biochem lecture 10 Flashcards
what do amino acids contain
nitrogen, in the form of amino groups
what is one important thing nitrogen cycle does
assimilation of nitrogen into organic structures
specifically what part of nitrogen cycle helps w/ assimilation of nitrogen into organic structures
nitrogen fixation
what is nitrogen fixation
the ability of certain microorganisms/bacteria that are able to take elemental/atmospheric nitrogen (N2 gas) and reduce it to form ammonia (NH4)
basically what is nitrogen fixation
N2 gas reduced to ammonia (NH4)
what kind of reaction is nitrogen fixation
reduction
what organisms do nitrogen fixing
micro organisms, bacterial, soil microbes/bacteria
why is the transformation of N2 gas into ammonia important
represents a gateway form of nitrogen that’s gonna be assimilated into AAs and other nitrogen containing carbon compounds (nucleotides, etc.)
what other processes are in nitrogen cycle
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
what is denitrification
certain microorganisms able to take nitrites, eliminate nitrogen in the form of N2 gas released into atmosphere
what enzyme is involved in nitrogen fixation
nitrogenase complex (nitrogenase enzyme complex)
what is nitrogen fixing overall
set of redox reactions
where do the electrons used in this reaction come from
things like pyruvate
what happens to those electrons in nitrogen fixation
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
is there a big ATP investment in nitrogen fixing
yup
how much ATP is invested in nitrogen fixing
16 ATP per N2 molecule that’s reduced
why does it still happen even though it’s energetically very expensive
highly conserved evolutionary process, so has to be important
what is nitrogen fixing important for
for bacteria and their ability to assimilate this nitrogen into their structures
what can certain types of plants do
form symbiotic relationships w/ nitrogen fixing bacteria
which plants form symbiotic relationships w/ nitrogen fixing bacteria
leguminous plants
where do these symbiotic bacteria live
in root nodules of leguminous plants; they’re enclosed in there
what is nitrogenase complex sensitive to
oxygen
why is oxygen toxic to nitrogenase complex
O2 is electronegative, can inhibit the series of redox rxns that are essential for reduction of N2 gas into ammonia
what is the purpose of those nodules
creates an anaerobic environment in which to carry out nitrogen fixation
how is leghemoglobin made
plants that form symbiotic relationship w/ nitrogen fixing bacteria produce this compound
what is leghemoglobin
can bind up any oxygen present to reduce levels of oxygen toxicity in nitrogenase enzyme
why do plants produce leghemoglobin
to minimize the effects of oxygen on nitrogen fixation
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
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
what does glutamine synthetase do
enzyme that catalyzes assimilation of NH4 into glutamate to yield glutamine
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
what is glutamine synthetase
large multi subunit enzyme complex, 12 identical subunits
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
what is a primary regulatory point in nitrogen metabolism
glutamine synthetase
how does glutamine synthetase regulation occur
2 ways; allosteric regulation, covalent modification
how does covalent modification occur
thru a process called adenylation
how many diff allosteric inhibitors for glutamine synthetase
8
what are many of the allosteric inhibitors of glutamine synthetase
end products of pathways that originated w/ conversion of glutamate to glutamine
what is needed in order for the enzyme to be completely inhibited
has to have all 8 allosteric inhibitors
describe these 8 allosteric inhibitors
has distinct sites for each of the inhibitors, they can all feedback inhibit the enzyme
what happens if you have 1 or 2 of these inhibitors
might lower activity of the enzyme somewhat
what is the second level of control for glutamine synthetase
covalent modification
what form of covalent modification found in glutamine synthetase
adenylation
what is adenylation
covalent attachment of a molecule of AMP (adenosine monophosphate)
describe adenylation in this case
attachment of AMP to tyrosine
what specific tyrosine is being adenylated
tyrosine at position 397 on each of the subunits of glutamine synthetase that are modified
what are the effects of this adenylation covalent modification
inhibits the enzyme
what enzymes carry out adenylation
adenyltransferases (At)
what can happen besides adenylation
de-adenylation
why is de-adenylation a thing
cuz forms of covalent modification like phosphorylation etc. are generally reversible
what is the effect of adenylation
inactivates glutamine synthetase
what is the effect of de-adenylation
activates glutamine synthetase
when does deadenylation occur
when we have low concentrations of some of those allosteric inhibitors, sow that we favor activation of synthetase overall
what enzymes are for de-adenylation
same as the enzymes that carry out adenylation
what do adenylate transferases do
carry out both reactions; attachment of AMP and its removal
what is adenylation mediated by
another form of covalent modification, uridylation
what is uridylation
attachment of uridine monophosphate (UMP
what is P2
regulatory subunit associated w/ adenylyl transferase enzyme
what dictates whether adenylyl transferase carries out adenylation or de-adenylation
whether P2 is uridylated or not
what happens when P2 is not uridylated
missing a UMP, AT enzyme will carry out adenylation, inactivating glutamine synthetase
what happens when P2 is uridylated
switches activity of AT to carry out de-adenylation, activating glutamine synthetase
what is uridylation controlled by
uridyltransferase
what favors activation of uridylyl transferase
high E state indicators like ATP, high [ ] of TCA cycle intermediates (a-ketoglutarate, etc.)
