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BIOL 3421 - molecular biochem > nitrogen metabolism > Flashcards

nitrogen metabolism Flashcards

1
Q

the atmosphere is __% nitrogen

A

78%

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2
Q

the the 4 forms of nitrogen that are useful

A

nitrate, nitrite, ammonia, ammonium

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3
Q

nitrate

A

NO3-

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4
Q

nitrite

A

NO2-

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5
Q

ammonia

A

NH3

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6
Q

ammonium

A

NH4+

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7
Q

NO3-

A

nitrate

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8
Q

NO2-

A

nitrite

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9
Q

NH3

A

ammonia

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10
Q

NH4+

A

ammonium

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11
Q

N2

A

atmospheric nitrogen

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12
Q

which organism can convert nitrogen to biologically useful forms

A

nitrogen fixing prokaryotes

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13
Q

nitrogen fixing prokaryotes fix over ___ kg of nitrogen per year

A

10^11

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14
Q

what does it mean to “fix” something

A

take it out of the atmosphere and make it an organic compound

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15
Q

when fixing N2, what form is it converted to?

A

NH3 (ammonia), and then will be converted to organic forms of nitrogen

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16
Q

out of the usable forms of nitrogen, which is the most oxidized?

A

nitrate (NO3-)

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17
Q

out of the usable forms of nitrogen, which is the most reduced?

A

ammonia (NH3)

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18
Q

what does nitrogen fixation produce

A

NH3, which is then converted to organic forms of nitrogen

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19
Q

what does nitrogen fixation use to make NH3

A

N2

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20
Q

T or F: most organisms can do nitrogen fixation

A

true

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21
Q

what does nitrification start with

A

NH3

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22
Q

what does nitrification produce

A

NO3-

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23
Q

is nitrogen fixation an oxidation or reduction

A

reduction

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24
Q

is nitrification an oxidation or reduction

A

oxidation

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25
Q

what does assimilation start with

A

NO2- or NO3-

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26
Q

what does assimilation produce

A

NH3

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27
Q

is assimilation an oxidation or reduction

A

reduction

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28
Q

what organisms use assimilation

A

plants

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29
Q

explain why plants use assimilation + what benefit this has for the plant

A

they take up nitrate and nitrite from the soil and convert it back to ammonia, which is used to build amino acids and nucleotides

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30
Q

in regards to the nitrogen cycle, what happens when an organism dies

A

decomposers return ammonia to the soil to be reused by nitrifying bacteria. Animals ingest these amino acids when they ingest plants or animals that ate plants

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31
Q

what does denitrification start with

A

NO3-

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32
Q

what does denitrification produce

A

N2

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33
Q

in what conditions does denitrification occur

A

anaerobic

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34
Q

does denitrification occur under aerobic or anaerobic conditions

A

anaerobic

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35
Q

in denitrification, what is the final electron acceptor instead of oxygen

A

NO3- or NO2-

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36
Q

is assimilation an oxidation or reduction

A

reduction

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37
Q

is denitrification an oxidation or reduction

A

reduction

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38
Q

in the nitrogen cycle, which step completes the cycle

A

denitrification

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39
Q

other than denitrification, which step can complete the cycle

A

anammox

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40
Q

what does anammox start with

A

NH3

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41
Q

what does anammox produce

A

N2

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42
Q

what electron acceptor does anammox use

A

NO2-

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43
Q

which organisms use anammox

A

anammox bacteria

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44
Q

does anammox happen aerobically or anaerobically

A

anaerobicaly

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45
Q

what makes anammox bacteria weird?

A

they create their ETC across an organelle membrane called the anammoxosome (weird that bacteria have an organelle)

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46
Q

what is the anammoxosome

A

an organelle in anammox bacteria where the ETC is located

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47
Q

what reaction does the nitrogenase complex mediate

A

reduction of atmospheric nitrogen to ammonia

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48
Q

T or F: converting N2 to NH3 (via nitrogenase complex) is spontaneous

A

true

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49
Q

T or F: converting N2 to NH3 (via nitrogenase complex) is easy to do

A

false; it’s very hard to do

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50
Q

why is the conversion of N2 to NH3 using the nitrogenase complex hard to do?

