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Biochemistry > Lecture 12 (Exam 2) > Flashcards

Lecture 12 (Exam 2) Flashcards

1
Q

This is the term for a modification and especially increase in the rate of a chemical reaction induced by material unchanged chemically at the end of the reaction.

A

Catalysis

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2
Q

This is the term for a substance that enables a chemical reaction to proceed at a usually faster rate or under different conditions (as at a lower temperature) than otherwise possible.

A

Catalyst

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3
Q

What do enzymes do?

A

1) Lower the activation energy

2) Stabilize the transition state

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4
Q

What do enzymes NOT do?

A

1) Change the Delta-G of the reaction

2) Irreversibly change shape

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5
Q

A catalyst is something that (INCREASES/DECREASES) the rate (speed) of a reaction but does not undergo any permanent chemical change as a result.

A

Increases

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6
Q

When the value of Delta-H is negative, that means energy is being (ADDED/RELEASED) to/from the system.

A

Released

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7
Q

When the value of Delta-H is positive, that means energy is being (ADDED/RELEASED) to/from the system.

A

Added

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8
Q

When the value of Delta-S (entropy) is negative, that means disorder is (INCREASING/DECREASING).

A

Decreasing

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9
Q

When the value of Delta-S (entropy) is positive, that means disorder is (INCREASING/DECREASING).

A

Increasing

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10
Q

When the value of Delta-G is negative, that means free energy is (RELEASED/REQUIRED).

A

Released

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11
Q

When the value of Delta-G is positive, that means free energy is (RELEASED/REQUIRED).

A

Required

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12
Q

When the value of Delta-G is negative, the reaction is (EXERGONIC/ENDERGONIC) and (UNFAVORABLE/FAVORABLE).

A

Exergonic

Favorable

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13
Q

When the value of Delta-G is positive, the reaction is (EXERGONIC/ENDERGONIC) and (UNFAVORABLE/FAVORABLE).

A

Endergonic

Unfavorable

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14
Q

When the value of Delta-G is negative, it is considered a (DRIVEN/SPONTANEOUS) reaction. When Delta-G is positive it is a (DRIVEN/SPONTANEOUS) reaction.

A

Spontaneous

Driven

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15
Q

When Delta-G equals zero, it is at…

A

Equilibrium

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16
Q

When Delta-H equals zero, it is considered a _______ system.

A

Closed

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17
Q

When Delta-S (entropy) equals zero, there is no net change in _______.

A

Disorder

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18
Q

This is a high energy, unstable form of the reactant(s) that is ready to form product(s).

A

Transition state

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19
Q

This is an energy barrier that must be overcome for the reaction to proceed.

A

Activation energy

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20
Q

Does the activation energy effect Delta G?

A

No

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21
Q

What is one way to speed up a reaction, but has too many negative effects to be used consistently (i.e., denaturation)?

A

Raise the temperature

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22
Q

What is the best way to speed up a reaction?

A

Stabilize the transition state (use an enzyme)

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23
Q

An enzyme will (LOWER/RAISE) the activation energy.

A

Lower

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24
Q

In the _______ _______ model, when a substrate binds, the enzyme changes shape so that the substrate is forced into the transition state.

A

Induced fit

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25
Q

T/F. The induced fit model is not reversible.

A

False. It can be reversed.

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26
Q

In covalent catalysis (strategy 1) – Enzyme (temporarily) covalently binds the transition state, in which _______ transfer (or shift).

A

Electrons

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27
Q

In acid-base catalysis (strategy 2) – There is partial _______ transfer to the substrate.

A

Proton

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28
Q

In approximation (catalysis strategy 3) – If electrons and/or protons must be exchanged, proper _______ _______ and close contact (proximity) of the reactant molecules must occur.

A

Spatial orientation

29
Q

In approximation (catalysis strategy 3) – If both pieces of the puzzle are “captured” and held in the proper orientation right next to each other, they are more likely to react with one another. We can also call this “_______ _______”.

A

Entropy reduction

30
Q

In electrostatic catalysis (strategy 4) – Stabilization of unfavorable charges on the transition state by ________ side chains in the enzyme and/or ______ ions (non covalent electrostatic interactions).

A

Polarizable

Metal

31
Q

One example of a catalyst is serine proteases, or _________. Its reaction substrate(s) are polypeptides/peptide bonds, and the reaction products are shorter polypeptides.

A

Chymotrypsin

32
Q

Chymotrypsin is what type of enzyme? What type of reaction does it perform?

A

Hydrolase

Hydrolysis

33
Q

With chymotrypsin, the reaction time uncatalyzed would take _______, but catalyzed it takes _______.

A

Years

Milliseconds

34
Q

The active site for chymotrypsin contains…

A

Catalytic triad

Oxyanion hole

35
Q

What does chymotrypsin contain that is important for its specificity?

A

Hydrophobic specificity pocket

36
Q

What catalytic strategies does chymotrypsin use?

A 
Covalent catalysis (1)
Acid-Base catalysis (2)
37
Q

Why do we need proteases?

A

Recycling
Regulation
Defense

38
Q

One component of the active site in chymotrypsin is a catalytic triad. Its 3 components are ________ (a nucleophile), _________ (a base – proton acceptor), and ________ ________ (an acid – proton donor).

A

Serine (S195)
Histidine (H57)
Aspartic Acid (D102)

39
Q

Another example of protease named for its active site is _________ protease. A classic example of this is Papain, or a human example is _________ and _________.

