Detailed Biochemistry Study Notes: Water, pH, Carbon, Functional Groups, and Macromolecules

Chemical and Physical Properties of Water

• Four Fundamental Characteristics of Water Supporting Life:

  • Cohesion and Adhesion: Water molecules adhere to each other via cohesion and stick to other non-water substances via adhesion.

  • Temperature Moderation: Water easily absorbs, stores, and transfers thermal energy, allowing it to cool or warm surroundings and moderate temperature fluctuations.

  • Lower Density of Solid Water ($H_2O_{(s)}$): Solid ice is less dense than liquid water, causing ice to float. This forms an insulating surface layer over bodies of water in freezing temperatures, preventing the liquid water underneath from freezing completely and preserving aquatic life.

  • Universal Solvent Capabilities: Water dissolves a wide variety of substances to form chemical solutions due to its polar nature.

• Molecular Structure and Polarity:

  • Chemical formula: $H_2O$. An oxygen atom is covalently bound to two hydrogen atoms.

  • Electronegativity: Oxygen is highly electronegative and acts as an electron hog, pulling shared electrons toward its nucleus.

  • Asymmetrical Charge Distribution: Because electrons spend more time orbiting oxygen, water forms a polar molecule with a pseudo-negative (partially negative) region near the oxygen atom and a pseudo-positive (partially positive) region near the hydrogen atoms.

• Solvent Action and Hydration Shells:

  • Positively charged particles are attracted to the pseudo-negative oxygen side of water.

  • Negatively charged particles are attracted to the pseudo-positive hydrogen side of water.

  • Hydration Shell Formation:

    • Cations (positively charged ions, such as sodium $Na^+$ in table salt) are surrounded by the partially negative oxygen atoms of water molecules.

    • Anions (negatively charged ions, such as chlorine $Cl^-$ in table salt) are surrounded by the partially positive hydrogen atoms of water molecules.

• Hydrophilic vs. Hydrophobic Classifications:

  • Hydrophilic ("Water-Loving"): Substances that dissolve readily in water. Includes charged ions and polar molecules.

  • Hydrophobic ("Water-Fearing"): Substances that do not dissolve in water or mix with it. Includes nonpolar molecules and neutral, uncharged atoms.

Acids, Bases, and the pH Scale

• Atomic Structure of Hydrogen:

  • Atomic number: $1$

  • Atomic mass: $1$

  • Composition: $1\text{ proton}$, $0\text{ neutrons}$, $1\text{ electron}$.

• Dissociation of Water and Reactivity:

  • Because oxygen is highly electronegative, a hydrogen atom in a water molecule can yield its single electron to oxygen and dissociate as a bare proton ($H^+$ cation).

  • This leaves behind a hydroxide ion ($OH^-$ anion) with a full negative charge.

  • Hydronium Ion Formation: Floating $H^+$ protons are extremely reactive. An $H^+$ ion can attach to another water molecule to form a hydronium ion ($H_3O^+$). By convention, both free $H^+$ protons and $H_3O^+$ ions are represented simply as $H^+$.

  • Hydroxide ions ($OH^-$) are equally reactive due to their full negative charge.

• Definitions of Acids and Bases:

  • Acid: Any chemical substance that increases the concentration of hydrogen ions ($H^+$) in a solution.

  • Base: Any chemical substance that increases the concentration of hydroxide ions ($OH^-$) or decreases hydrogen ions ($H^+$) in a solution.

• The pH Scale:

  • A logarithmic scale measuring the concentration of hydrogen ions ($H^+$) in a solution ("p" and "h" represent power of hydrogen).

  • Neutral ($pH = 7$): Occurs when the concentration of hydrogen ions equals the concentration of hydroxide ions ($[H^+] = [OH^-]$), as in pure water.

  • Acidic ($pH < 7$): Solutions containing a higher concentration of $H^+$ ions. Extreme acidic example: Battery acid.

  • Basic / Alkaline ($pH > 7$): Solutions containing a higher concentration of $OH^-$ ions. Extreme basic examples: Oven cleaner, bleach.

  • Both extremes of the pH scale (extreme acids and extreme bases) are highly reactive, caustic, and dangerous.

• Biological Fluid pH and Regulation:

  • Most biological fluids fall in a narrow pH range between $6$ and 8$.\n * **Gastric Acid Exception:** Stomach acid has an extremely low pH (highly acidic) necessary to break down and dissolve ingested food.\n * **Pathology of Acid Reflux:** When stomach acid escapes into the esophagus (heartburn/reflux), it burns and degrades esophageal tissue.\n * **Homeostatic Regulation:** Internal fluid pH is tightly regulated by the body regardless of food or drink consumption. Blood pH is strictly maintained at approximately 7.\n * **Buffers:** Substances that minimize changes in H^+$and$OH^-$concentrations by scavenging excess ions. Carbonic acid serves as a vital buffer in human blood to maintain a constant pH of$7$.

Carbon Chemistry and Hydrocarbons

• Atomic Properties of Carbon:

  • Atomic number: $6$

  • Atomic mass: $12$

  • Composition: $6\text{ protons}$, $6\text{ neutrons}$, $6\text{ electrons}$.

  • Valence Shell Configuration: Carbon has $4$ valence electrons in its outer shell (which can hold up to $8$ electrons).

  • Valence = $4$. Carbon's ability to form up to $4$ covalent bonds simultaneously makes it uniquely versatile as a molecular backbone.

• Organic Compounds:

  • Biological organisms consist primarily of water, followed by carbon-based compounds.

  • In chemistry and biochemistry, an organic compound is defined strictly as any chemical compound containing carbon.

• Hydrocarbons:

  • Definition: Molecules composed entirely of carbon and hydrogen.

  • Bonding Properties: Carbon and hydrogen share electrons evenly due to similar electronegativities, making hydrocarbon bonds nonpolar and hydrophobic.

  • Energy Content: Because electrons are shared equally in $C-H$ bonds, breaking these nonpolar bonds releases large amounts of potential energy.

  • Explosive Gases: Propane and butane are examples of highly energetic, explosive hydrocarbon gases.

  • Structural Plasticity: Hydrocarbons can form linear chains of varying lengths, branched networks, rings, planar configurations, and 3D geometric shapes (such as pyramids).

Functional Groups and Macromolecular Building Blocks

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