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, emitting radiation.

Electron Shells

• Electrons are arranged in shells around the nucleus.

• The arrangement determines chemical reactivity.

• First shell holds 2 electrons; second shell holds up to 8, and so on.

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 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 solute and solvent.

• 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 scale measures acidity/alkalinity: $pH = -\log[H^+]$

Chapter 3: Biological Molecules

Carbon Skeletons and Isomers

Carbon atoms form the backbone of organic molecules, allowing for a diversity of structures.

• Carbon skeletons can be straight, branched, or ring-shaped.

• Isomers are compounds with the same molecular formula but different structures (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 long chains of monomers.

• Polymers form via condensation (dehydration) reactions and break down via 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., starch, glycogen, cellulose, chitin).

Lipids

• Hydrophobic molecules including fats, oils, and steroids.

• Triglycerides: composed of glycerol and three fatty acids.

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

• Phospholipids: major component of cell membranes.

• Steroids: four fused carbon rings (e.g., cholesterol).

Proteins

• Polymers of amino acids joined by peptide bonds.

• Amino acid structure: central carbon, amino group, carboxyl group, R group.

• Protein structure levels:

  • Primary: amino acid sequence

  • Secondary: alpha helices and beta sheets (hydrogen bonding)

  • Tertiary: 3D folding (interactions among R groups)

  • Quaternary: multiple polypeptide chains

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

Nucleic Acids

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

• DNA (deoxyribonucleic acid) and RNA (ribonucleic acid) store and transmit genetic information.

• RNA vs. DNA: RNA is usually single-stranded, contains ribose sugar, and uracil instead of thymine.

Chapter 5: Cell Membranes and Transport

Plasma Membrane Structure

The plasma membrane is a selectively permeable barrier that surrounds cells, composed mainly of lipids and proteins.

• Phospholipid bilayer with embedded proteins, cholesterol, and carbohydrates.

• Membrane proteins serve as channels, receptors, and enzymes.

• Membrane carbohydrates are involved in cell recognition.

Fluid Mosaic Model

• Describes the dynamic and flexible nature of the membrane.

• Proteins and lipids can move laterally within the layer.

Membrane Fluidity

• Maintained by cholesterol and the types of fatty acids in phospholipids.

• Fluidity is essential for membrane function and cell signaling.

Cell Junctions

• Specialized structures that connect adjacent cells (e.g., tight junctions, desmosomes, gap junctions).

Transport Across Membranes

• Passive transport: movement of substances down their concentration gradient without energy input.

  • Simple diffusion: direct movement through the membrane.

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

  • Facilitated diffusion: movement via transport proteins.

• Active transport: movement against the concentration gradient, requiring 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 via carrier protein
Active Transport	Yes (ATP)	Low to High	Na+/K+ pump

Example: The sodium-potassium pump is an example of active transport, moving Na+ out of and K+ into the cell against their concentration gradients using ATP.