A

Cysteine
Calpains
Caspases

40
Q

Another example of protease named for its active site is _________ proteases. A classic example is HIV protease, or a human example is ________.

A

Aspartyl

Renin

41
Q

Another example of protease named for its active site is _________. A classic example is Thermolysin, or human examples are ________ ________ and _______ _______.

A

Metalloproteases
Matrix Metalloproteinases
Liver ADH

42
Q

The 2nd part of the chymotrypsin active site is the oxyanion hole. This stabilizes the tetrahedral intermediate (transition state) and is formed by ________ and _______.

A

Serine (S195)

Glycine (G193)

43
Q

The ______ ______ determines the placement of cut in chymotrypsin.

A

Specificity pocket

44
Q

In chymotrypsin, which amino acid fits best in the specificity pocket (hydrophobic)?

A

Phe

***Could also be Trp or Tyr

45
Q

In trypsin, its specificity pocket contains Asp 189 which is negatively charged. What would fit best inside this pocket?

A

His
Lys
Arg

***These are all positively charged amino acids

46
Q

In elastase, its specificity pocket contains two Val (Val 190 and Val 216). What would fit best inside this pocket?

A

Small, non polar amino acids

***i.e., Ala, Gly

47
Q

In the first step of catalysis with chymotrypsin, polypeptide substrate binds noncovalently in the enzyme active site. The catalytic triad includes a reactive Ser nucleophile that attacks the electrophilic ______ ______ atom.

A

Amide carbon

***See Lecture 12 Slide 23

48
Q

In the second step of catalysis with chymotrypsin, the resulting tetrahedral oxyanion is stabilized by H-bonding interactions with the _______ _______.

A

Oxyanion hole

***See Lecture 12 Slide 23

49
Q

In the third step of catalysis with chymotrypsin, the collapse of the tetrahedral intermediate and H+ transfer from His57 lead to the cleavage of the C–N bond. The N-terminal is bound through acyl linkage to _______. The C-terminal fragment is released.

A

Serine

***See Lecture 12 Slide 23

50
Q

In the fourth step of catalysis with chymotrypsin, a water molecule then binds to the active site and attacks the _____ _____ _____.

A

Acyl ester carbonyl

51
Q

In the fifth step of catalysis with chymotrypsin, the resulting tetrahedral oxyanion intermediate (due to binding of water from step 4) is stabilized via enthalpy interactions with the _______ _______.

A

Oxyanion hole

52
Q

In the sixth step of catalysis with chymotrypsin, the second ________ fragment is released and the enzyme returns to its initial state.

A

Peptide

53
Q

This enzyme is used to speed up the reaction of CO2 to HCO3- (bicarbonate) or vice versa.

A

Carbonic anhydrase

54
Q

Carbonic anhydrase is what type of enzyme? What type of reaction does it perform?

A

Hydrolase

Hydrolysis

55
Q

In an uncatalyzed reaction with CO2 and HCO3-, it would take ________, but catalyzed with carbonic anhydrase it takes _________.

A

Seconds

Microseconds

56
Q

What is the active site of carbonic anhydrase?

A

3 His
Zn++
Water (OH-)

57
Q

The specificity of carbonic anhydrase depends on what?

A

Size of entryway

58
Q

What catalytic strategies does carbonic anhydrase use?

A

Acid-base catalysis (2)
Approximate (3)
Electrostatic catalysis (4)

59
Q

What is the physiological relevance for carbonic anhydrase?

A

pH regulation

Enzyme pathway regulation

60
Q

What is the medical application for carbonic anhydrase?

A

Artificial lungs

61
Q

What is the industrial application for carbonic anhydrase?

A

CO2 scrubbers for reduction of greenhouse gases

62
Q

(1) In the carbonic anhydrase catalyzing reaction, CO2 is bound and a ________ and ________ assist with the reaction. Next, the ________ is added, forming carbonic acid.

A

Glutamate
Threonine
Hydroxide

***Study Lecture 12 Slide 25

63
Q

(2) The threonine has been mutated to ________ to help capture the complex. The histidine, which has been in two different conformations in the structure, assists with guiding one of the nearby _______ molecules to the zinc ion, and converting it to a hydroxyl.

A

Alanine
Water

***Study Lecture 12 Slide 25

64
Q

In the carbonic anhydrase catalyzing reaction, ______ facilitates the transition state. It is deprotonated and is responsible for the catalytic strategy of approximation.

A

Water

65
Q

For carbonic anhydrase, the specificity is determined by the ______ ______. This is responsible for determining the size of substrate. CO2 is small and weakly polar.

A

Entry channel

66
Q

In the first step of the reaction mechanism for carbonic anhydrase, water binds to ______, lowering its pKa. At physiological pH, water loses a proton.

A

Zn++

67
Q

In the second step of the reaction mechanism for carbonic anhydrase, the catalytic strategy of _________ is used as substrate enters the active site (substrate in this case is CO2).

A

Approximation

68
Q

In the third step of the reaction mechanism for carbonic anhydrase, there is a _________ addition (adds functional group to CO2).

A

Nucleophilic

69
Q

In the fourth step of the reaction mechanism for carbonic anhydrase, there is a release of product (product is HCO3-) and regeneration of ________ (histidine proton shuttle).

A

Enzyme

Biochemistry (10 decks)

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