Biochemistry

Course Administrative Notes and Reaction Energetics

  • Schedule and Calendar Announcements

    • The cellular level of organization begins on Thursday and concludes on Tuesday.
    • An examination covering the material is scheduled for one week from this coming Thursday.

  • Course Structure and Cumulative Nature

    • Examinations are administered over individual units; however, the course content is inherently cumulative.
    • The biological hierarchy builds directly from the chemical level of organization to the cellular level, which subsequently forms tissues.
    • Concepts introduced in foundational lectures are continuously integrated into downstream topics.

  • Feedback and Communication Loop

    • Student concerns communicated to Peer Enhanced Learning Leaders (PELL leaders) are brought to the instructor prior to the start of class to clarify complex topics.

  • Reaction Energetics: Laboratory Chemistry vs. Human Physiology

    • In human physiology, chemical energy is stored directly within chemical bonds.
    • Anabolic Reactions:
    • These are synthesis processes that build chemical bonds.
    • They are endothermic reactions, meaning energy must be input into the system to form the bonds.
    • The resulting products reside at a higher energy level than the initial reactants.
    • Catabolic Reactions:
    • These are breakdown processes that cleave chemical bonds.
    • They are exothermic reactions, meaning stored energy is released upon bond cleavage.
    • The resulting products reside at a lower energy level than the initial reactants.

Classification of Biocompounds and Properties of Water

  • Categorization of Biocompounds

    • Biological compounds are divided into two primary categories: inorganic compounds and organic compounds.

  • Inorganic Compounds

    • Traditional chemistry defines inorganic compounds as those lacking carbon.
    • In biological contexts, inorganic compounds are defined as substances that are water itself or substances that ionize (dissociate into charged particles) when dissolved in water.
    • Major biological inorganic compounds include:
    1. Water
    2. Salts
    3. Acids
    4. Bases
    • Electrolytes:
    • Dissociated charged particles in solution are called ions.
    • In the human body, ions are termed electrolytes because their movement can conduct electrical energy.
    • Consuming electrolyte replenishment solutions (such as Gatorade) after heavy sweating restores lost salt ions to the body.

  • Physiological Importance and Properties of Water

    • Water constitutes 60%60\% to 80%80\% of total human body mass, making it the most abundant inorganic compound.
    • Guided by the principle that form dictates function, water exhibits distinct physical properties critical for life:
    • High Heat Capacity:
      • Heat capacity is defined as the resistance to a change in temperature.
      • Water resists rapid temperature fluctuations, absorbing large amounts of metabolic heat generated by cellular activities while maintaining a stable body temperature.
    • High Heat of Vaporization:
      • Transitioning water from a liquid to a gaseous state requires a significant input of heat energy.
      • When water vaporizes (e.g., during sweating), it carries excess heat away from the body, providing an effective cooling mechanism.
    • Universal Solvent and Transport Medium:
      • Biological molecules must be in solution to undergo chemical reactivity.
      • Water is a polar solvent; polar solutes and ionic compounds readily dissolve (dissociate) within it.
      • Humorous analogy: A white bear dissolved when jumping into water because it was a polar bear.
      • Water acts as the primary transport medium, moving dissolved water-soluble (polar) substances throughout the body.
      • Solution Terminology:
      • Solvent: The dissolving medium (e.g., water).
      • Solute: The substance being dissolved (e.g., sodium chloride, NaClNaCl).
      • Solution: The homogeneous mixture of solute dissolved in solvent.
    • Reactivity in Metabolism:
      • Dehydration Synthesis (Condensation): An anabolic reaction that joins molecules together by removing a molecule of water.
      • Hydrolysis: A catabolic reaction that cleaves chemical bonds by adding a water molecule, splitting water into a hydrogen ion (H+H^+) and a hydroxyl ion (OH−OH^-).
    • Cushioning and Protection:
      • Fluid collections buffer sensitive organs against physical trauma.
      • Examples include pericardial fluid surrounding the heart, cerebrospinal fluid protecting the brain and central nervous system, and synovial fluid cushioning joints to prevent bone-on-bone friction.

Salts, Acids, Bases, and pH Dynamics

  • Salts

    • Salts dissociate in water into cations (positively charged ions) and anions (negatively charged ions), excluding H+H^+ and OH−OH^- ions.
    • Dissociated salt ions function as electrolytes capable of conducting electrical currents.
    • Essential for nerve impulse conduction and triggering muscle contraction.
    • The kidneys are the primary organs responsible for regulating ionic and salt-water homeostasis.
    • Solubilized salts can precipitate out of solution and crystallize to form solid structural matrices, such as those found in bones and teeth.

  • Acids

    • Acids dissociate in solution to release cations and anions, specifically releasing hydrogen ions (H+H^+).
    • Defined as proton donors.
    • Because they yield ions in solution, acids conduct electrical current.

  • Bases

    • Bases dissociate in solution to decrease free hydrogen ion concentration.
    • Defined as proton acceptors (often releasing hydroxyl ions, OH−OH^-).
    • Like acids and salts, bases dissociate into charged particles and conduct electrical current.

  • pH Scale and Calculations

    • pH is a logarithmic expression of hydrogen ion concentration:     pH=−log⁡[H+]\text{pH} = -\log[H^+]
    • The scale ranges from 00 to 1414:
    • Acidic: pH values from 00 to 6.996.99 (higher concentration of H+H^+ ions).
    • Neutral: pH of exactly 7.07.0 (equal concentrations of H+H^+ and OH−OH^-).
    • Basic / Alkaline: pH values from 7.017.01 to 1414 (lower concentration of H+H^+ ions).
    • Note on values: A pH of 7.17.1 is slightly basic; a pH of 6.96.9 is slightly acidic.
    • Inverse relationship: As the hydrogen ion concentration increases, the pH numerical value decreases.
    • Physiological Examples:
    • Stomach acid operates at approximately pH 22.
    • Blood pH is strictly regulated between 7.37.3 and 7.47.4 (optimal target centered around 7.47.4).

  • Neutralization vs. Buffering

    • Neutralization:
    • The active alteration of pH by adding a base to an acidic solution (or an acid to a basic solution) to drive the pH toward neutral.
    • Buffering:
    • The resistance to changes in pH when acids or bases are added.
    • Buffers present in human blood prevent physiological pH shifts, maintaining homeostatic limits.

Carbohydrates: Structure, Types, and Functions

  • General Properties
    • Composed of sugars and starches.
    • Account for 1%1\% to 2%2\% of total cellular mass.
    • Function primarily as an immediate source of cellular energy used to synthesize adenosine triphosphate ($$ATP