(Dr. Choy) (Unit A) Topic Note 5

Question 1

What are the molecules that enzymes act on called?

Answer 1

Substrates

Question 2

Are enzymes specific or general?

Answer 2

Specific, very specific

Question 3

Do enzymes themseles get changed by the reaction?

Answer 3

No, they may change transiently (temporarily) during the reaction though

Question 4

Do enzymes affect thermodynamics?

Answer 4

No, they do not affect the basic driving force behind chemcial transformations

Question 5

What is the intermediate form between the initial chemical reactant and the product known as?

Answer 5

Transition state

Question 6

What is the rate of the reaction controlled by?

Answer 6

Activation energy

Question 7

How do enzymes affect reaction rate?

Answer 7

By lowering activation energy

Question 8

Is the whole enzyme involved in catalysis?

Answer 8

No, only the active site of the enzyme is involved

Question 9

Where are active sites usually found in an enzyme?

Answer 9

Between two domains or subunits

Question 10

What factors contribute towards attaining the transition state?

Answer 10

• Bringing substrates together
• Orienting substrates in favorable geometry
• Supplying proton acceptors/donors, electron donors/acceptors
• Excluding water (sometimes)
• Stressing the substrate physically or electronically
• Selective binding of the transition state

Question 11

What is chymotrypsin?

Answer 11

An enzyme secreted by the pancreas
* Allows breakdown of dietary protein during digestion

Question 12

Chymotrypsin is a member of what family?

Answer 12

Serine protease
* Contains a critical serine residue in the active site

Question 13

What does each serine protease contain?

Answer 13

A catalytic triad
* Serine, histidine, and aspartic acid

Question 14

How does serine protease work?

Answer 14

Attack the peptide bond that joins amino acid residues to split the polypeptide in two at that site

Question 15

What type of reaction do serine proteases carry out? Why is it called that?

Answer 15

Hydrolysis, because a molecule of water is consumed

Question 16

How does chymotrypsin bind with substrate?

Answer 16

Binds such that the carbonyl carbon of the peptide bond is positioned for nucleophilic attack by the serine

Question 17

What is the responsibility of the histidine in serine protease?

Answer 17

Acts as a general base to abstract a proton from the serine hydroxyl

Question 18

What does the attack of the serine and histidine result in?

Answer 18

A tetrahedral intermediate

Question 19

How does the tetrahedral intermediate break down?

Answer 19

The protonated histidine acts as a general acid to donate its proton to the nitrogen of the peptide bond
* Splits bond, releases carboxyl-terminal part of the peptide

Question 20

When the peptide bond is split what happens to the serine?

Answer 20

Serine becomes covalently bound to the amino-terminal part of the peptide as an acyl-enzyme intermediate

Question 21

What happens in the second phase of chymotrypsin activity?

Answer 21

Water enters
* Acts as nucleophile, activated by the histidine once again acting as the general base

Question 22

What forms when water enters in chymotrypsin reaction?

Answer 22

Tetrahedral intermediate is formed

Question 23

What happens to the chymotrypsin in the second phase of the chymotrypsin reaction?

Answer 23

Decomposes with histidine acting as a general acid such that the amino-terminal part of the peptide is released

Question 24

What does the tetrahedral intermediate (transition state) contain? How is this managed?

Answer 24

An oxyanion
* Stabilized by entry into a special “hole” in the enzyme

Question 25

How else is the transition state in chymotrypsin stabilized?

Answer 25

The h-bond between histidine and aspartic acid side hains becomes shorter and stronger

Question 26

What strategies are used by chymotrypsin to lower transition states?

Answer 26

1. Orientating substrates in a favorable geometry
2. Supplying proton acceptors/donors
3. Selective binding of the transition state

Question 27

What are zymogens?

Answer 27

Enzymes synthesized that have a lack of enzymatic activity

Question 28

What is the purpose of zymogens?

Answer 28

Allows the elaboration of enzyme activity to be precisely controlled

Question 29

What is Vmax dependent on?

Answer 29

Enzyme concentration
* Doubling the amount of enzyme will double the rate of product formation

Question 30

What does the Michaelis Constant represent?

Answer 30

Affinity of the enzyme for the substrate
* The lower the constant, the higher the affinity

Question 31

Does enzyme concentration affect the Km?

Answer 31

No

Question 32

Where is the Vmax on a Lineweaver-Burk plot?

Answer 32

The intercept on the 1/v0 axis

Question 33

Where is Km on the Lineweaver-Burk Plot?

Answer 33

The intercept on the 1/[S] axis

Question 34

What are the two classes of inhibitors?

Answer 34

1. Irreversible: Forms covalent bond with enzyme
2. Reversible: Binds non-covalently

Question 35

What is a competitive inhibitor?

Answer 35

Bind directly in the active site and block substrate binding
* Many reversible inhibitors are this kind

Question 36

What affect do competitive inhibitors have on Km and Vmax?

Answer 36

Increases Km without affecting Vmax

Question 37

How can competitive inhibition be overcome?

Answer 37

High substrate concentration

Question 38

How is the potent activity of enzymes controlled?

Answer 38

1. Control of enzyme abundance (through gene expression)
2. Synthesis of enzymes as inactive precursors (zymogens)
3. Reversible modifications (phosphorylation etc.)
4. Allosteric regulation

Question 39

Where is allosteric regulation an important feature?

Answer 39

In metabolic pathways where precursor molecules are converted by a succession of enzymes into a product or products