Welcome To The New Term!

It has always seemed to me that the many parts that make up the subject of biology are related to each other more like the nodes of a web than as a linear collection of independent topics. So I believe that the power of hypertext is better suited to learning about specific topics in biology than is the linear structure of a printed textbook. But I do recognize that if you are trying to learn biology without the guidance of an instructor, the organization (or lack thereof!) of my pages can be bewildering. So for those who want to begin the study of biology on their own, here is a list of the topics in my pages in what I hope is an order where one can start at the beginning and gradually build up a body of knowledge as you proceed through the list. In other words, here the topics have been ordered as they might be in a printed textbook.

One further note: while my preference is to study systems as they occur in both animals and plants, many prefer to study the organismal biology of plants separate from that of animals, and I have followed that pattern here.

This is a preliminary effort. Please let me know by e-mail if you find any topics that appear to be in the wrong category or not in a logical order.

The Chemical Basis of Life

The following pages examine some of the principles of chemistry upon which an understanding of modern biology depends.

• Mixtures and Compounds — Follow the links to a discussion of ways to separate the components of mixtures.
• Elements and atoms
• Electronegativity and types of chemical bonds
• Noncovalent bonding
• Hydrogen bonds
• Acids and bases
• Molecular weight and the mole
• pH
• The International System of Units
• Parts per million (PPM), etc.

The Molecules of Life

• Organic molecules — types and functional groups
• Hydrocarbons
• Fats
• Phospholipids
• Cholesterol
• Carbohydrates
• Amino Acids
• Enantiomers — optical isomers (chiral molecules)
• Polypeptides
• Proteins — Follow the links at the bottom of its page to learn about the various levels of protein structure (primary, secondary, tertiary, quaternary).
• Rules of Protein Structure
• Glycoproteins
• Nucleotides — the subunits of nucleic acids

  You may wish to skip the more specialized topic below.

• Proteomics

The Cellular Basis of Life

• Animal cells (with links to the various organelles)
• Cell membranes
• The Nucleus
• Ribosomes
• Endoplasmic reticulum
• Golgi apparatus
• Centrosomes and Centrioles
• Lysosomes and Peroxisomes
• Protein Kinesis — how freshly-synthesized proteins are sent to their proper destinations in the cell
• The Proteasome
• The Cytoskeleton — actin microfilaments, intermediate filaments, microtubules.
• Cilia
• Animal tissues
• Adipose tissue
• Junctions between cells
• Plant cells
• Chloroplasts
• Chlorophylls and Carotenoids
• Plant tissues

  You may wish to skip the more specialized topics below.

• Apoptosis
• Collagens
• Chromatophores
• Culture media for growing cells
• Fluorescence-activated cell sorter (FACS)
• Limiting Dilution Analysis

How materials get in and out of cells

• Diffusion, active transport, and membrane channels
• Endocytosis
• Exocytosis

  You may wish to skip the more specialized topic below.

• Kinetics of membrane transport

Cell metabolism

• Enzymes
• ATP
• NAD
• Glycolysis
• Cellular respiration
• ATP synthase
• Photosynthesis: Pathway of Carbon Fixation
• Photosynthesis: The Role of Light
• Photosynthesis: how these details were discovered
• Chemiosmosis — a demonstration
• Metabolism (with links to specific examples)
• Intermediary metabolism
• G proteins
• Second messengers

  You may wish to skip the more specialized topics below.

• Free energy
• Redox potentials
• A quantitative analysis of the energy relationships in cellular respiration and photosynthesis.
• Cell signaling
• Reactive oxygen species (ROS)
• Bioluminescence

DNA: The Substance of the Genes

• Transformation in bacteria
• The Hershey-Chase Experiments
• The Double Helix: of DNA
• Base Pairing: in DNA and RNA
• DNA Replication
• The Meselson-Stahl Experiment

  Reading Genes: DNA Sequencing

• Restriction Enzymes: the tools upon which molecular biology and biotechnology depend
• DNA sequencing by the dideoxy method
• Genome Sizes
• The Human Genome Projects
• The Human and Chimpanzee Genomes

  You may wish to skip the more specialized topics below.

• Pyrosequencing
• DNA Repair
• Harlequin chromosomes
• Metagenomics: Exploring the Microbial World

Gene Expression

• One Gene - One Enzyme Theory
• The Transcription of DNA into RNA
• The Genetic Code
• The Translation of RNA into proteins

  You may wish to skip the more specialized topics below.

• RNA editing
• Expressed Sequence Tags
• Ribosomal RNA (rRNA) gene cluster

Cell Division

• Chromosomes
• The Cell Cycle
• Mitosis
• Polyploidy
• Endoreplication
• Sex Chromosomes
• Meiosis

The Genetic Consequences of Meiosis

• Mendel's monohybrid crosses
• Crossing Over and Genetic Recombination in Meiosis
• The Evidence of Creighton and McClintock
• Genetic linkage and genetic maps
• Gene mapping with three-point crosses
• Quantitative trait loci (QTL)

  The next pages describe gene mapping in viruses (where there is DNA recombination but no meiosis).

