Table of Contents with Internet Links

Chapter 1, Chapter 2, Chapter 3, Chapter 4, Chapter 5, Chapter 6, Chapter 7, Chapter 8, Chapter 9, Chapter 10, Chapter 11, Chapter 12, Chapter 13, Chapter 14, Chapter 15, Chapter 16, Chapter 17, Chapter 18

Chapter 1: Introduction to the Study of Cell Biology

How big is a...?
Scaled images of different types of cells, from virus particles to a human sperm cell.

Cells: O rigins
The evolution of cellular life, types of cells, and cellular components.

RES PlantPat Electron Micrographs
Electron micrographs of many plant viruses, organized by structure and nucleic acid.

Coronaviruses
One of the main causes of "the common cold"

Picornaviruses
A very old, diverse group of viruses that cause many diseases in humans, including polio, meningitis, colds, and Hepatitis A.

Virus Replication Tutorial
Tutorials in the form of quizzes linked to background information about different viruses.

Beginner's Guide to Molecular Biology
An introduction to cell structure.

Chapter 1: Types of Cells
A brief illustrated description of prokaryotes and eukaryotes.

BioMOO, the biologists' virtual meeting place
A MOO for biologists that is accessible via a Web browser or telnet.

Cells Alive!
Many animations and movies illustrating several aspects of cell biology.

Cell Biology Chapter
Part of MIT's Biology Hypertextbook. Covers membranes, cell types and cell division.

Microbiology - Introductory Lecture Notes
A discussion of microbes: bacteria and viruses.

The Microbe Zoo
Microbial ecology, diversity and protist-metazoan relationships.

Viruses, Viroids, Prions, and Bacteria
Descriptions of the different classes of prokaryotes.

The Microbial Underground
Many links to sites on the Web regarding microbiology, molecular biology, and medicine, as well as an online course in medical microbiology.

Bugs in the News
Recent events of a microbial nature, written for nontechnical audiences.

bionet.cellbiol
Discussions about cell biology.

Dictionary of Science and Biotechnology
A dictionary of over 5600 life science terms.

Virtual Cell
A clickable image of a cell, with options for viewing electron micrographs, diagrams, and stereographic images.

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Chapter 2: The Chemical Basis of Life

ExPASy - PROSITE
A database of protein families and domains. Search by author, citation, keyword or other criteria. Submit sequences for comparison against known families and domains.

IMB Jena Image Library of Biological Molecules
Links to information on amino acids and nucleic acids. Determination of secondary structure, Watson and Crick's paper on DNA structure, and three-dimensional models of macromolecules.

Molecules R Us
A database of biological molecule image files viewable as static or interactive three-dimensional images using the Rasmol program or Chime plugin.

HotMolecBase
A database of molecules that are promising targets for medical applications. Detailed descriptions of structure, metabolism, isolation and characterization, references and contacts are described for each entry.

Chemicals in the Cell, Part 1
Chemistry as it applies to living cells.

Chemicals in the Cell, Part 2
A continuation of the introduction to biochemistry started in the previous link.

Chemistry Review
A review of chemical principles necessary for the study of cell biology, with problems.

Introduction to Amino Acids
A quick introduction to amino acids, including composition, stereochemistry, and interactive models.

bionet.molecules.peptides
Chemica l and biological aspects of peptides.

Biotech: Protein Sequence Databases
Links, with descriptions, of the major protein sequence databases.

Biotech: Bio Informatics
How a protein is characterized, from its sequence to its three-dimensional structure

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Chapter 3: Energy, Enzymes and Metabolism

Glucose Metabolism
A brief comparison of anaerobic and aerobic metabolism.

Intracellular Energy Sources
Molecules that "carry" energy within cells.

Metabolism of Fatty Acids
How energy is obtained from fatty acids.

Chemical Energetics
The laws of thermodynamics applied to cellular metabolism.

WMU Biology Dept.:Bios 150 Enzymes Lab
Introduction to enzymes in general, with specific information on catechol oxidase.

Interactive Biochemistry
Enzyme tutorial covering kinetics, amino acid titration curves, and reversible inhibition (requires Java and Chime plugin).

Yale's metabolic database
A list-based metabolic database.

Enzyme Biochemistry
Chemical energetics, enzymatic mechanisms, kinetics, and regulation.

Enzymes
Ima ges, including interactive 3D models, of several enzymes. Note: to view the 3D models you will need the appropriate helper applications.

ExPASy - ENZYZME top page
A database of enzyme nomenclature.

ExPASy - Biochemical Pathways
A searchable database that displays graphical maps of biochemical pathways.

EC Enzyme

A searchable database of enzyme nomenclature, activity, and related diseases.

Catabolism of Amino Acids
A picture of amino acid breakdown pathways, linked to information on related enzymes and pathways.

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Chapter 4: The Structure and Function of the Plasma Membrane

Chapter 2 ..1: Phospholipid/Cell Membrane
The molecules that comprise the plasma membrane of cells, and how they affect water movement across the membrane.

