PHSC1212 Biochemistry - Lecture 7: Enzyme Catalysis pt 1

Chemical reaction

can only occur when colliding molecules possess the minimum amount of energy needed to break bonds or rearrange atoms in such a way to convert reactants into products

Increasing temperature or reactant concentrations

What can improve speed of reaction?

Enzymes

biological catalysts that facilitate proper orientation of reactant molecules and lower the energy needed to break bonds and rearrange atoms

Proteases and peptidases

can hydrolyze amide bonds (peptide bonds) rapidly and selectively, which is essential for protein metabolism and cellular function

Catalysis

the acceleration of a chemical reaction with the help of a substance that is chemically unchanged at the end of the reaction

Catalyst

a substance that helps accelerate the rate of a chemical reaction without being chemically changed

Free energy and activation energy

determine the likelihood of a chemical reaction taking place and how quickly a reaction takes place

Gibbs free energy

determines whether a reaction is thermodynamically favorable

Reaction spontaneous, energy released, thermodynamically favorable

What does ΔG < 0 mean?

Reaction nonspontaneous, energy consumed, thermodynamically unfavorable

What does ΔG > 0 mean?

Activation energy

represents an energy barrier reactants must overcome to form products in a chemical reaction; energy required to convert 1 mol of substrate from ground to transition state

Transition state

the highest-energy, most unstable configuration of atoms that occurs momentarily during the conversion of reactants to products

Some partially formed, some partially broken

What is happening with the bonds of the transition state?

Substrates

reactants in enzymatic reactions

Active site

specific place on an enzyme where a substrate binds that is used to optimally orient the substrate to achieve lower energy transition state

Substrate binding and catalytic process

What do the amino acid side chains of an enzyme's active site take an active role in?

Shape and charge distribution

parts of the active site that force the substrate to adopt a conformation more like that of the transition state

Induced fit model

flexibility of an enzyme and substrate to conform to each other better during the transition state

Intermediates

unstable and reactive state of a reaction with a finite lifetime; formed during progression of multi step reactions

Intermediate

Does an intermediate or transition state last longer?

Amino acid residues

found in the active site and help to stabilize the intermediate

Alternative reaction pathway with lower activation energy

What do enzymes catalyzing reactions provide?

Catalytic mechanism

the process by which enzymes break and form bonds during the conversion of substrate to product

Proximity and strain effects, acid base catalysis, covalent catalysis, metal ion catalysis

four important catalytic mechanisms of enzymes to convert a substrate into a product

Proximity and strain effects

enzyme catalytic mechanism that helps facilitate orientation and bond distortion

Noncovalent

Substrate binding to the active site occurs via what type of interactions?

Hydrophobic, electrostatic, hydrogen bonding

noncovalent interactions that allow substrate binging to the active site

Functional groups of substrate and R groups of active site amino acids

What do noncovalent interactions facilitating substrate binding occur between?

Precise orientation of substrate to active site catalytic groups and bond distortion

What do proximity and strain effects help facilitate?

Water

What molecules are often decreased or excluded by enzyme active sites in order to prevent interference between substrate and active site amino acid residues?

Acid base catalysis

enzyme catalysis mechanism when amino acid R groups in active sites can serve as proton donors or acceptors

Protonation state, their conjugate acid or base

R-groups can act as acids or bases depending on what?

Cysteine, tyrosine, serine, and threonine

What amino acids can behave as acids or bases in certain enzymes due to enzyme active site environment ability to alter pKa values?

Lysine

amino acid with high pKa (10.5) so it can only behave as a base in certain environments (pKa must be lowered); rare

Arginine

amino acid with a very high pKa (12.5), so it is essentially permanently charged and never behaves as a base

Metal ion catalysis

catalysis where ionic interactions between enzyme-bound metal ions and substrate can help orient substrate for a reaction

Covalent catalysis

enzyme catalysis mechanism involving the formation of a covalent bond between the enzyme and substrate

Covalent intermediate

What forms during covalent catalysis enzyme mechanism?