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
what does uridylation of Tyr do
stimulate deadenylation
where are AA carbon skeletons derived from
3 sources; glycolysis, TCA cycle, pentose phosphate pathway
what AA for ribose-5-phosphate
histidine
what AA for a-ketoglutarate
glutamate, glutamine, proline, arginine
what AAs for 3-phosphoglycerate
serine, glycine, cysteine
what AAs for oxaloacetate
aspartate, asparagine, methione, threonine, lysine
what AAs for pyruvate
alanine, valine, leucine, isoleucine
PEP and erythrose-4-phosphate
tryptophan, phenylalanine, tyrosine
how is isoleucine biosynthesis pathway regulated
allosteric regulation/feedback inhibition
what serves as an allosteric inhibitor for what enzyme in isoleucine pathway
isoleucine (end product) inhibits first enzyme of pathway, threonine dehydratase
what is the first enzyme in isoleucine biosynthesis pathwayt
threonine dehydratase
what is another type of feedback inhibition we see
sequential feedback inhibition
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]
basically what does sequential feedback inhibition do
prevents one endproduct from shutting down key steps in a pathway when other products are required
what are isozymes
multiple forms of the same enzyme; same enzyme, catalyzes same step, just regulated by different allosteric regulators
when do we see isozymes
conversion of aspartate into aspartyl-beta-phosphate
how many forms of the enzyme are there that catalyze this step
3; A1, A2, A3
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]
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
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
where do we get AAs from our diet
from proteins in the food we eat
what breaks down proteins
proteolytic enzymes that break down proteins into shorter peptides and individual AAs
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
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
do we derive a lot of E from nitrogen (in terms of energy metabolism)
not really
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
what happens to an excess of nitrogen
fed into urea cycle, excreted in the form of urea
where does excess of nitrogen come from
ammonia ions
what happens to carbon skeleton
separated from amino group
what happens to those carbon skeletons after separation
converted into diff types of alpha-keto acids, and fed into TCA cycle
what does TCA do
provides intermediates for synthesis of other things like glucose, etc. (gluconeogenesis)
what two pathways are connected
urea cycle and TCA cycle
how are urea cycle and TCA cycle connected
aspartate-argininosuccinate shunt
what does aspartate-arigninosuccinate shunt serve as
anaplerotic source of intermediates, allows us to replenish these intermediates
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
what happens to amino group nitrogen of AA
removed from AA by aminotransferases to yield ammonia (nitrogen not used in energy-producing pathways)
what happens to rest of carbon skeleton of AA
enters metabolic pathways as precursors of glucose or Krebs cycle intermediates
what are aminotransferases
enzymes that separate the amino group from carbon skeleton
what is the resulting compound that’s produced after enzymes separate amino group from carbon skeleton
ammonia
what is produced after aminotransferases do what they do
ammonia, and carbon skeletons
what happens to carbon skeletons
go into TCA cycle
what happens to excess ammonia in nitrogen
fed into urea cycle (for mammals)
are amino groups a source of energy
not typically
what are carbon skeletons gonna serve as
precursors for gluconeogenesis or fed into TCA cycle
what do aminotransferases do specifically
amino group in amino acid is transferred from AA to alpha-ketoglutarate
what does transferring of amino group from AA to a-ketoglutarate often yield
glutamate
what happens to glutamate after it’s generated
in biosynthesis pathways often used as an amino group donor to synthesize other AAs
what are we left with after AAs are synthesized
a-keto acids
what is Pyridoxal phosphate (PLP)
cofactor for aminotransferase
what is aminotransferase’s cofactor
pyridoxal phosphate
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
what is the amino group acceptor in aminotransferase reactions
alpha-ketoglutarate
what are the uses of nitrogen from ammonium ions
de novo synthesis of amino acids and nucleotides
what happens to excess ammonium ions
converted into urea (if mammal fed into urea cycle), etc., uric acid, ammonia
basically describe fate of ammonium ions
some used in synthesis of nitrogen compounds (AAs, nucleotides), excess is converted to ammonia, uric acid, urea, etc.
