Biological Chemistry I

🔬Biological Chemistry I Unit 2 – Water, pH, and Buffers

Water, pH, and buffers form the foundation of biological chemistry. These concepts explain how life processes function at the molecular level. Understanding water's unique properties, pH scales, and buffer systems is crucial for grasping how cells maintain homeostasis and carry out essential biochemical reactions. This unit covers water's polarity and hydrogen bonding, pH measurement, acids and bases, and buffer systems. It explores how these factors influence biological processes, from enzyme function to cellular compartmentalization. The knowledge gained here is essential for comprehending more complex biochemical interactions in living organisms.

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Key Concepts

  • Water's unique properties arise from its polar nature and hydrogen bonding capabilities
    • Polarity results from uneven distribution of electrons between hydrogen and oxygen atoms
    • Hydrogen bonding occurs between partially positive hydrogen and partially negative oxygen of neighboring water molecules
  • pH is a logarithmic scale that measures the concentration of hydrogen ions (H+) in a solution
    • Calculated as the negative log of the hydrogen ion concentration: pH=log[H+]pH = -log[H+]
    • pH values range from 0 to 14, with 7 being neutral, below 7 acidic, and above 7 basic
  • Acids are proton donors that increase the concentration of H+ ions in a solution
    • Strong acids (hydrochloric acid) dissociate completely in water
    • Weak acids (acetic acid) only partially dissociate in water
  • Bases are proton acceptors that decrease the concentration of H+ ions in a solution
    • Strong bases (sodium hydroxide) dissociate completely in water
    • Weak bases (ammonia) only partially dissociate in water
  • Buffer systems resist changes in pH when small amounts of acid or base are added
    • Consist of a weak acid and its conjugate base, or a weak base and its conjugate acid
    • Important in maintaining stable pH in biological systems (blood, cytoplasm)

Water's Unique Properties

  • High specific heat capacity enables water to absorb and release heat slowly
    • Helps regulate temperature in living organisms and Earth's climate
  • Strong cohesive and adhesive forces due to hydrogen bonding
    • Cohesion allows water to maintain column strength in xylem vessels of plants
    • Adhesion enables capillary action, which is crucial for water transport in plants and soil
  • High surface tension resulting from cohesive forces among water molecules
    • Allows some insects (water striders) to walk on water's surface
  • Universal solvent capabilities due to polarity and ability to form hydrogen bonds
    • Dissolves a wide range of polar and ionic compounds (salts, sugars, proteins)
    • Essential for transport of nutrients and waste products in living organisms
  • Density anomaly: water is most dense at 4°C and less dense as a solid (ice)
    • Ice floats on liquid water, insulating aquatic life in cold climates

pH Basics

  • pH is a measure of the acidity or basicity of a solution
    • Acidic solutions have a pH below 7 and a higher concentration of H+ ions
    • Basic solutions have a pH above 7 and a lower concentration of H+ ions
    • Neutral solutions have a pH of 7 and equal concentrations of H+ and OH- ions
  • The pH scale is logarithmic, meaning each unit change represents a tenfold difference in H+ concentration
    • A solution with pH 5 has 10 times more H+ ions than a solution with pH 6
    • A solution with pH 9 has 100 times fewer H+ ions than a solution with pH 7
  • The concentration of H+ and OH- ions in a solution are inversely related
    • In pure water at 25°C, [H+][OH]=1.0×1014[H+][OH-] = 1.0 \times 10^{-14} (the ion product constant of water, Kw)
    • As [H+] increases, [OH-] decreases proportionally to maintain Kw

Acids and Bases

  • Arrhenius definition: acids produce H+ ions in solution, while bases produce OH- ions
    • Limited to aqueous solutions and does not explain all acid-base behaviors
  • Brønsted-Lowry definition: acids are proton donors, while bases are proton acceptors
    • Accounts for acid-base reactions in both aqueous and non-aqueous solutions
    • Conjugate acid-base pairs differ by a single proton (H+)
  • Lewis definition: acids are electron pair acceptors, while bases are electron pair donors
    • Broadest definition, encompassing both Arrhenius and Brønsted-Lowry concepts
    • Explains the basicity of compounds without OH- ions (ammonia)
  • Acid and base strength depend on the extent of dissociation in solution
    • Strong acids and bases dissociate completely (hydrochloric acid, sodium hydroxide)
    • Weak acids and bases only partially dissociate (acetic acid, ammonia)
  • The acid dissociation constant (Ka) quantifies the strength of an acid
    • Higher Ka values indicate stronger acids and more complete dissociation

