Pharmaceutical Biochemistry PC 1112: Comprehensive Study Notes

Intermolecular and Intramolecular Forces of Attraction

Overview of Molecular Forces

Understanding the forces between and within molecules is fundamental to biochemistry, as these interactions dictate molecular behavior, solubility, and biological function.

• Intermolecular Forces: Forces between molecules, such as hydrogen bonding, van der Waals forces, and dipole-dipole interactions.

• Intramolecular Forces: Forces within a molecule, including covalent and ionic bonds.

• Polarity and Solubility: Polar molecules dissolve well in polar solvents (e.g., water), while nonpolar molecules dissolve in nonpolar solvents.

• Application: Why do some substances float on water? This relates to density and intermolecular forces.

• Example: Why does soap clean grease? Soap molecules have both hydrophilic and hydrophobic regions, allowing them to interact with both water and grease.

Acids and Bases

Titration and Buffer Systems

Acids and bases are central to biochemical reactions, affecting enzyme activity, metabolic pathways, and cellular homeostasis.

• Titration Curve: Graphical representation of pH changes during the addition of acid or base to a solution.

• Henderson-Hasselbalch Equation: Used to calculate the pH of buffer solutions.

• Equation: $pH = pK_a + \log \left( \frac{[A^-]}{[HA]} \right)$

• Buffer Systems: Maintain stable pH in biological systems.

• Example: Blood maintains pH using bicarbonate buffer system.

Gibbs Free Energy

Thermodynamics in Biochemistry

Gibbs free energy determines the spontaneity of biochemical reactions and is essential for understanding metabolism.

• Equation: $\Delta G = \Delta H - T\Delta S$

• Exergonic vs Endergonic: Exergonic reactions release energy ($\Delta G < 0$), endergonic reactions require energy ($\Delta G > 0$).

• ATP Hydrolysis: ATP breakdown is highly exergonic and drives many cellular processes.

• Example: Coupling of ATP hydrolysis to muscle contraction.

Carbohydrates

Structure and Function

Carbohydrates are vital for energy storage, structural integrity, and cell signaling.

• Monosaccharides: Simple sugars like glucose and fructose.

• Disaccharides: Two monosaccharides linked (e.g., sucrose).

• Polysaccharides: Long chains (e.g., starch, glycogen, cellulose).

• Glycosidic Bonds: Link monosaccharides in oligo- and polysaccharides.

• Example: Glycogen is the main storage form of glucose in animals.

Lipids

Types and Biological Roles

Lipids are hydrophobic molecules essential for membrane structure, energy storage, and signaling.

• Fatty Acids: Saturated (no double bonds) and unsaturated (one or more double bonds).

• Triglycerides: Main energy storage lipids.

• Phospholipids: Major component of cell membranes.

• Membrane Curvature: Influenced by lipid composition.

• Example: Cholesterol modulates membrane fluidity.

Enzymes and Enzyme Kinetics

Mechanisms and Regulation

Enzymes are biological catalysts that accelerate chemical reactions. Their kinetics and regulation are crucial for metabolic control.

• Michaelis-Menten Equation: Describes the rate of enzymatic reactions.

• Equation: $v = \frac{V_{max}[S]}{K_m + [S]}$

• Km Value: Substrate concentration at half-maximal velocity.

• Inhibition: Competitive, noncompetitive, and uncompetitive inhibition affect enzyme activity.

• Allosteric Regulation: Enzyme activity modulated by molecules binding at sites other than the active site.

• Example: Feedback inhibition in metabolic pathways.

Proteins

Structure and Function

Proteins are polymers of amino acids with diverse functions, including catalysis, transport, and structural support.

• Primary Structure: Sequence of amino acids.

• Secondary Structure: Alpha helices and beta sheets formed by hydrogen bonding.

• Tertiary Structure: 3D folding driven by interactions among side chains.

• Quaternary Structure: Assembly of multiple polypeptide chains.

• Peptide Bond: Covalent bond linking amino acids.

• Example: Hemoglobin is a quaternary protein that transports oxygen.

Nucleic Acids

DNA and RNA Structure and Function

Nucleic acids store and transmit genetic information. Their structure and processing are central to gene expression.

• DNA: Double helix composed of nucleotides (adenine, thymine, cytosine, guanine).

• RNA: Single-stranded, involved in protein synthesis and regulation.

• Base Pairing: Purines (A, G) pair with pyrimidines (T/U, C).

• Chromosomes: DNA packaged with proteins in eukaryotes.

• DNA Damage and Repair: Cells have mechanisms to correct mutations.

• Example: DNA polymerase proofreads and repairs errors during replication.

Protein Synthesis

Transcription and Translation

Protein synthesis involves transcription of DNA to RNA and translation of RNA to protein, with differences between prokaryotes and eukaryotes.

• Transcription: DNA is transcribed to mRNA in the nucleus (eukaryotes).

• Translation: mRNA is translated to protein in the ribosome.

• mRNA Processing: Includes addition of 5' cap, polyadenylation, and splicing.

• Mutations: Silent, missense, and frameshift mutations can affect protein function.

• Example: Sickle cell anemia is caused by a missense mutation in the hemoglobin gene.

Additional info:

• Some topics (e.g., nucleic acids, protein synthesis) extend beyond the provided chapter list but are foundational in biochemistry and relevant for comprehensive understanding.