Biochem Chapter 1

Section 1.1: Biochemical Unity Underlies Biological Diversity

  • Biochemistry: Study of life chemistry, involving macromolecules (proteins, DNA) and low-molecular-weight metabolites.

  • Unity: Conservation of structures (e.g., TATA-binding protein) suggests all organisms evolved from a common ancestor.

  • Domains: Life is classified into Eukarya (includes eukaryotes with nuclei), Bacteria, and Archaea (both prokaryotes).

Section 1.2: DNA Illustrates the Interplay Between Form and Function

  • Components: Nucleotides (sugar, phosphate, nitrogenous bases A, T, G, C).

  • Double Helix: Antiparallel strands with Watson-Crick base pairing held by hydrogen bonds: A−TA-T (2 bonds), G−CG-C (3 bonds).

  • Heredity: Each strand acts as a template for identical daughter helices.

Section 1.3: Chemistry Concepts in Biological Molecules

  • Covalent Bonds: Shared electrons; strong (1.54 A˚1.54 \text{ Å}, 355 kJ mol−1355 \text{ kJ mol}^{-1}).

  • Ionic Interactions: Attraction between charges described by Coulomb Energy: E=kq<em>1q</em>2DrE = \frac{k q<em>1 q</em>2}{Dr}.

  • Hydrogen Bonds: Interaction between an H-atom and an electronegative atom (4−20 kJ mol−14-20 \text{ kJ mol}^{-1}).

  • van der Waals: Weak attractions from transient dipoles (2−4 kJ mol−12-4 \text{ kJ mol}^{-1}) occurring at the van der Waals contact distance.

  • Water & Hydrophobic Effect: Water is polar and cohesive. Nonpolar molecules aggregate (the hydrophobic effect) to increase water entropy.

DNA and the Rules of Chemistry

  • Repulsion: Negatively charged phosphates repel each other but are stabilized by water's high dielectric constant and positive ions.

  • Specificity: Hydrogen bonds and base stacking (van der Waals forces) ensure precise sequence pairing.

Thermodynamics in Biochemical Systems

  • First Law: Energy is constant.

  • Second Law: Universal entropy (SS) always increases.

  • Gibbs Free Energy: Reactions are spontaneous if \Delta G < 0 , where ΔG=ΔH<em>system−TΔS</em>system\Delta G = \Delta H<em>{system} - T \Delta S</em>{system}.

  • Helix Formation: Spontaneous because heat release increases environmental entropy, offsetting the local entropy decrease in DNA.

Acid–Base Reactions

  • pH: Concentration of H+H^+, where pH=−log[H+]pH = - \text{log}[H^+].

  • Water Dissociation: KW=[H+][OH−]=10−14K_W = [H^+][OH^-] = 10^{-14}. At pH 7, [H+]=10−7M[H^+] = 10^{-7} M.

  • Denaturation: High pH removes protons (e.g., from Guanine, pKa=9.7pK_a = 9.7), disrupting hydrogen bonds and destabilizing the helix.

pKa and Buffers

  • pKa: Susceptibility of proton removal; at pH=pKapH = pK_a, a group is 50% deprotonated.

  • Henderson–Hasselbalch: pH=pKa+log⁡([A−][HA])pH = pK_a + \log\left(\frac{[A^-]}{[HA]}\right).

  • Buffers: Resist pH changes; most effective near their pKapK_a. Inorganic phosphate is a key physiological buffer (pH≈7.4pH \approx 7.4).

Genomic Sequences

  • Encoding: DNA encodes the sequence of 20 amino acids to build proteins.

  • Structure: The 3D structure and function of proteins are determined by their unique amino acid sequences.