BIOL 445 - 1997 Lecture Notes on the WWW
Ion channels and how they function in nerve cells.

BIOL 445 - 1997 Lecture Notes on the WWW
Voltage- and ligand-gated ion channels, and diseases affecting ion channels.

BIOL 445 - 1997 Lecture Notes on the WWW
Communication between nerve cells via electrical and chemical synapses.

Membrane Proteins Introduction
The major membrane protein classes: receptors and transporters.

Membrane S tructure and Composition
The architecture of cell membranes.

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Chapter 5: Aerobic Respiration and the Mitochondrion

Lecture 16
The Krebs Cycle in aerobic respiration.

Bioch emistry 2 Study Guides
A series of true/false questions (with answers) on oxidative phosphorylation and electron transport in the mitochondrian.

Lecture: C ellular Respiration
The Krebs (TCA) Cycle, electron transport, and oxidative phosphorylation and a quiz with links to related information.

Mitochondria and Chloroplasts
Mitochondrial structure, TCA Cycle and oxidative phosphorylation.

Glycolysis and the Krebs Cycle
Links to several Web sources on aerobic energy metabolism.

Glycolysis
Links to glycolysis materials as well as static and Interactive 3D images of glycolysis enzymes and intermediates. Note: to view the 3D models you will need the appropriate helper applications.

TCA Cycle
Static and Interactive 3D images of TCA Cycle molecules. Note: to view the 3D models you will need the appropriate helper applications.

Oxidative Phosphorylation
Static and Interactive 3D images of enzymes, transporters, and carriers involved in oxidative phosphorylation. Note: to view the 3D models you will need the appropriate helper applications.

Glycolysis
An image of glycolytic pathways linked to detailed information about related enzymes and pathways.

Metabolism of TCA Intermediates
An image of the TCA cycle linked to information about related metabolic pathways and enzymes.

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Chapter 6: Photosynthesis and the Chloroplast

Mitochondria and Chloroplasts
Chloroplast structure and CO2 fixation pathways.

Chloroplasts
Illustrated description of chloroplasts, with links to information on photophosphorylation, C3 and C4 pathways and the Calvin Cycle

Photosynthesis
Chloroplast structure, pathways and enzymes involved in photosynthesis.

Photosynthesis Problem Set 1
A self-test linked to a glossary and tutorials on photosynthesis.

Internet Directory for Botany - Subject Category List
Links to arboreta, botanical societies, taxonomic databases, images, ethnobotany, paleobotany, and other botanical sites.

Photosynthesis Directory
The physics of light, the light and dark reactions, and unusual forms of photosynthesis.

bionet.photosynthesis
Discussions about research on photosynthesis.

bionet.plants
Discussion about all aspects of plant biology.

Photosynthesis
The biochemistry of photosynthesis and different photosynthetic pathways.

Photosynthe sis
The nature of light, the structure of chlorophyll and chloroplasts, the light and dark reactions, and related links.

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Chapter 7: Interactions Between Cells and Their Environment

Lecture 5
Detailed discussion of cell adhesion and tight junctions between cells.

Dictyosteli um Lecture Notes
Cell-cell interactions in the slime mold, Dictyostelium discoideum.

Video s
Downloadable movies of phenomena related to Dictyostelium discoideum.

Dictyostelium: multicellular organisms
A Word 6.0 file describing the role of cell-cell communication in the evolution of multicellular organisms.

U of Minn. Medical School Lecture Abstracts
Morphogenesis and cell-cell adhesion.

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Chapter 8: Cytoplasmic Membrane Systems: Structure, Function, and Membrane Trafficking

Endoplasmic Reticulum
The structure and function of the endoplasmic reticulum, with links to information on the Golgi complex, peroxisomes, ribosomes, and secretory pathways.

Endoplasmic Reticulum and Golgi
ER, Golgi and protein targeting within eukaryotic cells.

Davis Biology 220 Spring 1998
Text only description of the way in which cells distribute proteins to their proper locations.

Intracellular protein sorting and transport
Illustrated lecture notes describing intracellular protein sorting.

The Cytoskeleton in Phagocytosis
How restructuring of the cytoskeleton facilitates the uptake of particles by cells, with a link to a movie showing phagocytosis of a yeast cell by Dictyostelium discoideum.

Mitochondria and Protein Sorting
Mitochondrial compartments, diseases, and protein signals for sorting between organelles.

Vesicle-Mediated Tr ansport
Membrane flow between the endoplasmic reticulum, Golgi bodies, and the plasma membrane.

bionet.cellbiol.insulin
Biology and chemistry of insulin and related receptors

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Chapter 9: The Cytoskeleton and Cell Motility

Structure, ultrastructure and biochemistry of the vertebrate myocyte
An overview of muscle cell components, illustrated with diagrams and micrographs.

Physiology and Biophysics of the Mycocyte
A discussion of muscle cell contraction that includes methods for studying contraction at the cellular level, the mechanism and the proteins that are involved.

Molecular Motors
Microtubules, intermediate filaments, and motor molecules.

