Essential Cell Biology: Foundation and Principles

Cell Theory: All living organisms are constructed from cells, which are small, membrane-enclosed units filled with an aqueous solution of chemicals. New cells are formed only by the growth and division of preexisting ones.
Central Dogma: In all living cells, genetic information flows from DNA to RNA (transcription) and from RNA to protein (translation). This shared chemistry suggests evolution from a common ancestral cell (3.5-3.8 billion years ago).
Evolution: The process of random mutation and natural selection leads to the diversity of life while maintaining fundamental biochemical similarities.

Light Microscopy: Uses visible light to magnify specimens up to 1000 times, with a resolution limit of roughly 0.2 \mu m.
Electron Microscopy: Uses beams of electrons to reveal fine details (organelles) at a resolution down to a few nanometers (nm).
- TEM: Transmits electrons through thin sections of tissue.
- SEM: Scatters electrons off the surface to see 3D detail.
Major Components: Cells are bounded by a plasma membrane. Eukaryotes contain a nucleus (storing DNA) and various membrane-enclosed organelles in the cytoplasm.

Three Domains: Life is categorized into Bacteria, Archaea, and Eukaryotes.
Prokaryotes: Lack a nucleus; include Bacteria and Archaea. They are diverse in chemistry and habitat.
Eukaryotes: Possess a nucleus and complex internal membranes.
- Mitochondria: Generate ATP through cell respiration; likely evolved from engulfed aerobic bacteria.
- Chloroplasts: Found in plants/algae; perform photosynthesis; likely evolved from engulfed photosynthetic bacteria.

Elements: 96\% of a cell's mass is composed of carbon (C), hydrogen (H), nitrogen (N), and oxygen (O).
Bonds:
- Covalent: Formed by sharing electrons; creates stable molecules.
- Ionic: Formed by electron transfer between atoms.
- Hydrogen Bonds: Weak noncovalent attractions between positive H and negative atoms like O or N.
Small Molecules: Cells contain four major families:
- Sugars: Energy sources and building blocks for polysaccharides.
- Fatty Acids: Components of lipids and cell membranes.
- Amino Acids: Subunits of proteins (20 standard types).
- Nucleotides: Subunits of DNA and RNA; includes ATP as an energy carrier.

Organization: Primary (amino acid sequence), Secondary (\alpha helices and \beta sheets), Tertiary (3D shape), and Quaternary (complex of multiple chains).
Domains: Independently folding structural units within a protein.
Binding: Protein function depends on specific binding to ligands via noncovalent interactions at a binding site.
Enzymes: Biological catalysts that lower the activation energy of chemical reactions at an active site.
Regulation: Controlled via feedback inhibition, allosteric switches, and covalent modifications like phosphorylation (catalyzed by kinases and phosphatases).
GTP-binding Proteins: Molecular switches toggled by the gain or loss of a phosphate group.
Molecular Motors: Use ATP hydrolysis to drive directed movement.

Laws of Thermodynamics: 1. Energy cannot be created or destroyed. 2. Disorder (entropy) in the universe always increases.
Free Energy (G): Chemical reactions proceed spontaneously only if the free-energy change (\Delta G) is negative.
Reaction Coupling: Cells drive energetically unfavorable reactions by coupling them to favorable ones, such as ATP hydrolysis.
Activated Carriers: Small molecules (ATP, NADH, NADPH) store energy in exchangeable forms for biosynthesis.