A

the N≡N triple bond is very stable, and this nitrogen fixation has such a high activation energy that it’s basically inert under normal temp/pressure

51
Q

since N2–> NH3 via nitrogenase complex is so hard to do, how do prokaryotes manage it?

A

ATP plays a role! (this is odd considering the reaction is exergonic)

52
Q

making 2 ammonia from N2 costs __ ATP

A

16

53
Q

which organisms can fix nitrogen

A

diazotrophs

54
Q

list 3 examples of diazotrophs

A

cyanobacteria, methanogens, rhizobia

55
Q

what are rhizobia

A

gram negative anaerobic bacteria living in the root nodules of legumes

56
Q

what two enzymes make up the nitrogenase complex

A

dinitrogenase and dinitrogenase reductase

57
Q

describe why the legume-rhizobium interaction is mutualistic

A

the plant provides sugars and phosphates, the bacteria provides nitrogen

58
Q

in the legume-rhizobium interaction, in what form do the bacteria give nitrogen to the plant

A

ammonium (NH4+)

59
Q

describe how the nitrogenase complex interacts with air

A

it’s rapidly inactivated in air due to instability around the presence of oxygen (it’s anaerobic)

60
Q

list 4 things that a bacteria with the nitrogenase complex might do

A

live anaerobically, inhibit complex activity when O2 is present, balance enzyme inactivation with enzyme synthesis, block O2 binding site by conformational changes

61
Q

describe how a bacteria (with the nitrogenase complex) living in the root nodule can solve the problem of oxygen toxicity

A

the plant provides the nodule with a hemoglobin-derivative called leghemoglobin, which binds and sequesters the oxygen in the nodule away from the anaerobic bacteria

62
Q

what hemoglobin derivative do plants have

A

leghemoglobin

63
Q

benefit of a plant providing its root nodule with leghemoglobin?

A

it binds and sequesters the oxygen in the nodule, keeping it away from the anaerobic bacteria

64
Q

structure of dinitrogen reductase (3)

A

homodimer, has an Fe-S redox center, and an ATP binding site on each subunit

65
Q

structure of dinitrogenase? (3)

A

tetramer, each with a P cluster and Fe-Mo cofactor

66
Q

list the 4 cofactors that dinitrogenase might have

A

Fe, S, molybdenum, vanadium

67
Q

in order to produce 2NH4+ from one N2, how many electrons are required

A

8

68
Q

where does dinitrogenase get the 8 electrons required for NH4+ formation?

A

from dinitrogenase reductase

69
Q

where does dinitrogenase reductase get the 8 electrons from required for NH4+ formation

A

came from pyruvate, which would then be oxidized to acetyl-CoA

70
Q

NH4+ formation: how does pyruvate get the 8 electrons to give to dinitrogenase reductase

A

it’s oxidized to acetyl-CoA, which produces 8 electrons

71
Q

NH4+ formation: how does pyruvate transfer the 8 electrons to dinitrogenase reductase

A

via ferredoxin or flavodoxin

72
Q

NH4+ formation: what does dinitrogenase reductase do with the 8 electrons

A

gives them one at a time to dinitrogenase

73
Q

NH4+ formation: T or F: dinitrogenase reductase gives all 8 electrons to dinitrogenase all at the same time

A

false; it gives them one at a time

74
Q

NH4+ formation: passage of 1 electron from dinitrogenase reductase to dinitrogenase requires __ ATP

A

2 ATP

75
Q

NH4+ formation: what is the result of ATP binding+hydrolysis to dinitrogenase reductase

A

causes a conformational change to bring DR and D cofactors together to promote electron transfer

76
Q

NH4+ formation: what does dinitrogenase do with the 8 electrons

A

uses 6 to reduce N2 to 2NH4+, and uses 2 to make H2

77
Q

NH4+ formation: what does dinitrogenase use 6/8 electrons for

A

reduction of N2 –> 2NH4+

78
Q

NH4+ formation: what does dinitrogenase use 2/8 electrons for

A

to make H2

79
Q

what is glutamate synthetase suppressed by? why?

