biochem lecture 10 Flashcards
(219 cards)
1
Q
what do amino acids contain
A
nitrogen, in the form of amino groups
2
Q
what is one important thing nitrogen cycle does
A
assimilation of nitrogen into organic structures
3
Q
specifically what part of nitrogen cycle helps w/ assimilation of nitrogen into organic structures
A
nitrogen fixation
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)
5
Q
basically what is nitrogen fixation
A
N2 gas reduced to ammonia (NH4)
6
Q
what kind of reaction is nitrogen fixation
A
reduction
7
Q
what organisms do nitrogen fixing
A
micro organisms, bacterial, soil microbes/bacteria
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.)
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
10
Q
what is denitrification
A
certain microorganisms able to take nitrites, eliminate nitrogen in the form of N2 gas released into atmosphere
11
Q
what enzyme is involved in nitrogen fixation
A
nitrogenase complex (nitrogenase enzyme complex)
12
Q
what is nitrogen fixing overall
A
set of redox reactions
13
Q
where do the electrons used in this reaction come from
A
things like pyruvate
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
15
Q
is there a big ATP investment in nitrogen fixing
A
yup
16
Q
how much ATP is invested in nitrogen fixing
A
16 ATP per N2 molecule that’s reduced
17
Q
why does it still happen even though it’s energetically very expensive
A
highly conserved evolutionary process, so has to be important
18
Q
what is nitrogen fixing important for
A
for bacteria and their ability to assimilate this nitrogen into their structures
19
Q
what can certain types of plants do
A
form symbiotic relationships w/ nitrogen fixing bacteria
20
Q
which plants form symbiotic relationships w/ nitrogen fixing bacteria
A
leguminous plants
21
Q
where do these symbiotic bacteria live
A
in root nodules of leguminous plants; they’re enclosed in there
22
Q
what is nitrogenase complex sensitive to
A
oxygen
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
24
Q
what is the purpose of those nodules
A
creates an anaerobic environment in which to carry out nitrogen fixation
25
how is leghemoglobin made
plants that form symbiotic relationship w/ nitrogen fixing bacteria produce this compound
26
what is leghemoglobin
can bind up any oxygen present to reduce levels of oxygen toxicity in nitrogenase enzyme
27
why do plants produce leghemoglobin
to minimize the effects of oxygen on nitrogen fixation
28
what happens once ammonia has been generated from the reduction of N2 gas
enzymes will act on ammonia to begin the process of incorporating nitrogen into organic structure
29
what happens to electrons from pyruvate
go to 8 ferredoxin or flavodoxin, then 8 dinitrogenase reductase, then 8 nitrogenase reductase again, then dinitrogenase. generate 2 ammonia molecules
30
what does glutamine synthetase do
enzyme that catalyzes assimilation of NH4 into glutamate to yield glutamine
31
why does glutamine synthetase add NH4 to glutamate to make glutamine
because it's one of the enzymes that begins process of incorporating nitrogen into organic structures
32
what is glutamine synthetase
large multi subunit enzyme complex, 12 identical subunits
33
what is the process of glutamate into glutamine conversion
one of the early rxns that allows for eventual assimilation of that nitrogen into other amino acids, and thus into proteins/other structures
34
what is a primary regulatory point in nitrogen metabolism
glutamine synthetase
35
how does glutamine synthetase regulation occur
2 ways; allosteric regulation, covalent modification
36
how does covalent modification occur
thru a process called adenylation
37
how many diff allosteric inhibitors for glutamine synthetase
8
38
what are many of the allosteric inhibitors of glutamine synthetase
end products of pathways that originated w/ conversion of glutamate to glutamine
39
what is needed in order for the enzyme to be completely inhibited
has to have all 8 allosteric inhibitors
40
describe these 8 allosteric inhibitors
has distinct sites for each of the inhibitors, they can all feedback inhibit the enzyme
