Enzymes as Catalyst

Question 1

Describe a catalyst

Answer 1

• A substance that increases the rate of a chemical reaction without undergoing
  changes in the process
• Enzyme catalyzed reactions usually occur under mild temperatures.
• Active sites of an enzyme is the region that binds the substrate and converts it into a
  product.
• The substrate is bound at the active sites by multiple weak forces (electrostatics int.,
  H-bonds, VDW-bonds & Hydrophobic int.).

Question 2

Explain how enzymes bind substrate

Answer 2

• When the substrate is bound to the active site, an enzyme-substrate complex is formed
• The active residues within the active sites will then transform it into the transition state complex and then into a product.
• Two models of the enzyme-substrate complex: Lock-and-key model & Induced-fit model

Question 3

Explain the lock-and-key model

Answer 3

The shape of the substrate and the active site fit together like a key into its lock.
They are rigid and fixed which perfectly compliment each other when binding together in the right alignment

Question 4

Explain the induced-fit model

Answer 4

The binding of substrate induces a conformational change in the active site.
The enzyme also can distort the substrate, forcing it into a conformation similar to its transition state.

Question 5

How do active sites of an enzyme determine the specific substrate to bind?

Answer 5

• At the active site, the properties and spatial arrangement of the amino acid residues will be the ones determining which molecules can bind to it.
• The amino acids at the substrate-binding sites must have a ‘differing specificity’ property that will attract certain substrates.
• Examples; Trypsin (enzyme) has a -ve charged Asp residue at its sites which will interact with the +ve charge of Lys or Arg sides-chains of a substrate

Question 6

How are enzymes being classified usually?

Answer 6

Enzyme is identifies with a four-digit classification number (Enzyme Commission, EC)

1) Class of enzyme
2) Substance causing the reaction
3) Amino acid residues at the active site
4) Number of enzyme assigned to the class

Question 7

List out the major classes of enzymes

Answer 7

• Oxidoreductases
• Transferases
• Hydrolases
• Lyases
• Isomerases
• Ligases

Question 8

Oxidoreductases

Answer 8

Transfer or electrons

Question 9

Transferases

Answer 9

Transfer of functional groups

Question 10

Hydrolases

Answer 10

Hydrolysis reactions

Question 11

Lyases

Answer 11

Cleavage of C-C, C-O, C-N and other bonds, often forming a double bond

Question 12

Isomerases

Answer 12

Transfer of groups within a molecule

Question 13

Ligases/Synthases

Answer 13

Bond formation coupled to ATP hydrolysis

Question 14

Explain what is enzyme assay

Answer 14

• Enzyme assay is the measure of the activity of an enzyme in terms of catalytic effect (conversion of substrate to product)
• It depends on the overall equation of the reaction, the rate of disappearance of substrate or appearance of the product, the presence of cofactors as well as the pH and temperature at which enzyme is optically active.
• Changes in concentration of substrate and product can be determined by the change in color (wavelength absorbance) using a spectrophotometer and the change in fluorescence using a fluorimeter

Question 15

What if the substrate/product didn’t absorb light at a certain wavelength?

Answer 15

We use the Linked Enzyme Assays method by linking it to a second enzyme reaction that involves the change in light absorbance.

Question 16

What are coenzymes?

Answer 16

A nonprotein cofactor that may be either one or more inorganic ions or a complex organic molecule

Question 17

Prosthetic group

Answer 17

Coenzymes that are covalently attached to the enzyme

Eq: NAD, NADP, FAD and FMN (carriers of electrons)

Question 18

Isozymes

Answer 18

Different forms of an enzyme that catalyze the same reaction but exhibit different physical or kinetic properties
Eg of properties: isoelectric point, pH optimum, substrate affinity, or inhibitors effect