Chapter 6: Enzymes Biochem Exam 2

Ribozymes

RNA molecules that are also enzymes

Cofactors

additional chemical components of one or more inorganic molecules such as iron, magnesium, manganese, or zinc

Coenzymes

complex organic or metallorganic molecules needed for enzyme function

Holoenzyme/holoprotein

enzyme with its cofactor(coenzyme)

Apoenzyme/apoprotein

enzyme part of the complex by itself, no cofactor or coenzyme

Six classes of enzymes

oxidoreductases, transferases, hydrolases, lyases, isomerases, ligases

Oxidreductases

transfer electrons; enzyme class 1

Transferases

group transfer reactions; enzyme class 2

Hydrolases

hydrolysis reactions (transfer of functional groups to water; enzyme class 3

Lyase

addition of groups to double bonds, or formation of double bonds aka cleavage and electron rearrangement; enzyme class 4

Isomerasese

transfer of groups within molecules to yield isomeric forms; enzyme class 5

Ligases

enzyme that is responsible for the formation of CC, CS, CO, CN bonds by condensation reactions coupled to cleavage of ATP or similar cofactor; enzyme class 6

Kinase

enzymes that transfer a phosphoryl group from a nucleoside triphosphate such as ATP to an acceptor molecule

Synthases

catalyze condensation reactions in which no nucleoside triphosphate (ATP, GTP) is needed for energy

Phosphorylases

enzyme that catalyzes the attachment of a phosphate to a point of bond breakage

Phosphatases

enzyme that catalyzes the removal of a phosphoryl group from a phosphate ester using water.

EC #

enzyme classification number; a 4 digit classification system with periods separating the enzyme ex. 2.9.1.1 where 2 is class, 1 is chemistry, and 1 is molecule

Ground state

the starting point for either the forward or the reverse reaction

Transition state

point at which the decay to the substrate (S) or product (P) state is equally probable; fleeting molecular moment where bond breakage, bond formation, and charge development have proceeded to a point that may produce products or substrates

Activation energy

difference between the energy levels of the ground state and the transition state; the higher this is, the slower a reaction, can be lowered with a catalyst

Reaction rates

the speed at which a reaction occurs; can be increased by raising the temperature or enhanced by

Reaction intermediates

any species/step on the reaction pathway involving the formation and decay of transient chemical species

Rate limiting step

the step in a chemical reaction with the highest activation energy; there can be multiple if they have similar activation energies

Rate constant

concentration of the reactant(s), denoted by k

The lower the activation energy

the faster the reaction as the rate constant (k) is inverse and exponential to the activation energy

Reaction energy diagrams

S= ground state energy of substrate; P= ground state energy of product

Weak bonds between enzyme and substrate

provide small amounts of free energy that provide a degree of stability for the interaction and drive enzymatic catalysis and specificity

Binding energy

energy derived from enzyme substrate interactions; major source of free energy used by enzymes to lower the activation energies of reactions

Acid base, covalent, and metal ion catalysis

mechanistic events occurring in enzymes that lead to enzymatic catalysis

Acid Base Catalysis

Bronsted/Lowry acid base reactions, proton transfers

Covalent Catalysis

lewis acid base reactions; nucleophilic attack on an electrophile that leads to formation of a new bond

Metal Ion catalysis

metal ion stabilization of a charged transition state group or oxidation reduction reaction

Enzyme Assay

protocol used to test for the presence of an enzyme

Enzyme Kinetics

the study of an enzyme’s catalytic efficiency

Specificity

the ability of an enzyme to discriminate between a substrate and a competing molecule; derived from formation of many weak interactions between enzyme and substrate

Michalis Menten/Steady state kinetics

when the rate limiting step is downstream (not the first step); analysis of the initial rates in the steady state

Steady state

when a reaction is in a state where the concentration of the enzyme and substrate [ES} are constant over time

Michaelis Menten equation

rate equation for a one substrate enzyme catalyzed reaction that defines the relationship between initial velocity, maximum velocity, and substrate concentration using the michaelis constant