Buffer Systems

  • Buffers minimize pH changes when small amounts of acid or base are added to a solution
    • Consist of a weak acid and its conjugate base, or a weak base and its conjugate acid
    • The weak acid or base component neutralizes added base or acid, respectively
  • The Henderson-Hasselbalch equation relates pH, pKa, and the ratio of base to acid concentrations in a buffer system:

pH=pKa+log[base][acid]pH = pK_a + log\frac{[base]}{[acid]}

  • Buffer capacity is the amount of acid or base that can be added before the pH changes significantly
    • Determined by the concentrations of the buffer components and the pKa of the acid or base
    • Buffers are most effective when the pH is within ±1 unit of the pKa
  • Preparing a buffer with a specific pH involves selecting an acid-base pair with a pKa close to the desired pH
    • The ratio of base to acid concentrations is adjusted according to the Henderson-Hasselbalch equation
  • Common biological buffers include bicarbonate (HCO3-/CO2) and phosphate (H2PO4-/HPO4-2) systems
    • Bicarbonate buffer helps maintain blood pH around 7.4
    • Phosphate buffer helps maintain intracellular pH around 7.2

Biological Importance

  • Maintaining stable pH is crucial for proper functioning of biological systems
    • Enzymes have optimal pH ranges for activity; deviations can lead to loss of function
    • Protein structure and solubility are sensitive to pH changes
    • Membrane potential and ion transport are affected by pH gradients
  • Blood pH is tightly regulated between 7.35 and 7.45 by buffer systems, respiratory control, and renal control
    • Bicarbonate buffer is the primary blood buffer, with hemoglobin and plasma proteins also contributing
    • Respiratory control adjusts blood pH by regulating CO2 levels through breathing rate
    • Renal control adjusts blood pH by excreting excess H+ or HCO3- ions in urine
  • Cellular compartments have specific pH ranges optimized for their functions
    • Cytoplasm: pH 7.2, favorable for most enzymatic reactions
    • Lysosomes: pH 4.5-5.0, optimal for acid hydrolase enzymes involved in digestion
    • Mitochondrial matrix: pH 7.8, supports efficient ATP synthesis during oxidative phosphorylation
  • pH gradients across membranes are harnessed for energy production and transport processes
    • Proton motive force drives ATP synthesis in mitochondria and chloroplasts
    • pH gradients facilitate secondary active transport of nutrients (glucose, amino acids) into cells

Lab Techniques and Measurements

  • pH meters measure the electrical potential difference between a reference electrode and a glass electrode in a solution
    • The potential difference is proportional to the pH of the solution
    • Calibration with standard buffer solutions (pH 4, 7, 10) is necessary for accurate measurements
  • pH paper and indicators change color depending on the pH of the solution
    • Litmus paper turns red in acidic solutions and blue in basic solutions
    • Universal indicator displays a range of colors corresponding to pH values from 0 to 14
    • Specific indicators (phenolphthalein, methyl orange) have distinct color changes at certain pH ranges
  • Titration is used to determine the concentration of an acid or base in a solution
    • A known concentration of base or acid (titrant) is gradually added to the unknown solution (analyte)
    • The endpoint is reached when the pH of the analyte changes abruptly, often indicated by a color change
    • The concentration of the analyte is calculated based on the volume and concentration of the titrant added
  • Spectrophotometric methods can measure pH-dependent changes in absorbance
    • Some compounds (phenol red) exhibit different colors and absorbance spectra at different pH values
    • The ratio of absorbance at two wavelengths can be used to calculate the pH of a solution

Real-World Applications

  • Environmental monitoring: pH measurements assess the health of aquatic ecosystems and soil quality
    • Acidification of lakes and streams due to acid rain can harm aquatic life
    • Soil pH affects nutrient availability and plant growth; lime is used to raise pH in acidic soils
  • Food and beverage industry: pH control ensures product safety, quality, and shelf life
    • Low pH in fermented foods (yogurt, pickles) prevents the growth of spoilage bacteria
    • Adjusting pH during cheese making influences texture and flavor development
  • Pharmaceutical industry: pH considerations are crucial in drug formulation and delivery
    • Drug solubility and absorption are pH-dependent; oral medications often have pH-sensitive coatings
    • Buffer systems maintain the stability and efficacy of liquid medications
  • Wastewater treatment: pH adjustment is necessary for effective removal of contaminants
    • Alkaline conditions (pH 10-11) promote the precipitation of heavy metals
    • Neutral pH is maintained in biological treatment stages to support microbial activity
  • Medical diagnostics: pH abnormalities in body fluids can indicate underlying health conditions
    • Blood pH outside the normal range (7.35-7.45) can signify respiratory or metabolic disorders
    • Urine pH can provide insights into kidney function, urinary tract infections, and metabolic status


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AP® and SAT® are trademarks registered by the College Board, which is not affiliated with, and does not endorse this website.