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601 EXAM 1 > 2.1 Enzymes > Flashcards

2.1 Enzymes Flashcards

1
Q

______ are the work horse of chemical/biological systems that catalyze biological reactions

A

Enzymes

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2
Q

Enzyme characteristics

A
  • highly specific for catalyzed reactions
  • encoded by majority of protein coding genes
  • end in “ase”: kinase, phosphatase, dehydrogenase (exceptions: trypsin, chymotrypsin)
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3
Q

how do enzymes act as catalysts? (what do they do to chemical reactions?

A

increase reaction rate, but do NOT change equilibrium

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4
Q

2 types of macromolecules with enzymatic functions?

A
  1. proteins (almost all enzymes = proteins)

2. RNA (ribozymes = catalytic RNA = RNA w enzymatic fxn)

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5
Q

how many proteinogenic AAs? and in eukaryotes?

A

22 total (pyrrolysine only found in archaea and bacteria), 21 in eukaryotes

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6
Q

How many essential AA? How to remember them?

A

9, Private Tim Hall
P V T T I M H A L L
phenylalanine, valine, threonine, tryptophan, isoleucine, methionine, histdine, arginine, leucine, lycine
(recognize structures in red on pic)

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7
Q

Differences in bonds for secondary structures?

A
  • both have H-bonds
  • a-helix: bond for every fourth base
  • B-sheet: bond with adjacent bases
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8
Q

what are the strong bonds in tertiary structures?

A

Di-sulfide

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9
Q

what is a basic enzymatic reaction? what are the transient complexes?

A

E + S <–> ES <–> EP <–> E + P

transient = ES, EP

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10
Q

enzymes affect _____ not ____, so they make reactions go faster

A

reaction rates, equilibria

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11
Q

Oxioreductases

A

do oxidation/reduction of molecules (e- transfer)

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12
Q

dehyderogenases

A

transfers e- to NAD+, NADP+, FMN, FAD

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13
Q

oxidases

A

transfer e- to Oxy

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14
Q

transferases

A

transfer groups (CH3, C2H3O, etc)

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15
Q

hydrolases

A

transfer functional groups to water; water to break chemical bonds

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16
Q

lysases

A

addition/removal of groups to form double bonds

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17
Q

isomerases

A

intramolecular group transfer (makes isomers)

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18
Q

ligases

A

ligation of 2 substances (joining)

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19
Q

what are tertiary and quaternary structures governed by?

A

weak non-covalent bonds

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20
Q

enzymes accelerate the reaction by ___________

A

lowering the activation energy of the reaction

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21
Q

The interaction of E and S release binding energy that contributes to _____

A

lowering the EA

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22
Q

Enzyme binds substrate in a way that makes it easier to _____

A

manipulate the substrate and break/form bonds

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23
Q

S binds to E initially with weak actions and the bond is strengthened by _____

A

formation of more interactions at the site

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24
Q

What is wrong with the lock and key model?

A

it does not produce enough energy

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25
Q

What is the induced fit model? why is it favored?

A
  • Initial ES formation =weak interactions, but full interactions in transition state
  • explains where extra energy to lower activation energy is derived from
26
Q

4 strategies for catalysis

A
  1. general acid-base (donate/accept protons)
  2. covalent catalysis (covalent bond forms bw SE)
  3. Metal ion catalysis (1/3 of all enzymes need metal for catalysis)
  4. catalysis by approximation (molecules so close that it is spontaneous)
27
Q

examples of AA commonly involved in acid-base catalysis? (dont have to memorize, but recognize them)

A

Glu, Asp, Lys, Arg, Cys, His, Ser, Tyr

28
Q

pKa definition

A

strength of acid, how likely to accept/lose H+

29
Q

pattern between pH and pKa

A

if pH > pkA, use acidic form (>i think, check this?)

30
Q

EX of enzyme using acid-base and covalent catalysis

A

Chymotrypsin= protease in pancreatic juice

- enzyme can use multiple strategies!

31
Q

Ex of metal-ion catalysis?

