Lecture 17 - Enzyme mechanisms

Question 1

What are 3 types of chemical reactions in metabolism?

Answer 1

1. nucleophilic substitutions
2. cleavage reactions
3. oxidation-reduction reactions

Question 2

what is a nucleophile?

Answer 2

-electron rich species with a negative charge or lone pair that is able to push its electron onto another atom (attack)

Question 3

what is an electrophile?

Answer 3

-electron poor species that can be attacked by a nucleophile

Question 4

are nucleophilic substitutions fast or slow reactions?

Answer 4

-usually slow unless the transition state can be stabilized

Question 5

nucleophilic substitutions are the basis of _______

Answer 5

most group transfer reactions

Question 6

What is a cleavage reaction?

Answer 6

• when a covalent bond cleaves

- the two electrons originally in the bond can go with one atom or each atom can take one with it

Question 7

are cleavage reactions fast or slow?

Answer 7

usually slow unless the carboanion/carbocation can be stabilized

Question 8

carbanions and carbocations are highly energetically _____

Answer 8

unstable

Question 9

When an electron pair splits up in a cleavage reaction ____ are produced

Answer 9

radicals

Question 10

what are radicals?

Answer 10

• high unstable
• causing oxidative damage to cells
• highly toxic

Question 11

can enzymes stabilize free radical production?

Answer 11

• no

- many enzymes are programmed to destroy and clean up radicals

Question 12

what are oxidation-reduction reactions?

Answer 12

• redox rxns are central to energy production in metabolism

- electrons are transferred during redox rxns

Question 13

what is an oxidizing agent?

Answer 13

-gains electrons and is reduced

Question 14

what is a reducing agent?

Answer 14

-loses electrons and is oxidized

Question 15

What are the 3 steps of oxidation?

Answer 15

1. removal of hydrogen, loss of a hydride ion H-
2. addition of oxygen, or
3. loss of electron

Question 16

what happens to the lost electron when a species is oxidized?

Answer 16

-the electron it loses are transferred to an oxidizing agent

Question 17

how do enzymes catalyze a reaction?

Answer 17

-by lowering its overall barrier

Question 18

What are 2 ways that enzymes work chemically?

Answer 18

1. enzyme must bind substrate

2. enzyme must turnover substrate

Question 19

what is an enzyme active site?

Answer 19

• location where substrate binds

- where the chemistry is carried out

Question 20

how many residues participate directly in catalysis?

Answer 20

• small number

- most contribute indirectly by holding together the fold + binding to the substrate

Question 21

what kind of residues are most frequently found at the catalytic site of enzymes?

Answer 21

charged or polar

Question 22

Which amino acid is found most often at the catalytic site?

Answer 22

-His (6x more than its abundance in the rest of all the proteins)

Question 23

____ is stabilized by the enzyme

Answer 23

an unstable intermrediate

Question 24

what are charges in the intermediate stabilized by?

Answer 24

1. electrostatics, or

2. acid/base chemistry

Question 25

What is acid-base catalysis?

Answer 25

-acid (proton donor) or base (proton acceptor) to stabilize the transition state of a leaving group

Question 26

what else can a base participate in?

Answer 26

the cleavage of C-N or C-O bonds EX glycosidic bonds

Question 27

what does protonation catalyze?

Answer 27

carbocation ion intermediates

Question 28

what is covalent catalysis?

Answer 28

- substrate bound covalently to the enzyme to form a reactive intermediate - the enzyme that transfer the group to a second substrate

Question 29

what does covalent catalysis allow the enzyme to do?

Answer 29

couple two different reactions EX: sucrose phosphorylase carries out the hydrolysis of the glycosidic bond in sucrose in 2 steps

Question 30

what do enzyme reactions often involve?

Answer 30

ions/and or acid-base catalysis

Question 31

what does the involvement of ions/acid-base catalysis cause?

Answer 31

the velocity can change with the pH EX: Papain is a cysteine protease found in papaya

Question 32

what type of reactions have some of the highest catalytic efficiencies?

Answer 32

diffusion-limited enzymatic reactions

Question 33

what happens when the substrate concentration is very low?

Answer 33

the enzyme-catalyzed reaction is bimolecular

Question 34

what happens if enzymatic efficiency is high?

Answer 34

the reaction then becomes diffusion limited

Question 35

What are 2 examples of high-efficiency enzymes?

Answer 35

1. triose phosphate isomerase | 2. superoxide dismutase

Question 36

what is triose phosphate isomerase?

Answer 36

- enzyme that is used in glycolysis and gluconeogensis | - catalyzes the conversion of dHAP to G3P

Question 37

what is a main feature about triose phosphate isomerase?

Answer 37

-employs a rare anionic form of His in its catalytic center

Question 38

what is superoxide dismutase?

Answer 38

-performs cleanup in an oxygen rich environment where metabolism produces toxic byproducts like the superoxide radical anion

Question 39

how is catalysis done with superoxide dismutase?

Answer 39

- a copper atom at the catalytic center | - first reduced, then oxidized

Question 40

why does superoxide dismutase work faster than the diffusion upper limit?

Answer 40

because it uses positively charged residues a the entrance to recruit superoxide

Question 41

what are 4 principles of enzymatic efficiencies?

Answer 41

1. proximity 2. weak binding of substrate to enzyme 3. induced fit 4. transition state stabilization

Question 42

what is proximity?

Answer 42

placing reactants in close contact encourages reactive collisions between them

Question 43

what is weak binding of substrate to enzyme?

Answer 43

- the enzyme should facilitate binding to the substrate | - but so strongly it is unable to release it to turnover products

Question 44

what is induced fit?

Answer 44

- enhances substrate specificity | - prevent unproductive reactions

Question 45

What is an example of induced fit?

Answer 45

- hexose kinase phosphorylates glucose to glucose 6 phosphate - conformational changes occur when glucose binds allowing ATP to only act in the close form

Question 46

what needs to happen to the transition state?

Answer 46

-needs to be stabilized, but not overstabilized

Question 47

what are transition state analogs?

Answer 47

- synthetic compounds/drugs taht mimic the transition state | - distorts the stability of the ES complex

Question 48

What is an example of transition state stabilization?

Answer 48

- 2-phosphoglycolate is a transition state analog for the enzyme triose phosphate isomerase and a strong inhibitor - 2-phosphoglycolate binds effectively to triose phosphate isomerase to mimic the transition state but overstabilize it