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 due to their unique active sites.
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 bind one substrate molecule and convert it to product. Their kinetics are often described by the Michaelis-Menten model.

Active Site: Region where substrate binds and reaction occurs.
Substrate Specificity: Determined by the shape and chemical properties of the active site.

Transition State Stabilization

Enzymes lower the activation energy by stabilizing the transition state, making the reaction proceed faster.

Transition State: High-energy intermediate between reactants and products.
Stabilization: Enzymes provide an environment that favors the formation of the transition state.

Michaelis-Menten Equation and Kinetic Parameters

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

Equation:

Plot: Hyperbolic curve showing velocity vs. substrate concentration.
Parameters: Km (Michaelis constant), Vm (maximal velocity), kcat (turnover number), kcat/Km (catalytic efficiency).
Lineweaver-Burk Plot: Double reciprocal plot used to determine kinetic parameters.

Pre-Steady-State and Steady-State Kinetics

Pre-steady-state kinetics examine the initial phase of the reaction, while steady-state kinetics focus on the period where the formation and breakdown of the enzyme-substrate complex are balanced.

Pre-Steady-State: Early reaction phase, often used to study enzyme mechanisms.
Steady-State: Most kinetic measurements are made during this phase.

Allosteric Activators and Inhibitors

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

Allosteric Activator: Increases enzyme activity, often shifts the Michaelis-Menten plot to the left.
Allosteric Inhibitor: Decreases enzyme activity, often shifts the plot to the right.

Enzyme Mechanisms

Exergonic vs. Endergonic Reactions

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

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

Proximity Effect

Enzymes increase reaction rates by bringing substrates close together in the correct orientation.

Proximity: 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 a better fit.

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.
Substrate Binding: Determines specificity (e.g., chymotrypsin prefers aromatic residues).

Chymotrypsin Mechanism

Chymotrypsin catalyzes peptide bond cleavage via a two-step mechanism involving acylation and deacylation.

Acylation: Formation of covalent enzyme-substrate intermediate.
Deacylation: Release of product and regeneration of enzyme.

Enzyme Inhibition

Types of Inhibition

Enzyme inhibitors reduce enzyme 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 enzyme or enzyme-substrate complex; decreases Vm, no change in Km.

Type	Km	Vm
Competitive	Increase	No change
Uncompetitive	Decrease	Decrease
Noncompetitive	No change	Decrease

Mechanism-Based Inhibitors

These inhibitors resemble substrates and are converted by the enzyme into a reactive form that irreversibly inactivates the enzyme.

Irreversible: Covalently modifies the enzyme.
Example: Penicillin inhibits bacterial transpeptidase.

Cofactors

Essential Ions vs. Coenzymes

Cofactors are non-protein molecules required for enzyme activity. They are classified as essential ions or coenzymes.

Essential Ions: Metal ions (e.g., Mg2+, Zn2+).
Coenzymes: Organic molecules, often derived from vitamins.

Types of Coenzymes

Coenzymes are divided into two types based on their association with enzymes.

Cosubstrates: Transiently associated, e.g., NAD+.
Prosthetic Groups: Permanently attached, e.g., FAD.

ATP in Group Transfer Reactions

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

Group Transfer: ATP donates phosphate to substrates (e.g., phosphorylation).

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 animals.
Signaling: Glycoproteins in cell recognition.

Classification of Saccharides

Saccharides are classified by the number of sugar units.

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

Aldoses vs. Ketoses

Monosaccharides are classified based on 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 their stereochemistry.

Chirality: Monosaccharides have multiple chiral centers.
Example: D-glucose has four chiral centers.

Stereochemical Terms

Monosaccharides exhibit various stereochemical relationships.

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 ring structures, creating new chiral centers.

Hemiacetal: Formed from aldoses.
Hemiketal: Formed from ketoses.
Anomeric Carbon: New chiral center formed during cyclization.

Haworth Projections, Pyranose, and Furanose Structures

Haworth projections depict cyclic forms of sugars.

Pyranose: Six-membered ring.
Furanose: Five-membered ring.

Disaccharides

Glycosidic Bonds and Connectivity

Disaccharides are formed by glycosidic bonds between monosaccharides.

Glycosidic Bond: Covalent bond between anomeric carbon and another sugar.
Reducing Sugar: Has free anomeric carbon.
Non-Reducing Sugar: Both anomeric carbons involved in bond.
Example: Sucrose (non-reducing), lactose (reducing).

Polysaccharides and Glycoproteins

Functional Roles and Structure of Polysaccharides

Polysaccharides serve as energy storage and structural molecules.

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

Glycoproteins: O-linked vs. N-linked

Glycoproteins are proteins with carbohydrate chains attached.

O-linked: Sugar attached to serine/threonine.
N-linked: Sugar attached to asparagine.
Functional Roles: Cell recognition, signaling.

ABO Blood Classification

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

Donor/Recipient Compatibility: Determined by presence/absence of A, B antigens.

Nucleic Acids

Components of a Nucleotide

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

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

Structures of Nucleotides

Nucleotides differ in their bases, sugars, and linkages.

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 and RNA differ in their sugar and base composition.

DNA: Deoxyribose, bases A, G, C, T.
RNA: Ribose, bases A, G, C, U.

DNA and RNA: Structures and Functions

Linking Nucleotides and Phosphodiester Bonds

Nucleotides are linked by phosphodiester bonds, forming the backbone of nucleic acids.

Phosphodiester Bond: Connects 5' phosphate to 3' hydroxyl of adjacent nucleotide.
Directionality: Nucleic acids are synthesized 5' to 3'.

Watson-Crick Base Pairing

Base pairs are formed by hydrogen bonds between complementary bases.

A-T (DNA) or A-U (RNA): Two hydrogen bonds.
G-C: Three hydrogen bonds.

Major Classes and Functions of RNA

RNA molecules serve various roles in the cell.

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

Secondary Structures of RNA

RNA can form complex secondary structures such as hairpins, loops, and bulges.

Hairpin: Stem-loop structure.
Bulge: Unpaired nucleotides in a stem.
Internal Loop: Unpaired regions between stems.