A
  • carbonic anhydrase (buffering system for pH)
  • Zn2+ = prosthetic group
  • Zn facilitates deprotonation of H2O and making OH a nucleophile
32
Q

10 factors effecting enzyme function

A
  1. substrate concentration
  2. Inhibitors
  3. Allosteric effectors (modulators)
  4. Cofactors
  5. reversible covalent modifications
  6. pH and temperature
  7. Proteolytic cleavage
  8. protein-protein interactions
  9. enzyme concentration
  10. isozymes
33
Q

At low Vo, [S] increases _______ and at high Vo, [S] increases ______

A
  1. linearly

2. slowly until approaches Vmax

34
Q

what does Michaelis Mentin curve describe?

A

the rate of catalysis of the enzyme at some particular substrate concentration.

35
Q

what is Km?

A

[S] at which half of E active sites are occupied

36
Q

Km = Michaelis constant = ______

A

1/2 Vmax

Vmax = when all enzymes are saturated with substrate

37
Q

High Km suggests ___________

Low Km suggests ____________

A
  1. weak binding of S to E (lower reaction rate)
  2. strong binding of S to E (higher reaction rate)

0.05 kM = stronger bond than 5 kM

38
Q

do hexokinase or glucokinase have a stronger binding?

A

hexokinase (lower kM)

39
Q

Inhibitors

A

therapeutic agents to control pathways (reversible, nonreversible)

40
Q

Reversible competitive inhibitor

A
  • Inhibitor binds to active site
  • you can overcome inhibitor by adding more S
  • binding is reversible`
41
Q

Non-Reversible competitive inhibitor

A
  • binds to a dif site than the catalytic site to alter proteins conformation
  • binding of NI alters conformation of E so S cant bind
42
Q

_______ are irreversible inhibitors that resemble the substrate and covalently modify the enzyme

A

Substrate analogs

43
Q

what do suicide inhibitors do?

A

Enzyme modifies and inactivates the substrate by forming a stable complex (enzyme modifies it and it can’t leave now)

44
Q

do Allosteric enzymes follow michaelis-mentin?

A

no because they have more than 1 binding site

45
Q

Allosteric enzymes

A

enzymes whose conformations are altered when an allosteric effector binds
- allosteric effectors can bind to the allosteric site and change the conformation of E to be more or less active

46
Q

how is ATCase a good example of how different allosteric effectors can effect a particular enzyme?

A
  • It has homo and hetero-regulation
  • homo: Substrate is also the effector; it binds and activates enzyme function (aspartate)
  • hetero: CTP netgatvely regulates and ATP positively regulates
47
Q

cooperative binding example

A
  • Hemoglobin has 4 spots for O2

- each time an O2 binds, there is a conformational change that makes it easier for the next to bind

48
Q

_____ are non-proteinaceous molecules for Enzyme activity

A

Cofactors

- can be organic or inorganic

49
Q

Inorganic co-factors

A

Zn, Mg, Mn, Fe, etc (remember, metal cofactors play a role in 1/3 of enzyme processes)

50
Q

What are coenzymes?

A

organic cofactors that act as transient carriers of moieties like e-, methyl-,acyl- etc

51
Q

Many enzymes need ______ for activity

A

cofactors

52
Q

Enzyme without cofactor = ______ = inactive

A

apoenzyme

53
Q

Enzyme with cofactor = ______ = active

A

holoenzyme

54
Q

covalent modifications can effect enzyme function by modifying groups such as ______

A

phosphoryl, acetyl, methyl, carboxyl, etc

ex: phosphorylation/dephos

55
Q

each enzyme has an optimal ______ and _____ range

A

pH, temperature

56
Q

What is Tm

A

melting point

57
Q

thermal denaturation

A

unfolding of protein due to heat

58
Q

______ are inactive precursors of enzymes that must be cleaved to becomes active

A

Zymogens

59
Q

Some proteins are inactive until _____

A

binding of a modulator protein causes a conformational change at the active site to activate or inhibit the enzyme
- Enzyme: GTP complex binds and regulates fxn of target protein

60
Q

______ catalyze the same reaction but have different primary structures (EX?)

A

isozymes

EX: hexokinase/glucokinase

601 EXAM 1 (12 decks)

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