Lecture 19

Question 1

What is the speed of a favorable biochemical reaction determined by?

Answer 1

The size of the activation energy barrier

Question 2

What is a transition state?

Answer 2

A high energy state that exists between the substrates and the products

Question 3

What is the thermodynamic aspect of a reaction about?

Answer 3

The difference in energy between products and reactants

Question 4

What does a negative 𝛥G indicate?

Answer 4

The reaction is spontaneous

Question 5

What is the activation energy?

Answer 5

The difference in energy between the transition state and substrate state that determines the rate of a reaction

Question 6

What happens to enzymes at the end of rxn?

Answer 6

They are returned to their original state

Question 7

How is 𝛥G for a rxn affected by an enzyme?

Answer 7

𝛥G is the same

Question 8

What leads to an increase in the rxn rate?

Answer 8

The decrease of the energy of the free energy state

Question 9

How do enzymes affect the transition state?

Answer 9

The lower the free energy that is associated with the transition state

Question 10

What are the four ways that enzymes use to reduce the free energy of the transition state?

Answer 10

• Removing substrates from aqueous solutions (desolvation)
• Proximity and orientation effects
• Taking part in the rxn mechanism
• Stabilizing the transition state

Question 11

What is an Active Site?

Answer 11

A region of an enzyme where catalysis occurs

Question 12

What do active sites determine?

Answer 12

Affinity, specificity and rate of a reaction

Question 13

What are active sites with oxygen binding?

Answer 13

Oxygen binding sites

Question 14

How much of a protein structure does an active site contain?

Answer 14

It is usually only a small part of the protein structure

Question 15

How can an active site be complementary to the substrate/transition state?

Answer 15

By shape, hydrophobic interaction, H-bonds, and ion pairs

Question 16

What does the design of an active site contribute to?

Answer 16

• Affinity

* Specificity

Question 17

What is Desolvation?

Answer 17

Exclusion of Water

Question 18

What are the three advantages that exclusion of water provides?

Answer 18

• Removal of water shell accelerates reactions
• Enhances polar interactions (Hbonds, ion pairs)
• Prevents side reaction

Question 19

Which interactions become much stronger with Desolvation?

Answer 19

H-bond interactions and ion pair interaction

Question 20

What is induced fit?

Answer 20

A change of shape of the enzyme active site as substrates bind into the active site

Question 21

How does induced fit affect the active sight?

Answer 21

It closes off the acte site and excludes more water

Question 22

How does induced fit affect catalytic groups?

Answer 22

It brings catalytic groups together

Question 23

Where is the active side of Hexokinase?

Answer 23

In a cleft found between two separate domains within the protein

Question 24

What happens to Enterokinase when glucose and ATP bind?

Answer 24

It closes around the substrate to prevent a hydrolysis reaction occurring

Question 25

What is the induced Fit Model?

Answer 25

When the active site changes shape as substrates bind

Question 26

How does Proximity and Orientation affect a reaction?

Answer 26

Chemical reactions only occur if substrates come together in the right orientation to react

Question 27

How do active sites affect proximity and orientation?

Answer 27

Active sites bind substrates close to each other (proximity) and in the correct geometry (orientation)

Question 28

What is Covalent Catalysis?

Answer 28

When the enzyme provides a nucleophile and becomes covalently attached to an intermediate during a reaction mechanism

Question 29

When can metal ions be important in reactions?

Answer 29

When they act as redox centers

Question 30

How can some enzymes participate in reactions?

Answer 30

By positioning functional groups near the substrates in the active site

Question 31

What may the functional groups in some enzymes that participate in reactions function as?

Answer 31

* Acid/base catalysis * Covalent catalysis * Metal ion catalysis

Question 32

What can enzyme participation in reaction be achieved by?

Answer 32

Amino acids, cofactors or both

Question 33

What property do all the amino acids that participate in acid base catalysis have?

Answer 33

They all have a pKa associated with it

Question 34

Which amino acids have pKa's?

Answer 34

* Asp * Glu * His * Lys * Cys * Tyr * Arg

Question 35

Which amino acids with pKa's are frequently associated with acid base catalysis?

Answer 35

* Asp * Glu * His * Lys

Question 36

Which amino acids can act as nucleophiles in Covalent Catalysis?

Answer 36

* Ser * Tyr * Thr * Cys * Lys

Question 37

How can Ser, Tyr and Thr act in covalent catalysis?

Answer 37

With their OH group that can act as nucleophiles

Question 38

In what from can Cys act as a good nucleophile?

Answer 38

In the deprotonated form

Question 39

Which amino acids can act as good nucleophiles in the deprotonated form?

Answer 39

Cys, Lys, His

Question 40

What can a nucleophile in covalent catalysis form?

Answer 40

The formation of a covalent bond of the enzyme and the substrate

Question 41

Which amino acids can act as nucleophiles on Covalent catalysis and with what conditions of the R group?

Answer 41

* Ser, Tyr, Thr (with their hydroxyl groups) * Cys, Lys, His (in their deprotonated form) * Asp, Glu (with their carboxylate groups)

Question 42

What are Cofactors?

Answer 42

Molecules that aren't specifically polypeptide structures but end up being part of reaction mechanisms for enzyme catalyzed reactions

Question 43

What are the two subtypes of Cofactors?

Answer 43

* Coenzymes | * Metal ions

Question 44

What are the two subtypes of metal ion cofactors?

Answer 44

* Prosthetic groups | * Loosely bound

Question 45

What are the two subtypes of coenzyme cofactors?

Answer 45

* Cosubstrates | * Prosthetic groups

Question 46

What is the difference between a cosubstrate and a prosthetic group?

Answer 46

Cosubstrates are converted within the active site and releases as products and prosthetic groups are a permanent part of protein tertiary structure and are permanent part of protein tertiary structure

Question 47

What is required of coenzymes after a reaction?

Answer 47

They need to be regenerated after reaction

Question 48

What is the difference between an apoprotein and a holoprotein?

Answer 48

Whether or not the prosthetic group is associated with the polypeptide chain

Question 49

What is a Holoenzyme?

Answer 49

When a polypeptide is combined with the prosthetic group to form the functional tertiary structure

Question 50

What is an Apoenzyme?

Answer 50

The name used to refer to an enzyme that contains a prosthetic group without the prosthetic group