Michaelis constant

equals the concentration of the substrate when ½ Vmax =Vo (half of the max velocity equals initial velocity)

Km

experimental evidence has shown that often the determined Km approaches the value of cellular [s]; can be considered an estimate of the enzyme substrate Kd(enzyme ability to bind the substrates.) Km is NOT the Kd

Lineweaver Burk equation

the inverse of the michaelis menten equation; slope of this straight line is the michaelis constant divided by Vmax, the y intercept is 1/Vmax, the x intercept is neg. 1/Km

Turnover number

the number of substrate molecules converted to product in a given unit of time on a single enzyme molecule aka Kcat ; determines the rate of rate limiting step

Sequential Reactions

when two or more substrates may bind to the enzyme in an ordered binding sequence or in a random order

Ping pong reactions

catalyzed reactions in which one or more products are released before all substrates have bound by enzyme

Double reciprocal Michaelis menten equation

equation used for ordered sequential reactions

Competitive inhibition

reversible inhibition where an inhibitor competes with the substrate for the active site of an enzyme

Uncompetitive inhibition

reversible inhibition where inhibitor binds at site distinct from the substrate active site; only binds to ES substrate

Mixed inhibition

reversible inhibition where inhibitor binds to site distinct form the substrate active site but binds to either the enzyme or the enzyme substrate (rare)

Dead end inhibitors

irreversible inhibitors that covalently bind the enzyme substrate complex and prevents catalysis

Suicide inhibitors

irreversible inhibitors that mimic the natural substrae and catalysis begins but stops and covalently binds within active site

Transition state analogs

irreversible inhibitors that mimic the transition state of the substrate; bind at active site, usually noncovalent, but very tight bond

Effect of pH on enzyme

enzymes have optimal pH ranges they can function in determined by amino acid side chains

Chemotrypsin

enzyme that belongs to the ser his asp proteases family that functions via a ser his asp catalytic triad (asp102, his57, ser195)

Catalytic triad

arrangement of three amino acids in an enzyme’s active site that activates a nucleophile for covalent catalysis

Nucleophile

electron rich atom such as negatively charged oxygen or sulfhydryl, uncharged amine (N), imidazole, hydroxide

Electrophile

electron deficient atom such as carbon of a carbonyl, protonated imine, phosphorous of a phosphate group, and a proton

Regulatory enzymes

found in the early stages of metabolic pathways and used as regulators to help control cell resources; don’t follow michaelis menten type kinetics

Feedback Inhibition

noncovalent binding of a downstream product.

Reversible covalent modification

covalent modification of one or more amino acid side chains with small functional groups; can affect the activity of a regulatory enzyme ex. phosphorylation

Common modifying groups for covalent modification

phosphoryl, acetyl, adenylyl, methyl, carboxyl, and ADP ribosylation

Proteolytic cleavage

process where precursor proteins are acted upon by a specific protease which cleaves part of the peptide chain off of the precursor protein with the active enzyme being all that remains

Phosphofructokinase PFK1

enzyme that catalyzes the committing step into glycolysis; has 5 allosteric regulators: AMP, ADP, ATP, citrate, and fructose 2,6 bisphosphate

AMP and ADP

PFK1 activators that build up when ATP is consumed triggering a need for more ATP

ATP

substrate, metabolic product of glycolysis, and inhibitor of PFK1; high levels of this indicates cell is happy; binds at allosteric sites and inhibits F6 P

Citrate

inhibitor of PFK1 an early intermediate of the citric acid cycle; indicates that cell needs are being met and glycolysis can be slowed down

Fructose 2,6 bisphosphate

powerful activator of PFK1

Fructose 2,6 bisphosphate (in liver)

increases PFK1’s affinity for F6P and reduces affinity for ATP and citrate;powerful activator of PFK1

PFK1 activity increases

as fructose 2,6 bisphosphate levels increases