BCH 351 Exam 2 Study Guide: Enzymes, Carbohydrates, and Nucleic Acids

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Enzyme Kinetics

General Properties of Enzymes

Enzymes are biological catalysts that accelerate chemical reactions without being consumed. They exhibit high specificity for their substrates and operate under mild physiological conditions.

Specificity: Enzymes recognize and bind specific substrates, often through precise molecular interactions.
Efficiency: Enzymes can increase reaction rates by factors of 106 or more.
Regulation: Enzyme activity can be modulated by various mechanisms, including allosteric regulation and covalent modification.
Example: Hexokinase catalyzes the phosphorylation of glucose in glycolysis.

Single Substrate Enzyme Features

Single substrate enzymes catalyze reactions involving one substrate molecule. Their kinetics are often described by the Michaelis-Menten model.

Substrate Binding: The substrate binds to the enzyme's active site, forming an enzyme-substrate complex.
Product Formation: The complex undergoes a chemical transformation, releasing the product.

Transition State Stabilization

Enzymes lower the activation energy by stabilizing the transition state, the high-energy intermediate between reactants and products.

Transition State: The configuration with the highest energy along the reaction pathway.
Stabilization: Enzymes provide an environment that favors the transition state, often through hydrogen bonding, electrostatic interactions, or induced fit.

Michaelis-Menten Equation and Kinetic Parameters

The Michaelis-Menten equation describes the rate of enzymatic reactions as a function of substrate concentration.

Equation:

Plot: The Michaelis-Menten plot is hyperbolic, showing velocity versus substrate concentration.
Key Parameters: Km (Michaelis constant), Vm (maximal velocity), kcat (turnover number), and kcat/Km (catalytic efficiency).
Lineweaver-Burk Plot: A double reciprocal plot linearizes the Michaelis-Menten equation.

Pre-Steady-State and Steady-State Kinetics

Pre-steady-state kinetics examines the initial formation of enzyme-substrate complexes, while steady-state kinetics analyzes the reaction once intermediate concentrations are constant.

Pre-Steady-State: Early phase, before equilibrium is reached.
Steady-State: The rate of formation and breakdown of the enzyme-substrate complex is balanced.

Allosteric Activators and Inhibitors

Allosteric enzymes are regulated by molecules that bind at sites other than the active site, affecting activity.

Allosteric Activator: Increases enzyme activity, often shifting the Michaelis-Menten plot to lower Km or higher Vm.
Allosteric Inhibitor: Decreases activity, shifting the plot to higher Km or lower Vm.

Enzyme Mechanisms

Exergonic vs. Endergonic Reactions

Enzyme-catalyzed reactions can be exergonic (energy-releasing) or endergonic (energy-consuming), as shown in reaction coordinate diagrams.

Exergonic: ; spontaneous.
Endergonic: ; non-spontaneous.

Proximity Effect

Enzymes increase reaction rates by bringing substrates into close proximity and proper orientation.

Effect: Reduces entropy and increases effective concentration of reactants.

Lock-and-Key vs. Induced-Fit Models

These models describe how substrates bind to enzymes.

Lock-and-Key: Substrate fits exactly into the active site.
Induced-Fit: Enzyme changes shape upon substrate binding for optimal interaction.

Serine Protease Catalysis and Specificity

Serine proteases use a catalytic triad (Ser, His, Asp) to hydrolyze peptide bonds.

Catalytic Triad: Serine acts as nucleophile, histidine as base, aspartate stabilizes histidine.
Substrate Binding: Specificity determined by the shape and charge of the binding pocket.
Example: Chymotrypsin cleaves peptide bonds adjacent to aromatic residues.

Enzyme Inhibition

Types of Inhibition

Enzyme inhibitors reduce activity by different mechanisms.

Competitive: Inhibitor binds active site; increases Km, no change in Vm.
Uncompetitive: Inhibitor binds only to enzyme-substrate complex; decreases both Km and Vm.
Noncompetitive: Inhibitor binds elsewhere; decreases Vm, no change in Km.

Type	Km	Vm
Competitive	Increase	Unchanged
Uncompetitive	Decrease	Decrease
Noncompetitive	Unchanged	Decrease

Mechanism-Based Inhibitors

These inhibitors mimic the substrate and irreversibly inactivate the enzyme by forming a covalent bond.

Distinction: Unlike reversible inhibitors, mechanism-based inhibitors permanently modify the enzyme.

Cofactors

Essential Ions vs. Coenzymes

Cofactors are non-protein molecules required for enzyme activity.

Essential Ions: Metal ions (e.g., Mg2+, Zn2+) that assist in catalysis.
Coenzymes: Organic molecules; can be prosthetic groups (tightly bound) or cosubstrates (loosely bound).