41
what happens if you have 1 or 2 of these inhibitors
might lower activity of the enzyme somewhat
42
what is the second level of control for glutamine synthetase
covalent modification
43
what form of covalent modification found in glutamine synthetase
adenylation
44
what is adenylation
covalent attachment of a molecule of AMP (adenosine monophosphate)
45
describe adenylation in this case
attachment of AMP to tyrosine
46
what specific tyrosine is being adenylated
tyrosine at position 397 on each of the subunits of glutamine synthetase that are modified
47
what are the effects of this adenylation covalent modification
inhibits the enzyme
48
what enzymes carry out adenylation
adenyltransferases (At)
49
what can happen besides adenylation
de-adenylation
50
why is de-adenylation a thing
cuz forms of covalent modification like phosphorylation etc. are generally reversible
51
what is the effect of adenylation
inactivates glutamine synthetase
52
what is the effect of de-adenylation
activates glutamine synthetase
53
when does deadenylation occur
when we have low concentrations of some of those allosteric inhibitors, sow that we favor activation of synthetase overall
54
what enzymes are for de-adenylation
same as the enzymes that carry out adenylation
55
what do adenylate transferases do
carry out both reactions; attachment of AMP and its removal
56
what is adenylation mediated by
another form of covalent modification, uridylation
57
what is uridylation
attachment of uridine monophosphate (UMP
58
what is P2
regulatory subunit associated w/ adenylyl transferase enzyme
59
what dictates whether adenylyl transferase carries out adenylation or de-adenylation
whether P2 is uridylated or not
60
what happens when P2 is not uridylated
missing a UMP, AT enzyme will carry out adenylation, inactivating glutamine synthetase
61
what happens when P2 is uridylated
switches activity of AT to carry out de-adenylation, activating glutamine synthetase
62
what is uridylation controlled by
uridyltransferase
63
what favors activation of uridylyl transferase
high E state indicators like ATP, high [ ] of TCA cycle intermediates (a-ketoglutarate, etc.)
64
what do these high E state indicators do
regulate overall activity of that particular transferase, and regulate the type of activity we see with adenylation and deadenylation of glutamine syntethase
65
what does uridylation of Tyr do
stimulate deadenylation
66
where are AA carbon skeletons derived from
3 sources; glycolysis, TCA cycle, pentose phosphate pathway
67
what AA for ribose-5-phosphate
histidine
68
what AA for a-ketoglutarate
glutamate, glutamine, proline, arginine
69
what AAs for 3-phosphoglycerate
serine, glycine, cysteine
70
what AAs for oxaloacetate
aspartate, asparagine, methione, threonine, lysine
71
what AAs for pyruvate
alanine, valine, leucine, isoleucine
72
PEP and erythrose-4-phosphate
tryptophan, phenylalanine, tyrosine
73
how is isoleucine biosynthesis pathway regulated
allosteric regulation/feedback inhibition
74
what serves as an allosteric inhibitor for what enzyme in isoleucine pathway
isoleucine (end product) inhibits first enzyme of pathway, threonine dehydratase
75
what is the first enzyme in isoleucine biosynthesis pathwayt
threonine dehydratase
76
what is another type of feedback inhibition we see
sequential feedback inhibition
77
why is sequential feedback inhibition a thing
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]
78
basically what does sequential feedback inhibition do
prevents one endproduct from shutting down key steps in a pathway when other products are required
79
what are isozymes
multiple forms of the same enzyme; same enzyme, catalyzes same step, just regulated by different allosteric regulators
80
when do we see isozymes
conversion of aspartate into aspartyl-beta-phosphate
81
how many forms of the enzyme are there that catalyze this step
3; A1, A2, A3
82
describe how A1, A2, A3 are inhibited
A1 inhibited by isoleucine and lysine, A2 not inhibited by anything, A3 inhibited by threonine [basically all by diff things]
83
