Use LEFT and RIGHT arrow keys to navigate between flashcards;
Use UP and DOWN arrow keys to flip the card;
H to show hint;
A reads text to speech;
44 Cards in this Set
- Front
- Back
3 common features of proteases
|
activate H2O or other nucleophile
polarize peptide carbonyl group stabilize tetrahedral intermediate |
|
chymotrypsin
|
digestive enzyme; protease that cleaves peptides at carboxy terminus of hydrophobic amino acids like tryptophan, tyrosine, Phe, and Met (in presence of water)
enzyme is acylated and X is released forming Acyl-enzyme intermediate then enzyme is deacylated with water and enzyme is restored |
|
structure of active site in chymotrypsin
|
side chain of Ser is H-bonded to His and NH group of His is H-bonded to carboxylate group of Asp--referred to as catalytic triad
|
|
carbonic anhydrase active site
|
Zn2+ atom bound to 3 His imidazole rings and one water molecule
|
|
mechanism for carbonic anhydrase
|
Zn2+ bound to H20 decreases pKa to 7, so loses H+. OH- attacks CO2
|
|
what do nucleoside monophosphate kinases do?
|
catalyze transfer of terminal phosphoryl group of a nucleoside triphosphate (usually ATP) to the phosphoryl group of a nucleoside monophosphate
|
|
what is the substrate for nucleoside monophosphate kinase reactions?
|
divalent metal--Mg2+ or Mn2+ (almost all NTPs are bound to one of these); usually bound to 2 O's of NTP + some water molecules
|
|
what does the magnesium ion do to the substrate/enzyme in NMP kinase reactions?
|
provides additional points of interaction btw ATP-Mg2+ and enzyme; coordinates the beta and gamma phosphates so that the gamma phosphate can be transferred to NMP
|
|
what is the p-loop on nucleoside monophosphate kinases? what does it do?
|
loop between beta strand and first helix; interacts with phosphoryl groups on bound nucleotide
|
|
name of the mechanism used by NMP kinases
|
catalysis by approximation
|
|
what metal ion is necessary for restriction enzymes? What does it do?
|
Mg2+; bound to 3 water molecules, 2 carboxylates of enzyme's Asp residues, 1 to O of the phosphoryl group at site of cleavage; holds water molecules in place so that it can attack phosphoryl group, and (with Asp) polarizes H2O molecule toward deprotonation
|
|
classic example of induced fit
|
nucleoside triphosphate kinase reactions; binding of substrate induces large structural changes in kinase
|
|
what are the changes induced by the binding of substrate in NMP kinase reactions?
|
P-loop closes down on top of polyphosphate chain, movement of P-loop brings down top domain of enzyme to form lid over bound nucleotide; ATP is held in position with gamma phosphoryl group positioned next to binding site of NMP
|
|
covalent catalysis
|
active site contains reactive group (usually powerful nucleophile) that becomes temporarily covalently bonded to substrate during reaction (i.e. chymotrypsin)
|
|
proteases (what do they do and 4 types)
|
cleave proteins by hydrolysis--add molecule of water to a peptide bond; aspartyl, serine, cysteine, metalloproteases
|
|
covalent catalysis
|
active site contains reactive group (usually powerful nucleophile) that becomes temporarily covalently bonded to part of substrate during reaction
|
|
chymotrypsin has 2 phases to reaction--what are they, why?
|
"burst" and steady-state; burst is first step of reaction--faster than second step, which is stead-state release of substrate
|
|
roles of residues in catalytic triad in chymotrypsin
|
His-positions Ser side chain and polarizes hydroxyl group so poised for deprotonation (in presence of substrate, it takes proton)
Asp-orients His residue, makes it a better proton acceptor Ser-binds to substrate Gly-also important--stabilizes oxyanion hole |
|
2 other catalytic triads
|
trypsin (replace Ser with Asp--attracts positively charged side chains)
Elastase (2 Val residues at top of active site limit size of side chains) |
|
example of a protease inhibitor used as a drug
|
HIV treatments inhibit HIV protease (an aspartyl protease)
|
|
catalysis by approximation
|
brings substrates into proximity at proper orientation
|
|
nucleoside monophosphate kinases
|
catalyze transfer of terminal phosphoryl group from a nucleoside triphosphate to phosphoryl group of nucleoside monophosphate
|
|
What structural motif do NMPases have?
|
p-loops (between first beta strand and first helix)
|
|
restriction enzymes
|
catalyze hydrolysis of phosphodiester backbone of DNA (bond between 3' O atom and phosphorous atom is broken)
|
|
structure of restriction enzymes
|
twofold rotational symmetry--enzyme surrounds DNA tightly
|
|
host DNA can't be distorted by restriction enzymes because...
|
methyl groups on adenine bases prevent H-bonding to Asn residue in enzyme
|
|
distortion of DNA increases binding energy by....this is canceled out by....
|
increasing points of contact; distortion
|
|
aspartate transcarbamoylase
|
catalyzes first step in biosynthesis of pyrimidine nucleotides like cytidine triphosphate; has T and R state (expands on substrate binding)
|
|
structure of ATCase
|
2 catalytic trimers stacked on top of eachother, 3 regulatory dimers link catalytic subunits together
|
|
PALA
|
resembles catalytic intermediate (bisubstrate analog) of ATCase, so inhibits it--stabilizes R state
|
|
mechanis for allosteric regulation of ATCase is
|
concerted--changes in enzyme are all or nothing--either in T or R state (not like hemoglobin=sequential)
|
|
CTP
|
product of ATCase reaction--inhibits reaction by stabilizing T state--higher apparent Km; ATP lowers apparent Km
|
|
isozymes
|
enzymes that differ in sequence but catalyze same reaction; lactate dehydrogenase
|
|
lactate dehydrogenase
|
catalyzes a step in anaerobic glucose metabolism/synthesis; humans have 2 isozymic polypeptide chains (H and M); can have different combinations--H3M
|
|
protein kinases
|
transfer phosphoryl groups from ATP (usually) to Ser, Thr, Tyr; turn on signaling pathways
|
|
protein phosphatases
|
reverse effects of protein kinases; turn off signaling pathways
|
|
effects of phosphorylation (6)
|
1) adds 2 neg. charges to protein
2) allows formation of new H-bonds 3) energetically favorable 4) reaction rates can be adjusted by [E] and Vmax 5) amplifies effects--activates many other enzymes 6) ATP is cellular energy currency--links energy status to metabolism |
|
trypsin
|
activates all pancreatic zymogens; cells that line duodenum secrete an enzyme that hydrolyzes peptide bond in trypsinogen to activate it
|
|
pancreatic trypsin inhibitor
|
6kDa protein; binds very tightly to active site of trypsin
|
|
intrinsic vs. extrinsic clotting pathways
|
intrinsic: occurs due to rupturing of endothelial lining of blood vessels
extrinsic: occurs due to trauma-related damage of blood vessels (exposure of tissue factor) |
|
thrombin
|
activates enzymes and factors that lead to generation of more thrombin, converts fibrinogen to fibrin
|
|
fibrinogen
|
made up of 2 alpha, beta, gamma chains; thrombin cleaves alpha and beta chains to make fibrin; cleaved ends of alpha/beta chains associate with globular domains of beta and gamma to clot
|
|
gamma carboxyglutamate
|
binds Ca2+ in Gla domain of prothrombin
|
|
inhibitors of Vit. K-dependent pathway of thrombin
|
warfarin, dicoumarol
|