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Biochemistry Study Notes (Lecture Transcript) 4

pH scale and acidity

  • pH scale ranges from 0 to 14; 7 is neutral. Values below 7 indicate increasing acidity (higher hydrogen ion, \[H^+]) concentration; values above 7 indicate increasing basicity (alkalinity) with higher hydroxide ion, \[OH^-], or lower \[H^+].
  • The transcript notes: from seven (neutral) down to zero increases acidity (more \[H^+]); on the high end (7.01 to 14) bases, where increasing numbers correspond to more \[OH^-] (less \[H^+]).

Units of measurement

  • Weight per volume (w/v): weight of solute per volume of solution.
    • Example: 8.5 g of sodium chloride in 1 L of solution.
  • Body-relevant units: milligrams per deciliter (mg/dL).
    • Example: cholesterol about \approx 200 \,\text{mg/dL}.
  • Percent (%): weight of solute per volume, interpreted as a percentage (solite per 100 units).
    • Example: 5% dextrose means 5 g sugar per 100 mL of solution (5 g per 100 mL).
  • Molarity (M): moles of solute per liter of solution.
    • Definition: M = \frac{n}{V} where n is moles and V is volume in liters.
    • A mole is defined as the amount of substance with a mass equal to its molecular (molar) weight; n can be found from mass: n = \frac{m}{Mr} where Mr is molar mass (g/mol).
  • Millimolar (mM): 1\,\text{mM} = 10^{-3}\,\text{M}; useful because body fluids are often in millimolar ranges.
  • Milliequivalents per liter (mEq/L):\text{mEq/L} = \text{mmol/L} \times z where z is the charge (valence) of the ion. Electrolyte measurements in IV fluids and physiology commonly use mEq/L.
  • Practical note: these units—mg/dL, %, M, mM, and mEq/L—appear on charts and are important when moving into cellular solute concentrations and transport.

Energy concepts

  • Energy is the ability to do work; to do work you must move something (e.g., muscles moving).
  • ATP is the cellular energy currency used for muscle contraction and many active processes.
  • Two main categories of energy:
    • Kinetic energy: energy of motion (e.g., muscles moving, eardrum vibration, heat).
    • Potential energy: stored energy that can do work when released (e.g., water behind a dam; chemical bonds).
  • Chemical energy: a form of potential energy stored in chemical bonds between atoms (ionic or covalent bonds).
  • Free energy: the amount of potential energy available to do work in a system.
  • Other energy forms: electromagnetic energy (photons/light) and electrical energy (can have both kinetic and potential components).
  • Quick takeaway: energy types will be revisited in the context of ATP and metabolism later in the course.

Chemical reactions: basics and terminology

  • A chemical reaction involves breaking chemical bonds (covalent or ionic) and forming new ones; reactions are described by reactants on the left and products on the right.
    • General form: \text{Reactants} \;\rightarrow\; \text{Products}
  • Major reaction types:
    • Decomposition: a large molecule breaks into smaller pieces.
    • Example: starch (polysaccharide) decomposes to glucose monomers: \text{Starch} \rightarrow \text{Glucose (monomers)}
    • Synthesis (anabolic): small molecules join to form a larger molecule.
    • Example: amino acids join to form a protein.
    • Exchange: atoms or groups are exchanged between reactants, producing new products.
    • Example pattern: \text{A} + \text{B} + \text{C} + \text{D} \rightarrow \text{A} + \text{D} + \text{B} + \text{C} or more specifically \text{AB} + \text{CD} \rightarrow \text{AD} + \text{CB}.
  • Reversible reactions: many reactions can proceed in both directions; represented with a double-headed arrow ( ⇌ ). Direction depends on circumstances (concentrations, temperature, etc.).
  • Buffer systems: buffers resist pH changes; example given:
    • CO₂ + H₂O ⇌ H₂CO₃ ⇌ HCO₃⁻ + H⁺.
    • If the system becomes too acidic (high H⁺), shift left to remove excess H⁺; if too basic, shift right to generate H⁺/H₂CO₃.
    • Buffers are important in respiratory, urinary, and digestive systems to maintain homeostasis.
  • Law of mass action and equilibrium:
    • The direction and extent of a reversible reaction depend on the relative concentrations of reactants and products.
    • Equilibrium is reached when forward and reverse rates are equal and concentrations become stable, though systems can be perturbed and shift away from equilibrium.
  • Factors influencing reaction rates:
    • Increasing reactant concentration increases collision likelihood.
    • Increasing temperature generally speeds up reactions.
    • Catalysts (e.g., enzymes) lower the activation energy and speed up reactions by bringing reactants into proper orientation.
    • Enzymes are biological catalysts and are proteins.
  • Catalysts and enzymes:
    • Enzymes bind reactants, stabilize transition states, and lower activation energy, allowing reactions to proceed more rapidly under physiological conditions.

