Chemistry/Physics 5

Chemical and Physical Foundations of Biological Systems

Foundational Concept 5

• The principles that govern chemical interactions and reactions provide a fundamental understanding of the molecular dynamics within living systems.
• Key points:
  • Chemical processes in organisms are understood through:
  • Behavior of solutions
  • Thermodynamics
  • Molecular structure
  • Intermolecular interactions
  • Molecular dynamics
  • Molecular reactivity

5A: Unique Nature of Water and Its Solutions

• An understanding of living systems begins with the unique properties of water and its ability to interact with various solutes, including ions.
• Properties of water include:
  • Ability to absorb energy.
  • Function as a buffer to maintain stability amid chemical changes essential for life.
• Topics covered include:
  • Nature of solutions, solubility, and characteristics of acids, bases, and buffers.

Acid-Base Equilibria (GC, BC)

• **Brønsted-Lowry definition: **
  • Acids are proton donors.
  • Bases are proton acceptors.
• Ionization of Water:
  • The ion product constant for water: $K_w = [H^+][OH^-] = 10^{-14}$ at 25°C, 1 atm.
  • Definition of pH:
  • pH of pure water is 7.
• Conjugate acids and bases:
  • Example: Ammonium ion ($NH_4^+$) is the conjugate acid of ammonia ($NH_3$).
• Strong Acids and Bases:
  • Examples include nitric acid and sulfuric acid.
• Weak Acids and Bases:
  • Examples: Acetic acid and benzoic acid.
  • Dissociation of weak acids can occur with or without added salt.
  • Hydrolysis of salts resulting from weak acids or bases.
  • Calculation of pH in salt solutions derived from weak acids or bases.
• Equilibrium Constants:
  • Acid dissociation constant $K_a$ and base dissociation constant $K_b$ analyzed via pKa and pKb.
• Buffers:
  • Definition and discussion of common buffer systems.
  • Effect on titration curves.

Ions in Solutions (GC, BC)

• Familiar ions include:
  • Cations: $NH_4^+$ (ammonium)
  • Anions: $PO_4^{3-}$ (phosphate), $SO_4^{2-}$ (sulfate).
• Hydration:
  • Formation of the hydronium ion (H3O+).

Solubility (GC)

• Units of Concentration:
  • Molarity and others.
• Solubility Product Constant:
  • Equilibrium expression is denoted as $K_{sp}$.
• Common-Ion Effect:
  • Utilized in laboratory separations.
  • Involves complex ion formation, impacting solubility.
  • Dependency of solubility on pH.

Titration (GC)

• Indicators:
  • Substances used to show pH changes visually.
• Neutralization:
  • A reaction between acids and bases.
• Interpretation of Titration Curves:
  • Graphical representation of pH changes.
• Redox Titration:
  • Involves reduction and oxidation reactions.

5B: Nature of Molecules and Intermolecular Interactions

• Covalent Bonding:
  • Involves the sharing of electrons between atoms.
  • If the interaction does not result in a network solid, the product will be discrete and molecular.
• Molecular Shape Prediction:
  • Can be determined based on electrostatic principles and quantum mechanics (e.g., only two electrons can occupy the same orbital).
• Bond Polarity:
  • Direction and magnitude predictable via knowledge of electron structure.
• Strength of Intermolecular Interactions:
  • Depends on molecular shape and covalent bond polarity.
  • Solubility and other physical properties are influenced.

Covalent Bond (GC)

• Lewis Electron Dot Formulas:
  • Visual representation of bonding pairs and lone pairs of electrons.
  • Resonance Structures:
  • Illustrates delocalized electrons.
  • Formal Charge:
  • Concept used to determine charges in molecules.
  • Lewis Acids and Bases
  • Acid: Electron pair acceptor.
  • Base: Electron pair donor.
• Partial Ionic Character:
  • Influenced by electronegativity, determining charge distribution.
  • Dipole Moment: A measure of polarity in a bond.
• Bond Types:
  • Sigma (σ) Bonds:
  • Formed by head-on overlapping of atomic orbitals.
  • Pi (π) Bonds:
  • Result from the side-on overlap of p-orbitals.
• Hybrid Orbitals:
  • Types: $sp^3$, $sp^2$, $sp$; specific geometries associated.
  • Valence Shell Electron Pair Repulsion (VSEPR):
  • Used to predict shapes of molecules (e.g., ammonia $NH_3$, water $H_2O$, carbon dioxide $CO_2$).
• Structural Formulas:
  • Chemical representations for H, C, N, O, F, S, P, Si, Cl.
• Delocalized Electrons and Resonance:
  • Role in the stability of molecules and ions.
• Multiple Bonding Effects:
  • Influence on bond length and energies.
  • Rigidity introduced in molecular structure.

