Biochemistry Exam 2

Biochemistry Exam 2

Enzymes

Catalysts that can accelerate the rate of a reaction without being consumed, usually proteins.

Gibbs Free Energy

A thermodynamic property that measures the energy capable of doing work.

Transition State

The state in which reactants are partially converted into products during a chemical reaction, facilitated by enzymes.

Reaction Velocity

The rate at which a reaction occurs, used to characterize enzyme activity.

KM

The Michaelis constant, a measure of the substrate concentration at which an enzyme works at half its maximum velocity.

kcat

The turnover number, a measure of the number of substrate molecules converted into product per unit time by a single enzyme molecule.

Reversible Inhibitors

Molecules that can bind to an enzyme and inhibit its activity, but can be easily dissociated.

Enzyme Specificity

The ability of enzymes to catalyze specific reactions and bind to specific substrates.

Proteases

Enzymes that catalyze the hydrolysis of peptide bonds.

Enzyme Cofactors

Small molecules, such as coenzymes and metals, that many enzymes require for catalytic activity.

Exergonic Reactions

Reactions that can take place spontaneously as the Gibbs free energy change (ΔG) is negative.

Endergonic Reactions

Reactions that cannot take place spontaneously as the Gibbs free energy change (ΔG) is positive.

ΔG

The free energy change of a reaction, which depends on the difference between the free energy of the products and the reactants.

Standard Free-Energy Change

The change in free energy that occurs in a reaction under standard conditions.

Equilibrium Constant

The ratio of the concentrations of products to reactants at equilibrium for a chemical reaction.

Molar Concentrations

The amount of a substance present in a given volume of a solution, expressed in moles per liter.

Gas Constant

A constant that relates the energy of a system to its temperature and pressure.

Absolute Temperature

The temperature measured on the Kelvin scale, which starts at absolute zero.

Kilojoules (kJ)

A unit of energy equal to 1000 joules.

Kilocalories (kcal)

A unit of energy equal to 1000 calories.

Equilibrium

The state in which the forward and reverse reactions of a chemical reaction occur at equal rates.

pH

A measure of the acidity or alkalinity of a solution.

Activation Energy

The energy required to initiate a chemical reaction.

Enzyme

A biological catalyst that speeds up chemical reactions in living organisms.

Substrate

The molecule or molecules on which an enzyme acts.

Transition State

A high-energy intermediate state that forms during a chemical reaction.

Enzyme-Substrate Complex

The temporary complex formed when an enzyme binds to its substrate.

Active Site

The specific region of an enzyme where the substrate binds and the catalytic reaction occurs.

Binding Energy

The energy released when an enzyme binds to its substrate.

Michaelis-Menten Model

A mathematical model that describes the kinetics of enzyme-catalyzed reactions.

First-Order Reaction

A reaction whose rate is directly proportional to the concentration of a single reactant.

Second-Order Reaction

A reaction whose rate is proportional to the product of the concentrations of two reactants.

Steady-State Assumption

An assumption made in enzyme kinetics that the rate of formation of the enzyme-substrate complex is equal to the rate of its breakdown.

Reaction Velocity (V0)

The rate at which a reaction proceeds.

Substrate Concentration

The amount of substrate present in a reaction.

Michaelis-Menten Model

A mathematical model that describes the relationship between reaction velocity and substrate concentration in enzyme-catalyzed reactions.

Michaelis constant (KM)

A constant that represents the substrate concentration at which the reaction rate is half its maximal value.

Enzyme-Substrate (ES) complex

The intermediate complex formed when an enzyme binds to its substrate.

Vmax

The maximum reaction velocity that can be achieved in an enzyme-catalyzed reaction.

Lineweaver-Burk plot

A graphical representation of the Michaelis-Menten equation that yields a straight-line plot.

Turnover number (kcat)

The number of substrate molecules converted into product per second by an enzyme.

Catalytic efficiency (kcat/KM)

A measure of how efficiently an enzyme converts substrate into product.

Specificity constant

The rate constant kcat/KM, which represents the efficiency and specificity of an enzyme for a particular substrate.

Substrate Preferences

The specific amino acids and their corresponding kcat/KM values that chymotrypsin prefers as substrates.

Enzymes with kcat/KM Near the Diffusion-Controlled Limit

Enzymes that have high catalytic efficiency (kcat/KM) close to the diffusion-controlled limit.

Sequential Reactions

Reactions where all substrates must bind to an enzyme before any product is released.

Ordered Sequential Mechanisms

Sequential mechanisms where the substrates bind the enzyme in a defined sequence.

Random Sequential Mechanisms

Sequential mechanisms where the order of substrate addition and product release is arbitrary.

Double-Displacement Reactions

Reactions where one or more products are released before all substrates bind the enzyme, characterized by the formation of an enzyme intermediate.

Allosteric Enzymes

Enzymes that do not obey Michaelis-Menten kinetics and display sigmoidal plots of reaction velocity versus substrate concentration.

Temperature Affects Enzymatic Activity

The effect of temperature on the rates of enzyme-catalyzed reactions.

Single-Molecule Kinetics

Studying enzyme behavior at the level of individual molecules.

Single-Molecule Michaelis-Menten Equation

The equation that describes the relationship between average time increments at different substrate concentrations in single-molecule kinetics.

Irreversible Enzyme Inhibitors

Inhibitors that bind covalently to the enzyme and do not dissociate at any appreciable rate.

