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CHEM 350 > Lecture 17 - Enzyme mechanisms > Flashcards

Lecture 17 - Enzyme mechanisms Flashcards

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1
Q

What are 3 types of chemical reactions in metabolism?

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

what is a nucleophile?

A

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

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3
Q

what is an electrophile?

A

-electron poor species that can be attacked by a nucleophile

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4
Q

are nucleophilic substitutions fast or slow reactions?

A

-usually slow unless the transition state can be stabilized

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5
Q

nucleophilic substitutions are the basis of _______

A

most group transfer reactions

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6
Q

What is a cleavage reaction?

A
  • 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

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7
Q

are cleavage reactions fast or slow?

A

usually slow unless the carboanion/carbocation can be stabilized

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8
Q

carbanions and carbocations are highly energetically _____

A

unstable

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9
Q

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

A

radicals

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10
Q

what are radicals?

A
  • high unstable
  • causing oxidative damage to cells
  • highly toxic
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11
Q

can enzymes stabilize free radical production?

A
  • no

- many enzymes are programmed to destroy and clean up radicals

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12
Q

what are oxidation-reduction reactions?

A
  • redox rxns are central to energy production in metabolism

- electrons are transferred during redox rxns

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13
Q

what is an oxidizing agent?

A

-gains electrons and is reduced

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14
Q

what is a reducing agent?

A

-loses electrons and is oxidized

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15
Q

What are the 3 steps of oxidation?

A
  1. removal of hydrogen, loss of a hydride ion H-
  2. addition of oxygen, or
  3. loss of electron
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16
Q

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

A

-the electron it loses are transferred to an oxidizing agent

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17
Q

how do enzymes catalyze a reaction?

A

-by lowering its overall barrier

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18
Q

What are 2 ways that enzymes work chemically?

A
  1. enzyme must bind substrate

2. enzyme must turnover substrate

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19
Q

what is an enzyme active site?

A
  • location where substrate binds

- where the chemistry is carried out

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20
Q

how many residues participate directly in catalysis?

A
  • small number

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

21
Q

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

A

charged or polar

22
Q

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

A

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

23
Q

____ is stabilized by the enzyme

A

an unstable intermrediate

24
Q

what are charges in the intermediate stabilized by?

A
  1. electrostatics, or

2. acid/base chemistry

25
Q

What is acid-base catalysis?

A

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

26
Q

what else can a base participate in?

A

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

27
Q

what does protonation catalyze?

A

carbocation ion intermediates

28
Q

what is covalent catalysis?

A
  • substrate bound covalently to the enzyme to form a reactive intermediate
  • the enzyme that transfer the group to a second substrate
29
Q

what does covalent catalysis allow the enzyme to do?

A

couple two different reactions EX:

sucrose phosphorylase carries out the hydrolysis of the glycosidic bond in sucrose in 2 steps

30
Q

what do enzyme reactions often involve?

A

ions/and or acid-base catalysis

31
Q

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

A

the velocity can change with the pH

EX: Papain is a cysteine protease found in papaya

32
Q

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

A

diffusion-limited enzymatic reactions

33
Q

what happens when the substrate concentration is very low?

A

the enzyme-catalyzed reaction is bimolecular

34
Q

what happens if enzymatic efficiency is high?

A

the reaction then becomes diffusion limited

35
Q

What are 2 examples of high-efficiency enzymes?

A
  1. triose phosphate isomerase

2. superoxide dismutase

36
Q

what is triose phosphate isomerase?

A
  • enzyme that is used in glycolysis and gluconeogensis

- catalyzes the conversion of dHAP to G3P

37
Q

what is a main feature about triose phosphate isomerase?

A

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

38
Q

what is superoxide dismutase?

A

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

39
Q

how is catalysis done with superoxide dismutase?

A
  • a copper atom at the catalytic center

- first reduced, then oxidized

40
Q

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

A

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

41
Q

what are 4 principles of enzymatic efficiencies?

A
  1. proximity
  2. weak binding of substrate to enzyme
  3. induced fit
  4. transition state stabilization
42
Q

what is proximity?

A

placing reactants in close contact encourages reactive collisions between them

43
Q

what is weak binding of substrate to enzyme?

A
  • the enzyme should facilitate binding to the substrate

- but so strongly it is unable to release it to turnover products

44
Q

what is induced fit?

A
  • enhances substrate specificity

- prevent unproductive reactions

45
Q

What is an example of induced fit?

A
  • hexose kinase phosphorylates glucose to glucose 6 phosphate
  • conformational changes occur when glucose binds allowing ATP to only act in the close form
46
Q

what needs to happen to the transition state?

A

-needs to be stabilized, but not overstabilized

47
Q

what are transition state analogs?

A
  • synthetic compounds/drugs taht mimic the transition state

- distorts the stability of the ES complex

48
Q

What is an example of transition state stabilization?

A
  • 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

CHEM 350 (22 decks)

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