Enzymes

Enzymes

• Drastically increase rates of reactions, allowing cellular function (and more specifically metabolism) to occur
• Are highly specific in their substrates (even showing stereo-specificity)
• Increase reaction rate through stabilization of the transition state (lowering the energy)
• Each enzyme has a specific substrate and active site
• There are six classes of enzymes:

• Catalyze oxidation-reduction reactions
• Named: oxidases, dehydrogenases, reductases
• One substrate is oxidized (loses electrons)
• The other is reduced (gains electrons)

• Group transfer reactions
• Kinases transfer phosphate groups (phosphorylation)
• Transketolase reaction:

• Catalyzes hydrolysis reactions (breaking apart molecules with water)
• Largest group of enzymes
• Group transfers to water
• Proteases, lipases, nucleases, esterases

• Addition of groups to double bonds or removal of groups to form double bonds
• Also referred to as synthases (perform addition reactions)
• Methylisocitrate lyase:

• Transfer groups within molecules (create isomers)
• Mutases
• Isopentenyl pyrophosphate isomerase:

• Joins to molecules through the use of ATP (energy source)
• Synthetase

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

Enzyme Mechanisms

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

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

• 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

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