Biochemistry > Chapter 11 > Flashcards

Chapter 11 Flashcards

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1
Q

What is enzymology?

A

study of enzymes

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2
Q

What do enzymes do?

A

Catalyze thermodynamically favorable reactions

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3
Q

True or False: Enzymes have an effect on ΔG

A

False

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4
Q

What is catalytic power?

A

Ratio of the enzyme-catalyzed rate of a reaction to the uncatalyzed rate

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5
Q

What type of reaction do oxidoreductases catalyze?

A

Oxidation-reduction reactions (electron transfers)

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6
Q

What type of reaction do transferases catalyze?

A

Transfer of functional groups

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7
Q

What type of reaction do hydrolases catalyze?

A

Hydrolysis reactions

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8
Q

What type of reaction do lyases catalyze?

A

group elimination to form double bonds

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9
Q

What type of reaction do isomerases catalyze?

A

Isomerization

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10
Q

What type of reaction do ligases catalyze?

A

Bond formation coupled with ATP hydrolysis

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11
Q

What are the 6 enzyme classifications?

A
  1. Oxidoreductases
  2. Transferases
  3. Hydrolases
  4. Lyases
  5. Isomerases
  6. Ligases
    “Oh Ted Has Leukemia I Lied”
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12
Q

What are enzyme cofactors?

A

Nonprotein components essential to enzyme activity

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13
Q

What are the enzyme cofactors?

A

Metal ions, Coenzymes (Cosubstrates and Prosthetic Groups)

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14
Q

What is the difference between cosubstrates and prosthetic groups?

A

Cosubstrates: free to move in or out of enzyme
Prosthetic Groups: covalently attached to protein

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15
Q

What is a holoenzyme?

A

Active enzyme-cofactor complex

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16
Q

What is an apoenzyme?

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A

Enzyme without needed cofactor, likely not functional

17
Q

What is the difference between ΔG and ΔG-cross?

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A

ΔG: Overall free energy change for a reaction
ΔG-cross: Free energy of activation for a reaction

18
Q

What is ΔG related to?

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A

Equilibrium constant

19
Q

What is ΔG-cross related to?

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A

Rate constant

20
Q

Does the direction of the reaction depend on ΔG or ΔG-cross?

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A

ΔG
ΔG = (+) spontaneous in the reverse direction
ΔG = (-) spontaneous in the forward direction

21
Q

What are the 5 mechanisms for enzyme catalysis?

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A

Acid-Base Catalysis
Covalent Catalysis
Metal Ion Catalysis
Proximity and Orientation Effect
Transition State Binding

22
Q

How does the RNAse mechanism work?

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A
  1. Base nitrogen on His12 attacks 2’ hydroxyl
  2. Electrons in the O-H bond attack the P
  3. The bond between P and the oxygen that leads to the second RNA sugar accepts acid H on His119
  4. New base nitrogen on HIs119 attacks a H on water
  5. Water bond attacks P and oxygen attacks base H His12
23
Q

What is the mechanism of carbonic anhydrase (metal ion catalysis)?

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A
  1. Alcohol on Zn2+ attacks carbon of CO2
  2. Water attacks Zn2+ and breaks the oxygen bond
24
Q

What is faster intramolecular or intermolecular reactions?

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A

Intramolecular (within molecule)

25
What is electrostatic catalysis?
Charged groups stabilize transition state
26
What is the mechanism of proline racemase?
1. Hydrogen is removed from central carbon 2. Creates planer transition state 3. Hydrogen is added on in other position, switching sides
27
What is the function of lysozyme?
Hydrolyzes bacterial cell wall glycosidic linkages
28
Where does lysozyme hydrolyze?
On β-1,4-glycosidic linkage between NAM and NAG
29
What structural change does lysozyme force upon binding?
Forces chair conformation into half chair conformation (Switches C5 and O5)
30
What two amino acids carry out the lysozyme mechanism?
Asp52 and Glu35
31
What is the mechanism for lysozyme?
1. Glycosidic bond between NAM and NAG attacks alcohol on Glu35 2. Negative oxygen on Asp52 binds to the now positive carbon on NAM 3. Water is cleaved by the now negative oxygen on Glu35 and the oxygen attacks the 1' carbon 4. Upon getting attacked, the carbon loses the bond to the oxygen on Asp52
32
What are the serine proteases?
Trypsin Chymotrypsin Elastase Thrombin Substilism Plasmin TPA
33
What is the catalytic triad?
Ser, His, Asp
34
What makes up the binding pocket for chymotrypsin?
Gly 226, Ser 189, Gly 216
35
What makes up the binding pocket for trypsin?
Gly 226, Asp 189, Gly 216
36
What makes up the binding pocket for elastase?
Val 226, Thr 216
37
What is the serine protease mechanism?
1. Nucleophilic attack of the alcohol on serine on carbon of substrate, removing C=O 2. Double bond reformation between oxygen and carbon, removing the bond to nitrogen 3. Nitrogen of histidine attacks water and oxygen forms a bond with carbon, removing the double bond to oxygen 4. Covalent bond between carbon and serine's oxygen attacks histidine's hydrogen 5. HO-C(O)-R leaves as product
38
What is a zymogen?
Inactive molecule that is converted to an enzyme when activated by another enzyme
Biochemistry
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