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Biochemistry > Biochem Exam #2 Study Guide > Flashcards

Biochem Exam #2 Study Guide Flashcards

(80 cards)

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1
Q

Enzymes

A

proteins that catalyze specific reactions

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2
Q

Each Enzyme is

A

unique
catalyze specific reactions
speed up reactions

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3
Q

What attracts an enzyme to a substrate?

A

intermolecular forces

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4
Q

Active Site

A

catalytic center where the substrate fits into the enzyme

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5
Q

What happens when the enzyme undergoes a conformational change?

A
  • creates tighter induced fit

- bring chemical groups in position to catalyze the reaction

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6
Q

When S binds to E

A
  • there is a conformational change
  • transition state is stabilized
  • create environment for rxn
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7
Q

cofactor

A

any organic or inorganic molecule that aids in catalysis

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8
Q

What are the 2 types of cofactors? Protein or Non-protein?Organic or inorganic?

A

coenzyme & prosthetic group
nonprotein
organic

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9
Q

How do the 2 cofactors bind?

A

coenzyme: binds with IMFs

prosthetic group: bind with covalent bond

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10
Q

Holoenzyme vs. Apoenzyme

A

holoenzyme: has cofactor
apoenzyme: does not have cofactor

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11
Q

Oxidoreductase (dehyrogenase)

A

cataylze redox reactions

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12
Q

Transferases

A

transfer functional group

G+ATP->G6P+ ADP

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13
Q

Hydrolase

A

use H20 to break covalent bonds

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14
Q

Lyase

A

adds or removes covalent bond without H2O

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15
Q

Isomerase

A

creates an isomer (molecule with same EF but arranged differently)

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16
Q

Ligase

A

make covalent bond and use energy (ATP)

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17
Q

What does enzyme kinetics give us? (5)

A 
info on:
purity of enzyme
catalytic efficiency
specificity
inhibition
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18
Q

Lock & Key Theory

A

Enzyme binds S like a lock fits a key

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19
Q

Induced Fit

A

S binds to E, but “fit” to accommodate transition state

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20
Q

The conformational change during cataylsis allows for what?

A

Stabilization of the transition state

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21
Q

How does an enzyme speed up a reaction?

A

by lowering its activation energy

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22
Q

What are the 2 things we need to know about the enzyme?

A
  1. how good the substrate binds (km)

2. Production of product

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23
Q

k1 is; k-1

A

the association of S to E; disassociation of S from E

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24
Q

Rate=____: which is?

A

Velocity: the quantity of S that disappears and quantity of P that appear in a specific time

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25
1st order rate
exponential | rate depends on substrate concentration
26
Zero order rate
horizontal line | rate does not depend on substrate concentration; there is no difference
27
ka
rate constant | indicator of strength of acid
28
2nd order rate
sigmodial | rate depends on concentration of both substrate 1 and 2
29
Steady State Assumption was created by?
Briggs Haldene
30
Steady State
As the [S] decrease the [P] increases, but the ES complex is still the same
31
Vmax
theoretical max rate of an enzyme that is never reached
32
Km
"affinity" | concentration of S at 1/2 Vmax
33
Small Km= | High Km=
small=tight fit (better affinity) | high=weak fit
34
Kcat;equation
"turnover number" -number of S molecules converted to P the bigger the number the more product made -Kcat=Vmax/[Et]
35
Kcat/Km
catalytic efficiency
36
Types of Inhibition
Competitive Noncompetitive Uncompetitive
37
Competitive Inhibition: reversible?
-inhibitor binds the to the same place that the substrate binds reversible -can be overcome by adding more substrate
38
Affects of competitive inhibitor
Lowers the Km, but Km will appear to increase
39
Noncompetitive Inhibition:reversible?
- inhibitor binds to a spot on the enzyme other than the active site - can not be overcome by adding more substrate
40
Affects of noncompetitive inhibitor
Vmax is decreased; Km is unchanged
41
Uncompetitive Inhibitor
inhibitor binds to ES only | prevents S from detaching or become P
42
Affects of uncompetitive inhibitor
Km & Vmax are decreased
43
Cleland Notations
for enzymes with 2 substrates
44
What are the 2 types of notations for cleland diagrams
sequential & double displacement
45
Ordered Sequential
S1:S2:P1:P2 | order matters
46
Double Displacement
S1:P1:S2:P2
47
catalytic residue (2)
- amino acid side chains in active site that are involved in the mechanism - alter pka - stabilize transitional state
48
Acidic Residue
want charge: pka decrease (-) | not want charge: pka increases (+)
49
Basic Residue
want charge: pka increase (+) | not want charge: pka decreases (-)
50
Nu
nucleus loving has extra electrons reacts with + or partial +
51
E+
electron loving has lack of electrons react with - or partial -
52
proteases
enzyme the cut peptide bonds
53
Acid Catalysis
uses a strong E+ a molecule other than water acts as an acid positive charge pulls on oxygen
54
Base Catalysis
uses a strong Nu a molecule other than water acts as a base negative charge pulls on hydrogen
55
Acid/Base Catalysis
uses both strong E+ and Nu
56
Carboxypeptidase A
CPA metalloprotease cuts off C-terminal residue uses Zn+2 for catalytic activity
57
MetalloPR
uses a metal for catalytic mechanism | metal acts as E+
58
Mechanism of CPA (6)
1. Substrate binds to active site 2. Zn attacks the double bonded oxygen 3. Glu takes H+ from water 4. Attack N-term leaves 5. Tetrahedral intermediate forms 6. Enzyme resets
59
CPA: substrate binds active site
Arg attacks the C term
60
CPA:Zn attacks double bonded oxygen
makes carbon better E+(acts as an acid)
61
CPA:Glu take H+ from water
water acts as a base
62
CPA:Tetrahedral intermediate form
Transition state stabilized by Tyr | Tyr acts as an acid
63
CPA: Enzyme reset
Tyr accepts H from Glu
64
Chymotrypsin
Serine PR has a catalytic triad cuts after WMFYL
65
What amino acids are in the catalytic triad?
aspartic acid histidine serine
66
Mechanism of Chymo (9)
1. substrate binds active site and activates catalytic triad 2. Asp takes H+ from His, then His takes from Ser 3. Nu attack bu Ser 4. Tetrahedral intermediate formed 5. Reform pi bond 6. 2nd Nu attack 7. Shiff N of His gives es to water 8. Attack on tetrahedral intermediate 9. N term released
67
Cutting locations of chymo
WMFYL
68
Cutting locations of trypsin
K and R
69
Cutting locations of elastase
A and G
70
Feed forward activation
ATP binds Enz to make go
71
Feedback inhibition
E binds Enz to make slow
72
Enzyme catalyze with step in the pathway
rate limiting step-committing step
73
T State
Active site is blocked; little S bind
74
R State
Active site open; S bind readily
75
What types of domains do enzymes have?
active site domain | regulatory domain
76
Effector binds the _____ domain w/ + effector= w/ - effector=
regulatory domain activator (more in R) inhibitor (more in T)
77
Isozymes
2 enzymes
78
Zymogen
inactive precusor | ex.chymotrypsiongen
79
post translational modifications
"after protein made change"
80
Kinase
- enzyme that catalyze the transfer of a phosphate from ATP to an aa side chain in an enzyme - reversed by phosphatases

Biochemistry (14 decks)

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