzymes is deficient?

A

a protein-rich diet –> build up of toxic free NH4+ or of urea cycle intermediates in blood and urine. But sufferers still have to eat some protein to acquire essential amino acids that we can’t synthesize

50
Q

when might someone want to take an arginine supplement

A

when enzymes earlier in the cycle are deficient. Arginine can help generate urea, complete the cycle, and eliminate at least some of the excess amino groups

51
Q

which molecule is an intermediate of both the urea cycle and the CAC

A

fumarate

52
Q

why can the urea cycle + CAC be easily linked

A

fumarate is an intermediate of both

53
Q

between which parts of the cell do the urea cycle and CAC communicate

A

mito matrix and cytosol

54
Q

what is the name of the cycle that physically links the urea cycle and the CAC

A

aspartate argininosuccinate shunt

55
Q

what is the a-keto acid of aspartate? where is this molecule found?

A

OAA is the a-keto acid. It’s a CAC intermediate

56
Q

If fumarate is a CAC intermediate, why does it get converted to malate in the cytosol after leaving the urea cycle and then enter the CAC as malate?

A

it doesn’t have a mito matrix transporter, but there IS a malate/a-KG transporter

57
Q

where does the ATP cost come from in the urea cycle

A

2 ATP equivalents are used to make carbamoyl from bicarbonate. As well, 2 ATP equivalents are used to make argininosuccinate from citrulline

58
Q

how many ATP total are required for the urea cycle

A

4

59
Q

how many ATP are indirectly produced due to the shunt? explain

A

2.5: fumarate from the urea cycle is converted to malate, enters the matrix, and produces NADH upon conversion to OAA during the CAC. NADH helps generate ATP in the ETC

60
Q

what is the NET cost of ATP in the urea cycle

A

1.5 ATP per turn

61
Q

purpose of the malate-aspartate shuttle?

A

get NADH produced by glycolysis/cytosolic processes into the mito matrix (it lacks a transporter)

62
Q

NADH from which process is already in the matrix (malate-aspartate shuttle)

A

NADH produced by aspartate-argininosuccinate shunt is already in the right place (bc it will be used for the ETC)

63
Q

malate-aspartate shuttle: how do we solve the problem of needing to bring the rest of the NADH into the matrix? (ie describe the steps of the shuttle)

A

take OAA in the cytosol, convert it to malate using NADH (reduction), ship malate across, convert malate back to OAA and NADH (oxidation)

64
Q

malate-aspartate shuttle: once malate comes into the matrix and is oxidized to OAA and NADH, what happens to the OAA to complete the cycle

A

OAA is transaminated to aspartate (glutamate is the amino donor). Aspartate leaves the matrix, and is reconverted to OAA in the cytosol

65
Q

malate-aspartate shuttle: by which transporter does aspartate leave the mito matrix

A

aspartate-glutamate transporter

66
Q

what is the net effect of the malate-aspartate shuttle

A

brings NADH from the cytosol into the matrix (shifts the location of NADH)

67
Q

malate-aspartate shuttle: now that aspartate is in the cytosol, what are its two fates?

A
  1. return to the CAC via OAA and the malate-aspartate shuttle, and bring reducing equivalents to the mito
  2. enter the urea cycle by helping form argininosuccinate, producing fumarate as a byproduct for the aspartate-argininosuccinate shunt
68
Q

after the urea cycle, what happens to all the leftover carbon skeletons

A

all are degraded into CAC intermediates

69
Q

in which tissue types does carbon skeleton degradation occur

A

extra-hepatic tissues

70
Q

why does carbon skeleton degradation occur in extra-hepatic tissues

A

this is where we need the fuel

71
Q

list the 7 intermediates that can be formed via carbon skeleton degradation

A

pyruvate
acetyl-CoA
acetoacetyl-CoA
a-Kg
succinyl-CoA
fumarate
OAA

72
Q

once carbon skeletons are degraded to CAC intermediates, list the 3 fates

A
  1. end products are completely oxidized to CO2
  2. end products are diverted from CAC for GNG
  3. end products are diverted from CAC for ketogenesis
73
Q

define ketogenic

A

making of ketones from degradation of amino acids

74
Q

define glucogenic

A

making of glucose from degradation of amino acids

75
Q

T or F: degradation of a few amino acids can be ketogenic or glucogenic

A

true

76
Q

T or F: almost all amino acids are glucogenic when degraded

A

true

77
Q

which two amino acids are strictly ketogenic

A

leucine and lysine

78
Q

which amino acids are both ketogenic and glucogenic

A

isoleucine, Phe, Trp, Thr, Tyr

79
Q

which amino acids are degraded to pyruvate (6)

A

Ala, Cys, Gly, Ser, Thr, Trp

80
Q

once amino acids are degraded to pyruvate, what are the two fates

A

generate acetyl-CoA and enter the CAC, or generate OAA and undergo GNG

81
Q

which 7 amino acids are degraded to acetyl-CoA

A

Iso, Leu, Lys, Phe, Thr, Trp, Tyr

82
Q

once amino acids are degraded to acetyl-CoA, what are the two fates

A

acetyl-CoA can then generate ketone bodies or join OAA to make citrate in the CAC

83
Q

what does PKU stand for

A

phenylketonuria

84
Q

what is PKU

A

a genetic defect in Phe degradation

85
Q

which step of Phe degradation is disturbed in PKU? how?

A

defective enzyme in the first step of Phe degradation: Phe to Tyr

86
Q

PKU: what is the result of having a defective enzyme in the first step of Phe degradation

A

Phe builds up. Excessive Phe may outcompete other amino acids trying to pass the blood brain barrier, resulting in deficits of other amino acids in the brain

87
Q

symptoms of PKU?

A

seizures, microcephaly, delayed development, behavioral problems, hyperactivity

88
Q

how do you combat PKU

A

keep Phe levels very low

89
Q

T or F: in PKU patients, a normally rare pathway becomes active to deal with the high Phe levels in the blood

A

true

90
Q

describe the normally rare pathway that becomes active in PKU patients

A

amino group of Phe is donated to pyruvate to form alanine (transamination). These phenyl products then accumulate in the blood and are excreted in urine. Produces a musty odor

91
Q

list some dietary restrictions of someone with PKU

A

no nuts, no aspartame, no corn/kale/peas/rice

92
Q

how does one get albinism

A

results from an inability to degrade tyrosine into melanin

93
Q

melanin is a derivative of which amino acid

A

tyrosine

94
Q

describe how PKU relates to albinism

A

PKU patients often have albinism, because Phe can produce tyrosine, which is required for melanin

95
Q

which amino acids are degraded to a-KG

A

Arg, Glu, Gln, His, Pro

96
Q

describe how Arg is degraded to a-KG

A

arginine degradation releases urea and produces ornithine. Removal of the first amine group on ornithine requires a transamination that converts a-KG to glutamate

97
Q

which amino acids are degraded to succinyl-CoA

A

Iso, Met, Thr, Val

98
Q

describe how Iso, Met, Thr, Val are degraded to succinyl-CoA

A

they’re first degraded to propionyl-CoA, which can then be modified to succinyl-CoA with a mutase

99
Q

which amino acids are degraded to OAA

A

Asp, Asn

100
Q

describe how Asn and Asp are converted to OAA

A

Asn is converted to Asp by asparaginase, releasing NH4+. A transamination converts Asp to OAA. But to be used in the CAC, OAA must be converted to malate to enter the matrix. Or instead, OAA can be diverted to GNG in the liver cytosol

BIOL 3421 - molecular biochem (20 decks)

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