what do isozymes being inhibited by different allosteric inhibitors allow for
allows you to achieve a balanced pool of all the diff amino acids here
84
why does sequential feedback inhibition ensures we have a balanced pool of AAs
we're not gonna be lacking in any one AA, cuz we can keep some of these pathways active while we inhibit others
85
where do we get AAs from our diet
from proteins in the food we eat
86
what breaks down proteins
proteolytic enzymes that break down proteins into shorter peptides and individual AAs
87
what would happen if this proteolytic breakdown was occurring in upper portions of small intestine
absorption of those AAs into intestinal epithelial cells, those AAs transported into blood where they can undergo oxidation/degradation
88
what 2 things are we talking about when we talk about degradation of AAs
what happens to amino groups in AAs, what happens to carbon skeletons that are separated from amino group
89
do we derive a lot of E from nitrogen (in terms of energy metabolism)
not really
90
what can nitrogen be used for once separated from the cell
in biosynthesis of new AAs in the cell, nucleotide synthesis, synthesis of other nitrogen containing compounds
91
what happens to an excess of nitrogen
fed into urea cycle, excreted in the form of urea
92
where does excess of nitrogen come from
ammonia ions
93
what happens to carbon skeleton
separated from amino group
94
what happens to those carbon skeletons after separation
converted into diff types of alpha-keto acids, and fed into TCA cycle
95
what does TCA do
provides intermediates for synthesis of other things like glucose, etc. (gluconeogenesis)
96
what two pathways are connected
urea cycle and TCA cycle
97
how are urea cycle and TCA cycle connected
aspartate-argininosuccinate shunt
98
what does aspartate-arigninosuccinate shunt serve as
anaplerotic source of intermediates, allows us to replenish these intermediates
99
basically what happens to amino acids once cleaved from larger proteins
2 fats; fate of amino group nitrogen of AA, fate of rest of carbon skeleton of AA
100
what happens to amino group nitrogen of AA
removed from AA by aminotransferases to yield ammonia (nitrogen not used in energy-producing pathways)
101
what happens to rest of carbon skeleton of AA
enters metabolic pathways as precursors of glucose or Krebs cycle intermediates
102
what are aminotransferases
enzymes that separate the amino group from carbon skeleton
103
what is the resulting compound that's produced after enzymes separate amino group from carbon skeleton
ammonia
104
what is produced after aminotransferases do what they do
ammonia, and carbon skeletons
105
what happens to carbon skeletons
go into TCA cycle
106
what happens to excess ammonia in nitrogen
fed into urea cycle (for mammals)
107
are amino groups a source of energy
not typically
108
what are carbon skeletons gonna serve as
precursors for gluconeogenesis or fed into TCA cycle
109
what do aminotransferases do specifically
amino group in amino acid is transferred from AA to alpha-ketoglutarate
110
what does transferring of amino group from AA to a-ketoglutarate often yield
glutamate
111
what happens to glutamate after it's generated
in biosynthesis pathways often used as an amino group donor to synthesize other AAs
112
what are we left with after AAs are synthesized
a-keto acids
113
what is Pyridoxal phosphate (PLP)
cofactor for aminotransferase
114
what is aminotransferase's cofactor
pyridoxal phosphate
115
basically what do aminotransferases do
transfer amino group from AA to alpha ketoglutarate to form glutamate (can synthesize other AAs), AA becomes alpha-keto acid
116
what is the amino group acceptor in aminotransferase reactions
alpha-ketoglutarate
117
what are the uses of nitrogen from ammonium ions
de novo synthesis of amino acids and nucleotides
118
what happens to excess ammonium ions
converted into urea (if mammal fed into urea cycle), etc., uric acid, ammonia
119
basically describe fate of ammonium ions
some used in synthesis of nitrogen compounds (AAs, nucleotides), excess is converted to ammonia, uric acid, urea, etc.