what are the sources we derive nitrogen from
glutamine, amino acids, alanine cycle
describe how nitrogen comes from glutamine
glutamine, comes from tissues that AREN’T liver (extrahepatic tissues)
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
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
are there multiple sources of nitrogen in body or just one
at least 3 diff forms of nitrogen
what happens to nitrogen that comes from diff sources
can all be utilized, funneled into urea cycle
where do we derive small amount of oxidative energy from
catabolism of amino acids
where are amino acids derived from
breakdown of cellular proteins, ingested proteins, body proteins (when other forms of fuel aren’t available)
what do proteases do
degrade ingested proteins in stomach and small intestine
what happens to these various sources of amino gruops
transported to places like liver
what happens to glutamine
imported into liver/hepatocytes, then transported into mitochondria
what happens after glutamine goes into the liver
transporters move it into mitochondria
what do glutamine/glutamate undergo
removal of amino group nitrogen
what removes amino group from glutamine/glutamate
aminotransferase and glutamate dehydrogenase
what happens after aminotransferase and glutamate do their thing
amino group is released
what acts on amino group
carbamoyl phosphate synthetase I
why is carbamoyl phosphate synthetase I important
cuz this is how nitrogen enters the urea cycle
what is first intermediate of urea cycle
citrulline
what is end product of urea cycle
ornithine
what is the first rxn in urea cycle
combines carbamoyl phosphate and ornithine to produce citrulline
why is carbamoyl phosphate important
cuz its the form of nitrogen that enters the urea cycle
what step in urea cycle takes place in mitochondria
first step only
what happens to citrulline
citrulline in mitochondrial matrix transported out of mitochondria by transporters
what happens to citrulline once it’s in the cytoplasm
citrulline is acted on, taken into the rest of urea cycle
what kinds of steps do we have in urea cycle
where it indirectly connects to TCA cycle
what do we have in step 4 of urea cycle
production of urea
how is urea produced
conversion of arginine into ornithine (last compound in cycle), results in production of urea
what is excreted from the body eventually
urea
what happens early on in amino acid catabolism
separation of AA group from carbon skeleton
what happens in most cases
amino group transferred to a-ketoglutarate to form glutamate
what does formation of glutamate from a-ketoglutarate require
pyridoxal phosphate
what happens to glutamate
transported to liver mitochondria
what happens when glutamate transported to liver mito
glutamate dehydrogenase releases amino group as NH4+
how is ammonia from other tissues transported to liver
1) amide nitrogen of glutamine or 2) amino group of alanine (from skeletal muscle)
how is pyruvate produced
by deamination of alanine (liver) is converted to glucose (transported back to muscle)
basically how is pyruvate produced
glucose alanine-cycle
how is NH4+ excreted
in diff forms, depending on the organism
what is produced from urea cycle
urea
what are ureotelic animals
organisms that excrete urea
uricotelic animals
organisms that excrete nitrogen in form of uric acid
who are ureotelic animals
many terrestrial vertebrates, sharks
who are uricotelic animals
birds, reptiles
what are ammonotelic animals
excrete nitrogen as ammonia
who are ammonotelic animals
bony fish, amphibians (basically aquatic vertebrates)
are there diff strategies for nitrogen excretion
yup; diff animals excrete nitrogen in diff forms (urea, uric acid, ammonia)
how is ammonia excreted in most terrestrial organism
converted to urea
what is the connection b/w urea cycle and TCA cycle
aspartate argininosuccinate shunt
how os carbamoyl phosphate formed
from carbon dioxide and amino group derived from earlier rxns involving diff AAs
what step of urea cycle involves actual production of urea
last step; generates ornithine as end product from arginine, urea is produced
what is the krebs bicycle
aspartate-argininosuccinate; link b/w urea and TCA cycles
what is urea cycle (for AAs)
