UCM Biochem Chapter 5

catalyst

agent that enhances rate of chemical rxn without being consumed by it

enzyme

biological macromolecule that acts as a catalyst for biochem rxn

• although almost all enzymes are composed of protein, some RNA molecules are catalytically active

• dramatically enhance and control rates of chem rxn

substrates

a reactant in chem rxn

• An enzyme catalyzes a single chemical rxn or set of closely related rexns, and the components of those rxns are called the …

protease

This enzyme class hydrolyzes the peptide bonds between amino acids, thus digesting proteins

free energy of products minus free energy of reactants

What does delta (change in) G of a rxn depend on?

transition state

What is image shown?

• has higher free energy than either S or P

Gibbs free energy of activation

The difference in free energy between the transition state and the substrate is called…

• Enzymes accelerate reactions by decreasing this.

active site

A specific region of an enzyme that binds the enzyme’s substrate and carries out catalysis

• 3D cleft or crevice formed by groups that come from different parts of the AAs sequence

kinetics

study of reaction rates

competitive inhibitor

What inhibitor competes with substrate for binding to the enzyme and thus reduces the proportion of enzyme molecules bound to substrate?

• Can be relieved by increasing substrate concentration

uncompetitive inhibitor

What inhibitor binds not to the enzyme itself but to the enzyme-substrate complex?

• It is a substrate dependent

pure noncompetitive inhibitor

What inhibitor along with substrate can bind simultaneously to an enzyme molecule at two different binding sites?

• binds to either free enzyme or ES complex, but will decrease the rate catalysis

• cannot be overcome by increasing substrate mix

exergonic reactions

A reaction will occur without the input of energy, or spontaneously, only if ΔG is negative

at equilibrium

there is no net change in the amount of reactant or product. ΔG =0

endergonic reactions

A reaction will not occur spontaneously if the ΔG is positive

ΔG of a reaction

What depends only on the free energy difference between reactants and products and is independent of how the reaction occurs

• And provides no information about the rate of the reaction

transition state

Enzymes Accelerate Reactions by Facilitating the Formation of the…

• a molecular form that is no longer substrate but not yet product

activation energy

The energy required to form the transition state from the substrate is called

The rate of reaction is proportional to the concentration of X‡

because only X‡ can be converted into product.

The concentration of X‡ depends on the energy difference between X‡ and S, the activation energy.

enzyme decrease the activation energy

overall reaction rate of V

• depends on ΔG‡

• k = Boltzmann’s constant

• h is Planck’s constant

• Using this equation, we can show that a 20% decrease in ΔG‡ results in a 10-fold increase in rate

• Enzymes function by lowering the activation energy

enzyme active sites list

• 1. Cleft or Crevice in the enzyme typically composed amino acids from different parts of primary structure

• 2. Small part of whole protein

• 3. Create unique microenvironments

• 4. Substrates bind through many weak interactions

• 5. Specificity for substrate depends on unique position of atoms

• 6. Active site is designed to stabilize the reaction’s transition state

induced fit model of substrate binding

steady state conditions

Reaction Velocity –vs- Enzyme Conc. At Steady State Conditions

Reaction Velocity –vs- Substrate Conc. At Steady State Conditions

Michaels-Menten Diagram

A Lineweaver—Burk plot

• allows for you to find enzyme saturation at a given [S]

• related to the rate constants of each step in the pathway

• equal to the dissociation constant of the ES complex when k-1 >> k2. Measurement of binding affinity

• Most [S] in the cell are similar to KM values

• no dependent on enzyme

Significance of Km

• if VMax is known, then kcat or Turnover # can be determined

• Number of substrate molecules converted to product molecules by an enzyme molecule in a unit time when the enzyme is full saturated

• kcat cannot be greater than the diffusion controlled limit ≈10^6 - 10^7

• randomly bouncing in solution until it reaches active sites

significance of VMax

k2*[Etot]

VMax equation

• can be found experimentally

• you know [Etot] cause you set up the experiment'

enzyme efficiency

kcat / KM

• temp changes

• pH change (picking up proton/protonated or deprotonated states)

• inhibitor molecules (slow rxn down)

  • Reversible Inhibitors

    • Competitive, Uncompetitive & Noncompetitive

  • Irreversible Inhibitors

    • considered negative allosteric effector'

    • control rxn rates of enzyme in cells

modulating enzyme activity

the rxn unfolds

Rxn rates increase …

• substrate can’t get into active sites

• enzyme is out of actions

• once binded, cant be undone

• completely inactivate the enzyme

• usually form an unbreakable covalent bond with functional group in active site

• could bind enzyme so tightly that it does not dissociate from the enzyme

irreversible inhibitors

• A molecule that inhibits substrate binding at the active site

• Can bind to the active site or obstruct the substrate from binding through steric clash

• Can be overcome by increasing [S]

• Vmax is unchanged, but Km values change

• binds to active site on enzyme

• looks similar to substrate/product

• competitive inhibition

  

uncompetitive inhibition

• Binds to the enzyme-substrate complex and alters the active site conformation

• Often acts upon enzymes with multiple substrates

• Both Km and vmax are decreased.

mixed inhibition

• Binds to sites unique from the active site

• Can bind to both the enzyme and the enzyme-substrate complex

• Lowers vmax and may increase or decrease Km