Moore section post midterm Flashcards
is there a protein whose sole job is to act as a storage depot for amino acids?
nope.
What is the main source for amino acid input to the pool?
Cellular protein turnover
What is the weight of proteins recycled in a day due to cellular turnover?
300/400g of protein in a day
What are some examples of protein halflife being variable?
regulatory proteins degrade in minutes to hours
- collagens or eye lens proteins take months or years
What is the major protein degradation pathway?
ubiquitin-proteasome pathway
Give an overview of the ubiquitin proteasome pathway
Ubiquitin molecules are linked to a specific lysine residue in the target protein
- protein becomes polyubiquinated which is recognized by the proteosome
- protein is processed into peptides , ubiquitin is cleaved and re utilized.
What links the ubiquitin to the target protein? type of linkage?
isopeptide bond - to lysine not amino terminus
Why do we have to degrade proteins to peptides?
because they fat as fuck
What is proteolysis?
breakdown of protein by hydrolysis, cleavage of proteins by digestive proteinases - enzymes are secreted into stomach and small intestine
What is the benefit of the gastric environment for proteolysis?
gastric acid environment denatures proteins and thus enhances proteolysis - due to low pH
- gastric acid also acts as an antiseptic, killing bacteria and viruses
what is the important pump in the stomach?
K/H pump in membrane of specialized stomach cells pump protons into the stomach in exchange for K at the expense of ATP hydrolysis - generates acidic environment
What is GERD?
gastroesophageal reflux disease
- K/H pump is overactive which results in reflux
what are proteinase zymogens?
inactive proteolytic enzymes - activated by proteolysis
- proteinases are synthesized and stored as zymogens so they dont break down proteins in the cells where they are made stored and dont digest themselves prior to secretion
What can pepsin cleave?
preferentially cleaves peptide bonds between hydrophobic amino acids or aromatic amino acids
What can trypsin cleave?
cleaves bonds following an Arg or Lys residue
What can chymotrypsin cleave?
preferentially cleaves peptide bonds after an aromatic amino acid
What can elastase cleave?
not as specific - cuts amino acids with smaller hydrophobic side chains such as glycine, alanine or valine
Proteases eventually self _____
inactivate - digest themselves
What are endopeptidases?
proteolytic enzymes that cleave internal peptide bonds in a substrate
What are aminopeptidases and carboxypeptidases?
can only cleave amino or carboxy residue of a peptide - works further down in the intestine - chew up one by one until only amino acids are left
What happens to excess amino acids?
not excreted or stored, must be converted to other molecules that can be excreted or repurposed
What is the transamination reaction?
- transfers amino group to aKG
— donor - L amino acids
— acceptor - a KG - funnels amino groups to glutamate
- obligatory step in degradation of amino acids except for Lys and Thr
- Reversible reaction
- Enzymes - aminotransferases - specific amino group donor and acceptor
What are the two different aminotransferases? And what tissues / cell locations
Aspartate aminotransferase - liver mitochondria - see urea cycle
- Alanine aminotransferase - muscle cytosol - muscle amino groups converted to alanine which is transported to liver via blood
What is the ultimate acceptor of donated amino groups - what does this lead to?
alpha ketoglutarate - glutamate
what converts glutamate into alphaketoglutarate?
mitochondrial glutamate dehydrogenase
What is PLP?
Pyridoxal Phosphate - cofactor for transaminases
- amino group acceptor
Pyridoxamine phosphate is an aketo group acceptor
- bound by default in active site to lys side chain NH3 group
What does the amino group of incoming amino acids do with PLP?
forms covalent linkage with aldehyde group - a-keto group leaves
What does the ketone group of incoming a-keto acids do with pyridoxamine phosphate?
forms covalent linkage with amino group
- amino group displaves by active site lysine amino group
- glutamate leaves
What is a Schiff base / aldimine?
chemical term that defines an imine C—N group derived from an aldehyde
Aminotransferases are important molecules for what?
liver or heart damage
What are the fates of glutamate when it enters the mitochondria in the liver/
Enters liver - acted on by glutamate dehydrogenase
- some is converted to NH4 and goes to urea cycle
- some is converted back to aKG and goes into TCA cycle
Is NH3 or NH4 odorless?
