Chapter 2: Chemical Components of Cells

Atomic Structure and Subatomic Particles

Atoms are the basic units of matter, composed of three main subatomic particles: protons, neutrons, and electrons. Understanding their properties is essential for grasping the chemical basis of cellular processes.

• Protons: Positively charged particles located in the nucleus; determine the atomic number and identity of an element.

• Neutrons: Neutral particles found in the nucleus; contribute to atomic mass and isotopic variation.

• Electrons: Negatively charged particles orbiting the nucleus in electron shells; involved in chemical bonding and reactions.

Atomic Number: The number of protons in an atom, defining the element. For example, carbon has an atomic number of 6.

Isotopes: Atoms of the same element with different numbers of neutrons. Isotopes can be stable or radioactive and are used in biological tracing.

Ions: Atoms or molecules that have gained or lost electrons, resulting in a net charge.

• Cation: Positively charged ion (loss of electrons).

• Anion: Negatively charged ion (gain of electrons).

Chemical Bonding

Chemical bonds hold atoms together in molecules and influence the structure and function of biological molecules.

• Ionic Bonds: Formed by the transfer of electrons from one atom to another, resulting in oppositely charged ions that attract each other.

• Covalent Bonds: Formed when two atoms share one or more pairs of electrons. Covalent bonds can be single, double, or triple.

• Hydrogen Bonds: Weak attractions between a hydrogen atom covalently bonded to an electronegative atom (like oxygen or nitrogen) and another electronegative atom.

Polar Molecule: A molecule with an uneven distribution of charge due to differences in electronegativity (e.g., water).

Nonpolar Molecule: A molecule with an even distribution of charge; atoms share electrons equally.

Electronegativity: The tendency of an atom to attract electrons in a covalent bond. Oxygen is highly electronegative, influencing water's properties.

Properties of Water

Water's unique properties are critical for life and cellular function.

• High Heat Capacity & Heat of Evaporation: Water absorbs and retains heat, stabilizing temperatures in organisms and environments.

• Cohesiveness & Adhesiveness: Water molecules stick to each other (cohesion) and to other substances (adhesion), facilitating transport in plants and cells.

• Expansion Upon Freezing: Water becomes less dense as it freezes, allowing ice to float and insulate aquatic environments.

• Solvent Ability: Water dissolves many substances, making it the universal solvent for biological reactions.

Acids, Bases, and pH

Acids and bases influence cellular processes by altering hydrogen ion concentration.

• Acid: Substance that increases the concentration of H+ ions in solution.

• Base: Substance that decreases the concentration of H+ ions (or increases OH-).

pH Scale: Measures the concentration of hydrogen ions; ranges from 0 (acidic) to 14 (basic), with 7 as neutral.

Buffers: Substances that minimize changes in pH by absorbing or releasing H+ ions, maintaining homeostasis in cells.

Chapter 3: Organic Molecules and Macromolecules

Organic Chemistry and Functional Groups

Organic chemistry studies carbon-containing compounds, which form the backbone of biological molecules. Functional groups are specific groups of atoms within molecules that confer characteristic chemical properties and reactivity.

• Functional Groups: Examples include hydroxyl (-OH), carboxyl (-COOH), amino (-NH2), phosphate (-PO4), and methyl (-CH3).

• Role: Functional groups determine the behavior and interactions of organic molecules in cells.

Isomers and Molecular Shape

Isomers are molecules with the same chemical formula but different structures. The shape of a molecule affects its function, as structure determines how molecules interact with other cellular components.

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

• Cis-trans Isomers: Differ in spatial arrangement around a double bond.

• Enantiomers: Mirror-image isomers, important in pharmaceuticals and biochemistry.

Monomers, Polymers, and Synthesis

Macromolecules are large molecules formed by joining smaller units called monomers. The process of building and breaking down polymers is central to cell biology.

• Monomer: A single subunit (e.g., glucose, amino acid, nucleotide).

• Polymer: A chain of monomers linked by covalent bonds (e.g., starch, protein, DNA).

• Dehydration Synthesis: Reaction that joins monomers by removing a water molecule.

• Hydrolysis: Reaction that breaks polymers into monomers by adding water.

Macromolecules: Structure and Function

Cells contain four major classes of macromolecules, each with distinct structures and functions.

Carbohydrates

• Purpose: Energy storage and structural support.

• Structure: Composed of monosaccharides (simple sugars) linked to form polysaccharides.

• Examples: Glycogen (animal storage), cellulose (plant structure), starch (plant storage).

• α-glucose vs. β-glucose: Differ in the orientation of the hydroxyl group on carbon 1; affects polysaccharide structure and function.

Lipids

• Purpose: Long-term energy storage, membrane structure, signaling.

• Structure: Mostly hydrophobic molecules, including fats, phospholipids, and steroids.

• Unsaturated vs. Saturated Fats: Unsaturated fats have one or more double bonds (liquid at room temperature); saturated fats have no double bonds (solid at room temperature).

• Steroids: Lipids with a four-ring structure (e.g., cholesterol).

• Phospholipids: Major component of cell membranes; contain hydrophilic head and hydrophobic tails.

Proteins

• Purpose: Catalysis (enzymes), structure, transport, signaling, defense.

• Structure: Polymers of amino acids; structure organized into four levels:

  • Primary: Sequence of amino acids.

  • Secondary: Local folding (α-helix, β-sheet).

  • Tertiary: Overall 3D shape of a polypeptide.

  • Quaternary: Association of multiple polypeptide chains.

Nucleic Acids

• Purpose: Storage and transmission of genetic information.

• Structure: Polymers of nucleotides (sugar, phosphate, nitrogenous base).

• DNA vs. RNA: DNA contains deoxyribose sugar and is double-stranded; RNA contains ribose sugar and is single-stranded.

Summary Table: Major Macromolecules

Example: The difference between α-glucose and β-glucose leads to the formation of starch (digestible by humans) and cellulose (indigestible by humans), respectively.

Additional info: Functional groups and isomerism are foundational for understanding enzyme specificity and metabolic diversity in cells.