where amino groups from AAs are gonna be sent
what is TCA cycle
carbon skeletons from AAs are gonna be used and incorporated in TCA
where do these cycles occur
TCA cycle occurs in mitochondria, urea cycle only first step occurs in miotochondria
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
where do rest of steps in urea cycle occur
cytoplasm
what do we need to get in and out of mitochondria
transportesr
what is one of three sources of amino groups
muscle
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
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
what happens when amino groups separted from AAs in muscle
specific aminotransferase that generates alanine
what aminotransferase generates alanine
alanine aminotransferase
what is alanine
represents the major carrier form of nitrogen from muscle, from AAs that were present in muscle
what does alanine serve as
carrier of ammonia and a carbon skeleton of pyruvate from skeletal muscle to liver
what happens to alanine
transported thru bloodstream, taken up into liver cells, where amino group of alanine is separated from carbon skeleton
what happens to alanine in liver cells
amino group separated from carbon skeleton
what does the separation of amino group from carbon skeleton in alanine result in
production of pyruvate
where is pyruvate used
gluconeogenesis (glucose synthesis)
what happens to ammonia
excreted
what happens to excess nitrogen
amino group converted into glutamate or used in glutamate synthesis, then eventual excretion thru urea cycle
how is pyruvate produced
deamination of alanine
describe where pyruvate goes
produced in liver thru deamination of alanine; then transported back to muscle when converted to glucose
what happens to pyruvate after is produced
converted to glucose
what can carbon atoms produced in AA synthesis be used for
to feed various metabolic intermediates
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
what are 2 main categories of AAs based on
based on how they’re handled after they’ve been degraded: glucogenic and ketogenic
what are glucogenic amino acids
AAs that feed into TCA cycle
what are ketogenic amino acids
AAs that result in production of ketone/ketone bodies
talk about alanine
carbon skeletons from alanine can be used in pyruvate production
what happens to pyruvate produced from alanine
used in gluconeogenesis pathway
basically what are glucogenic AAs
carbon skeletons which can be used in synthesis of glucose
what are ketogenic AAs
AAs used in synthesis of ketone containing compounds like ketone bodies
when are ketone bodies produced
long-term starvation conditions, provides energy for CNS
what do many genetic disorders involve
defects or inability to produce certain enzymes involved in AA catabolism/anabolism
phenylketonuria
defects in ability to produce enzyme phenylalanine hydroxylase
what is phenylalanine hydroxylase
converts phenylalanine into tyrosine
what is phenylalanine hydroxylase involved in
affects aspects of aromatic AA metabolism, esp in mamammals
what do people with phenylketonuria have (or not have)
phenylalanine hydroxylase
what do phenylketonurics have to avoid
diets w/ phenylalanine
what happens if they consume phenylalanine while lacking hydroxylase
phenylalanine will be converted into phenylpyruvic acid
what is phenylpyruvic acid
toxic byproduct
what does phenylpyruvic acid cause
toxic to CNS, cause serious complications
what are ketogenic AAs
leucine, lysine, phenylalanine, tryptophan, tyrosine, isoleucine, threonine
what are AAs for acetoacetyl CoA
leucine, lysine, phenylalanine, tryptophan
what are AAs for acetyl CoA
isoleucine, leucine, threonine, tryptophan
what are AAs for glutamate
arginine, glutamine, histidine, proline
what are AAs for succinyl CoA
isoleucine, methionine, threonine, valine
what are AAs for fumarate
phenylalanine, tyrosine
what are AAs for oxaloacetate
asparagine, aspartate
what are AAs for pyruvate
alanine, cysteine, glycine, serine, threonine, tryptophan
what are glucogenic AAs
alanine, cysteine, glycine, serine, threonine, tryptophan, asparagine, aspartate, phenylalanine, tyrosine, isoleucine, methionine, threonine, valine, arginine, glutamine, histidine, proline
