General Biology: Acids, Bases, pH, Carbon Chemistry, and Isomerism

Acids, Bases, and the pH Scale

Introduction to pH

The pH scale is a logarithmic scale used to measure the concentration of hydrogen ions (H+) in a solution, indicating its acidity or basicity. The scale ranges from 0 (most acidic) to 14 (most basic), with 7 being neutral.

• pH: A measure of H+ ion concentration in a solution.

• Logarithmic scale: Each unit change represents a tenfold change in H+ concentration.

• Formula: $\text{pH} = -\log_{10}[\text{H}^+]$

• Neutral pH: pH 7, where [H+] = [OH-]

Acid: A substance that can donate H+ ions (pH < 7). Base: A substance that can accept H+ ions (pH > 7).

Examples and Applications

• pH 7 = 0.0000001 moles/liter of H+

• pH 6 = 0.000001 moles/liter of H+

• pH 7 is 10x less acidic than pH 6; pH 13 is 10,000,000x more basic than pH 6.

• Normal blood pH: 7.2–7.4. Deviations can cause coma (<6.95) or convulsions (>7.5).

pH Value	Acidity/Basicity	[H+]
0–6	Acidic	High
7	Neutral	Equal [H+] and [OH-]
8–14	Basic	Low

Example: In petunias, red color indicates more acidic vacuole contents, while blue color indicates less acidic vacuole contents. This affects pollinator attraction.

The Element of Carbon

Properties and Importance

Carbon is a fundamental element in biology, making up a significant portion of the dry weight of living organisms. Its ability to form four covalent bonds allows for a diversity of stable organic molecules.

• Bonding versatility: Carbon can form single, double, or triple bonds, and can create chains, rings, and branched structures.

• Hydrocarbons: Compounds composed only of hydrogen and carbon; generally nonpolar and hydrophobic.

Hydrocarbons

• Definition: Molecules consisting entirely of carbon and hydrogen.

• Properties: Nonpolar, hydrophobic, and do not dissolve in water.

• Example: Vegetable oil (hydrocarbon) does not mix with water due to nonpolarity.

Polarity and Water Interaction

• Polar molecules: Have regions of partial positive and negative charge; interact well with water.

• Nonpolar molecules: Lack charged regions; do not interact with water (hydrophobic).

Type	Interaction with Water
Polar	Hydrophilic (water-loving)
Nonpolar	Hydrophobic (water-fearing)

Functional Groups

Introduction

Functional groups are specific groups of atoms within molecules that confer characteristic chemical properties and reactivity. Adding functional groups to hydrocarbons increases their solubility and reactivity, especially with water.

• Hydroxyl group (-OH): Polar, forms hydrogen bonds, increases solubility in water.

• Carbonyl group (C=O): Polar; found in aldehydes (end of molecule) and ketones (middle of molecule).

• Carboxyl group (-COOH): Acts as an acid, donates H+, becomes negatively charged.

• Amino group (-NH2): Acts as a base, accepts H+, positively charged at physiological pH.

• Phosphate group (-PO42-): Negatively charged, important in energy transfer (e.g., ATP).

Example: Adding functional groups to hydrocarbons allows them to interact with water, making them biologically active.

Hydrophilic and Hydrophobic Interactions

Definitions and Examples

• Hydrophilic: "Water-loving"; substances that dissolve or interact well with water (e.g., polar molecules, ions).

• Hydrophobic: "Water-fearing"; substances that do not dissolve in water (e.g., nonpolar molecules like oils).

Example: In a demonstration with red and blue dyes, the hydrophobic dye ended up in the oil layer, while the hydrophilic dye dissolved in water.

Drawing Organic Molecules

Structural Representation

Organic molecules are often represented as line structures, where each vertex or unlabeled angle represents a carbon atom. Hydrogen atoms attached to carbons are often omitted for simplicity.

• Every angle in a ring not labeled with an element is a carbon atom.

• Each carbon forms four bonds; missing bonds are assumed to be with hydrogen.

Example: The ring structure of glucose, where each corner is a carbon atom unless otherwise labeled.

Isomers

Introduction

Isomers are compounds with the same molecular formula but different arrangements of atoms, resulting in different properties.

• Isomer: Same formula, different structure or spatial arrangement.

• Types of isomers:

  • Enantiomers: Mirror-image isomers; important in biology because organisms may only use one form.

  • Structural isomers: Differ in the covalent arrangement of atoms.

  • Cis-trans (geometric) isomers: Differ in arrangement around a double bond.

Type	Description	Example
Enantiomer	Mirror images, not superimposable	Hands, some amino acids
Structural	Different bonding patterns	Butane vs. isobutane
Cis-trans	Different positions around double bond	cis-2-butene vs. trans-2-butene

Examples and Biological Relevance

• Enantiomers: Only one enantiomer of a drug may be biologically active.

• Structural isomers: Butane (straight chain) and isobutane (branched) have different properties.

• Cis-trans isomers: Retinal in the eye changes from cis to trans form when absorbing light.

Example: The liver uses glucose for energy, storage, or conversion to fat, depending on the body's needs. Fructose is metabolized differently, often bypassing certain regulatory steps.

Additional info: The notes have been expanded with standard definitions, examples, and context for clarity and completeness.