Enzymes

Enzyme Active Site

• A pocket on the enzyme that provides a specific environment, within which a reaction can occur more rapidly
• Can have varying levels of specificity
• High degree of specificity: Only acts properly on only one substrate

• Functional group specificity: Acts on multiple substrates with a key functional group

• Broader specificity: Acts on substrates with the same molecular "scaffold"

• The shape of the active site is complementary to the substrate "lock and key"
• The enzyme can also change shape to accept a substrate
• Is its own microenvironment

https://commons.wikimedia.org/wiki/File:227_Steps_in_an_Enzymatic_Reaction-01.jpg. OpenStax College. This file is licensed under the Creative Commons Attribution 3.0 Unported license.

Enzyme Mechanisms

Nucleophilic Substitution:

https://commons.wikimedia.org/wiki/File:AcylSubstitution.svg. V8rik. This file is licensed under the Creative Commons Attribution-Share Alike 3.0 Unported license.

Proximity Effect:

• Brings components close together, increasing the chance of completing the reaction

Stabilization of Transition State:

• Transition states are fleeting and unstable
• The enzyme binds to the transition state and stabilizes it

Acid-Base Catalysis:

• Electrons are either transferred from an acid catalyst to the substrate or from the substrate to a base catalyst

Roles of Amino Acid Functional Groups:

Cofactors

• Can either be Essential Ions (Mg2+, Ca2+, Fe2+, Co+)
• Activator ions are loosely bound
• Metal ions (tightly bound)
• Or Coenzymes (Organic compounds)
• Cosubstrates are loosely bound
• Prosthetic groups are tightly bound

https://commons.wikimedia.org/wiki/File:FAD_FADH2_equlibrium.png

https://commons.wikimedia.org/wiki/File:ATP_chemical_structure.png

Chymotrypsin

• A digestive protein, responsible for hydrolyzing proteins allowing for absorption of amino acids by the small intestine
• Cleaves peptide bond on the carboxyl side of large hydrophobic residues (eg. Phe and Met)
• Contains a catalytic triad in its active site consisting of His57, Ser 195, and Asp 102
• The hydrolysis of the peptide bond occurs in 2 stages: the burst and then steady state
• These stages are separated by the formation of an acyl-enzyme intermediate (stabilized by an oxyanion hole consisting of Ser 195 and Gly 193)
• A water molecules is also used as a substrate
• During the reaction the His residues alternates between acting like an acid and a base

https://commons.wikimedia.org/wiki/File:Mechanism_of_peptide_bond_cleavage_in_%CE%B1-chymotrypsin.gif. Felix Plasser. Creative Commons Attribution-Share Alike 3.0 Unported license.

Which class of enzyme is catalyzing this reaction?

a) Hydrolase

b) Isomerase

c) Oxidoreductase

d) Lyase

Which of the following is NOT a method that enzymes use to catalyze reactions?

a) Acid-base catalysis

b) Proximity effect

c) Stabilization of Product

d) Nucleophilic substitution

Which of the following is NOT a coenzyme?

a) NADH

b) Fe2+ ion

c) Heme

d) NADPH

e) None of the above

Chymotrypsin contains a catalytic triad consisting of His57, Ser 195, and Asp 102. Choose the statement that is TRUE about this active site.

a. The His residue acts exclusively as a base due to the pH in the micro-environment around the residue.

b. The Asp 102 residue is involved in the oxyanion hole, which stabilizes the intermediate.

c. It binds polar amino aicds and cleaves the peptide bond on the carboxyl side.

d. H2O is a substrate involved in the reaction.

e. More than one of than the above.