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biochem > biochem lecture 10 > Flashcards

biochem lecture 10 Flashcards

1
Q

what do amino acids contain

A

nitrogen, in the form of amino groups

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2
Q

what is one important thing nitrogen cycle does

A

assimilation of nitrogen into organic structures

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3
Q

specifically what part of nitrogen cycle helps w/ assimilation of nitrogen into organic structures

A

nitrogen fixation

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4
Q

what is nitrogen fixation

A

the ability of certain microorganisms/bacteria that are able to take elemental/atmospheric nitrogen (N2 gas) and reduce it to form ammonia (NH4)

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5
Q

basically what is nitrogen fixation

A

N2 gas reduced to ammonia (NH4)

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6
Q

what kind of reaction is nitrogen fixation

A

reduction

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7
Q

what organisms do nitrogen fixing

A

micro organisms, bacterial, soil microbes/bacteria

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8
Q

why is the transformation of N2 gas into ammonia important

A

represents a gateway form of nitrogen that’s gonna be assimilated into AAs and other nitrogen containing carbon compounds (nucleotides, etc.)

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9
Q

what other processes are in nitrogen cycle

A

other transformations involving diff forms of nitrogen; oxidation rxns: nitrification, converting ammonia to nitrites, nitrites to nitrates

reductive processes: nitrogen fixation, reduction of nitrates into ammonia

deinitrification

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10
Q

what is denitrification

A

certain microorganisms able to take nitrites, eliminate nitrogen in the form of N2 gas released into atmosphere

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11
Q

what enzyme is involved in nitrogen fixation

A

nitrogenase complex (nitrogenase enzyme complex)

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12
Q

what is nitrogen fixing overall

A

set of redox reactions

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13
Q

where do the electrons used in this reaction come from

A

things like pyruvate

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14
Q

what happens to those electrons in nitrogen fixation

A

funneled along a set of electron acceptors and donors, culminating in the donation of electrons to the N2 gas to generate 2 ammonia molecules per N2

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15
Q

is there a big ATP investment in nitrogen fixing

A

yup

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16
Q

how much ATP is invested in nitrogen fixing

A

16 ATP per N2 molecule that’s reduced

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17
Q

why does it still happen even though it’s energetically very expensive

A

highly conserved evolutionary process, so has to be important

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18
Q

what is nitrogen fixing important for

A

for bacteria and their ability to assimilate this nitrogen into their structures

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19
Q

what can certain types of plants do

A

form symbiotic relationships w/ nitrogen fixing bacteria

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20
Q

which plants form symbiotic relationships w/ nitrogen fixing bacteria

A

leguminous plants

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21
Q

where do these symbiotic bacteria live

A

in root nodules of leguminous plants; they’re enclosed in there

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22
Q

what is nitrogenase complex sensitive to

A

oxygen

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23
Q

why is oxygen toxic to nitrogenase complex

A

O2 is electronegative, can inhibit the series of redox rxns that are essential for reduction of N2 gas into ammonia

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24
Q

what is the purpose of those nodules

A

creates an anaerobic environment in which to carry out nitrogen fixation

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25
Q

how is leghemoglobin made

A

plants that form symbiotic relationship w/ nitrogen fixing bacteria produce this compound

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26
Q

what is leghemoglobin

A

can bind up any oxygen present to reduce levels of oxygen toxicity in nitrogenase enzyme

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27
Q

why do plants produce leghemoglobin

A

to minimize the effects of oxygen on nitrogen fixation

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28
Q

what happens once ammonia has been generated from the reduction of N2 gas

A

enzymes will act on ammonia to begin the process of incorporating nitrogen into organic structure

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29
Q

what happens to electrons from pyruvate

A

go to 8 ferredoxin or flavodoxin, then 8 dinitrogenase reductase, then 8 nitrogenase reductase again, then dinitrogenase. generate 2 ammonia molecules

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30
Q

what does glutamine synthetase do

A

enzyme that catalyzes assimilation of NH4 into glutamate to yield glutamine

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31
Q

why does glutamine synthetase add NH4 to glutamate to make glutamine

A

because it’s one of the enzymes that begins process of incorporating nitrogen into organic structures