NH4
Go back and look at second lecture of stan
yes maam
What are the three ways of removing nitrogen / ammonia?
NH4+ - ammonium in aquatic vertebrates and fish
Urea - most terrestrial vertebrates
Uric acid - reptiles and birds
What happens in the urea cycle?
converts NH4 to urea
- occurs in liver
- urea is secreted into blood, filtered by kidney and excreted in urine
What are the three precursors of urea?
NH4, CO2, Aspartate
What is a major regulation point of urea cycle?
Carbamoyl Phosphate Synthetase I
(not actually part of the cycle)
What occurs in step 1 of the urea cycle? forming carbamoyl phosphate?
- Bicarbonate turns into carboxyphosphate using ATP
-Carboxyphosphate turns into carbamic acid - carbamic acid goes to carbamoyl phosphate using ATP
- effectively NH2, Co2 and phosphate
- occurs in mito matrix
- enzyme is CPS1
- Allostericaly regulated
-uses 2 ATP - N-acetylglutamate is a required allosteric activator
What is N-Acetyl-Glutamate and how is it formed?
Required allosteric activator of CPSI
- Acetyl coa plus glutamate
- forms amide bond
- only occurs with excess amino acids in liver
What occurs in step 2 - forming citrulline in the urea cycle?
- formed in mito
- Ornithine (basically Lys) amide bonds with Carbamoyl phosphate using ornitihine transcarbamoylase
- makes citrulline
What occurs in step 3 - forming argininosuccinate in the urea cycle?
occurs in cytosol so citrulline has to exit mito
- citrulline and aspartate - aspartate is thedonor of the second NH3 group to urea
- uses 1 ATP
- forms arginosuccinate via arginosuccinate synthetase
- also forms L-citrulline intermediate
What happens in step 4 - forming arginine in the urea cycle?
Arginosuccinate gets broken down to arginine and fumarate by arginosuccinase
- fumarate goes to TCA
- arginine continues in urea cycle
Do we need arginine in our diet?
No, we make enough in the urea cyc;e
What happens in the 5th step, hydrolysis or arginine in the urea cycle?
Arginine is converted into ornithine and urea via arginase
- ornithine is regenerated and goes back to the start
How many ATP are used in the urea cycle?
3 - 2ATP, one AMP (whatever the activated form is)
What is a common treatment for deficiencies in Urea cycle enzymes?
supplement diet with benzoate phenybutyrate
- these molecules can form enzyme catalyzed amide linkages with glycine or glutamine
- can help deplete liver nitrogen eventually lowering ammonia levels in blood
Give a summary of the major sources of free NH4+? 4
- Major source is dietary and body protein
- glutamate dehydrogenase activity in liver leads to free NH4 - urea
- Ser and Thr dehydratase in liver generates NH4- urea
-glutaminase in liver releases NH4+ - urea
- Amino groups from other tissues come to liver in the form of alanine and glutamine- nh4 is released by transanimation/glutamate dehydrogenase and glutaminase - Kidney
- Amines
- purines in pyrimidines
In the liver, free ammonium can also be produced from the breakdown of what two amino acids?
Serine and threonine by respective dehydratases
- serine turns to pyruvate + NH4
- threonine turns to aketobutyrate + NH4
Ammonia can be secreted ___ by the kidney
Directly - ammonia is generated by the metabolism of glutamate by enzymes glutamate dehydrogenase and glutaminase - secreted in the urine as free ammonium
What are the ketogenic amino acids and what do ketogenic amino acids become?
- Iso, Leu, Thr, Trp, Lys, Phe, Tyr
- becomes acetylCoA or AcetoacetylCoA
What do glucogenic aminoacids become?
pyruvate
oxaloacetate
aketoglutarate
succinyl coa
fumarate
Which two amino acids are ONLY ketogenic?
Leucine Lysine
What does ketogenic mean?
Can make ketone bodies - metabolites its broken down into
What are glucogenic amino acids used for?
Glucogenic metabolites - will be used to make molecules for glycolysis or atp synthesis
Phenylalanine breakdown generates products that are ____ and ____
ketogenic and glucogenic
- acetoacetate is ketogenic
- fumarate is glucogenic via gluconeogenesis
What are the fates of B branched amino acids + methionine? Why is isoleucine special?