Stereochemistry of Covalently Bonded Molecules (OC)

• Isomers:
  • Species with the same molecular formula but different structures.
  • Structural Isomers:
  • Differ in the covalent arrangement of atoms.
  • Stereoisomers:
  • Have the same connectivity but differ in spatial arrangement (e.g., diastereomers, enantiomers, cis-trans isomers).
  • Conformational Isomers:
  • Polarization of Light:
  • Ability of chiral molecules to rotate plane-polarized light; measured via specific rotation.
  • Configuration:
  • Absolute (R and S) and relative (E and Z) configurations for stereoisomers.

Liquid Phase – Intermolecular Forces (GC)

• Hydrogen Bonding:
  • Strongest type of dipole-dipole interaction; occurs when H is bonded to highly electronegative atoms (N, O, F).
• Dipole Interactions:
  • Attraction between polar molecules due to permanent dipoles.
• Van der Waals Forces:
  • Includes London dispersion forces, the weakest type of molecular interaction.

5C: Separation and Purification Methods

• Separation techniques are necessary for analyzing complex mixtures, particularly biological materials.
• The chosen method is often based on the component types of mixtures, leveraging differences in intermolecular forces.

Separations and Purifications (OC, BC)

• Extraction:
  • Involves partitioning a solute between two immiscible solvents.
• Distillation:
  • Separation based on differences in boiling points.
• Chromatography:
  • Fundamental principles for separation processes include:
  • Column Chromatography
  • Gas-Liquid Chromatography
  • High-Pressure Liquid Chromatography (HPLC)
  • Paper Chromatography
  • Thin-Layer Chromatography (TLC)
• Separation and Purification of Peptides and Proteins (BC):
  • Techniques employed:
  • Electrophoresis:
    • Separates molecules based on charge and size.
  • Quantitative Analysis:
    • Measurement of substance amounts.
  • Chromatography:
    • Includes various types like:
    • Size-exclusion chromatography
    • Ion-exchange chromatography
    • Affinity chromatography
  • Racemic Mixtures:
  • Separation of enantiomers is important in biological applications.

5D: Structure, Function, and Reactivity of Biologically Relevant Molecules

• The structural composition of biological molecules dictates their chemical reactions such as oligomerization and polymerization.
• Different types of biological molecules play roles in structure, information storage, fueling cellular processes, and acting as catalysts.

Nucleotides and Nucleic Acids (BC, BIO)

• Nucleotides and Nucleosides:
  • Comprised of:
  • Sugar-phosphate backbone
  • Pyrimidine and purine residues.
• Deoxyribonucleic Acid (DNA) and Ribonucleic Acid (RNA):
  • Structure of DNA: Double helix.
  • RNA structures: varied configurations.

Amino Acids, Peptides, Proteins (OC, BC)

• Amino Acids Description:
  • Absolute configuration at the α position.
  • Exist as dipolar ions.
  • Classified as:
  • Acidic or basic
  • Hydrophilic or hydrophobic.
• Synthesis of α-amino acids (OC):
  • Strecker Synthesis and Gabriel Synthesis.
• Peptides and Proteins Reactions:
  • Cysteine and Cystine: Formation of sulfur linkages.
  • Peptide linkages create polypeptides and proteins.
  • Hydrolysis: Breaks down polypeptides.
• General Principles:
  • Primary Structure: Sequence of amino acids.
  • Secondary Structure: Local folding patterns (e.g., α-helices, β-sheets).
  • Tertiary Structure: 3D configuration of a single polypeptide.
  • Isoelectric Point (pI): pH at which a molecule has no net charge.

The Three-Dimensional Protein Structure (BC)

• Conformational Stability:
  • Influences biological function; based on hydrophobic interactions and solvation layers.
• Quaternary Structure:
  • Assembly of multiple polypeptide chains.
• Denaturing and Folding:
  • How proteins regain or lose biological activity depending on their conformation.

Nonenzymatic Protein Function (BC)

• Functions of proteins beyond enzymatic activity include:
  • Binding: Specific molecule interactions (e.g., receptors).
  • Immune System: Role of antibodies and defense mechanisms.
  • Motor Functions: Movement facilitated by proteins (e.g., myosin, actin).

Lipids (BC, OC)

• Description and Types:
  • Storage Lipids:
  • Triacyl glycerols and free fatty acids.
  • Structural Lipids:
  • Phospholipids, phosphatidylcholine, sphingolipids, and waxes.
  • Signals and Cofactors:
  • Include fat-soluble vitamins, steroids, and prostaglandins.

Carbohydrates (OC)

• Description:
  • Nomenclature and classification, common names.
  • Absolute Configuration: Determine D and L representations.
  • Cyclic Structure: Conformations of hexoses, epimers, and anomers.
  • Hydrolysis of Glycosidic Linkages: Breaks down polysaccharides.
  • Keto-Enol Tautomerism: Interconversion of ketoses and aldoses.

