Introduction to the Chemistry of Life

pH, Acids, and Bases

The acidity or alkalinity of a solution is determined by the concentration of hydrogen ions $[H^+]$. We measure this using the pH scale via the following logarithmic formula:

$$pH = -\log[H^+]$$

A neutral solution has a pH of 7. Acids are substances that increase the $[H^+]$ concentration in water, while bases are substances that combine with $H^+$ to reduce its concentration. Furthermore, water can undergo ionization, a process where covalent bonds break spontaneously to form a hydroxide ion ($OH^-$) and a hydrogen ion ($H^+$):

$$H_2O \rightleftharpoons OH^- + H^+$$

Study Tip: Remember that "hydrophilic" means "water-loving" (polar/ionic substances that dissolve in water), while "hydrophobic" means "water-fearing" (nonpolar substances that are sheltered from water).

Osmosis and Tonicity

Because water is a polar solvent, it moves across biological membranes to balance solute concentrations—a process known as osmosis. The movement of water is determined by the tonicity of the surrounding environment:

• Hypotonic Solution: The solution has a lower solute concentration (and more water) than the cell. Water moves into the cell, causing it to swell.
• Hypertonic Solution: The solution has a higher solute concentration than the cell. Water moves out of the cell, causing it to shrink.
• Isotonic Solution: The solute concentration is equal inside and outside the cell, resulting in no net movement of water.

This mechanism is vital for plants. For example, in a plant's stomata (small openings in leaves), guard cells become turgid (swollen) via osmosis to open the pore for gas exchange, or they become flaccid (shrunken) to close it.

Carbon Chemistry and Functional Groups

Carbon is the fundamental building block of organic chemistry because it has four valence electrons. This allows a single carbon atom to form up to four covalent bonds, creating complex skeletons through single, double, or triple bonds.

The specific behavior of a carbon-based molecule is dictated by its functional groups—specific clusters of atoms attached to the carbon skeleton:

• Hydroxyl ($-OH$): Found in alcohols and sugars; water-soluble.
• Carboxyl ($-COOH$): Acidic and water-soluble; found in amino acids.
• Amino ($-NH_2$): Basic and water-soluble; found in amino acids.
• Phosphate ($-PO_4^{2-}$): Acidic and water-soluble; found in DNA, RNA, and ATP.

Biological Macromolecules

Living things build large molecules, called polymers, by linking smaller subunits called monomers together. This process is called dehydration synthesis, where enzymes remove a hydroxyl group ($-OH$) from one molecule and a hydrogen ($-H$) from another to create a new covalent bond.

Carbohydrates

Carbohydrates are composed of sugar monomers called monosaccharides (e.g., glucose, $C_6H_{12}O_6$). These can link to form disaccharides (two sugars) or polysaccharides (long chains).

• Energy Storage: Plants use starch, while animals use glycogen.
• Structure: Plants use cellulose for cell walls, and arthropods use chitin for their shells.

Lipids

Lipids are nonpolar and do not dissolve in water. Key types include:

• Triglycerides: Used for energy storage, consisting of glycerol and three fatty acids. They can be saturated (straight chains, solid at room temperature) or unsaturated (kinked chains due to double bonds, liquid at room temperature).
• Phospholipids: Essential for cell membranes, featuring a hydrophilic (polar) head and hydrophobic (nonpolar) tails.
• Steroids: Such as cholesterol.

Nucleic Acids

Nucleic acids, such as DNA, are the blueprints of life. They are polymers made of monomers called nucleotides. Each nucleotide consists of three parts: a phosphate group, a sugar, and a nitrogenous base. ATP (Adenosine Triphosphate) is a specialized nucleotide used to store and transfer energy via its phosphate bonds.