• Mapping the genes of T2
• rII locus of T4

Regulation of Gene Expression

• Regulation of Gene Expression in Bacteria
• The Tryptophan Repressor — how the presence of tryptophan shuts down the genes needed for its synthesis.
• Regulation of Gene Expression in Eukaryotes
• Steroid Response Elements — how steroid hormones regulate gene expression

  You may wish to skip the more specialized topics below.

• Epigenetics
• Visualization of Transcription and Translation in Bacteria
• Footprinting
• Chromatin Immunoprecipitation (ChIP)
• Isolating Transcription Factors
• Palindromes
• Cell-specific gene expression
• Imprinted Genes
• Ribozymes

Mutation

• Mutations: causes and significance
• Testing for mutagenic chemicals in bacteria and in mice
• Radiation and its effect on DNA
• Transposons: "jumping genes"

Genomics: manipulating genes

• Recombinant DNA and Gene Cloning
• Polymerase chain reaction (PCR)
• Gene Therapy: methods and prospects and recent advances
• Transgenic Animals
• Transgenic Plants
• Restriction Fragment Length Polymorphisms (RFLPs) and their use in medical diagnosis and law enforcement
• Gel blotting
• Genetic Screening for Phenylketonuria (PKU)
• Antisense RNA
• Antisense Oligodeoxynucleotides and their therapeutic potential
• "Forward" and "Reverse" genetics
• Metagenomics

Cancer

• Cancer (general discussion)
• Cancer Cells in Culture
• Oncogenes — genes whose disregulation leads to cancer
• Tumor Suppressor Genes
• BCL-2 — the role of this proto-oncogene in leukemia and apoptosis
• Burkitt's Lymphoma — the molecular basis of this B-cell tumor
• Chronic Myelogenous Leukemia (CML) — its molecular basis

  You may wish to skip the more specialized topics below.

• Fighting cancer with inhibitors of angiogenesis
• Immunotherapy of cancer
• Cancer: The Causes and Prevention of Cancer as described by Bruce Ames, who has studied these questions for many years.
• Estimating cancer risks
• The LD₅₀ test
• Dioxin
• Magnetic fields — do they cause cancer?

Aging

• Aging
• Telomeres

Embryonic Development and its Regulation

• Embryonic Development — the mechanisms at work in first steps followed by links to descriptions of the mechanisms at work during the later phases
• Frog Embryology
• Cleavage
• The Organizer
• Segmentation: Organizing the Embryo
• Homeobox Genes — their role in embryonic development
• Stem cells
• Embryonic Stem Cells
• Germline vs. Soma and the biological significance of their distinction
• Regeneration

The Anatomy and Physiology of Animals

Nutrition

• The Human Gastrointestinal Tract
• Metabolism (with links to specific examples)
• Nutrition
• RDAs — Recommended dietary allowances

Gas Exchange

• Breathing (respiratory system): [Human] [Control of breathing] [of frogs, lizards, and birds] [Insect]

Circulatory Systems

• Circulatory system of humans: anatomy and physiology
• Heart, control of
• The Lymphatic System
• Blood
• Blood Groups
• Heat, transport of

  You may wish to skip the more specialized topics below.

• Blood Clotting
• Sickle-cell disease
• Serine proteases
• Circulatory systems of fish, frog, lizard, squid

The Immune System

• Clonal selection and immunological memory
• Antibody-Antigen Binding
• B Cells and T Cells — lymphocytes of the immune system
• Antigen Receptors — on B cells and T cells
• Histocompatibility Molecules and their role in eliciting an immune response
• Antigen Receptor Diversity: how a virtually limitless variety of antigen-binding sites is created by the immune system
• Anatomy of the immune system
• T Helper cells
• Cytotoxic T lymphocytes (CTL)
• Cell-Mediated Immunity
• Transplants: [ organ ] [bone marrow]
• Antigen Presentation — how antigens are "presented" to B cells and T cells
• The Immunological Synapse
• Dendritic Cells
• Passive Immunity
• Innate Immunity
• The Complement System
• Inflammation
• Allergies
• Asthma: its immunological basis
• AIDS: acquired immune deficiency syndrome
• Vaccines

  You may wish to skip the more specialized topics below.

