chapter 6 enzymes biochemistry 299

The transition state of an enzyme-catalyzed reaction that converts a substrate to a product..is-

1. a transient intermediate formed along the reaction coordinate of the reaction. 2. has higher free energy than either the substrates or products. 3. is increased in concentration because the enzyme binds tightly to it. 4. determines the velocity of the reaction(the velocity of a reaction is directly proportional to the concentration of the transition state)

common features of active sites of enzymes

1. three-dimensional cleft of crevice 2. the site takes up a small part of total volume of an enzyme 3. active sites are unique microenviroments 4. Substrates are bound to enzymes by multiple weak attractions. 5. The specificity of binding depends on the precisely defined arrangement of atoms in an active site

The Free Energy Change provides info about the spontaneity but not the rate of a reaction

A reaction can take place spontaneously only if delta G is negative...(without the input of energy- exergonic) i.e. more product than reactant

Enzymes are powerful and highly specific catalysts

The specificity of an enzyme is due to the precise interaction of the substrate with the enzyme. This precision is a result of the intricate 3D structure of the enzyme protein.

Enzymes facilitate the formation of the transition state

Transition state is the least-stable and also in rxn pathway the state with the highest free energy.

Explain why the thermodynamic parameter delta S cannot be used to predict the direction in which a reaction will proceed.

delta S for a chemical reaction is not easily measured. Even if it were easily determined, its value depends on changes that occur not only in the system under study but also in the surroundings (Chapt 2) Intrinsically unfavourable reactions (deltaG*knot > than zero) can take place if a change in the surroundings compensates for a decrease in the entropy (neg delta S) of the reaction

Induced fit model of enzyme -substrate binding

the enzyme changes shape on substrate binding. the active site forms a shape complementary to the substrate only after the substrate has been bound.

The Binding Energy between enzyme and substrate is important for catalysis

the full compliment of such interactions is formed only when the substrate is in the transition state (transition state analogs are potent inhibitors of enzymes i.e. antibiotics

The essence of catalysis is stabilization of the transition state.

Enzymes accelerate reactions by decreasing G**, the free energy of activation( Ea)

An enzyme cannot alter the laws of thermodynamics and consequently cannot alter the equilibrium of a chemical reaction

Enzymes accelerate the attainment of equilibria but do not shift their positions. The eqm position is a function only of the free energy difference between reactants and products

Explain briefly how enzymes accelerate the rate of reactions

Enzymes have evolved to bind tightly the transition state of the reaction they catalyze. By binding the transition state with high affinity, they facilitate its formation. Hydrogen bonds and ionic and hydrophobic interactions can be involved in binding the transition state. The more transition state formed, the faster the reaction.

Free energy is a useful thermodynamic function for understanding Enzymes

Enzymes speed up the rate of chemical reactions but the properties of rxn depends on free energy differences. Delta G is a thermodynamic property that is a measure of useful energy, or energy that is capable of doing work

The Standard free energy change of a reaction is related to the equilibrium constant

Important to stress that whether the delta G for a reaction is larger, smaller, or the same as delta G * depends on the concentrations of the reactants and products

Six major classes of enzymes

Oxidoreductases (transfer electrons between molecules i.e.. redox, Tranferases (transfer functional groups between molecules) Hydrolyases (hydrolyase cleaves molecules by addition of water i.e.. proteolytic enzyme is a hydrolyase) Lyases(add to double bond or remove something to make ) , Isomerases (move functional groups in a molecule) Ligases (join 2 molecules rqr' atp hydrolysis)

The delta G of a reaction depends only on the free energy of the products minus the free energy of the reactants

The delta G of a reaction is independent of the path(or molecular mechanism) of the transformation. Also G does not provide info about the rate of a reaction. Its just the altitude (height of the graph)

Explain why the forces that bind a substrate at the active site of an enzyme are usually weak.

The enzyme-substrate and enzyme-product complexes must be reversible for catalysis to proceed; therefore, weak forces are involved in the binding of substrates to enzymes.

Why is there a high degree of sterospecificity in the interaction of enzymes with their substrates?

The formation of an enzyme-substrate complex involves a close, complementary fitting of the atoms of the amino-acid-residue side chains that make up the active site of the enzyme with the atoms of the substrate. Since stereoisomers have different spatial arrangements of their atoms, only a single steroisomer of the substrate usually fits into the active site in a form capable of being acted upon by the enzyme.

list the true statements to Enzyme catalysis of a chemical reaction..

increases the forward and reverse reaction rates. The enzyme speeds up the rate of attainment of equilibrium.

The formation of an Enzyme - Substrate complex is the first step in enzymatic catalysis

the active site of an enzyme is the region that binds the substrates(and cofactor if any) The interaction of the enzyme and substrate at the active site promotes the formation of the transition state.

Lock and key model of enzyme substrate binding

the active site of the unbound enzyme is complementary in shape to the substrate

Activation energy

the difference in free energy between the transition state and the substrate is G** Enzymes facilitate the formation of the transition state