enzyme structure/mechanism

Question 1

what is gibbs free energy change?

Answer 1

free energy change for any transformation

it can predict if a reaction will occur spontaneously

Question 2

what does a delta G less than 0 mean?

Answer 2

reaction will occur spontaneously

Question 3

what does a delta G greater than 0 mean?

Answer 3

it will not occur spontaneously

Question 4

what does a delta G equal to 0 mean?

Answer 4

the system is in equilibrium

Question 5

how is activation energy related to G

Answer 5

it is NOT related to delta G. the RATE of the reaction is the thing that depends on activation energy

Question 6

can enzymes change the delta G for a reaction?

Answer 6

no!

Question 7

can enzymes change the activation energy for a reaction?

Answer 7

yes! they can lower it

Question 8

what are the two ways enzymes can lower the activation energy of a rxn?

Answer 8

1. by direct stabilization of the transition state

2. creation of new reaction pathway

Question 9

What theory of binding do most enzyme-substrate interactions exhibit?

Answer 9

the induced fit (rather than the lock and key)

Question 10

with what type of interactions do enzymes bind to substrates?

Answer 10

multiple weak non covalent interactions

electrostratic interactions, H bonds, van der waal forces, hydrophobic effect

Question 11

does this statement describe a prosthetic group or a cofactor? “more loosely bound and generally come on and off the enzyme”

Answer 11

cofactor

Question 12

explain what “proximity and orientation effects” regarding chemical strategies in enzymatic catalysis means

Answer 12

reactants come together with proper spatial orientation for reaction to occur

Question 13

what does general acid catalysis mean?

Answer 13

weak acid on enzyme provides a partial proton transfer during the enzymatic reaction

Question 14

in acid/bad catalysis, what groups are typically at the enzyme’s active site?

Answer 14

HISTIDINE (because it can be an acid or a base)

aspartate, glutamate

Question 15

in covalent catalysis, what 4 amino acids and 1 group isnormally involved at the enzyme’s active site?

Answer 15

cysteine, serine, lysine, histidine, prosthetic groups

Question 16

what occurs in covalent catalysis?

Answer 16

transient formation of a covalent bond between enzyme and substrate (creating new intermediate)

Question 17

what is occurring in electrostatic catalysis?

Answer 17

charge distribution in active site helps stabilize the transition state

Question 18

what 5 amino acids and 1 cofactor group is usually seen in electrostatic catalysis?

Answer 18

aspartate, glutamate, arginine, histidine, lysine, metal ions cofactors

Question 19

how do proteases carry out their chemical reaction?

Answer 19

cleavage of a peptide bond by addition of water across the bond

Question 20

what are the 4 major classes of proteases?

Answer 20

serine protease
aspartyl protease
thiol protease
Zn+2 protease

Question 21

what 3 amino acids make up the catalytic triad?

Answer 21

serine
aspartate
histidine
all 3 are hydrogen bonded when substrate is not bound

Question 22

what four catalysis happen in the 1st step of serine proteases?

Answer 22

Preferential binding for transition state
covalent catalysis
general base catalysis
elecrostatic catalysis

Question 23

what two catalysis happen in the 2nd step of serine proteases?

Answer 23

general acid/base catalysis

Preferential binding for transition state

Question 24

what is the rate limiting step in the serine protease reactions

Answer 24

formation of the acyl-enzyme intermediate

Question 25

on the graph, where is the rate limiting step occur?

Answer 25

in the semi stable dip between the two peaks

Question 26

how do chymotrypsin, trypsin and elastase differ?

Answer 26

they are all serine proteases (so same mechanism) but they differ in their substrate specificities

Question 27

how is substrate specificity achieved?

Answer 27

the different serine proteases will have different amino acids/confirmations around the invariant catalytic triad that will determine the specificity. *the catalytic triad itself does NOT provide specificity

Question 28

what type of inhibitor is penicillin?

Answer 28

a suicide inhibitor

irreversible inhibitor

Question 29

how do suicide inhibitors work?

Answer 29

they bind to the enzyme because of their resemblance to the substrate and are converted to an irreversible inhibitor by the initial steps of the enzyme’s reaction mechanism