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32
Q

what is glutamine synthetase

A

large multi subunit enzyme complex, 12 identical subunits

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33
Q

what is the process of glutamate into glutamine conversion

A

one of the early rxns that allows for eventual assimilation of that nitrogen into other amino acids, and thus into proteins/other structures

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34
Q

what is a primary regulatory point in nitrogen metabolism

A

glutamine synthetase

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35
Q

how does glutamine synthetase regulation occur

A

2 ways; allosteric regulation, covalent modification

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36
Q

how does covalent modification occur

A

thru a process called adenylation

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37
Q

how many diff allosteric inhibitors for glutamine synthetase

A

8

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38
Q

what are many of the allosteric inhibitors of glutamine synthetase

A

end products of pathways that originated w/ conversion of glutamate to glutamine

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39
Q

what is needed in order for the enzyme to be completely inhibited

A

has to have all 8 allosteric inhibitors

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40
Q

describe these 8 allosteric inhibitors

A

has distinct sites for each of the inhibitors, they can all feedback inhibit the enzyme

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41
Q

what happens if you have 1 or 2 of these inhibitors

A

might lower activity of the enzyme somewhat

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42
Q

what is the second level of control for glutamine synthetase

A

covalent modification

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43
Q

what form of covalent modification found in glutamine synthetase

A

adenylation

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44
Q

what is adenylation

A

covalent attachment of a molecule of AMP (adenosine monophosphate)

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45
Q

describe adenylation in this case

A

attachment of AMP to tyrosine

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46
Q

what specific tyrosine is being adenylated

A

tyrosine at position 397 on each of the subunits of glutamine synthetase that are modified

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47
Q

what are the effects of this adenylation covalent modification

A

inhibits the enzyme

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48
Q

what enzymes carry out adenylation

A

adenyltransferases (At)

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49
Q

what can happen besides adenylation

A

de-adenylation

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50
Q

why is de-adenylation a thing

A

cuz forms of covalent modification like phosphorylation etc. are generally reversible

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51
Q

what is the effect of adenylation

A

inactivates glutamine synthetase

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52
Q

what is the effect of de-adenylation

A

activates glutamine synthetase

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53
Q

when does deadenylation occur

A

when we have low concentrations of some of those allosteric inhibitors, sow that we favor activation of synthetase overall

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54
Q

what enzymes are for de-adenylation

A

same as the enzymes that carry out adenylation

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55
Q

what do adenylate transferases do

A

carry out both reactions; attachment of AMP and its removal

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56
Q

what is adenylation mediated by

A

another form of covalent modification, uridylation

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57
Q

what is uridylation

A

attachment of uridine monophosphate (UMP

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58
Q

what is P2

A

regulatory subunit associated w/ adenylyl transferase enzyme

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59
Q

what dictates whether adenylyl transferase carries out adenylation or de-adenylation

A

whether P2 is uridylated or not

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60
Q

what happens when P2 is not uridylated

A

missing a UMP, AT enzyme will carry out adenylation, inactivating glutamine synthetase

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61
Q

what happens when P2 is uridylated

A

switches activity of AT to carry out de-adenylation, activating glutamine synthetase

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62
Q

what is uridylation controlled by

A

uridyltransferase

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63
Q

what favors activation of uridylyl transferase

A

high E state indicators like ATP, high [ ] of TCA cycle intermediates (a-ketoglutarate, etc.)

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64
Q

what do these high E state indicators do

A

regulate overall activity of that particular transferase, and regulate the type of activity we see with adenylation and deadenylation of glutamine syntethase