- All can be broken down into propionyl coa which is eventually turned into succinyl coa which is a glucogenic precursor
- Iso is special because it can also become acetyl coa
What does maple syrup urine disease cause?
mental deficits and death
What are the most common results of amino acid breakdown?
aketoglutarate and pyruvate
What is phenylketonuria?
genetic disorder of phenylalanine metabolism
- caused by defect in phenylalanine hydroxylase that does not work so phenylalanine builds up in the blood
- if not caught early can cause sever mental defects.
What is the only way we can synthesize argenine?
urea cycle
Where does the majority of earths fixed nitrogen come from>
60% comes from nitrogen fixing microorganisms like rhizobium
Give a brief overview of the biotic nitrogen cycle
- nitrogen is assimilated to biomolecules
- nitrates are reduced to ammonium
what is indirectly required for nitrogen fixation?
oxygen - for ATP formation in oxidative phosphorylation
Why must nitrogen fixation be done in relatively anoxic conditions?
because nitrogenase is very sensitive to inactivation by O2
Reductase and nitrogenase are both what kind of proteins?
iron sulfur cluster proteins
What can glutamate and glutamine both donate in other biosynthetic pathways?
can both donate amino groups
- Glutamate - amino for other amino acids through aminotransferase
- Glutamine - source of amino group in many biosynthetic processes
What is the primary control point in nitrogen metabolism?
glutamine synthetase
- allosteric dodecamer
- controlled by 8 allosteric inhibitors
- can also be covalently modified by adenylating glutamine synthetase which makes the enzyme more responsive to allosteric inhibitors
What are some known allosteric regulators of glutamine synthetase?
carbamoyl phosphate
alanine
CTP
Adenylation of glutamine synthetase occurs on ___
a tyr residue
- leads to inactivation
What is an example of an amino group transfer reaction?
asparagine synthesis - glutamine and asparagine synthetase move the amino group from glutamine onto aspartate to make asparagine
All amino acids are built from intermediates of what three pathways?
- glycolysis
- TCA
- PPP
What are the nonessential amino acids?
Alanine
Asparagine
Aspartate
Glutamate
Serine
What three amino acids are conditionally essential and why?
Arginine, Glutamine and Tyrosine
Why? unsure - go review pg 90 ish in set 3
How do we synthesize serine (go check slides)
3 phosphoglycerate to 3 phosphohydroxypyruvate to 3 phosphoserine to serine
Why is arginine conditionally essential?
in newborns, urea cycle cannot compensate for arginine so it is needed in diet
Why do we get some amino acids from diet as opposed to synthesizing them?
because it is energetically expensive to do so - cheaper to get from diet
What is an important reaction in amino acid and nucleotide synthesis?
1 carbon transfer reactions using tetrahydrofolate (TH4)
What is tetrahydrofolate?
single carbon carrier
What is serine a precursor for?
glycine and cystine
What 2 nitrogens do 1 carbon tranfers occur on?
N5 and/or N10
What is used as the reduction agent for TH4 reactions?
NADPH
What modification occurs on both N5 and N10?
methylene modification
What modification only occurs on N5?
methyl modification
What does TH4 do for amino acid synthesis?
acts as a single carbon donor for making certain amino acids?
How is methionine synthesized and how is TH4 involved?
methionine is synthesized from homocysteine using methionine synthase, it gains a methyl group from N5 methylTH4 and turns the N5 TH4 to just TH4 (coenzyme b12)
What does the adenylation of methionine form?
S- adenosylmethionine (SAM)
What is important about S -adenosylmethionine?
methyl donor in many reacitions
- can eventually form homocysteine - which can then be turned back into methionine
What type of inhibition regulates amino acid biosynthesis?
feedback inhibition
- 3 phosphate dehydrogenase is the first step in serine biosynthesis
- enzyme is allosterically regulated
- domain binds the end product serine
- binding serine lowers vmax and inhibits enzyme
-
What amino acid is a precursor for epinephrine?
tyrosine but go check
What amino acid is a orecursor for serotonin?
tryptophan
What percent of nucleosides are absorbed for nucleic acid synthesis?
only 5%
What do 25% of the nucleosides we consume in our diet go towards?
rapidly regenerating enterocytes which are specialized intestinal cells
What are the three main uses for raw nucleotides?
