Enzymes

Question 1

What are enzymes?

Answer 1

Enzymes are biological catalysts

–> Speed up chemical reactions without being consumed or changed

Question 2

What is the difference between apoenzyme and holoenzyme?

Answer 2

Apoenzyme - without the prosthetic group

Holoenzyme - with the prosthetic group

Question 3

Two general ways to increase the

speed of a chemical reaction:

Answer 3

• Heat (denature, speeds up everything (nonspecific) problem is that cell needs specificity)
• Add a catalyst

Question 4

Enzymes are typical globular proteins:

Answer 4

 Biological catalyst
 Same structure as other proteins
 1o, 2o, 3o (not regulated often) and sometimes 4o (regulated by allostery)
 Structure determined and/or stabilized by the same non-covalent interactions (hydrophobic interactions, H-bonds, ion pairs, van der waals, disulphide bonds)

Question 5

Enzymes are Highly ….

Answer 5

Specific and Non-random

Question 6

General properties of enzymes vs.

non-biological catalysts

Answer 6

-Higher reaction rates
- Milder reaction conditions (37 degree C, ph of 7, high pressure)
- Greater reaction specificity (act on certain number of molecules)
- Capacity for regulation
 BECAUSE conformational change in protein structure is possible
 Also important in cooperativity

Question 7

Why is ATP a “high energy” molecule?

Answer 7

1. decreased electrostatic repulsion
2. resonance stabilization
3. increase entropy via breaking phosphoanhydride bond
4. Free energy released for breaking a
   phosphoanhydride bond is -30 kJ/mol (more than -25 kJ/mol)

Question 8

In biological systems, a reaction will proceed only if the free energy of the ____ is less than the free energy of the _____.

Answer 8

products; reactants

Question 9

delta G = negative means

Answer 9

-Reaction is exergonic and
“thermodynamically favorable” (energy released)
-R>P
-doesnt mention speed!

Question 10

Define Enthalpy and Spontaneous

Answer 10

Enthaply: type/number of bonds
Spontaneous: rate/speed –> does the reaction want to go, when it does move what speed?

Question 11

Increase entropy means …

Answer 11

decrease enthalpy, decrease in high energy bonds

Question 12

The Speed of a Favourable Biochemical

Reaction is Determined by the Size of the _________________

Answer 12

Activation Energy Barrier

Question 13

Facts about ∆G‡

Answer 13

• ∆G‡ = GTS - GR
• Increase ∆G‡ = slower rxn
• Decrease ∆G‡ = faster rxn

Question 14

How does enzymes affect reaction rates (kinetics)?

Answer 14

Increasing temp will increase speed of rxn, therefore more collisions

Question 15

Enzyme do not influence __, they influence ___. Enzymes effect ___, they do not effect ___.

Answer 15

1. ∆G
2. ∆G‡
3. Kinetics
4. Thermodynamics

Question 16

Catalysts lower the activation energy

barrier by:

Answer 16

1. Removing substrates from aqueous solution (desolvation) - H2O
2. Proximity and orientation effects -> physically bring correct orientation
3. Taking part in the reaction mechanism -> change transition state
4. Stabilizing the transition state -> decrease transition state

Question 17

Design of the active site in enzymes contributes to:

Answer 17

• Affinity (how tightly the molecules bind)

* Specificity (what molecules bind)

Question 18

Induced Fit Model?

Answer 18

Substrate binding changes the shape
of an active site - induced fit
New interactions between the substrate and active site influence the enzyme conformation (shape).

Question 19

Desolvation?

Answer 19

Removing substrates from

aqueous solution

Question 20

The sequestering of substrates in a
non-aqueous environment has
several advantages:

Answer 20

• Prevents interference by water molecules
• Formation of H-bonds is more effective in a non-aqueous environment
• It eliminates the energy barrier imposed by ordered solvent molecules (water)

Question 21

Proximity and Orientation

Effects in Catalysis

Answer 21

May account for a thousand-fold increase in reaction rates

Question 22

Enzymes assist in the formation of the
transition state by taking part in the
reaction mechanism

Answer 22

• Positioning certain aa side chains in the active site where they can react with the substrates
• -acid-base catalysis (residue taking part in rxn)
• • covalent catalysis/nucleophilic catalysis
• –transient covalent bond between substrate and enzyme
• Provide other chemical substances at the active site-cofactors
• -metal ion catalysis

Question 23

Amino Acid Side Chains in Acid-Base

Catalysis

Answer 23

These groups can

act as acid (with hydrogen) or base (without hydrogen) catalysts, depending on their state of protonation.

Question 24

4.Stabilizing the transition state

Answer 24

• The Active Site Binds the Transition State Better Than it Binds the Substrate
• Free energy of the transition state is lowered

Question 25

The more tightly an enzyme binds the transition state relative to the substrate the _____ the catalytic activity of the enzyme

Answer 25

greater

Question 26

Transition state analogs are POTENT inhibitors of many enzymes b/c

Answer 26

* bind to enzyme with higher affinity compared to substrate (compete with substrate) * rational basis for drug design (take new info, and design molecules) * versus serendipitous drug discovery

Question 27

Relationship between Kd and affinity:

Answer 27

- decrease kd = increase affinity | - increase kd = decrease affinity

Question 28

Competitive Inhibition of | Enzyme Activity

Answer 28

- Inhibitors are similar to the substrate in shape and size but differ chemically in such a way that they cannot react - CO is a competitive Inhibitor of O2 binding to HB - Substrate and inhibitor compete for the same site on the enzyme - overcome by increase number of substrates, decrease inhibitor = non covalent bonds break -> substrate gets in

Question 29

Allosteric enzymes show a _______ relationship between reaction velocity and substrate concentration

Answer 29

sigmoidal

Question 30

Heteroallostery?

Answer 30

An allosteric enzymes catalytic activity is | modulated by the noncovalent binding of specific molecules at a site other than the active site

Question 31

Effector vs inhibitor

Answer 31

Negative effector, allosteric inhibitor Positive effector, allosteric activator

Question 32

Allosteric enzymes have two states:

Answer 32

T (tense, low activity) --> Allosteric Activator | R (relaxed, high activity) --> Allosteric Inhibitor

Question 33

The addition of a phosphate | group results in:

Answer 33

-A large increase in size. -A large increase in polarity/hydrophilicity. -The addition of two negative charges. -The capability of making multiple new H bonds. Phosphorylation CHANGES enzyme activity by modifying the protein’s precise 3-D shape.