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65
Q

what does uridylation of Tyr do

A

stimulate deadenylation

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66
Q

where are AA carbon skeletons derived from

A

3 sources; glycolysis, TCA cycle, pentose phosphate pathway

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67
Q

what AA for ribose-5-phosphate

A

histidine

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68
Q

what AA for a-ketoglutarate

A

glutamate, glutamine, proline, arginine

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69
Q

what AAs for 3-phosphoglycerate

A

serine, glycine, cysteine

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70
Q

what AAs for oxaloacetate

A

aspartate, asparagine, methione, threonine, lysine

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71
Q

what AAs for pyruvate

A

alanine, valine, leucine, isoleucine

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72
Q

PEP and erythrose-4-phosphate

A

tryptophan, phenylalanine, tyrosine

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73
Q

how is isoleucine biosynthesis pathway regulated

A

allosteric regulation/feedback inhibition

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74
Q

what serves as an allosteric inhibitor for what enzyme in isoleucine pathway

A

isoleucine (end product) inhibits first enzyme of pathway, threonine dehydratase

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75
Q

what is the first enzyme in isoleucine biosynthesis pathwayt

A

threonine dehydratase

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76
Q

what is another type of feedback inhibition we see

A

sequential feedback inhibition

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77
Q

why is sequential feedback inhibition a thing

A

even if we have enough of a certain AA, we don’t wanna shut everything down cuz we may still have lower concentrations than the cell needs for other AAs. [when we have pathways with common intermediates, we can’t assure that every single AA that’s produced by these diff pathways that have these common intermediates that we’re gonna have enough of these AAs at the same time]

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78
Q

basically what does sequential feedback inhibition do

A

prevents one endproduct from shutting down key steps in a pathway when other products are required

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79
Q

what are isozymes

A

multiple forms of the same enzyme; same enzyme, catalyzes same step, just regulated by different allosteric regulators

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80
Q

when do we see isozymes

A

conversion of aspartate into aspartyl-beta-phosphate

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81
Q

how many forms of the enzyme are there that catalyze this step

A

3; A1, A2, A3

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82
Q

describe how A1, A2, A3 are inhibited

A

A1 inhibited by isoleucine and lysine, A2 not inhibited by anything, A3 inhibited by threonine [basically all by diff things]

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83
Q

what do isozymes being inhibited by different allosteric inhibitors allow for

A

allows you to achieve a balanced pool of all the diff amino acids here

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84
Q

why does sequential feedback inhibition ensures we have a balanced pool of AAs

A

we’re not gonna be lacking in any one AA, cuz we can keep some of these pathways active while we inhibit others

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85
Q

where do we get AAs from our diet

A

from proteins in the food we eat

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86
Q

what breaks down proteins

A

proteolytic enzymes that break down proteins into shorter peptides and individual AAs

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87
Q

what would happen if this proteolytic breakdown was occurring in upper portions of small intestine

A

absorption of those AAs into intestinal epithelial cells, those AAs transported into blood where they can undergo oxidation/degradation

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88
Q

what 2 things are we talking about when we talk about degradation of AAs

A

what happens to amino groups in AAs, what happens to carbon skeletons that are separated from amino group

89
Q

do we derive a lot of E from nitrogen (in terms of energy metabolism)

A

not really

90
Q

what can nitrogen be used for once separated from the cell

A

in biosynthesis of new AAs in the cell, nucleotide synthesis, synthesis of other nitrogen containing compounds

91
Q

what happens to an excess of nitrogen

A

fed into urea cycle, excreted in the form of urea

92
Q

where does excess of nitrogen come from

A

ammonia ions

93
Q

what happens to carbon skeleton

A

separated from amino group

94
Q

what happens to those carbon skeletons after separation

A

converted into diff types of alpha-keto acids, and fed into TCA cycle

95
Q

what does TCA do

A

provides intermediates for synthesis of other things like glucose, etc. (gluconeogenesis)

96
Q

what two pathways are connected

A

urea cycle and TCA cycle

97
Q

how are urea cycle and TCA cycle connected

A

aspartate-argininosuccinate shunt

98
Q

what does aspartate-arigninosuccinate shunt serve as

A

anaplerotic source of intermediates, allows us to replenish these intermediates

99
Q

basically what happens to amino acids once cleaved from larger proteins

A

2 fats; fate of amino group nitrogen of AA, fate of rest of carbon skeleton of AA

100
Q

what happens to amino group nitrogen of AA

A

removed from AA by aminotransferases to yield ammonia (nitrogen not used in energy-producing pathways)

