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Biochemistry I > Exam 2 > Flashcards

Exam 2 Flashcards

1
Q

Many diseases are caused by an excess of _____ or deficiency of a ______

A

product, substrate

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2
Q

Active site

A

region where catalysis occurs

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3
Q

Substrate

A

Reactant of the enzyme

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4
Q

Product

A

Molecules produced as the result of a reaction

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5
Q

Enzymes work best in what conditions

A

temps below 100 C and a neutral pH

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6
Q

How much faster is a catalyzed reaction than an uncatalyzed one

A

10^6-10^14 times faster

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7
Q

Why are side products rare in enzyme reactions

A

because enzymes are usually highly specific in terms of reaction selectivity

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8
Q

How are enzymes regulated (3 ways)

A
  1. covalent modification
  2. levels of enzyme synthesized
  3. allosteric regulation
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9
Q

Oxidoreductases

A

used in redox reactions

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10
Q

Transferases

A

used when functional groups are being transferred

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11
Q

Hydrolases

A

water cleaving bonds

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12
Q

Lyases

A

forms a double bond

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13
Q

Isomerases

A

intermolecular rearrangement

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14
Q

Ligases

A

creating a bond with ATP

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15
Q

How do enzymes work

A

by lowering the energy of activation

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16
Q

Rate enhancement

A

e^(ΔΔG‡/RT)

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17
Q

When ΔG‡ is larger, the reaction is

A

slower

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18
Q

At 298K, decreasing ΔG‡ by 5.7 kJ/mol, the speed of reaction increases

A

10 fold

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19
Q

Catalytical enzyme mechanisms (5 types)

A
  1. acid-base
  2. covalent
  3. metal ion
  4. proximity and orientation effects
  5. preferential binding of the transition state
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20
Q

Example of acid-base catalysis

A

RNAase A

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21
Q

Covalent catalysis

A

transient formation of an enzyme-substrate covalent bond

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22
Q

Covalent catalysis usually involves a reaction between ______ on the catalyst and the _____ group on the substrate

A

nucleophilic, electrophilic

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23
Q

What are the 4 amino acids that are typically used as substrates in covalent catalysis

A

ser, cys, his, lys

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24
Q

Metal ion participation in metal ion catalysis (3)

A
  1. binding to substrates to orient them properly
  2. Mediating redox reactions
  3. Electrostatic stabilization and shielding negative charges
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25
Q

What metal ion catalyzes carbonic anhydrase formation

A

zinc

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26
Q

What is the purpose of metal ion catalysis

A

to create a stronger nucleophile

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27
Q

Net reaction of glycolysis

A
  • 1 molecule of glucose consumed
    -2 molecules of ADP are converted to ATP
    -2 molecules of NAD+ are reduced to NADH
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28
Q

Step 1 glycolysis

A

Hexokinase
Requires Mg2+
Generates G6P

29
Q

G6P activates _____ and then _____

A

glucose, traps it in the cell

30
Q

Step 3 glycolysis

A

Phosphofructokinase (PFK)
F6P-> 1,6 FBP

31
Q

Hexokinase is a

A

transferase

32
Q

Step 3 of glycolysis is

A

irreversible, critical regulatory point/committed step

33
Q

PFK2 generates _____ which is a regulator for ______ and _____

A

2,6 FBP, gluconeogenesis, glycolysis

34
Q

Irreversible steps of glycolysis

A

1, 3, 10

35
Q

What steps in glycolysis use ATP

A

1 and 3

36
Q

Step 4 of glycolysis

A

Aldolase
1,6 FBP -> 2 triose compounds
operates via aldol cleavage

37
Q

Step 6 of glycolysis

A

GAPDH
NAD+ reduced to NADH
GAP -> 1,3-BPG

38
Q

Step 6 of glycolysis is the only ________ step

A

oxidation

39
Q

Step 7 glycolysis

A

Phosphoglycerate kinase (PGK)
1,3-BPG + ADP -> 3-PG + ATP

40
Q

Steps 7 and 10 of glycolysis are examples of

A

substrate level phosphorylation

41
Q

Step 10 of glycolysis

A

Pyruvate Kinase
Phosphoenol pyruvate (PEP)-> pyruvate

42
Q

Catalytic triad

A

ASP - HIS- SER

43
Q

High energy phosphates (4)

