Enzymology 1-3

Enzymes

Biological catalysts, primarily proteins that increase rates of chemical reaction w/o being consumed in the process

except: ribozymes(catalytic RNA)

Possess a region known as an active site where the substrate binds—resulting in a product

Catalytic power

A characteristic feature of an enzyme which specifies its ability to accelerate the rxn rate of noncatalyzed reaction as much as 10²⁶

Specificity

A characteristic feature of an enzyme which demonstrates it extreme selectivity to the substances it interacts with and the rxn it catalyzes

Regulation

A characteristic feature of an enzyme which allows it to be regulated (increased or decreased) so that the rate of product formation responds to cellular needs

Oxidoreductase

Type of enzyme which catalyzes oxidation-reduction reactions

Oxidoreductase

What type of enzyme is this: dehydrogenase

Oxidoreductase

What type of enzyme is this: oxidase

Oxidoreductase

What type of enzyme is this: reductase

Oxidoreductase

What type of enzyme is this: catalase

Oxidoreductase

What type of enzyme is this: peroxidase

oxido-reductase

What type of enzyme is this: oxygenase

transferase

What type of enzyme is this: transfer of glucosyl

transferase

What type of enzyme is this: transfer of methyl

transferase

What type of enzyme is this: transfer phosphoryl groups

Hydrolase

What type of enzyme is this: Urease

Hydrolase

What type of enzyme is this: Phosphatase

Hydrolase

What type of enzyme is this: lipase

Hydrolase

What type of enzyme is this: peptidase

lyase

What type of enzyme is this: Decarboxylase

Lyase

What type of enzyme is this: dehydratases

Lyase

What type of enzyme is this: aldolases

isomerase

What type of enzyme is this: mutase

isomerase

What type of enzyme is this: epimerase

transferase

Type of enzyme which catalyzes transfer of moieties

hydrolase

Type of enzyme which catalyzes cleavage of bonds(by addition of water)

Lyase

Type of enzyme which catalyzes cleavage of bonds (i.e C—C, C—S, C—N bonds)

Isomerase

Type of enzyme which catalyzes the rearrangement of optical or geometric isomers

Ligase

Formation of bonds between two molecules coupled to hydrolysis of high-energy phosphates

ligase

What type of enzyme is this: carboxylase

ligase

What type of enzyme is this: synthetase

Active site

A special cleft or crevice that provides the environment where substrate binds and catalysis occurs

Is able to bind through weak forces—hydrogen bonds, ionic bonds and van der waals interaction

Cofactor

Metal ions or organic molecules (nonprotein moiety) that participate directly in substrate binding or catalysis

Coenzyme

Organic molecules that participate directly in substrate binding or catalysis

• Usually, vitamins or vitamin derivatives

• Extend the mechanistic capabilities of an enzyme

Metal-activated enzyme

Enzymes that require a metal ion factor

Metallo-enzyme

Metal ions that serve as prosthetic groups

Prosthetic Group

Permanently associated with the enzyme

Cosubstrate

Transiently associated with the enzyme

Free Enzyme

The structure of the active site is formed by the folding of the protein, which is the complementary to the structure of the substrate

Enzyme-substrate complex

Amino acid side chains and non-protein components participate in substrate binding

Transition-state complex

The enzyme stabilizes the high unstable transition-state intermediate by binding to the substrate, to not return to starting reactants, but not too strong in order not to form product. Substrates are NOT consumed in the process but it can be modified during the rxn

Note that it will always return to its original form

Original Enzyme

Products are released and enzymes could attach to another substrate to repeat the process

Lock and Key Model

Proposed by German Chemist Emil Fischer

Enzymes resemble a lock and its particular substrate the key

Implied that enzymes are rigid, falling to account for the dynamic changes that accompany catalytic transformations

Induced Fit Model

States that an enzymes active site is not rigid, preformed shape but a flexible one that changes shape to fit the substrate
Binding of a substrate to the enzyme induces a conformational change that is analogous to placing a hand in a glove

• This occurs in the active site for the enzyme to accommodate the substrate—resulting in better fit and enhanced catalytic activity

Catalysis by proximity and orientation

Substrate molecules must come within bond-forming distance in order to interact

• Substrates should be organized in a specific orientation wherein the reactants are close together within the active site

  • Increase in proximity of reactants> increase collision frequency > faster rate of rxn

Acid-base catalysis

Ionizable functional groups of the amino acyl side chanins contirbutes to catalysis by acting as acids and bases in the active side

• Functional groups can act as acids/bases

• Acceleration of rxn is achieved by the catalytic transfer of a proton

Catalysis by bond strain

Enzymes bind substrates in a conformation that weakens the bond targeted for cleavage through physical distortion and electric polarization

Covalent Catalysis

Involves the formation of a transient covalent bond between enzyme and one or more substrate. The modified enzyme becomes a reactant but would eventually return to its original state

Participating residues on the enzyme are cysteine or serine and occasionally histidine

Often follows a pingpong mechanism

Ribozymes

Enzymes that satisfy the enzymatic criteria but most act in RNA processing

• It is part of a ribosome which acts as the catalytic core composed of ribosomal RNA which joins amino acids to form proteins

• Large rRNA that catalyzes the peptidyl transferase reaction

  • The formation of peptide bonds during the translation of proteins

Kinetics

General study of chemical reaction rates

Enzyme kinetics

The study of how the rates of enzyme-catalyzed chemical reactions are affected by changing the reaction conditions

Transition State

A state where the molecules have the energy necessary to achieve a reactive condition

• It is the highest energy point along the reaction pathway

• However, due to its high energy and instability, it has a fleeting existence and is the least probable configuration for molecules to adopt at any given time

• Can revert back to its reactant

Initial state

The state of average free energy of molecule A

Final state

The state of average free energy of molecule P

Free energy change or Gibbs free energy

Difference between the average free energy of the energies of the product and reactants for the given reaction; typically describes the direction the reaction will tend to proceed

• Negative value(-)

  • Rxn is favored from left to right

  • Spontaneous

  • Independent of the mechanism

Energy of Activation

Energy required to initiate the reaction

• Energy required ot raise the ave. energy of 1 mol of reactant (at a given temperature) to transition-state energy

  • The higher the activation energy, the slower the reaction

Temperature, Hydrogen Ion Concentration and Substrate Concentration

Factors affecting the rates of enzyme catalysis

High Temperature

Factor leads to heat energy to disrupt noncovalent interaction that 3D structures of proteins > loss of activity from the denaturation of enzymes

High Hydrogen Ion Concentration

Factor which is caused when pH extremes can denature enzymes as the structure of catalytically active protein molecules depend on the ionic character of the amino acid chain

Pepsin

A gastric digestive enzyme that is maximally active at pH 2

Chymotrypsin

A digestive enzyme produced in the pancreas that operates at an optimal pH of 7

Vmax

Maximum value of the reaction rate

Also indicates that all the enzymes are saturated

All enzymes are saturated

The vmax indicates…

Michaelis-Menten

Describes how reaction velocity varies with substrate concentration and is hyperbolic in shape