Catalytic Strategies

Question 1

what are the 6 catalytic strategies an enzyme can use?

Answer 1

1. preferential transition state binding
2. proximity and orientation effects
3. general acid base catalysis
4. covalent catalysis
5. electrostatic catalysis
6. metal ion catalysis

Question 2

amino acid side chains are the main determinants of enzyme __ and __

Answer 2

structure and function

Question 3

the active site of an enzyme has what 2 types of residues?

Answer 3

those that form bonds with the substrate and those that catlyse

Question 4

what type of amino acids have the most important roles in the active site>

Answer 4

polar, especially if ionizable

Question 5

what are catalytic amino acids?

Answer 5

play a direct role in catalysis

Question 6

“cation and anion binding” and “hydrogen bonding” indicates what type of role in the active site?

Answer 6

accessory

Question 7

“proton transfer” and “covalent binding” indicates what type of role in the active site?

Answer 7

catalytic

Question 8

what are the various roles of polar amino acids? (3)

Answer 8

1. proton transfer
2. transient covalent bonds to substrate
3. substrate and TS bonding through charge–chrage interactions

Question 9

why is histidine such a common catalytic residue?

Answer 9

side chain pka 6-7 (close to physiological pH), both protonated and unprotonated form will be present and it can therefore accept or donate protons

Question 10

what is preferential transition state binding?

Answer 10

catalytic strategy where the enzyme binds better to the TS than the substrate of products

Question 11

in preferential TS binding, the max binding energy is released when?

Answer 11

at the TS

Question 12

how does preferential TS binding increase reaction rate?

Answer 12

the enzyme strains the substrate to the TS shape, possibly bringing reacting groups closer together

Question 13

what are TS analogues?

Answer 13

stable molecules that bind strongly to enzymes because the mimic the TS shape

Question 14

why are TS analogues bad for reaction progression?

Answer 14

they can’t become products, so the enzyme is stuck and inhibited from turning actual TS to products

Question 15

TS analogues are an example of what type of inhibition?

Answer 15

competitive

Question 16

HIV has 3 main replication enzymes

Answer 16

1. reverse transcriptase
2. integrase
3. protease

Question 17

what is the function of reverse transcriptase?

Answer 17

turns viral RNA into dsDNA

Question 18

what is the function of intergrase?

Answer 18

inserts viral genome into host chromosomes

Question 19

what is the function of protease>

Answer 19

processes viral proteins so they can assemble into new viruses

Question 20

proximity effect in single substrate reactions

Answer 20

the substrate molecule may be contorted to bring the reacting functional groups to clover together

Question 21

proximity effect in multi-substrate reactions

Answer 21

binding of substrate to enzyme increases their local or effective concentration

Question 22

orientation effect

Answer 22

enzymes orient reacting molecules to promote reaction

Question 23

what is the most common ( not most important) catalytic strategy?

Answer 23

general acid base catalysis

Question 24

general acid-base catalysis relies on amino acid side chains that can ___

Answer 24

donate and accept a proton

Question 25

what is the goal of acid base catalysis?

Answer 25

lower the free energy of TS

Question 26

a general acid __ an H to an atom that develops a __ charge in the TS

Answer 26

donates ; negative

Question 27

a general base ___ an H to an atom that develops a ___ charge in the TS

Answer 27

accepts ; positive

Question 28

what is covalent catalysis (catalytic strategy?

Answer 28

a side chain with a nucleophilic group makes a transient bond with an electrophilic group on the substrate

Question 29

in covalent catalysis, what changes about the reaction pathway?

Answer 29

there is an extra intermediate state

Question 30

what does the intermediate state in covalent catalysis look like?

Answer 30

similar to TS but lower free energy

Question 31

what is the effect of the extra intermediate in covalent catalysis?

Answer 31

lowers the overall free energy of the TS

Question 32

what amino acids can act as nucleophiles?

Answer 32

serine, cysteine, aspartate and glutamate

Question 33

some proteases (like chymotrypsin) use serine to __

Answer 33

hydrolyze peptide bonds in their proteins

Question 34

role of chymotrypsin in the body

Answer 34

Diest proefins in the small intestine

Question 35

T/F chymotrypsin, trypsin, and elastase come from a common ancestor

Answer 35

t

Question 36

chymotrypsin, trypsin, and elastase have the same substrate and cleavage site preferences

Answer 36

f

Question 37

chymotrypsin selectively cleaves the peptide bond at the __ side of large __ amino acids

Answer 37

carboxyl-terminal; hydrophobic

Question 38

chymotrypsin is composed of __ different polypeptides held together by ___ bonds

Answer 38

3; disulphide

Question 39

what acts as the nucleophile in chymotrypsin?

Answer 39

serine residue

Question 40

chymotriopsin is known as a __ because it is made of 3 catalytic amino acids in its active site

Answer 40

catalytic triad

Question 41

what part of chymotrypsin its as the general base?

Answer 41

HIS 57