Biological Chemistry, Acidity, and Carbon

Alkalinity and Acidity in the Human Body

  • Inside the Intestine

    • The environment within the intestine is alkaline.
    • This alkalinity is crucial for digesting acidic foods consumed.

  • Neutralization of Stomach Acids

    • Examples of substances used for neutralization:
    • Milk of Magnesia: A common antacid, neutralizes gastric acidity.
    • Pepto-Bismol: Helps soothe upset stomachs by neutralizing stomach acid.
    • Ammonia, Bleach, Oven Cleaner: Highly alkaline substances that react to neutralize acidic residues.

  • Reactivity of Acids and Bases

    • Acids and bases are equally reactive.
    • However, bases do not typically cause damage to materials as acids do.

Stomach Acidity in Animals

  • Stomach Acid Comparison

    • Various animals have different acidic levels in their stomachs, measured on a pH scale (7 being neutral).
    • Monkeys: Stomach acid is close to neutral, slightly acidic.
    • Howler Monkeys: pH around 4.7 (acidic).
    • Dogs: pH around 4.5 (acidic).
    • Cats: pH around 3.6 (more acidic).
    • Humans: pH around 1.5 (very acidic) - one of the strongest stomach acids.
    • Possums and Vultures: Even more acidic stomach acids due to their carrion diet (consuming decomposing flesh).

  • Implications for Evolution

    • Strong human stomach acids suggest an ancestral diet that included decomposed and contaminated food sources.
    • This selective dietary adaptation differentiates humans from other primates with milder acidic levels in their stomach.

Definitions of Acids and Bases

  • Acids

    • Defined as substances that release free protons (H⁺) into a solution, thus lowering the pH.

  • Bases

    • Substances that reduce the number of free protons in a solution either by:
    • Adding hydroxide ions (OH⁻).
    • Reacting with and neutralizing free protons.

  • Buffers

    • Substances in biological systems that resist changes in pH by absorbing or releasing free protons.
    • Example: Carbonic Acid (H₂CO₃), which can convert to bicarbonate ion (HCO₃⁻) as a buffering capacity in blood.

Blood pH and Health Implications

  • Importance of Maintaining Blood pH
    • Deviations from normal pH range can be detrimental to health, often caused by consuming acidic foods.
    • Diet adjustments may be necessary to maintain proper blood pH levels.

Physiological Effects of Acids and Bases

  • Buffers' Mechanisms
    • Carbonic acid and bicarbonate interconvert to stabilize blood pH upon proton or hydroxide ion addition.
    • Example reaction:
      H₂CO₃
      ightleftharpoons HCO₃⁻ + H⁺
    • The ability of buffers to regulate pH is critical for physiological stability.

important: Overwhelming a buffer's capacity results in a shift in pH.

Acidification of Oceans

  • Impact of Increased CO₂

    • Increased carbon dioxide from human activities dissolves in ocean water, forming carbonic acid, which consequently lowers ocean pH.
    • Coral reefs and marine life face challenges due to competition between the carbonate ions needed for shell formation and the increased availability of protons (leading to the dissolution of calcium carbonate).

  • Consequences

    • Coral Bleaching: Reduced availability of carbonate results in less calcium carbonate for coral skeleton formation.
    • Food Chains: Disruption of marine ecosystems leading to larger threats to biodiversity and food security.

Thermodynamics Laws

  • First Law of Thermodynamics

    • Energy cannot be created or destroyed, only transformed.
    • Implication: Organisms must obtain energy from external sources such as food.

  • Second Law of Thermodynamics

    • Energy transfers are never 100% efficient, generating waste heat and entropy.
    • In biological systems, energy is often lost during conversion processes (e.g., metabolism).

Energy, Heat, and Gradients

  • Energy Transfer

    • Energy moves from areas of high concentration to low concentration (heat flows from hot to cold).

  • Gradients

    • An uneven distribution of substances (heat, electrical charge, solutes) where particles tend to move down the gradient.
    • Important for biological processes like diffusion and osmosis.

Importance of Carbon

  • Carbon-Based Life

    • Carbon is fundamental in biology due to its ability to form four covalent bonds, allowing for complex molecular structures.
    • Carbon's versatility gives rise to various biological molecules like carbohydrates, proteins, lipids, and nucleic acids.

  • Monomer and Polymer Formation

    • Monomers (basic building blocks) can join to form polymers (long chains).

  • Chemical Structure and Functional Groups

    • Various functional groups (e.g., hydroxyl, carbonyl, carboxyl) influence the properties and reactivity of biological molecules.

Carbon Cycles in Ecosystems

  • Carbon Cycle
    • Carbon dioxide absorbed by plants during photosynthesis becomes organic matter.
    • Animals consume plants, obtaining carbon, and return carbon to the atmosphere as CO₂ through respiration.
    • Carbon storage and release occur in various life cycles affecting global carbon levels.

Formation and Breakdown of Macromolecules

  • Polymers & Macromolecules

    • Polymers consist of repeating units (monomers).
    • Macromolecules like proteins and nucleic acids are complex structures essential for biological function.
    • Formation typically occurs through dehydration (condensation) reactions, breaking down through hydrolysis reactions.

  • Condensation and Hydrolysis

    • Condensation Reaction: Two molecules combine, releasing water.
    • Example: Forming disaccharides from monosaccharides.
    • Hydrolysis Reaction: A molecule is broken down by adding water.
    • Reverse of condensation, releasing energy.

  • Naming Conventions:

    • Monomer = one part, Dimer = two parts, Oligomer = few parts, Polymer = many parts.