Howenzymes Work

Question 1

Explain the basic principles of enzyme catalysis, including binding and specificity, proximity and orientation effects and transition state stabilization

Answer 1

The transition state is a barrier to chemical reactions
Catalysis lowers the activation energy for a reaction
At a lower delta G, more molecules will react. Increasing molecules, temperature or adding a catalyst will increase reaction rates.
Enzymes have active sites that bind substrate/product. If the substrates are in proximity, with the correct orientation and provide functional groups for catalysis then there will be a decrease in the activation energy
Catalysts are not chemically changed by the reaction and do not change the reaction equilibrium
Enzymes stabilize the transition state

Question 2

What is the purpose of cofactors?

Answer 2

Cofactors provide additional chemistries for carrying out catalysis
Cofactors can be metal ions or coenzymes which are cosubstrates or prosthetic groups
Enzymes that don’t have a cofactor are apoenzymes and the ones that have one are called holoenzymes

Question 3

Describe the types of catalysis used by enzymes

Answer 3

Acid base catalysis: transfer or removal of H+
Covalent catalysis: transient formation of a covalent bond between enzyme and substrate—-> nucleophiles attack electron-deficient centers to create covalent bonds
Metal catalysis: direct or indirect role in catalysis; often oxidation-reduction reactions —-> metal ions can mediate oxidation reactions, promote reactivity of the substrate or other functional groups

Question 4

Describe how chymotrypsin uses catalytic triad to hydrolysis a peptide bond

Answer 4

The catalytic triad is Asp 102, His 57 and Ser 195
Chymotrypsin uses both covalent and acid-base catalysis to hydrolysis a peptide bond
His accepts a proton from serine ( base catalyst ) allowing the nucleophilic oxygen of serine to attack the carbonyl carbon of the substrate ( covalent catalysis)
Tetrahedral intermediate: His donates a proton to the new NH2 of the C- terminal peptide fragment, breaking the peptide bond
Acyl- enzyme intermediate ( a stable covalent intermediate): Departure of the Rc leaves the enzymes covalently bound to the Rn region of the substrate
Water donates a proton to His 57 and resulting OH - sttscks the carbonyl group of substrate.
Second tetrahedral intermediate: His 57 donating a proton leads to collapse of the second tetrahedral intermediate
Chymotrypsin returns to its original state: N-terminal portion of substrate diffuses away, regenerating chymotrypsin

Question 5

Explain the basic principles for enzyme catalysis, including binding specificity, proximity and orientation effect, and transition state stabilization

Answer 5

Catalysis lowers the activation energy for a reaction, this allows more molecules to react (increasing the number of molecules, increasing the temperature, or adding a catalyst will increase reaction rates.
Enzymes have active sites that bind to substrate/product. If the substrates are put into proximity, with the correct orientation and provide functional groups for catalysis, there is a decrease in activation energy.
They stabilize the transition state because they decrease the energy which makes the transition state unstable The enzyme causes a conformational change which makes it more likely to proceed.

Question 6

Describe the three types of catalysis used by enzymes

Answer 6

1. Acid-base catalysis: transfer or removal of H+
2. Covalent catalysis: transient formation of a covalent bond between enzyme and substrate
3. Metal catalysis: direct or indirect role in catalysis; often oxidation reduction reactions
   *enzymes have a character tic pH and temperature optima

Question 7

Enzymes function by stabilizing
A) their substrates
B) their products
C) the transition state
D) their substrates and the transition state
E) all of the above

Answer 7

C) the transition state

Question 8

Describe how chymotripsin uses a catalytic triad to hydrolysis a peptide bond

Answer 8

Chymotrypsin uses both covalent and acid-base catalysis to hydrolysis a peptide bond
Base catalysis: His accepts a proton from Ser.
Covalent catalysis: the nucleophilic oxygen of serine attacks the carbonyl carbon of the substrate

Question 9

In the following step of chymotrypsin catalysis:
A) His 57 is undergoing acid catalysis
B) Ser 195 is undergoing base catalysis
C) Asp 102 is undergoing acid catalysis
D) Ser 193 is undergoing covalent catalysis
E) none of the above

Answer 9

D) Ser 193 is undergoing covalent catalysis

Question 10

What stabilizes the transition state in chymotrypsin?

Answer 10

Gly 193 and a backbone amide