BCH 451 EXAM 3 QUESTIONS AND ANSWERS WITH COMPLETE
SOLUTIONS VERIFIED LATEST UPDATE
structure of coenzyme A
can dissociate from PDC
-accept and carry acetal groups
Structure of Lipoyllysine
-prosthetic group, longer chain so lipoate can anchor to lysine (E2) to serve as a
biological tether to sway substrate around
-lipoate can serve as an electron (hydrogen) carrier and as a acyl carrier
biological tether
allow flexibility, swings substrate from one active site and donate it to other side
biological tethers
-TPP: ethanol fermentation with pyruvate decarboxylase (acetylaldehyde serves as a
schiff base e- holder)
-Biotin: carries CO2 with pyruvate carboxylase in gluconeogenesis
-Lipoate: pyruvate to acetyl-CoA with E2 of PDC
pyruvate dehydrogenase complex
large multienzyme complex (E1, E2, E3) coordinates different active sites together
-substrate channeling from one active site to another (rxn, faster, reduce side reactions,
and regulation of activity of one subunit - E1 (pyruvate DH), affects entire complex)
citrate synthase
,Oxaloacetate + Acetyl CoA --> Citrate
-conformational change upon binding OAA
-induced fit depends on OAA which fits into binding pocket to change from open
concentration (does not have binding site for acetyl-CoA) to closed confirmation
(binding of OAA creates binding for acetyl-CoA)
acetyl-CoA is a high energy molecule bc of its thioester so this process prevents
acetyl-CoA from going through hydrolysis or any side rxn
what kind of mechanism is citrate synthase
double substrate - order sequential
mechanism of citrate synthase
Asp at active site acts as a general base to take away a H+
-acetyl-CoA now as a nucleophile can attack carbonyl carbon of OAA (stabilized by His)
-thioester is hydrolyzed which regenerates CoA-SH and produces citrate
aconitase structure
iron-sulfur core (Fe stabilized by 4 Cys, catalyze the +/- H2O)
-stereospecific (only R isocitrate produce)
-catalyzes citrate to isocitrate
Step 3 of Citric Acid Cycle
oxidative decarboxylation #2 (first one was losing a carbon when pyruvate converted to
acetyl-CoA)
what is alpha ketoglutarate dehydrogenase complex similar to?
PDC
-they have the same coenzymes and mechanisms but slightly different E1 and E2 to
,accommodate for the different substrates, but E3 are the same (FADH2 donates H to
NAD+)
what is alpha ketoglutarate dehydrogenase and PDC relationship an example of?
gene duplication and divergent evolution
synthase
a synthetic rxn without ATP
synthetase
require ATP or GTP
Phosphohistidine enzyme
used in step 5 of CAC with succinyl-CoA synthetase b/c His can be phosphorylated but
not the same type of phosphorylation regulation as Ser, Thr, Tyr (with -OH so use
kinases and phosphorylase) b/c on HIs, it only in active site of enzyme
FAD
covalently attached prosthetic group
-can take up to 2 e- but donate 1 e- at a time
-e- will hop down Fe-S clusters and feed into ETC
L-malate dehydrogenase
catalyzes the oxidation of L-malate to oxaloacetate
-in the mitochondria and cytosol for gluconeogenesis (in cytosol when ow NADH in cell
so need more for process)
why does succinyl-CoA feedback inhibit citrate synthase
b/c alpha ketoglutarate important for making other molecules/aa
, why is ATP an inhibitor of CAC when isocitrate is converted to alpha
ketoglutarate by isocitrate DH?
