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Molecular Biology
Table of Contents
Unit 2 Overview: Chemical Foundations of Molecular Biology
2.1 Chemical bonds and interactions
2.2 Water and its role in biological systems
2.3 pH and buffers
2.4 Biological macromolecules: carbohydrates, lipids, proteins, and nucleic acids

pH and buffers are crucial concepts in molecular biology, affecting enzyme activity and cellular function. This section explores how pH measures hydrogen ion concentration on a logarithmic scale, and how buffers maintain stable pH levels in biological systems.

Understanding pH and buffers is essential for grasping how molecules interact in living organisms. We'll examine acid-base chemistry, the importance of pH in biological processes, and how buffer systems work to maintain optimal conditions for life.

pH and its logarithmic scale

Understanding pH measurement

  • pH measures hydrogen ion concentration [H+] in aqueous solutions on a logarithmic scale from 0 to 14
  • Defined as negative logarithm (base 10) of hydrogen ion concentration: pH=−log[H+]pH = -log[H+]
  • One unit change on pH scale represents tenfold change in [H+] (lemon juice pH 2, vinegar pH 3)
  • Inversely related to [H+] as [H+] increases, pH decreases (battery acid pH 0, bleach pH 13)
  • Neutral solutions have pH 7, acidic solutions pH < 7, basic (alkaline) solutions pH > 7 (pure water pH 7, milk pH 6.5, ammonia pH 11)

Complementary pOH scale

  • pOH measures hydroxide ion concentration [OH-]
  • Complementary to pH sum of pH and pOH always equals 14 in aqueous solutions at 25°C
  • Calculated using equation: pOH=−log[OH−]pOH = -log[OH-]
  • Useful for determining [OH-] when pH is known (seawater pH 8, pOH 6)

Acids, Bases, and Neutrality in Solutions

Acid-Base Definitions and Properties

  • Acids donate protons increase [H+] in solution, lowering pH (hydrochloric acid, sulfuric acid)
  • Bases accept protons decrease [H+] in solution, raising pH (sodium hydroxide, potassium hydroxide)
  • Brønsted-Lowry definition describes acids as proton donors and bases as proton acceptors in chemical reactions
  • Strong acids and bases completely dissociate in water (HCl, NaOH)
  • Weak acids and bases partially dissociate in water (acetic acid, ammonia)

Neutrality and Dissociation Constants

  • Neutrality occurs when [H+] equals [OH-] resulting in pH 7 at 25°C
  • Acid dissociation constant (Ka) quantifies strength of weak acids
  • Base dissociation constant (Kb) quantifies strength of weak bases
  • Henderson-Hasselbalch equation relates pH to concentrations of weak acids and conjugate bases: pH=pKa+log([A−]/[HA])pH = pKa + log([A-]/[HA])
  • pKa negative logarithm of Ka used to compare acid strengths (acetic acid pKa 4.76, formic acid pKa 3.75)

Buffers for Stable pH in Biology

Buffer Composition and Function

  • Buffers resist pH changes when small amounts of acids or bases are added
  • Consist of weak acid and conjugate base, or weak base and conjugate acid, in roughly equal concentrations
  • Buffering capacity depends on concentration of buffer components and relative proportions
  • Biological buffers maintain pH homeostasis in living organisms (bicarbonate buffer system, phosphate buffer system)
  • Henderson-Hasselbalch equation calculates pH of buffer solutions: pH=pKa+log([base]/[acid])pH = pKa + log([base]/[acid])

Buffer Limitations and Effectiveness

  • Buffer systems have limited capacity can be overwhelmed by large acid or base additions
  • Buffer range describes pH range where buffer is most effective typically ±1 pH unit of buffer's pKa
  • Optimal buffer composition determined for desired pH range using Henderson-Hasselbalch equation
  • Multiple buffer systems work together in biological systems to maintain pH across wider ranges (blood pH 7.35-7.45)

pH Significance in Biological Processes

Enzyme Activity and Protein Structure

  • Enzymes have optimal pH range for maximum activity (pepsin pH 2, trypsin pH 8)
  • pH changes alter ionization state of amino acid side chains affecting enzyme active sites and catalytic efficiency
  • Extreme pH changes lead to protein denaturation by disrupting hydrogen bonds and electrostatic interactions
  • Isoelectric point (pI) pH at which protein carries no net electrical charge influences solubility and behavior in solution (casein pI 4.6, albumin pI 4.7)

Cellular pH Regulation and Gradients

  • Intracellular pH regulation crucial for proper cellular function (energy production, signal transduction, membrane transport)
  • pH gradients across cellular membranes essential for various physiological processes (ATP synthesis in mitochondria, lysosomal function)
  • Cellular compartments have distinct pH values optimized for specific functions (lysosomes pH 4.5-5.0, mitochondria pH 7.8)
  • Disruption of cellular pH regulation can lead to various pathological conditions (acidosis, alkalosis)