Types of Coenzymes

Prosthetic Groups: Permanently attached to enzyme (e.g., FAD).
Cosubstrates: Transiently associated (e.g., NAD+).

ATP in Group Transfer Reactions

ATP acts as a cofactor by transferring phosphate groups in metabolic reactions.

Example: Phosphorylation of glucose by hexokinase.

NAD(P)+/NAD(P)H and FAD/FADH2 in Redox Reactions

These cofactors participate in oxidation-reduction reactions by accepting or donating electrons.

NAD(P)+: Accepts electrons, becomes NAD(P)H.
FAD: Accepts electrons, becomes FADH2.

Monosaccharides

Functions of Carbohydrates

Carbohydrates serve as energy sources, structural components, and signaling molecules.

Energy: Glucose is a primary energy source.
Structure: Cellulose in plants, chitin in fungi.
Signaling: Glycoproteins in cell recognition.

Classification of Saccharides

Monosaccharides: Single sugar units (e.g., glucose).
Disaccharides: Two monosaccharides linked (e.g., sucrose).
Oligosaccharides: 3-10 monosaccharides.
Polysaccharides: Many monosaccharides (e.g., starch).

Aldoses vs. Ketoses

Monosaccharides are classified by their carbonyl group.

Aldoses: Have an aldehyde group (e.g., glucose).
Ketoses: Have a ketone group (e.g., fructose).

Fischer Projections and Chirality

Fischer projections are 2D representations of monosaccharides, showing stereochemistry.

Chirality: Monosaccharides have multiple chiral centers.
Example: D- and L-glucose differ at the chiral center furthest from the carbonyl.

Stereochemical Terms

Stereoisomer: Same formula, different spatial arrangement.
Enantiomer: Mirror images.
Diastereomer: Not mirror images.
Epimer: Differ at one chiral center.

Cyclization of Monosaccharides

Monosaccharides cyclize to form hemiacetals (aldoses) or hemiketals (ketoses).

Anomeric Carbon: New chiral center formed during cyclization.
Haworth Projection: Shows cyclic structure.
Pyranose: Six-membered ring.
Furanose: Five-membered ring.

Disaccharides

Glycosidic Bonds and Connectivity

Disaccharides are formed by glycosidic bonds between monosaccharides.

Reducing Sugar: Has a free anomeric carbon.
Non-Reducing Sugar: Both anomeric carbons are involved in the bond.
Example: Sucrose (non-reducing), lactose (reducing).

Polysaccharides and Glycoproteins

Functional Roles and Structure of Polysaccharides

Polysaccharides serve as energy storage and structural materials.

Starch: Storage in plants; composed of amylose and amylopectin.
Glycogen: Storage in animals; highly branched.

Glycoproteins

Proteins with covalently attached carbohydrate chains.

O-linked: Carbohydrate attached to serine/threonine.
N-linked: Carbohydrate attached to asparagine.
Function: Cell recognition, signaling.

ABO Blood Classification

Blood types are defined by specific glycoprotein antigens on red blood cells.

Donor/Recipient: Compatibility depends on antigen presence.

Nucleic Acids

Components of a Nucleotide

Nucleotides are composed of a nucleobase, a pentose sugar, and a phosphate group.

Nucleobase: Purine (A, G) or pyrimidine (C, T, U).
Nucleoside: Nucleobase + sugar.
Nucleotide: Nucleoside + phosphate.

Structures of Nucleotides

Purines: Adenine (A), Guanine (G).
Pyrimidines: Cytosine (C), Thymine (T), Uracil (U).
Ribose: Sugar in RNA.
Deoxyribose: Sugar in DNA.
Phosphoanhydride: Between phosphate groups.
Phosphoester: Between phosphate and sugar.

DNA vs. RNA Nucleotides

DNA: Contains deoxyribose and T.
RNA: Contains ribose and U.

DNA and RNA: Structures and Functions

Linking Nucleotides

Nucleotides are linked by phosphodiester bonds, forming polynucleotide chains.

Directionality: 5' to 3' end.
Watson-Crick Base Pairs: A-T (or A-U in RNA), G-C.
Hydrogen Bonds: A-T: 2 bonds; G-C: 3 bonds.

Major Classes of RNA and Functions

mRNA: Messenger RNA; carries genetic information.
tRNA: Transfer RNA; brings amino acids to ribosome.
rRNA: Ribosomal RNA; structural and catalytic role in ribosome.

Secondary Structures of RNA

Hairpin: Stem-loop structure.
Bulge: Unpaired nucleotides in a loop.
Pseudoknot: Complex folding pattern.

Additional info: Where original notes were brief, academic context and examples were added for completeness.