120
what are the sources we derive nitrogen from
glutamine, amino acids, alanine cycle
121
describe how nitrogen comes from glutamine
glutamine, comes from tissues that AREN'T liver (extrahepatic tissues)
122
describe how nitrogen comes from AAs
often times those AAs will be sent to liver tissue for separation of amino group from rest of carbon skeleton
123
describe how nitrogen comes from in alanine cycle
alanine cycle is mainly the form of nitrogen that is transported from muscle to liver, and utilized in excretory pathway in urea cycle
124
are there multiple sources of nitrogen in body or just one
at least 3 diff forms of nitrogen
125
what happens to nitrogen that comes from diff sources
can all be utilized, funneled into urea cycle
126
where do we derive small amount of oxidative energy from
catabolism of amino acids
127
where are amino acids derived from
breakdown of cellular proteins, ingested proteins, body proteins (when other forms of fuel aren't available)
128
what do proteases do
degrade ingested proteins in stomach and small intestine
129
what happens to these various sources of amino gruops
transported to places like liver
130
what happens to glutamine
imported into liver/hepatocytes, then transported into mitochondria
131
what happens after glutamine goes into the liver
transporters move it into mitochondria
132
what do glutamine/glutamate undergo
removal of amino group nitrogen
133
what removes amino group from glutamine/glutamate
aminotransferase and glutamate dehydrogenase
134
what happens after aminotransferase and glutamate do their thing
amino group is released
135
what acts on amino group
carbamoyl phosphate synthetase I
136
why is carbamoyl phosphate synthetase I important
cuz this is how nitrogen enters the urea cycle
137
what is first intermediate of urea cycle
citrulline
138
what is end product of urea cycle
ornithine
139
what is the first rxn in urea cycle
combines carbamoyl phosphate and ornithine to produce citrulline
140
why is carbamoyl phosphate important
cuz its the form of nitrogen that enters the urea cycle
141
what step in urea cycle takes place in mitochondria
first step only
142
what happens to citrulline
citrulline in mitochondrial matrix transported out of mitochondria by transporters
143
what happens to citrulline once it's in the cytoplasm
citrulline is acted on, taken into the rest of urea cycle
144
what kinds of steps do we have in urea cycle
where it indirectly connects to TCA cycle
145
what do we have in step 4 of urea cycle
production of urea
146
how is urea produced
conversion of arginine into ornithine (last compound in cycle), results in production of urea
147
what is excreted from the body eventually
urea
148
what happens early on in amino acid catabolism
separation of AA group from carbon skeleton
149
what happens in most cases
amino group transferred to a-ketoglutarate to form glutamate
150
what does formation of glutamate from a-ketoglutarate require
pyridoxal phosphate
151
what happens to glutamate
transported to liver mitochondria
152
what happens when glutamate transported to liver mito
glutamate dehydrogenase releases amino group as NH4+
153
how is ammonia from other tissues transported to liver
1) amide nitrogen of glutamine or 2) amino group of alanine (from skeletal muscle)
154
how is pyruvate produced
by deamination of alanine (liver) is converted to glucose (transported back to muscle)
155
basically how is pyruvate produced
glucose alanine-cycle
156
how is NH4+ excreted
in diff forms, depending on the organism
157
what is produced from urea cycle
urea
158
what are ureotelic animals
organisms that excrete urea
159
uricotelic animals
organisms that excrete nitrogen in form of uric acid
160
who are ureotelic animals
many terrestrial vertebrates, sharks
161
who are uricotelic animals
birds, reptiles
162
what are ammonotelic animals
excrete nitrogen as ammonia
163
who are ammonotelic animals
bony fish, amphibians (basically aquatic vertebrates)
164
are there diff strategies for nitrogen excretion
yup; diff animals excrete nitrogen in diff forms (urea, uric acid, ammonia)
165
how is ammonia excreted in most terrestrial organism
converted to urea
166
what is the connection b/w urea cycle and TCA cycle
aspartate argininosuccinate shunt
167
how os carbamoyl phosphate formed
from carbon dioxide and amino group derived from earlier rxns involving diff AAs
168
what step of urea cycle involves actual production of urea
last step; generates ornithine as end product from arginine, urea is produced
169
what is the krebs bicycle
aspartate-argininosuccinate; link b/w urea and TCA cycles
170
what is urea cycle (for AAs)
where amino groups from AAs are gonna be sent