101
Q

what happens to rest of carbon skeleton of AA

A

enters metabolic pathways as precursors of glucose or Krebs cycle intermediates

102
Q

what are aminotransferases

A

enzymes that separate the amino group from carbon skeleton

103
Q

what is the resulting compound that’s produced after enzymes separate amino group from carbon skeleton

A

ammonia

104
Q

what is produced after aminotransferases do what they do

A

ammonia, and carbon skeletons

105
Q

what happens to carbon skeletons

A

go into TCA cycle

106
Q

what happens to excess ammonia in nitrogen

A

fed into urea cycle (for mammals)

107
Q

are amino groups a source of energy

A

not typically

108
Q

what are carbon skeletons gonna serve as

A

precursors for gluconeogenesis or fed into TCA cycle

109
Q

what do aminotransferases do specifically

A

amino group in amino acid is transferred from AA to alpha-ketoglutarate

110
Q

what does transferring of amino group from AA to a-ketoglutarate often yield

A

glutamate

111
Q

what happens to glutamate after it’s generated

A

in biosynthesis pathways often used as an amino group donor to synthesize other AAs

112
Q

what are we left with after AAs are synthesized

A

a-keto acids

113
Q

what is Pyridoxal phosphate (PLP)

A

cofactor for aminotransferase

114
Q

what is aminotransferase’s cofactor

A

pyridoxal phosphate

115
Q

basically what do aminotransferases do

A

transfer amino group from AA to alpha ketoglutarate to form glutamate (can synthesize other AAs), AA becomes alpha-keto acid

116
Q

what is the amino group acceptor in aminotransferase reactions

A

alpha-ketoglutarate

117
Q

what are the uses of nitrogen from ammonium ions

A

de novo synthesis of amino acids and nucleotides

118
Q

what happens to excess ammonium ions

A

converted into urea (if mammal fed into urea cycle), etc., uric acid, ammonia

119
Q

basically describe fate of ammonium ions

A

some used in synthesis of nitrogen compounds (AAs, nucleotides), excess is converted to ammonia, uric acid, urea, etc.

120
Q

what are the sources we derive nitrogen from

A

glutamine, amino acids, alanine cycle

121
Q

describe how nitrogen comes from glutamine

A

glutamine, comes from tissues that AREN’T liver (extrahepatic tissues)

122
Q

describe how nitrogen comes from AAs

A

often times those AAs will be sent to liver tissue for separation of amino group from rest of carbon skeleton

123
Q

describe how nitrogen comes from in alanine cycle

A

alanine cycle is mainly the form of nitrogen that is transported from muscle to liver, and utilized in excretory pathway in urea cycle

124
Q

are there multiple sources of nitrogen in body or just one

A

at least 3 diff forms of nitrogen

125
Q

what happens to nitrogen that comes from diff sources

A

can all be utilized, funneled into urea cycle

126
Q

where do we derive small amount of oxidative energy from

A

catabolism of amino acids

127
Q

where are amino acids derived from

A

breakdown of cellular proteins, ingested proteins, body proteins (when other forms of fuel aren’t available)

128
Q

what do proteases do

A

degrade ingested proteins in stomach and small intestine

129
Q

what happens to these various sources of amino gruops

A

transported to places like liver

130
Q

what happens to glutamine

A

imported into liver/hepatocytes, then transported into mitochondria

131
Q

what happens after glutamine goes into the liver

A

transporters move it into mitochondria

132
Q

what do glutamine/glutamate undergo

A

removal of amino group nitrogen

133
Q

what removes amino group from glutamine/glutamate

A

aminotransferase and glutamate dehydrogenase

134
Q

what happens after aminotransferase and glutamate do their thing

A

amino group is released

135
Q

what acts on amino group

A

carbamoyl phosphate synthetase I

136
Q

why is carbamoyl phosphate synthetase I important

A

cuz this is how nitrogen enters the urea cycle

137
Q

what is first intermediate of urea cycle

A

citrulline

138
Q

what is end product of urea cycle

A

ornithine

139
Q

what is the first rxn in urea cycle

A

combines carbamoyl phosphate and ornithine to produce citrulline

140
Q

why is carbamoyl phosphate important

A

cuz its the form of nitrogen that enters the urea cycle

141
Q

what step in urea cycle takes place in mitochondria

A

first step only

142
Q

what happens to citrulline

A

citrulline in mitochondrial matrix transported out of mitochondria by transporters