when ATP increases, isocitrate goes back to citrate and leaves mitochondria to go to
cytosol and inhibit PFK1 in glycolysis to stop glycolysis
why are CAC intermediates amphibolic
-they are anabolic (make molecules) or catabolic (break down for energy)
anaplerotic reactions
replenish OAA in case they are drained to make sure CAC is not stopped
-OAA made from PEP or pyruvate using diff types of enzymes (pyruvate carboxylase -
gluconeogenesis and PEP carboxylase - does not exist in human)
mutations in isocitrate dehydrogenase
decreased affinity to NADP+, isocitrate, and Mg2+ (substrates) while increased affinity
for product alpha ketoglutarate (so enzyme binds with product well)
how did reseachers discovery the mutation in isocitrate DH (IDH)
cloned the gene for isocitrate DH and made it express mutant protein/do kinetic analysis
old theory of isocitrate DH mutation
increased alpha ketoglutarate = shut down CAC = increased glycolysis (abandoned
when measured metabolites in cycle and concentration consistent for mutation and WT)
new theory of isocitrate DH mutation
the Arg132 mutated is IDH is making contact with isocitrate
-IDH mutation causes a gain of function mutation due to increased alpha ketoglutarate,
making oncogenic D-2-hydroxyglutarate (2HG)
what happens to NADH and FADH2 after CAC
SOLUTIONS VERIFIED LATEST UPDATE
structure of coenzyme A
can dissociate from PDC
-accept and carry acetal groups
Structure of Lipoyllysine
-prosthetic group, longer chain so lipoate can anchor to lysine (E2) to serve as a
biological tether to sway substrate around
-lipoate can serve as an electron (hydrogen) carrier and as a acyl carrier
biological tether
allow flexibility, swings substrate from one active site and donate it to other side
biological tethers
-TPP: ethanol fermentation with pyruvate decarboxylase (acetylaldehyde serves as a
schiff base e- holder)
-Biotin: carries CO2 with pyruvate carboxylase in gluconeogenesis
-Lipoate: pyruvate to acetyl-CoA with E2 of PDC
pyruvate dehydrogenase complex
large multienzyme complex (E1, E2, E3) coordinates different active sites together
-substrate channeling from one active site to another (rxn, faster, reduce side reactions,
and regulation of activity of one subunit - E1 (pyruvate DH), affects entire complex)
citrate synthase
,Oxaloacetate + Acetyl CoA --> Citrate
-conformational change upon binding OAA
-induced fit depends on OAA which fits into binding pocket to change from open
concentration (does not have binding site for acetyl-CoA) to closed confirmation
(binding of OAA creates binding for acetyl-CoA)
acetyl-CoA is a high energy molecule bc of its thioester so this process prevents
acetyl-CoA from going through hydrolysis or any side rxn
what kind of mechanism is citrate synthase
double substrate - order sequential
mechanism of citrate synthase
Asp at active site acts as a general base to take away a H+
-acetyl-CoA now as a nucleophile can attack carbonyl carbon of OAA (stabilized by His)
-thioester is hydrolyzed which regenerates CoA-SH and produces citrate
aconitase structure
iron-sulfur core (Fe stabilized by 4 Cys, catalyze the +/- H2O)
-stereospecific (only R isocitrate produce)
-catalyzes citrate to isocitrate
Step 3 of Citric Acid Cycle
oxidative decarboxylation #2 (first one was losing a carbon when pyruvate converted to
acetyl-CoA)
what is alpha ketoglutarate dehydrogenase complex similar to?
PDC
-they have the same coenzymes and mechanisms but slightly different E1 and E2 to
,accommodate for the different substrates, but E3 are the same (FADH2 donates H to
NAD+)
what is alpha ketoglutarate dehydrogenase and PDC relationship an example of?
gene duplication and divergent evolution
synthase
a synthetic rxn without ATP
synthetase
require ATP or GTP
Phosphohistidine enzyme
used in step 5 of CAC with succinyl-CoA synthetase b/c His can be phosphorylated but
not the same type of phosphorylation regulation as Ser, Thr, Tyr (with -OH so use
kinases and phosphorylase) b/c on HIs, it only in active site of enzyme
FAD
covalently attached prosthetic group
-can take up to 2 e- but donate 1 e- at a time
-e- will hop down Fe-S clusters and feed into ETC
L-malate dehydrogenase
catalyzes the oxidation of L-malate to oxaloacetate
-in the mitochondria and cytosol for gluconeogenesis (in cytosol when ow NADH in cell
so need more for process)
why does succinyl-CoA feedback inhibit citrate synthase
b/c alpha ketoglutarate important for making other molecules/aa
, why is ATP an inhibitor of CAC when isocitrate is converted to alpha
ketoglutarate by isocitrate DH?
when ATP increases, isocitrate goes back to citrate and leaves mitochondria to go to
cytosol and inhibit PFK1 in glycolysis to stop glycolysis
why are CAC intermediates amphibolic
-they are anabolic (make molecules) or catabolic (break down for energy)
anaplerotic reactions
replenish OAA in case they are drained to make sure CAC is not stopped
-OAA made from PEP or pyruvate using diff types of enzymes (pyruvate carboxylase -
gluconeogenesis and PEP carboxylase - does not exist in human)
mutations in isocitrate dehydrogenase
decreased affinity to NADP+, isocitrate, and Mg2+ (substrates) while increased affinity
for product alpha ketoglutarate (so enzyme binds with product well)
how did reseachers discovery the mutation in isocitrate DH (IDH)
cloned the gene for isocitrate DH and made it express mutant protein/do kinetic analysis
old theory of isocitrate DH mutation
increased alpha ketoglutarate = shut down CAC = increased glycolysis (abandoned
when measured metabolites in cycle and concentration consistent for mutation and WT)
new theory of isocitrate DH mutation
the Arg132 mutated is IDH is making contact with isocitrate
-IDH mutation causes a gain of function mutation due to increased alpha ketoglutarate,
making oncogenic D-2-hydroxyglutarate (2HG)
what happens to NADH and FADH2 after CAC