171
what is TCA cycle
carbon skeletons from AAs are gonna be used and incorporated in TCA
172
where do these cycles occur
TCA cycle occurs in mitochondria, urea cycle only first step occurs in miotochondria
173
what step in urea cycle occurs in mitochondria
incorporation of carbamoyl phosphoate in that amino group nitrogen into urea cycle w/ ornithine to produce citrulline
174
where do rest of steps in urea cycle occur
cytoplasm
175
what do we need to get in and out of mitochondria
transportesr
176
what is one of three sources of amino groups
muscle
177
describe muscle
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
basically what happens to muscle proteins
if proteins damaged, they're gonna be further degraded. AAs are gonna be either recycled or amino groups separated
179
what happens when amino groups separted from AAs in muscle
specific aminotransferase that generates alanine
180
what aminotransferase generates alanine
alanine aminotransferase
181
what is alanine
represents the major carrier form of nitrogen from muscle, from AAs that were present in muscle
182
what does alanine serve as
carrier of ammonia and a carbon skeleton of pyruvate from skeletal muscle to liver
183
what happens to alanine
transported thru bloodstream, taken up into liver cells, where amino group of alanine is separated from carbon skeleton
184
what happens to alanine in liver cells
amino group separated from carbon skeleton
185
what does the separation of amino group from carbon skeleton in alanine result in
production of pyruvate
186
where is pyruvate used
gluconeogenesis (glucose synthesis)
187
what happens to ammonia
excreted
188
what happens to excess nitrogen
amino group converted into glutamate or used in glutamate synthesis, then eventual excretion thru urea cycle
189
how is pyruvate produced
deamination of alanine
190
describe where pyruvate goes
produced in liver thru deamination of alanine; then transported back to muscle when converted to glucose
191
what happens to pyruvate after is produced
converted to glucose
192
what can carbon atoms produced in AA synthesis be used for
to feed various metabolic intermediates
193
just like in AA synthesis, what can Cs produced from AA degradation be used for
to feed various metabolic intermediates, specifically TCA cycle and some gluconeogenesis
194
what are 2 main categories of AAs based on
based on how they're handled after they've been degraded: glucogenic and ketogenic
195
what are glucogenic amino acids
AAs that feed into TCA cycle
196
what are ketogenic amino acids
AAs that result in production of ketone/ketone bodies
197
talk about alanine
carbon skeletons from alanine can be used in pyruvate production
198
what happens to pyruvate produced from alanine
used in gluconeogenesis pathway
199
basically what are glucogenic AAs
carbon skeletons which can be used in synthesis of glucose
200
what are ketogenic AAs
AAs used in synthesis of ketone containing compounds like ketone bodies
201
when are ketone bodies produced
long-term starvation conditions, provides energy for CNS
202
what do many genetic disorders involve
defects or inability to produce certain enzymes involved in AA catabolism/anabolism
203
phenylketonuria
defects in ability to produce enzyme phenylalanine hydroxylase
204
what is phenylalanine hydroxylase
converts phenylalanine into tyrosine
205
what is phenylalanine hydroxylase involved in
affects aspects of aromatic AA metabolism, esp in mamammals
206
what do people with phenylketonuria have (or not have)
phenylalanine hydroxylase
207
what do phenylketonurics have to avoid
diets w/ phenylalanine
208
what happens if they consume phenylalanine while lacking hydroxylase
phenylalanine will be converted into phenylpyruvic acid
209
what is phenylpyruvic acid
toxic byproduct
210
what does phenylpyruvic acid cause
toxic to CNS, cause serious complications
211
what are ketogenic AAs
leucine, lysine, phenylalanine, tryptophan, tyrosine, isoleucine, threonine
212
what are AAs for acetoacetyl CoA
leucine, lysine, phenylalanine, tryptophan
213
what are AAs for acetyl CoA
isoleucine, leucine, threonine, tryptophan
214
what are AAs for glutamate
arginine, glutamine, histidine, proline
215
what are AAs for succinyl CoA
isoleucine, methionine, threonine, valine
216
what are AAs for fumarate
phenylalanine, tyrosine
217
what are AAs for oxaloacetate
asparagine, aspartate
218
what are AAs for pyruvate
alanine, cysteine, glycine, serine, threonine, tryptophan
219
what are glucogenic AAs
alanine, cysteine, glycine, serine, threonine, tryptophan, asparagine, aspartate, phenylalanine, tyrosine, isoleucine, methionine, threonine, valine, arginine, glutamine, histidine, proline