A
  • acetyl phosphate
    -1,3-BPG
    -Phosphocreatine
    -Phosphoarginine
44
Q

Low energy phosphates (2)

A
  • alpha-D-glucose-6-phosphate
  • 1-glycerol-3-phosphate
45
Q

Preferential binding of the transition state

A

this is the concept that the enzyme will bind tighter to the transition state so the complex is forced to complete the original reaction instead of reacting with a different compound

46
Q

_____ bonds link the anomeric carbon to other compounds

A

Glycosidic

47
Q

Why can humans not digest cellulose

A

We cannot digest the 1,4-beta linkages found in cellulose

48
Q

True/False: A low Kcat/Km ratio is favorable because it indicates a higher enzyme efficiency

A

False. A high Kcat/Km ratio indicates a higher enzyme efficiency

49
Q

____ Kcat is favorable, ______ Km is favorable

A

high, low

50
Q

Competitive inhibitors bind to

A

enzyme only

51
Q

Competitive inhibition increases _____ and does not affect ____

A

Km, Vmax

52
Q

Catalytic mechanism by serine proteases

A
  1. preferential binding of transition state
  2. Covalent catalysis (Ser195 binds substrate)
  3. Proximity/orientation effects (Ser195 positioned for nucleophilic attack)
  4. Acid/base catalysis (His57 acts as both an acid and a base, Asp102 acts somewhat as a base)
53
Q

Summary of lysozyme mechanism

A
  1. Binds hexasaccharide unit, distorts D residue
  2. Glu35 transfers proton to O1 bridging D and E rings
  3. Asp52 nucleophilically attacks C1 of D ring to form glycosyl-enzyme intermediate
  4. Water replaces E ring product in active site and Glu35 hydrolyzes covalent bond
54
Q

Km=[S] when

A

V0=1/2Vmax

55
Q

Enzymes with small Km achieve maximal efficiency at ____ substrate concentrations

A

low

56
Q

Trypsin specificity pocket

A

Deep. Trypsin binds lysine and arginine

57
Q

Chymotrypsin specificity pocket

A

binds aromatic compounds. specificity pocket is large

58
Q

Elastase specificity pocket

A

Small uncharged residues

59
Q

What is alpha in liveweaver-burke plots

A

a factor by which substrate concentration must be increased in order to overcome the effects of the inhibitor

60
Q

Uncompetitive inhibitors bind

A

ES

61
Q

T/F: Uncompetitive inhibition cannot be overcome by addition of S

A

true

62
Q

Uncompetitive inhibition _____ Vmax and Km

A

decreases

63
Q

Lines on uncompetitive lineweaver-burke are

A

parallel

64
Q

Noncompetitive inhibitors bind

A

E and ES

65
Q

Pure noncompetitive inhibition

A

Vmax decreases
Km stays the same

66
Q

Mixed noncompetitive

A

If K1 is larger -> inhibitor favors binding enzyme, mimics competitive inhibition
If K1’ is larger -> inhibitor favors binding ES which mimics uncompetitive inhibition
Lines on Linewever-burke do not intersect on an axis
Vmax decreases

67
Q

Inactivation of serine proteases

A

-irreversible
-DIPF inactivates
-Lovers Vmax but doesn’t affect Km

68
Q

Enzymes that catalyze reactions near equlibrium (delta G near 0)

A

not good sites to control pathway flux
rate is almost entirely controlled by substrate/product concentrations

69
Q

Enzymes that catalyze far from equilibrium (delta G«0)

A

-act as chokepoints that can be used to control entire pathway

Biochemistry I (13 decks)

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