A

low ATP, high NH4+
this is because the process is very costly (ATP), and it produces NH4+

80
Q

NH4+ is incorporated into all biomolecules starting with ___ and ___

A

glutamate and glutamine

81
Q

once in glutamate, what happens to NH4+ to generate most other amino acids

A

it can be transaminated

82
Q

once in glutamine, what happens to NH4+

A

incorporated into other biomolecules

83
Q

__ + ___ = glutamine

A

NH4+ and glutamate = glutamine

84
Q

T or F: synthesis of glutamine from NH4+ and glutamate uses ATP

A

true

85
Q

once glutamine is produced from NH4+ and glutamate, what can it combine with + what is produced

A

combines with a-ketoglutarate to make two glutamate molecules

86
Q

how many glutamates are made from a-ketoglutarate and glutamine joining

A

2

87
Q

what does glutamine join with to make glutamate

A

a-ketoglutarate

88
Q

during glutamine + a-keto –> glutamate, what else is produced

A

NADPH

89
Q

what is formed when a-keto gains a backbone amine

A

glutamate

90
Q

what is formed when glutamate gains an R group amine

A

glutamine

91
Q

how many amines does a-keto have

A

0

92
Q

how many amines does glutamate have

A

1

93
Q

how many amines does glutamine have

A

2

94
Q

when pairing glutamine and glutamate synthesis, what are the net products?

A

glutamate, NADP+, ADP, Pi

95
Q

how many types of glutamine synthetase are there

A

2

96
Q

type I of glutamine synthetase is present in ____

A

bacteria

97
Q

type II of glutamine synthetase is present in ____

A

eukaryotes

98
Q

how many subunits does type I glutamine synthetase have

A

12

99
Q

how many subunits does type II glutamine synthetase have

A

10

100
Q

in glutamine synthetase, each subunit has an active site where __ and __ bind

A

ATP and glutamate

101
Q

type I glutamine synthetase is regulated by __ other molecules

A

8

102
Q

how is type I glutamine synthetase regulated

A

all 8 inhibitory molecules must be present to shut it down. The effects of each one are additive

103
Q

define cumulative feedback inhibition

A

the downstream products act as inhibitors of an enzyme, but all of them are required in order to shut down the enzyme

104
Q

other than the downstream products, which molecule is able to inhibit the activity of glutamine synthetase

A

AMP

105
Q

how does AMP inhibit glutamine synthetase activity

A

it covalently binds to a tyrosine (adenylation) near the enzyme active site

106
Q

which enzyme promotes adenylation and deadenylation of glutamine synthetase

A

adenylyltransferase (AT)

107
Q

which regulatory protein modules adenylyltransferase activity

A

PII

108
Q

result of PII binding to adenylyltransferase?

A

stimulates adenylation of glutamine synthetase

109
Q

when glutamine synthetase is adenylylated, is it active or inactive

A

inactive

110
Q

what regulates PII activity

A

uridylylation

111
Q

how is glutamine synthetase deadenylylated

A

via UMP-PII binding to adenylyltransferase

112
Q

which enzyme promotes uridylylation and deurifylylation

A

uridylyltransferase (UT)

113
Q

UT uridylylation activity is inhibited by ___

A

glutamine

114
Q

UT uridylylation activity is stimulated by __ and ___

A

a-keto and ATP

115
Q

PII inhibits or promotes transcription of glutamine synthetase gene

A

inhibits

116
Q

UMP-PII inhibits or promotes transcription of glutamine synthetase gene

A

promotes

117
Q

which enzyme incorporates nitrogen in glutamine into other biological molecules

A

glutamine amidotransferases

118
Q

after glutamine amidotransferase activity to incorporate nitrogen into other molecules, what happens to the glutamine that donated the N

A

it converts back to glutamate

119
Q

how many active sites does glutamine amidotransferase have

A

2

120
Q

what do the 2 active sites of glutamine amidotransferase fit

A

one fits glutamine, other fits various nitrogen acceptors

121
Q

during the transfer of nitrogen from glutamine to other molecules, which enzyme acts as the nucleophile that cleaves the amide bond in glutamine

A

cysteine

122
Q

after cysteine cleaves the amide bond in glutamine, what is released

A

NH3

123
Q

after cysteine cleaves the amide bond in glutamine, where does the freed NH3 go

A

it’s transferred to a second product

124
Q

after cysteine cleaves the amide bond in glutamine and the NH3 is transferred to a second product, what happens

A

the residual glutamate and new aminated product leave

BIOL 3421 - molecular biochem (20 decks)

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