Reversible Inhibition

Inhibition characterized by the dissociation of the enzyme-inhibitor complex formed by noncovalent interactions.

Competitive Inhibition

Inhibition where the inhibitor competes with the substrate for binding to the enzyme.

Uncompetitive Inhibition

Inhibition where the inhibitor binds only to the enzyme-substrate complex.

Noncompetitive Inhibition

Inhibition where the inhibitor binds either the enzyme or the enzyme-substrate complex.

Pure Noncompetitive Inhibitors

Inhibitors that bind equally well to the enzyme with or without substrate bound.

Mixed Noncompetitive Inhibitors

Inhibitors that bind preferentially to either the free enzyme or the enzyme-substrate complex.

Competitive Inhibitors

Inhibitors that mimic the substrate and compete for binding to the enzyme.

Kinetics of a Competitive Inhibitor

The effect of a competitive inhibitor on enzyme kinetics, including changes in KM and the Lineweaver-Burk plot.

Uncompetitive inhibitor

An inhibitor that binds to the enzyme-substrate complex (ES) to form an enzyme-substrate-inhibitor complex (ESI), depleting the concentration of ES and lowering the apparent value of KM.

Vmax

The maximum rate of an enzyme-catalyzed reaction, which is lower in the presence of an uncompetitive inhibitor compared to its absence.

KM

The Michaelis constant, which represents the substrate concentration at which the reaction rate is half of Vmax. Uncompetitive inhibitors lower the apparent value of KM.

Lineweaver-Burk plot

A graphical representation of enzyme kinetics that shows the reciprocal of reaction velocity (1/Vo) plotted against the reciprocal of substrate concentration (1/[S]). It can be used to analyze the effects of uncompetitive inhibitors and yields a straight-line plot.

Noncompetitive inhibitor

An inhibitor that binds to the enzyme or the enzyme-substrate complex (ES) without affecting the binding of the substrate. It lowers the concentration of functional enzyme and decreases the apparent value of Vmax, but does not change KM.

Pure Noncompetitive Inhibitors

Inhibitors that bind equally well to the enzyme with or without substrate bound.

Mixed Noncompetitive Inhibitors

Inhibitors that covalently bind to enzymes and cannot be easily removed. They can be used to map the active site and elucidate enzyme mechanisms.

Competitive Inhibitors

Inhibitors that mimic the substrate and compete for binding to the enzyme.

Affinity labels

Inhibitors that structurally resemble the substrate and covalently bond to active-site residues, inhibiting enzyme activity.

Mechanism-based (suicide) inhibitors

Inhibitors that bind to the enzyme as a substrate and generate a chemically reactive intermediate during catalysis, which inactivates the enzyme through covalent modification.

Central Dogma

The flow of genetic information from DNA to RNA to proteins.

DNA

Deoxyribonucleic acid, a long linear polymer that carries genetic information.

RNA

Ribonucleic acid, a long linear polymer that carries genetic information and is involved in protein synthesis.

Irreversible inhibitors

Inhibitors that covalently bind to enzymes and cannot be easily removed. They can be used to map the active site and elucidate enzyme mechanisms.

Nucleotide

The monomer unit within a nucleic acid, consisting of a sugar, a phosphate, and one of four bases.

Double helix

The structure formed by base-paired DNA strands, held together by hydrogen bonds.

Base pairs

Specific pairs of bases in DNA that form the rungs of the double helix.

Group-specific reagents

Inhibitors that react with specific side chains of the enzyme's amino acids, inhibiting enzyme activity.

Phosphodiester bond

The bond that links the sugars in the backbone of DNA and RNA.

Purines

A type of base found in DNA and RNA, including adenine and guanine.

Pyrimidines

A type of base found in DNA and RNA, including cytosine, thymine (in DNA), and uracil (in RNA).

Nucleoside

A unit consisting of a base bonded to a sugar.

Nucleotide

A nucleoside joined to one or more phosphoryl groups by an ester linkage.

Complementary sequences

Two nucleic acid strands with base sequences that can form specific base pairs.

Hydrogen bonds

Weak chemical bonds that hold the base pairs together in the double helix.

Van der Waals interactions

Weak attractive forces between atoms or molecules that contribute to the stability of the double helix.

Replication

The process of copying DNA to produce two identical DNA molecules.

Gene expression

The process by which DNA information is used to produce functional molecules, such as proteins.

Introns

Non-coding regions within genes that are transcribed but not translated into proteins.

Exons

Coding regions within genes that are transcribed and translated into proteins.

Watson-Crick Model of DNA

A model proposed by Watson and Crick that describes the structure of DNA as a double helix with sugars and phosphates on the outside and purines and pyrimidines on the inside.

Base pairs

Pairs of nucleotides that hold the two strands of DNA together, consisting of adenine with thymine and guanine with cytosine.

Hydrogen bonds

Weak bonds that hold the base pairs together in DNA.

Chargaff's rules

The observation made by Erwin Chargaff that the ratios of adenine to thymine and guanine to cytosine are nearly 1:1 in DNA.

Base stacking

The stacking of base pairs on top of each other, which contributes to the stability of the DNA double helix.

B-form DNA

The most common form of DNA under physiological conditions, characterized by a right-handed double helix with Watson-Crick base pairs.

A-form DNA

A form of DNA similar to B-form, but wider and shorter with tilted base pairs relative to the helix axis, often seen in RNA double helices.

Z-form DNA

A left-handed double helix with zigzagged phosphoryl groups, with an unknown biological role.