how enzymes work Flashcards
What are enzymes?
protein catalysts!!
what are three ways to increase the rate of chemical reactions?
increase the temperature
increase the concetration
add a catalyst
Do enzymes alter the equilibrium?
NO, just the speed of the reaction
What part of enzymes is involved in the chemistry?
the active site
are enzymes normally present in high amounts compared to the substrates?
NO
what do enzymes lower?
the free energy of activation for a reaction
how do enzymes lower the free energy?
residues at the active site bind the substrates and put them in proximity (the correct orientation), and provide functional groups for catalysis
What do enzymes preferentially bind and stabilize?
the transition state (induced fit)
what is the time to catalyze on reaction called?
turn over time
what are the mechanisms of catalysts?
acid-base: transfer or removal of H+ lowers the ∆Gt
covalent: transient formation of reversible covalent bond between an enzyme and a substrate
metal: indirect or direct; red/ox reactions
do the AA side chains often play a direct role in acid-base and covalent catalysis at the active site?
YES
What is something that some catalytic mechanisms require?
enzyme co-factors (organic co-enzymes or metal ions)
with cofactor= holoenzyme
w/out cofactor= apoenzyme
nucleophiles in enzymes (5)
ser, tyr, cys, lys, his
how do metal ions catalyze reactions?
metal ions at the active site can mediate oxidation/reduction reactions, promote further reactivity of other functional groups, or interact directly with the reacting substrate
what type of catalysis does chymotrypsin use?
acid-base and covalent in the hydrolysis of a peptide bond
what does chymotrypsin prefer as residues on the carbonyl side of the peptide bond?
bulky non-polar, part of the serine protease family
what form the catalytic triad?
asp 102, his 57, ser 195
what is serines role?
acts as nucleophile
what is histidines role?
act as a general base
what is asparagines role?
anchor
what happens if you use mutations to affect chymotrypsin?
if you replace Asp you decrease rate by 1000x, replace ser decrease by 10^6x BUT it still acts as a catalyst because of the specificity of the active site
is chymotrypsin flexible? How so?
Yes, it adopts slightly different conformations as it goes through the catalytic cycle (induced fit)
How does chymotrypsin preferentially stabilize the transition state?
through gly 193 and a backbone amide (oxyanion hole)
how do different proteases have different specificities at the active site?
different residues lining the substrate binding pocket
despite similar tertiary structure (divergent evolution)
what is an example of convergent evolution with enzymes?
some proteases that are not homologous to the serine proteases and have little sequence and 3D structure similarities but use a similar catalytic mechanism involving a triad
What is a zymogin?
an inactive pre-cursor protease that needs to be activated by cleavage by other proteases
are some proteases regulated by specific inhibitors?
YES
what are isozymes?
a set of different enzymes which catalyze the same reaction, they different primary structure
what are cyclooxegenases?
catalyze the first step in the synthesis of prostaglandins
AKA COX and they are isoenzymes
what is COX-1 required for?
required for basal PG production
what is COX-2 required for?
it is inducible and involved in pain and inflammation
what is the advantage of COX-2?
it has a slightly larger active site due to val instead of ile at position 523 which has allowed for the development of COX 2 specific drugs such as vioxx and celebrex