143
Q

what happens to citrulline once it’s in the cytoplasm

A

citrulline is acted on, taken into the rest of urea cycle

144
Q

what kinds of steps do we have in urea cycle

A

where it indirectly connects to TCA cycle

145
Q

what do we have in step 4 of urea cycle

A

production of urea

146
Q

how is urea produced

A

conversion of arginine into ornithine (last compound in cycle), results in production of urea

147
Q

what is excreted from the body eventually

A

urea

148
Q

what happens early on in amino acid catabolism

A

separation of AA group from carbon skeleton

149
Q

what happens in most cases

A

amino group transferred to a-ketoglutarate to form glutamate

150
Q

what does formation of glutamate from a-ketoglutarate require

A

pyridoxal phosphate

151
Q

what happens to glutamate

A

transported to liver mitochondria

152
Q

what happens when glutamate transported to liver mito

A

glutamate dehydrogenase releases amino group as NH4+

153
Q

how is ammonia from other tissues transported to liver

A

1) amide nitrogen of glutamine or 2) amino group of alanine (from skeletal muscle)

154
Q

how is pyruvate produced

A

by deamination of alanine (liver) is converted to glucose (transported back to muscle)

155
Q

basically how is pyruvate produced

A

glucose alanine-cycle

156
Q

how is NH4+ excreted

A

in diff forms, depending on the organism

157
Q

what is produced from urea cycle

A

urea

158
Q

what are ureotelic animals

A

organisms that excrete urea

159
Q

uricotelic animals

A

organisms that excrete nitrogen in form of uric acid

160
Q

who are ureotelic animals

A

many terrestrial vertebrates, sharks

161
Q

who are uricotelic animals

A

birds, reptiles

162
Q

what are ammonotelic animals

A

excrete nitrogen as ammonia

163
Q

who are ammonotelic animals

A

bony fish, amphibians (basically aquatic vertebrates)

164
Q

are there diff strategies for nitrogen excretion

A

yup; diff animals excrete nitrogen in diff forms (urea, uric acid, ammonia)

165
Q

how is ammonia excreted in most terrestrial organism

A

converted to urea

166
Q

what is the connection b/w urea cycle and TCA cycle

A

aspartate argininosuccinate shunt

167
Q

how os carbamoyl phosphate formed

A

from carbon dioxide and amino group derived from earlier rxns involving diff AAs

168
Q

what step of urea cycle involves actual production of urea

A

last step; generates ornithine as end product from arginine, urea is produced

169
Q

what is the krebs bicycle

A

aspartate-argininosuccinate; link b/w urea and TCA cycles

170
Q

what is urea cycle (for AAs)

A

where amino groups from AAs are gonna be sent

171
Q

what is TCA cycle

A

carbon skeletons from AAs are gonna be used and incorporated in TCA

172
Q

where do these cycles occur

A

TCA cycle occurs in mitochondria, urea cycle only first step occurs in miotochondria

173
Q

what step in urea cycle occurs in mitochondria

A

incorporation of carbamoyl phosphoate in that amino group nitrogen into urea cycle w/ ornithine to produce citrulline

174
Q

where do rest of steps in urea cycle occur

A

cytoplasm

175
Q

what do we need to get in and out of mitochondria

A

transportesr

176
Q

what is one of three sources of amino groups

A

muscle

177
Q

describe muscle

A

metabolically active; can have protein damage in muscle tissue, those AAs that are released from muscle during protein breakdown can be exported from muscle in form of alanine

178
Q

basically what happens to muscle proteins

A

if proteins damaged, they’re gonna be further degraded. AAs are gonna be either recycled or amino groups separated

179
Q

what happens when amino groups separted from AAs in muscle

A

specific aminotransferase that generates alanine

180
Q

what aminotransferase generates alanine

A

alanine aminotransferase

181
Q

what is alanine

A

represents the major carrier form of nitrogen from muscle, from AAs that were present in muscle