Metabolism: catabolic vs anabolic; energy considerations

  • Metabolism comprises all chemical reactions in the body.
  • Catabolic reactions (decomposition): release energy; break large molecules into smaller ones (e.g., starch to glucose).
  • Anabolic reactions (synthesis): require input of energy; build larger molecules from smaller ones (e.g., amino acids to proteins).
  • Endergonic vs exergonic (as mentioned):
    • Catabolic reactions are generally exergonic (energy-releasing).
    • Anabolic reactions are often endergonic (energy-requiring).
  • The continuous balance of breaking down and building up supports growth, repair, and function of tissues and organ systems, including digestive, muscular, and nervous system activities.

Oxidation-reduction (redox) reactions

  • Oxidation: loss of electrons; the oxidized species is the one that loses electrons.
  • Reduction: gain of electrons; the reduced species is the one that gains electrons.
  • Oxidizing agent: the species that accepts electrons (causes oxidation of another).
  • Reducing agent: the species that donates electrons (causes reduction of another).
  • Redox reactions always occur in pairs and are often coupled in metabolic pathways.

Organic chemistry and carbon fundamentals

  • Organic chemistry studies carbon-containing compounds; carbon is central to biology.
  • Carbon basics:
    • Carbon has four valence electrons, enabling it to form four bonds.
    • It readily forms carbon backbones: long chains that can be branched or arranged in rings.
    • It bonds readily with hydrogen, oxygen, sulfur, and other elements.
  • Functional groups (clusters of atoms attached to a carbon) are key to chemical behavior.
    • hydroxyl group: –OH
    • methyl group: –CH₃
    • carboxyl group: –COOH
    • amino group: –NH₂
    • phosphate group: –PO₄H₂
  • Context for these groups in biology:
    • Hydroxyl: common in sugars and alcohols.
    • Methyl: found in lipids (fats, oils, steroids) and in some amino acids.
    • Carboxyl: present in amino acids and sugars; contributes to acidic properties.
    • Amino: present in amino acids, the building blocks of proteins.
    • Phosphate: found in nucleic acids and ATP; important for energy transfer and storage.

Macromolecules, polymers, and monomers

  • Macromolecule: large organic molecule, often polymers; typically have high molecular weights.
  • Polymer: large molecule made of repeating subunits (monomers).
    • Monomers can be identical or different.
  • Major biological polymers and their monomers:
    • Carbohydrates: monomer = glucose; polymer example = starch (polysaccharide).
    • Proteins: monomer = amino acids; polymer = proteins.
    • Nucleic acids: monomer = nucleotides; polymer = DNA or RNA.
    • Lipids: not always polymers; include fats, oils, phospholipids, steroids; organized differently but essential as energy stores and membranes.
  • Polymerization (dehydration synthesis): joining monomers to form a polymer with loss of water.
    • General form: \text{Monomer}1 + \text{Monomer}2 \rightarrow \text{Polymer} + \mathrm{H_2O}
    • Mechanism: a hydroxyl from one monomer is removed along with a hydrogen from another, producing water (HOH).
  • Hydrolysis (opposite of dehydration synthesis): breaking polymers into monomers with the addition of water.
    • General form: \text{Polymer} + \mathrm{H2O} \rightarrow \text{Monomer}1 + \text{Monomer}_2
  • Moiety: a component or part of a macromolecule; a useful term when discussing parts of a larger molecule.
  • Visual examples and directions given in the lecture:
    • Starch is a carbohydrate polymer broken down into glucose monomers.
    • Amino acids (monomers) join to form proteins (polymers).
    • DNA is a polymer of four different nucleotide monomers.
  • Real-world context and links:
    • Dehydration synthesis is the process by which cells build complex biomolecules (e.g., proteins, polysaccharides) from simpler units.
    • Hydrolysis is used in digestion to break down carbohydrates, proteins, and nucleic acids into absorbable monomers.
    • The balance of synthesis and decomposition is essential for growth, tissue repair, and energy production.

Summary of interconnections and real-world relevance

  • The different units (mg/dL, %, M, mM, mEq/L) connect laboratory measurements with physiological processes, including nervous system function, muscle contraction, and IV fluid management.
  • Buffers and reversible reactions are essential for maintaining homeostasis across respiratory, urinary, and digestive systems; they help stabilize pH during metabolic and environmental fluctuations.
  • Understanding energy types and metabolism (catabolic vs anabolic pathways) explains how dietary nutrients are converted into usable energy and building blocks for tissues.
  • Organic molecules, carbon chemistry, and functional groups underpin how carbohydrates, lipids, proteins, and nucleic acids perform their structural and functional roles in cells and tissues.
  • Enzymes as catalysts illustrate how biological systems increase reaction rates without requiring prohibitive amounts of energy, enabling life-sustaining processes to occur at body temperature.
  • The concepts of equilibrium, mass action, and reaction rates link chemistry principles to physiological outcomes, including how the body adapts to maintain homeostasis under varying conditions.

Note: The lecture references a plan to cover ATP and further details on carbohydrates, lipids, proteins, and nucleic acids in upcoming sections. The four major organic molecule categories (carbohydrates, lipids, proteins, nucleic acids) form the framework for the remainder of the course content.