Aldehydes and Ketones (OC)

• Description:
  • Nomenclature and physical properties outlined.
• Important Reactions:
  • Involvement in nucleophilic addition at carbonyl (C=O) bonds:
  • Formation of acetals, hemiacetals, imines, and enamines.
  • Introduction of cyanohydrin and oxidation reactions.
  • Aldol Condensation and Retro-Aldol Reactions:
    • Discussed along with kinetic vs. thermodynamic enlate control.

Alcohols (OC)

• Description:
  • Nomenclature and analysis of physical properties (acidity and hydrogen bonding).
• Important Reactions:
  • Oxidation processes, substitution (SN1/SN2), protection strategies, preparation of mesylates and tosylates.

Carboxylic Acids (OC)

• Description:
  • Analysis covering nomenclature and physical properties.
• Important Reactions:
  • Reactions pertinent to the carboxyl group, formation of amides, esters, lactones, and anhydrides.

Acid Derivatives (Anhydrides, Amides, Esters) (OC)

• Description:
  • Nomenclature and physical properties.
• Important Reactions:
  • Nucleophilic substitution reactions, transesterification, hydrolysis of amides.
  • General principles regarding reactions include:
  • Relative reactivity of acid derivatives, steric effects, electronic effects, and strain in cyclic structures.

Phenols (OC, BC)

• Oxidation and Reduction:
  • Involvement of phenols as 2-electron redox centers including hydroquinones and ubiquinones.

Polycyclic and Heterocyclic Aromatic Compounds (OC, BC)

• Examination of biological aromatic heterocycles.

5E: Principles of Chemical Thermodynamics and Kinetics

• Biological processes are dynamic and governed by the laws of thermodynamics and kinetics.
• Factors influencing chemical equilibrium include relative energies of products and reactants.
• Factors that impact the rate of equilibrium attainment include:
  • Concentration of reactants
  • Temperature
  • Catalyst presence
• Biological systems optimize energy use for life processes such as homeostasis and anabolism.
• Enzymes serve as biological catalysts facilitating chemical reactions rapidly and efficiently under specified conditions.

Enzymes (BC, BIO)

• Classification:
  • Based on reaction type.
• Mechanism:
  • Interaction with substrates demystifies enzyme specificity.
  • Models include:
  • Active-site model
  • Induced-fit model
• Cofactors, Coenzymes, and Vitamins:
  • Require additional molecules to function properly.
• Kinetics:
  • General principles of catalysis studied, including:
  • Michaelis-Menten kinetics
  • Cooperativity effects.
  • Local conditions such as pH and temperature impact enzyme activity.
  • Types of inhibition and regulatory enzyme mechanisms:
  • Allosteric effects
  • Covalent modification.

Principles of Bioenergetics (BC)

• Bioenergetics/Thermodynamics:
  • Concepts of free energy and equilibrium constant (Keq) discussed.
  • Mechanisms of phosphorylation and ATP:
  • ATP hydrolysis characterized by ext{ΔG} << 0 signifies a spontaneous reaction.
  • Group transfer reactions of ATP.
• Biological Oxidation-Reduction:
  • Study of half-reactions and the role of soluble electron carriers, including flavoproteins.

Energy Changes in Chemical Reactions – Thermochemistry and Thermodynamics (GC, PHY)

• Thermodynamic Systems:
  • Characterized as state functions.
• Laws of Thermodynamics:
  • Zeroth Law: Defines temperature concept.
  • First Law: Conservation of energy during processes.
  • PV Diagram:
  • Defines work done as area under curve.
  • Second Law: Entropy as a disorder measure.
  • Relative values for gas, liquid, solid states.
• Measurement of Heat Changes:
  • Involves calorimetry, heat capacity, and specific heat.
• Heat Transfer Mechanisms:
  • Modes include conduction, convection, and radiation.
• Reactions Classification:
  • Endothermic vs. Exothermic studies.
  • Enthalpy (H):
  • Investigates standard heats of reaction and formation and Hess's Law of heat summation.
• Free Energy Analysis (G):
  • Discusses spontaneous reactions and $ext{ΔG}^°$ significance.
• Phase Diagrams:
  • Relationships of pressure and temperature mapped out.

Rate Processes in Chemical Reactions – Kinetics and Equilibrium (GC)

• Reaction Rate Investigations:
  • Factors impacting rate include concentration and temperature.
• Rate Law Definitions:
  • Incorporates rate constants and reaction order.
• Rate-Determining Step:
  • The slowest step dictates overall reaction rate.
• Activation Energy Concepts:
  • Study of activated complexes and energy profiles detailing reactant/product energies, activation energy, and $ext{ΔH}$ changes.
• Use of Arrhenius Equation:
  • Exemplifies temperature dependence of reaction rates.
• Kinetic vs. Thermodynamic Control:
  • Exploration of reaction pathways.
• Equilibrium Dynamics:
  • Law of Mass Action: governs concentrations at equilibrium.
  • Equilibrium constants analyzed.
• Le Châtelier’s Principle:
  • Applications regarding shifts in equilibrium with varying conditions.