General Biology: Core Concepts and Molecular Foundations

Chapter 2: Chemical Foundations of Life

Atomic Structure

The structure of atoms forms the basis of all matter. Understanding atomic structure is essential for studying chemical reactions and biological molecules.

• Atoms are composed of protons, neutrons, and electrons.

• Protons (positive charge) and neutrons (neutral) are found in the nucleus; electrons (negative charge) orbit the nucleus.

• Atomic number is the number of protons; mass number is protons plus neutrons.

Elements and Isotopes

• Elements are pure substances consisting of only one type of atom.

• Isotopes are atoms of the same element with different numbers of neutrons.

• Some isotopes are radioactive and decay over time, releasing energy.

Electron Shells

• Electrons are arranged in shells around the nucleus.

• The valence shell is the outermost shell and determines chemical reactivity.

Covalent and Ionic Bonds

• Covalent bonds involve the sharing of electron pairs between atoms.

• Ionic bonds form when electrons are transferred from one atom to another, creating charged ions.

• Hydrogen bonds are weak attractions between a hydrogen atom and an electronegative atom (e.g., oxygen or nitrogen).

Solutions, Properties of Water, and Acids/Bases

• Solutions are homogeneous mixtures of solutes dissolved in solvents.

• Water is a polar molecule, leading to unique properties such as cohesion, adhesion, high specific heat, and solvent abilities.

• Acids release H+ ions in solution; bases accept H+ or release OH- ions.

• pH is a measure of hydrogen ion concentration: $pH = -\log[H^+]$

Chapter 3: Biological Molecules

Carbon Skeletons and Isomers

Carbon's versatility allows for a variety of molecular structures essential for life.

• Carbon skeletons form the backbone of organic molecules and can be straight, branched, or ring-shaped.

• Isomers are compounds with the same molecular formula but different structures (e.g., structural, geometric, and enantiomers).

Functional Groups

• Groups of atoms that confer specific chemical properties to molecules (e.g., hydroxyl, carboxyl, amino, phosphate).

Monomers and Polymers

• Monomers are small building blocks; polymers are large molecules made from monomers.

• Polymers form via condensation (dehydration) reactions and are broken down by hydrolysis.

Carbohydrates

• Composed of carbon, hydrogen, and oxygen (CH2O).

• Monosaccharides: simple sugars (e.g., glucose, fructose).

• Disaccharides: two monosaccharides joined by a glycosidic linkage (e.g., sucrose).

• Polysaccharides: long chains (e.g., cellulose, starch, glycogen, chitin).

Lipids

• Hydrophobic molecules including fats, oils, and steroids.

• Saturated fats have no double bonds; unsaturated fats have one or more double bonds.

• Triglycerides: three fatty acids linked to glycerol.

• Phospholipids: major component of cell membranes.

• Other lipids: carotenoids, steroids, vitamins, waxes.

Proteins

• Polymers of amino acids joined by peptide bonds.

• Functional classes: enzymes, structural, transport, etc.

• Structure:

  • Primary: amino acid sequence

  • Secondary: alpha helices and beta sheets

  • Tertiary: 3D folding

  • Quaternary: multiple polypeptides

• Denaturation: loss of structure and function due to environmental changes.

Nucleic Acids

• Polymers of nucleotides (DNA and RNA).

• Nucleotide structure: phosphate group, sugar (deoxyribose or ribose), nitrogenous base.

• DNA: double helix, stores genetic information.

• RNA: single-stranded, involved in protein synthesis.

• RNA vs. DNA: DNA contains deoxyribose and thymine; RNA contains ribose and uracil.

Chapter 5: Cell Membranes and Transport

Plasma Membrane Structure

The plasma membrane is a selectively permeable barrier that surrounds cells.

• Composed of a phospholipid bilayer with embedded proteins, cholesterol, and carbohydrates.

• Membrane lipids & cholesterol: provide fluidity and stability.

• Membrane proteins: transport, signaling, structural support.

• Membrane carbohydrates: cell recognition and signaling.

Fluid Mosaic Model

• Describes the membrane as a mosaic of components that move fluidly.

Membrane Fluidity

• Determined by lipid composition and temperature.

• Cholesterol acts as a buffer, maintaining fluidity across temperatures.

Cell Junctions

• Structures that connect cells together (e.g., tight junctions, desmosomes, gap junctions).

Transport Across Membranes

• Passive transport: movement down a concentration gradient, no energy required.

  • Simple diffusion: movement of small, nonpolar molecules.

  • Osmosis: diffusion of water across a selectively permeable membrane.

  • Facilitated diffusion: transport via membrane proteins.

• Active transport: movement against a concentration gradient, requires energy (usually ATP).

Table: Types of Membrane Transport

Type	Energy Required?	Direction	Example
Simple Diffusion	No	High to Low	O2, CO2
Osmosis	No	High to Low (water)	Water movement
Facilitated Diffusion	No	High to Low	Glucose transport
Active Transport	Yes (ATP)	Low to High	Na+/K+ pump

Example: The sodium-potassium pump uses ATP to move Na+ out of and K+ into the cell, maintaining electrochemical gradients.