182
Q

what does alanine serve as

A

carrier of ammonia and a carbon skeleton of pyruvate from skeletal muscle to liver

183
Q

what happens to alanine

A

transported thru bloodstream, taken up into liver cells, where amino group of alanine is separated from carbon skeleton

184
Q

what happens to alanine in liver cells

A

amino group separated from carbon skeleton

185
Q

what does the separation of amino group from carbon skeleton in alanine result in

A

production of pyruvate

186
Q

where is pyruvate used

A

gluconeogenesis (glucose synthesis)

187
Q

what happens to ammonia

A

excreted

188
Q

what happens to excess nitrogen

A

amino group converted into glutamate or used in glutamate synthesis, then eventual excretion thru urea cycle

189
Q

how is pyruvate produced

A

deamination of alanine

190
Q

describe where pyruvate goes

A

produced in liver thru deamination of alanine; then transported back to muscle when converted to glucose

191
Q

what happens to pyruvate after is produced

A

converted to glucose

192
Q

what can carbon atoms produced in AA synthesis be used for

A

to feed various metabolic intermediates

193
Q

just like in AA synthesis, what can Cs produced from AA degradation be used for

A

to feed various metabolic intermediates, specifically TCA cycle and some gluconeogenesis

194
Q

what are 2 main categories of AAs based on

A

based on how they’re handled after they’ve been degraded: glucogenic and ketogenic

195
Q

what are glucogenic amino acids

A

AAs that feed into TCA cycle

196
Q

what are ketogenic amino acids

A

AAs that result in production of ketone/ketone bodies

197
Q

talk about alanine

A

carbon skeletons from alanine can be used in pyruvate production

198
Q

what happens to pyruvate produced from alanine

A

used in gluconeogenesis pathway

199
Q

basically what are glucogenic AAs

A

carbon skeletons which can be used in synthesis of glucose

200
Q

what are ketogenic AAs

A

AAs used in synthesis of ketone containing compounds like ketone bodies

201
Q

when are ketone bodies produced

A

long-term starvation conditions, provides energy for CNS

202
Q

what do many genetic disorders involve

A

defects or inability to produce certain enzymes involved in AA catabolism/anabolism

203
Q

phenylketonuria

A

defects in ability to produce enzyme phenylalanine hydroxylase

204
Q

what is phenylalanine hydroxylase

A

converts phenylalanine into tyrosine

205
Q

what is phenylalanine hydroxylase involved in

A

affects aspects of aromatic AA metabolism, esp in mamammals

206
Q

what do people with phenylketonuria have (or not have)

A

phenylalanine hydroxylase

207
Q

what do phenylketonurics have to avoid

A

diets w/ phenylalanine

208
Q

what happens if they consume phenylalanine while lacking hydroxylase

A

phenylalanine will be converted into phenylpyruvic acid

209
Q

what is phenylpyruvic acid

A

toxic byproduct

210
Q

what does phenylpyruvic acid cause

A

toxic to CNS, cause serious complications

211
Q

what are ketogenic AAs

A

leucine, lysine, phenylalanine, tryptophan, tyrosine, isoleucine, threonine

212
Q

what are AAs for acetoacetyl CoA

A

leucine, lysine, phenylalanine, tryptophan

213
Q

what are AAs for acetyl CoA

A

isoleucine, leucine, threonine, tryptophan

214
Q

what are AAs for glutamate

A

arginine, glutamine, histidine, proline

215
Q

what are AAs for succinyl CoA

A

isoleucine, methionine, threonine, valine

216
Q

what are AAs for fumarate

A

phenylalanine, tyrosine

217
Q

what are AAs for oxaloacetate

A

asparagine, aspartate

218
Q

what are AAs for pyruvate

A

alanine, cysteine, glycine, serine, threonine, tryptophan

219
Q

what are glucogenic AAs

A

alanine, cysteine, glycine, serine, threonine, tryptophan, asparagine, aspartate, phenylalanine, tyrosine, isoleucine, methionine, threonine, valine, arginine, glutamine, histidine, proline

biochem (15 decks)

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