General Biology: Acids, Bases, Carbon Chemistry, and Organic Molecules

pH, Acids, and Bases

Understanding pH and Its Biological Importance

The pH scale is a measure of the concentration of hydrogen ions (H+) in a solution, which determines its acidity or basicity. This concept is fundamental in biology because many biochemical processes are pH-dependent.

• pH Definition: pH is the negative logarithm of the hydrogen ion concentration.

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

• Neutral pH: A pH of 7 is considered neutral, where [H+] = [OH-].

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

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

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

Example: pH 7 = 0.0000001 moles/liter of H+; pH 6 = 0.000001 moles/liter of H+. Thus, pH 6 is 10 times more acidic than pH 7.

Biological Relevance: Normal blood pH is tightly regulated between 7.2 and 7.4. Deviations can lead to coma (if pH < 6.95) or convulsions (if pH > 7.5).

pH	Acidity/Basicity	[H+]
0	Most acidic	1 M
7	Neutral	10-7 M
14	Most basic	10-14 M

Application: The color of petunia flowers is affected by vacuole pH: red (more acidic), blue (less acidic). This can influence pollinator attraction.

The Element of Carbon

Properties and Importance of Carbon in Biology

Carbon is the backbone of all organic molecules and makes up a significant portion of living organisms. Its unique bonding properties allow for a diversity of molecular structures.

• Valence: Carbon has 4 valence electrons and needs 4 more to complete its shell, allowing it to form up to 4 covalent bonds.

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

• Organic Molecules: Molecules containing carbon atoms bonded to hydrogen and often other elements.

Hydrocarbons

Structure and Properties of Hydrocarbons

Hydrocarbons are compounds composed solely of hydrogen and carbon. They are generally nonpolar and hydrophobic.

• Nonpolar Covalent Bonds: The electronegativity difference between carbon (2.5) and hydrogen (2.1) is small, resulting in nonpolar bonds.

• Hydrophobicity: Hydrocarbons do not mix well with water because water is polar and hydrocarbons are nonpolar.

• Example: When oil (a hydrocarbon) and water are mixed, oil floats on top because it is less dense and hydrophobic.

Key Terms: Hydrophobic ("water-fearing"), Hydrophilic ("water-loving").

Functional Groups

Common Functional Groups in Organic Molecules

Functional groups are specific groups of atoms within molecules that have characteristic properties and reactivity. They determine the chemical behavior of organic molecules.

• 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, can donate H+, becomes negatively charged in water.

• Amino Group (-NH2): Acts as a base, can accept H+, positively charged in water.

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

Application: Adding functional groups to hydrocarbons increases their reactivity and allows them to interact with water.

Hydrophobic and Hydrophilic Interactions

Water Interactions and Biological Examples

The interaction of molecules with water is crucial for biological structure and function. Hydrophobic molecules avoid water, while hydrophilic molecules interact readily with it.

• Hydrophobic: Nonpolar molecules (e.g., oils, fats) that do not dissolve in water.

• Hydrophilic: Polar or charged molecules (e.g., salts, sugars) that dissolve in water.

• Example: In the eye, the corneal epithelium is hydrophobic, while the underlying corneal layer is hydrophilic. Hydrophilic dyes will stick to damaged areas where the hydrophilic layer is exposed.

Drawing Organic Molecules

Conventions for Representing Organic Structures

Organic molecules are often represented using line-angle formulas, where each vertex represents a carbon atom unless otherwise labeled. Hydrogen atoms attached to carbons are usually omitted for simplicity.

• Line-Angle Formula: Each angle or endpoint is a carbon atom unless labeled otherwise.

• Example: The ring structure of glucose is often drawn with each corner representing a carbon atom.

Isomers

Types and Biological Importance of Isomers

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

• Enantiomers: Isomers that are mirror images of each other (e.g., left and right hands). Important in biology because only one enantiomer may be biologically active.

• Structural Isomers: Differ in the covalent arrangement of atoms (e.g., butane vs. isobutane).

• Cis-Trans (Geometric) Isomers: Differ in the arrangement of atoms around a double bond. Cis isomers have substituents on the same side; trans isomers have them on opposite sides.

Type of Isomer	Description	Example
Enantiomer	Mirror images, not superimposable	L- and D- forms of amino acids
Structural	Different covalent arrangements	Butane vs. isobutane
Cis-Trans	Different spatial arrangement around double bond	cis-2-butene vs. trans-2-butene

Biological Example: Retinal in the photoreceptors of the eye exists as cis and trans isomers, which are important for vision.

Metabolic Note: The liver processes glucose based on the body's needs (energy, fat storage, or glycogen storage), while fructose is metabolized differently and is more readily converted to fat.