Basics of enzyme and enzyme regulation

Question 1

What are enzymes?

Answer 1

Biological catalysts

1. All enzymes are proteins
   * EXCEPT: Ribozymes (catalytic ribonucleic acids invoking catalyst in RNA processing)

Question 2

How do enzymes stabilize the transition state?

Answer 2

Via the formation of:

1. Enzyme-Substrate(ES) Procuct
2. Transition State Complex (T)
3. Products

Question 3

Without an enzyme or catalyst, a reaction will proceed extremely slowly, if at all

Answer 3

Question 4

Cofactor, coenzyme, prosthetic group

Answer 4

Cofactor – a component other than the protein portion of an enzyme (i.e. metal ions/minerals, vitamins, GSH, ATP, CoQ, etc.)

Coenzyme – _organic cofacto_r that is loosely bound to the apoenzyme and can be easily separated from it (i.e. most vitamins)

Prosthetic group – cofactor that is tightly bound to the apoenzyme (i.e. many minerals)

Question 5

Isozyme

Answer 5

• Enzymes that differ in amino acid sequence but catalyze the same chemical reaction
• May have different kinetic parameters, expressed in different tissues, and/or regulated differently
• Permits the fine-tuning of metabolism to meet the particular needs of a given tissue or developmental stage
• I.e. ALA synthase, heme oxygenase, hexokinase, COX, lactate dehydrogenase (LDH), etc.

Image:

In the example shown here, lactate dehydrogenase has 2 isoforms (A and B) which gives rise to 5 different active forms of the LDH tetramer. Because of the differences in the isozymes, the 5 isoforms of LDH run differently on a protein gel (this is not the case for all isozymes).

Question 6

Define Activation energy and transition state

Answer 6

Activation energy – energy needed for the reactants (substrates) to reach the transition state

• New bonds are forming and old bonds are breaking (transition state complex)

Transition state (point) – molecules have the highest potential energy

• Can have multiple transition states for coupled (or successive) reactions
• Endergonic and exergonic only refer to comparison of reactant & products values

Question 7

How enzymes lower the activation energy

Answer 7

• Enzymes (catalysts) lower the activation energy (barrier), thus speeding up a reaction (stabilize the transition state) – typical catalytic power: 106-1014
• Does not change the overall ΔG values
• Would actually see 2 “hills” or “peaks” on the curve with enzyme

image:

Enzymes can act as catalysts and speed up reactions by lowering the activation energy. This is noted by a smaller “hill” on an energy diagram. Because the substrates have to bind the enzyme, there would actually be at least peaks on the Energy Diagram.

Notice that the overall deltaG does not change because the energy values of the reactants and products did not change.

Question 8

3-D structure of Enzymes

Answer 8

• Active site
• Substrate-binding site
  
  • Lock and key
  • Induced Fit
• Transition state complex

Question 9

The enzyme active site

Answer 9

1. Site (usually an opening or cleft) where the chemical reaction takes place
2. Contains functional groups that are actively involved in the reaction

• Coenzymes – enzymes that utilize cofactors (metals or complex organic molecules) as functional groups too

Question 10

Substarte binding and TS

Answer 10

Substrate binds to the substrate binding site

• Non-covalent bonds form
• Amino acids from enzyme or atoms of cofactors

Additional bonds form with the enzyme to stabilize the substrate in its transition state

• Stabilization is how the activation energy is lowered