- precursors of DNA and RNA
-ATP - energy currency - Adenine nucleotides - components of 3 major coenzymes
What 3 coenzymes are Adenine nucleotides components of?
NAD, FAD, CoA
What are four more uses for nucleotides - specific examples
- activated intermediates for many pathways - UDP glucose
- metabolic and physiologic regulators - cAMP
- GTP is used by G proteins in signal transduction pathways
- CTP is used in the biosynthesis of glycerophospholipids
Give an overview of the de novo pathway for pyrimidine synthesis
bicarbonate and nh3 and 2 atp are used to make carbamoyl phosphate
- joins with aspartate to make the pyrimidine ring
- pyrimidine ring and PRPP (activated ribose) join to make UTP or CTP
What is the rate limiting step in pyrimidine synthesis?
the synthesis of carbamoyl phosphate
What are the differences between carbamoyl phosphate synthetase I and II? Which is used in pyrimidine synthesis?
CPS I is used in urea synthesis and is located in the mito matrix
- the N donor is NH4+
CPS II is used in pyrimidine synthesis and is located in the cytosol
- the N donor is Glutamine
What is ATCase?
- Aspartate transcarbamoylase
- allosterically regulated control point in nucleotide synthesis
- enzyme that changes carbamoyl phosphate into carbamoylaspartate which leads to the end product of CTP
- allosterically inhibited by CTP (product) and activated y ATP
How is the ring closed in carbamoyl aspartate to form ?
- dihydroorotate synthetase forms an amide bond on carbamoylaspartate to close the ring, creating dihydroorotate
- dihydroorotate loses to H to FMN via dihydroorotate dehydrogenase to form orotate, forming a double bond in the ring
you missed nov 29 lecture?
yes go back
What two chemicals are effective competitive inhibitors of dihydrofolate reductase?
methotrexate and aminopterin
methotrexate can be used to treat what disorders?
arthritis and eczema
What does trimethoprim do to dihydrofolate reductase?
competitive inhibitor of DHFR, but not in humans, mainly in bacteria and protozoa meaning it can target bacterial infection without damaging humans
What does acyclovir do?
inhibits biosynthesis of deoxynucleotides in viruses, can be used to treat herpes, chicken pox and shingles
- effectively terminates viral DNA synthesis
What does zidovudine do?
reverse transcriptase inhibitor which is a nucleoside analog
- used in HIV medication
- cellular enzymes will convert it to the 5’ triphosphate but the azido group on C3 prevents further DNA elongation
what happens when a nucleoside monophosphate is added to ATP?
will become the nucleoside diphosphate of the specific base and ADP
What happens when a nucleoside diphosphate is added to ATP?
Will become the nucleotide triphosphate of the specific base and then ADP
What are the precursors needed for the de novo pathway of purine synthesis?
Ribose 5p. Asp, CO2, Gly, Gln, Formate
What molecule acts as the backbone for purine synthesis?
ribose 5 phosphate
Which N atom is the starting point for purine synthesis?
N 9
What is the first step in purine synthesis?
Adding ammonia to C1 of ribose 5p
- glutamate is the origin of the amino group
- does not require ATP bc good leaving group
- product is very unstable so next reaction must happen quickly
What is the second step in denovo synthesis of purines?
glycine comes in and tons of complicated shit happens
turning inosinate (IMP) to AMP and GMP requires what?
GMP - requires ATP and aspartate
AMP - requires GTP and Gln
What inhibitors are used in the split pathway after making IMP in purine synthesis?
AMP inhibits AMP synthesis
IMP inhibits IMP synthesis
Purine degradation results in _____
uric acid
Most purines from diet are converted to uric acid which is ____
excreted
What can purine synthesis be salvaged from?
- PRPP + Adenine to AMP via APRT
- PRPP + guanine to GMP via HGPRT
- PRPP + Hypoxanthine to IMP via HGPRT
Gout is caused by what?
high blood levels of uric acid or urate due to overproduction of uric acid
