Chapter 6: Mechanisms of Enzymes

Question 1

what are the 4 chemical modes of enzymatic catalysis?

Answer 1

1. polar amino acids in the active site
2. acid-base catalysis
3. covalent catalysis
4. pH effects on enzymatic rates

Question 2

what are the non-chemical modes of enzymatic catalysis?

Answer 2

• proximity effect
• weak binding of substrate to enzymes
• induced fit
• transition state stabilization

Question 3

what are the mechanisms of action for serine proteases?

Answer 3

• zymogens

- catalytic triad

Question 4

what is the mechanism of action for lysozyme?

Answer 4

substrate conformation and specificity

Question 5

what is the mechanism of action for arginine kinase?

Answer 5

transition state analog as a tool to understand reactivity

Question 6

• an electron rich ion or atom
• nucleus seeking
• has a negative charge or an unshared electron pair

Answer 6

nucleophile

Question 7

• an electron poor ion or atom

- electron seeking

Answer 7

electrophile

Question 8

what type of reactions are most biochemical reactions?

Answer 8

group transfer reactions

Question 9

the nucleophile attacks while the leaving group leaves, creating an unstable transition state with five groups around the central atom

Answer 9

direct displacement reaction

Question 10

• *can occur in two ways:
• the electrons of the breaking covalent bond stay with one atom (most common)
• the electrons split and one electron remains with each atom

Answer 10

cleavage reaction

Question 11

reaction in which both electrons go in one direction

Answer 11

heterolytic cleavage

Question 12

reaction in which both electrons go in opposite directions

Answer 12

homolytic cleavage

Question 13

• the loss of electrons
• gain of C–O bonds
• loss of C–H bonds

Answer 13

oxidation

Question 14

• the gain of electrons
• loss of C–O bonds
• gain of C–H bonds

Answer 14

reduction

Question 15

causes oxidation and is reduced in the process

Answer 15

oxidizing agent

Question 16

causes reduction and is oxidized in the process

Answer 16

reducing agent

Question 17

what causes changes between the pKa values of the ionizable groups of amino acids residues compared to the same groups in a free amino acid?

Answer 17

the microenvironment of the active site

Question 18

how many catalytic residues do enzymes have?

Answer 18

between 2-6

Question 19

which residues account for almost 2/3 of all catalytic residues?

Answer 19

• *the charged residues (HDREK)
• histidine
• arginine
• lysine
• aspartate
• glutamate

Question 20

how is reaction acceleration achieved?/

Answer 20

catalytic transfer of a proton

Question 21

which residue is an ideal group for proton transfer at neutral pH?

Answer 21

histidine (side chain pka of 6-7)

Question 22

what happens during covalent catalysis?

Answer 22

a substrate is bound covalently to the enzyme to form a reactive intermediate

Question 23

what are the steps of Schiff base formation?

Answer 23

1. attack of nucleophile on the carbonyl
2. transfer of proton from weak acid to strong base
3. protonation of -OH to establish leaving group
4. leaving group departs, double bond forms

Question 24

what can the effects of pH on enzyme activity tell us?

Answer 24

• effect of pH on the reaction rate of any enzyme can suggest which amino acid residues are in its active site
• sensitivity to pH reflects an alteration in the ionization state of one or more residues involved in catalysis

Question 25

- a reaction that occurs with every collision between reactant molecules - can only go as fast as two things bind to each other in solution

Answer 25

diffusion controlled reaction

Question 26

- catalyzes the interconversion of dihydroxyacteone to glyceraldehyde 3-phosphate - mechanism has 4 kinetically measurable steps

Answer 26

triose phosphate isomerase

Question 27

- catalyzes the removal of the superoxide radical anion - structure creates a positively charged pocket in the active site that enhances the formation of the ES complex - happens in two steps during which a metal bound to the enzyme is reduced and then oxidized

Answer 27

superoxide dismutase

Question 28

- enzymes are often called entropy traps since they collect highly mobile reactants from dilute solution and position them for reaction - often involves the rotation of bonds

Answer 28

proximity effect

Question 29

why can't binding of substrate to enzyme be extremely tight?

Answer 29

- the enzyme decreases the activation energy, so if the substrate is bound tightly to the enzyme, it would take just as much energy to reach ES as it does without catalysis - excessive ES stability is a thermodynamic pit - if ES binding is too tight, products will not be formed

Question 30

- the enzyme shifts from an inactive to active form | - not a catalytic mode, but rather a substrate specificity mode

Answer 30

induced fit

Question 31

mimic the transition state

Answer 31

transition state analogs

Question 32

- explains a large part of the rate acceleration of enzymes | - increased interaction of the enzyme with the substrate in the transition state

Answer 32

transition state stabilization

Question 33

- cleave the peptide bond of proteins - characterized by a serine residue in the active site - regulated by zymogen activation

Answer 33

serine proteases

Question 34

- inactive enzyme precursors that undergo hydrolysis to generate active enzyme - also called proezymes

Answer 34

zymogens

Question 35

enzymatic cleavage of specific peptide bonds

Answer 35

selective proteolysis

Question 36

what are some examples of serine proteases?

Answer 36

- pepsin - trypsin - chymotrypsin - elastase

Question 37

trypsin, chymotrypsin, and elastase are all examples of ______ because they have ____________ in the active site

Answer 37

homologous proteins; the same 3 residues

Question 38

what gives rise to structural differences/specificity in the enzyme pockets?

Answer 38

size and polarity

Question 39

- the three amino acid residues that function together at the center of the active site of some enzymes - generate a powerful nucleophile that eventually attacks a peptide bond

Answer 39

catalytic triad

Question 40

catalyzes the hydrolysis of some polysaccharides, especially those found in bacterial cell walls

Answer 40

lysozyme

Question 41

what is the most stable form of a six-membered ring?

Answer 41

chair conformation

Question 42

- catalyzes the phosphorylation of arginine | - is an induced fit enzyme

Answer 42

arginine kinase

Question 43

What are the residues in Chymotrypsin?

Answer 43

- tyrosine | - serine

Question 44

What are the residues of trypsin?

Answer 44

- arginine | - aspartate

Question 45

What are the residues of elastase?

Answer 45

- alanine - valine - threonine - has a shallow pocket