Lecture 12 (Exam 2)

Question 1

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.

Answer 1

Catalysis

Question 2

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.

Answer 2

Catalyst

Question 3

What do enzymes do?

Answer 3

1) Lower the activation energy

2) Stabilize the transition state

Question 4

What do enzymes NOT do?

Answer 4

1) Change the Delta-G of the reaction

2) Irreversibly change shape

Question 5

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

Answer 5

Increases

Question 6

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

Answer 6

Released

Question 7

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

Answer 7

Added

Question 8

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

Answer 8

Decreasing

Question 9

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

Answer 9

Increasing

Question 10

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

Answer 10

Released

Question 11

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

Answer 11

Required

Question 12

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

Answer 12

Exergonic

Favorable

Question 13

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

Answer 13

Endergonic

Unfavorable

Question 14

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.

Answer 14

Spontaneous

Driven

Question 15

When Delta-G equals zero, it is at…

Answer 15

Equilibrium

Question 16

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

Answer 16

Closed

Question 17

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

Answer 17

Disorder

Question 18

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

Answer 18

Transition state

Question 19

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

Answer 19

Activation energy

Question 20

Does the activation energy effect Delta G?

Answer 20

No

Question 21

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

Answer 21

Raise the temperature

Question 22

What is the best way to speed up a reaction?

Answer 22

Stabilize the transition state (use an enzyme)

Question 23

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

Answer 23

Lower

Question 24

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

Answer 24

Induced fit

Question 25

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

Answer 25

False. It can be reversed.

Question 26

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

Answer 26

Electrons

Question 27

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

Answer 27

Proton

Question 28

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

Answer 28

Spatial orientation

Question 29

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 "_______ _______".

Answer 29

Entropy reduction

Question 30

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).

Answer 30

Polarizable | Metal

Question 31

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

Answer 31

Chymotrypsin

Question 32

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

Answer 32

Hydrolase | Hydrolysis

Question 33

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

Answer 33

Years | Milliseconds

Question 34

The active site for chymotrypsin contains...

Answer 34

Catalytic triad | Oxyanion hole

Question 35

What does chymotrypsin contain that is important for its specificity?

Answer 35

Hydrophobic specificity pocket

Question 36

What catalytic strategies does chymotrypsin use?

Answer 36

``` Covalent catalysis (1) Acid-Base catalysis (2) ```

Question 37

Why do we need proteases?

Answer 37

Recycling Regulation Defense

Question 38

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).

Answer 38

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

Question 39

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

Answer 39

Cysteine Calpains Caspases

Question 40

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

Answer 40

Aspartyl | Renin

Question 41

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

Answer 41

Metalloproteases Matrix Metalloproteinases Liver ADH

Question 42

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

Answer 42

Serine (S195) | Glycine (G193)

Question 43

The ______ ______ determines the placement of cut in chymotrypsin.

Answer 43

Specificity pocket

Question 44

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

Answer 44

Phe ***Could also be Trp or Tyr

Question 45

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

Answer 45

His Lys Arg ***These are all positively charged amino acids

Question 46

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

Answer 46

Small, non polar amino acids ***i.e., Ala, Gly

Question 47

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.

Answer 47

Amide carbon ***See Lecture 12 Slide 23

Question 48

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

Answer 48

Oxyanion hole ***See Lecture 12 Slide 23

Question 49

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.

Answer 49

Serine ***See Lecture 12 Slide 23

Question 50

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

Answer 50

Acyl ester carbonyl

Question 51

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 _______ _______.

Answer 51

Oxyanion hole

Question 52

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

Answer 52

Peptide

Question 53

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

Answer 53

Carbonic anhydrase

Question 54

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

Answer 54

Hydrolase | Hydrolysis

Question 55

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

Answer 55

Seconds | Microseconds

Question 56

What is the active site of carbonic anhydrase?

Answer 56

3 His Zn++ Water (OH-)

Question 57

The specificity of carbonic anhydrase depends on what?

Answer 57

Size of entryway

Question 58

What catalytic strategies does carbonic anhydrase use?

Answer 58

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

Question 59

What is the physiological relevance for carbonic anhydrase?

Answer 59

pH regulation | Enzyme pathway regulation

Question 60

What is the medical application for carbonic anhydrase?

Answer 60

Artificial lungs

Question 61

What is the industrial application for carbonic anhydrase?

Answer 61

CO2 scrubbers for reduction of greenhouse gases

Question 62

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

Answer 62

Glutamate Threonine Hydroxide ***Study Lecture 12 Slide 25

Question 63

(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.

Answer 63

Alanine Water ***Study Lecture 12 Slide 25

Question 64

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

Answer 64

Water

Question 65

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

Answer 65

Entry channel

Question 66

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

Answer 66

Zn++

Question 67

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).

Answer 67

Approximation

Question 68

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

Answer 68

Nucleophilic

Question 69

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).

Answer 69

Enzyme