• Clonal Selection — experimental evidence
• Natural Killer (NK) Cells
• Immune Tolerance
• Regulatory T cells
• Antibody affinity
• Nude Mice
• Cancer Immunotherapy
• Games Parasites Play: some ways of evading the immune responses of their host
• Monoclonal Antibodies
• ELISA (enzyme-linked immunosorbent assay)
• Radioimmunoassay
• DNA vaccines

Excretion

• Kidney physiology: [ human ] [other vertebrates]
• Urea cycle

Hormones

• Human Hormones and a summary table listing them with links to the individual hormones
  • Thyroid and parathyroids
  • Hormones of the Gut
  • Pancreas, hormones of
  • Pituitary
  • Hypothalamus, hormones of
  • Adrenal Glands
  • Sex Hormones
  • Progesterone
  • Pineal gland
  • Melatonin and the pineal gland
  • Kidney Hormones
  • Leptin: the fat hormone
  • Liver, hormones of
  • Melanocyte-stimulating hormone (MSH)
• Insect hormones

Sexual Reproduction

• Sexual Reproduction
• Asexual reproduction in animals
• Birth Control
• Prenatal screening
• Extraembryonic membranes and the physiology of the placenta
• Genetic Mosaics
• Can Humans Be Cloned?

The Nervous System

• Neurons and other "excitable cells"
• Synapses
• The Central Nervous System — the brain and spinal cord.
• The Peripheral Nervous System

  You may wish to skip the more specialized topics below.

• Drugs: how psychoactive drugs affect the brain
• Nitric Oxide (NO) — its physiological functions
• Prions

The Senses

• Mechanoreceptors (touch, pressure, stretch, proprioception)
• Hearing
• Vision
• Processing visual information
• Vision in arthropods
• Heat, cold, and pain receptors
• Taste
• Olfaction — the sense of smell
• Electric organs and electroreceptors
• Magnetoreceptors

Muscles

• Bone
• Muscles: skeletal, cardiac, smooth
• Muscles: testing the sliding-filament hypothesis

Behavior

• Innate Behavior
• Taxes
• Learned Behavior
• Long-Term Potentiation (LTP)
• Honeybee Navigation
• Avoiding Predation
• Pheromones
• Circadian Rhythms in Drosophila and Mammals

The Anatomy and Physiology of Plants

Plant Anatomy

• Plant tissues
• Roots
• Stems
• The Leaf
• Arabidopsis thaliana: a "model" organism

Plant Physiology

• Xylem and the transport of water and minerals
• Phloem and the transport of food
• Transpiration
• Gas exchange in plants
• Photorespiration and C₄ plants
• Tropisms

Reproduction in Plants

• Alternation of generations in plants
• Moss life cycle
• Fern life cycle
• Angiosperm life cycle
• Asexual reproduction in plants

  You may wish to skip the more specialized topics below.

• Self-incompatibility: how plants avoid inbreeding
• Transgenic Plants

Plant Development

• Plant Growth
• Germination of seeds
• Plant Hormones: Abscisic acid (ABA), Auxin, Cytokinins, Ethylene, Gibberellins, Strigolactones
• Etiolation
• Flowering: its genetic control
• Photoperiodism and phytochrome

Ecology

Energy Flow through the Biosphere

• Net Productivity of ecosystems
• Food chains and food webs
• Biomes
• Freshwater ecosystems
• Marine ecosystems

  You may wish to skip the more specialized topic below.

• Biomagnification of pesticides

Cycles of Matter in the Biosphere

• Carbon cycle
• Nitrogen cycle
• Nitrogen fixation, symbiotic
• Soil
• Sewage Treatment
• Chlorination, MX, and the Law of Unintended Consequences
• Air pollution
• Acid Rain
• Ozone

The Growth of Populations

• The Human Population
• Principles of Population Growth

Interactions between Species

• Symbiosis
• Insecticides
• Biological control of pests

Evolution

• Evolution and Adaptation
• Speciation
• The Evolution of Body Form in Animals
• Recapitulation
• Mutation and Evolution
• The Hardy-Weinberg Equilibrium
• Polymorphisms
• Kin Selection
• The Origin of Life: abiotic synthesis of organic molecules
• Mars — Is (or was) there life on Mars?
• Endosymbiosis and the origin of eukaryotes
• Geologic eras

The Diversity of Life

Eukaryotic Life

• Taxonomy
• Protists
• Ciliates
• Volvox
• Diversity and evolutionary relationships of the plants
• Arabidopsis thaliana: a "model" organism
• Fungi
• Yeast
• Barcoding
• Invertebrates
• Drosophila melanogaster
• Caenorhabditis elegans: a model organism
• Vertebrates
• Zebrafish
• Monotremes

Microbes

• Bacteria (Eubacteria)
• Archaea
• Antibiotics
• E. coli
• Anthrax
• Bacillus thuringiensis: and the use of its toxin gene in agriculture
• The Rapid Identification of Microorganisms

Viruses

• Viruses
• Influenza — the "flu"
• PhiX174
• Smallpox
• Retroviruses: including HIV, the cause of AIDS

General Science

• Epidemiology: the criteria for establishing causation
• Types of Clinical Studies
• Scientific Methods
  • a case study
• Scientific Papers
• Statistical Methods
• Drugs: how new drugs are tested