Biology 590 Related Resource Links
Links to movies showing muscle cell contraction, cell motility as well as interactive Shockwave titles on mitosis, heart function and how Parkinson's Disease affects basal ganglia cells.

Mucking about with myosin motor mutants
One laboratory's efforts to better understand how molecular motors function, with links to related information at other sites.

Bacterial Motility
How some bacteria "swim" with flagella.

bionet.cellbiol.cytonet
The cytoskeleton, plasma membrane and cell wall.

U of Minn. Medical School Lecture Abstracts
Morphogenesis: cell motility and shape changes.

Neural Crest Cell Movies in FishScope
Movies showing the migration of cells destined to become neural crest cells during zebrafish gastrulation.

Fish Epi dermal Cell Movies
Movies portraying several examples of cellular and organellar motility.

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Chapter 10: The Nature of the Gene and the Genome

Biology 210
The anatomy of eukaryotic chromosomes: centromeres, telemeres and chromatin (graphics-rich).

Biology 210
How DNA is coiled and packed (graphics-rich).

Supercoiled DNA on Gels
Annotated animation demonstrating how different DNA conformations migrate at different rates in agarose gels.

Baylor College of Medicine's Search Launcher
Several links to DNA and protein analysis tools.

Kyoto Encyclopedia of Genes and Genomes
A set of interwoven databases that relate genetic and functional information about biomolecules. It consists of maps for metabolic and some regulatory pathways, a molecular catalog, gene catalog, and genome maps for some species.

FlyBase
A database of the Drosophila genome.

Nucleic Acid Sequence Databases
Links, with descriptions, to the major sequence databases.

Fundamenta l Concepts in Genetics
Genes, inheritance, and investigative methods of genetics.

Primer on Molecular Genetics (Department of Energy)
dAn introduction to DNA, transcription and translation.

Microbiology -- Nucleic Acids in Microbial Cells
Replication and transcription in prokaryotes.

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Chapter 11: Utilization of Genetic Information: From Transcription to Translation

Codon Usage Database
The frequency of codon use in each organism from the GenBank sequence database is searchable through this World Wide Web site.

DNA Binders
Interactive models of different classes of DNA binding proteins (requires Chime plugin).

PolIII Beta Subunit
Interactive model of the subunit of E. coli DNA polymerase III, which is responsible for the holoenzyme's ability to replicate a new strand very quickly (requires Chime plugin).

Swiss-PDB Viewer
A program for comparing the three-dimensional structure of several proteins at once, view electron density maps, and generating ray-traced model images.

Tr anscription
A brief description of transcription using E. coli as an example.

RNA P rocessing
Capping, polyadenylation, and spliceosomes.

Ribozy mes
How RNA acts as a catalyst in Tetrahymena thermophila.

The Central Dogma of Biology
How cells convert the information contained in DNA to make proteins.

Translation
Translating mRNA into proteins, with an emphasis on prokaryotes.

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Chapter 12: The Cell Nucleus and the Control of Gene Expression

Control of Gene Expression
How gene expression is controlled in both prokaryotes and eukaryotes.

Bioluminescence Lecture Notes
Quorum sensing in bacteria via the Lux operon

Lac Operon lecture notes
How the Lac operon functions in E. coli.

Multidrug Resistance lecture notes
Operons involved in the spread of bacterial drug resistance.

Induci ble Genes
Well illustrated description of inducible operons, with a link to a problem set on the molecular genetics of prokaryotes.

Prokaryoti c Gene Expression
Transcriptional control, regulatory sequences and proteins, and operons.

Regul ation of Gene Expression
Eukaryotic gene regulation: transcriptional and post-translational control, mRNA transport, and post-translational modifications.

Prokaryotic Gene Regulation
Operons, including one responsible for light production in a marine bacterium.

Prokaryotic Genetics Mutants
How gene expression can be studied in prokaryotes.

The Human Transcript Map
Chromosomal maps of disease alleles, from the Human Genome Project.

Microbiology -- Genetic Code/Regulation Lecture Notes
Eukaryotic gene regulation.

1 ..26.96.html
Eukaryotic gene structure and RNA splicing.

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Chapter 13: DNA Replication and Repair

DNA Da mage and Repair
How UV light damages DNA and the enzymes that can repair it.

Defective DNA Repair
Descriptions of diseases caused by errors involving DNA repair enzymes.

DNA Repair
Causes of DNA damage and mechanisms of repair in prokaryotes.

DNA Replication
How DNA makes copies of itself.

The Central Dogma of Biology
How cells convert the information contained in DNA to make proteins.

Mic robiology -- DNA and RNA Lecture Notes
DNA structure, replication, repair and transcription.

Microbiology -- Nucleic Acids in Microbial Cells
Replication and transcription in prokaryotes.

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Chapter 14: Cellular Reproduction

Eukaryotic Cell Growth and Cell Cycle Part I
A short history of research on the cell cycle.

Cell Cycle Part 2
The transition from G2 to M phase.

Cell Cycle Part 3
The transition from G1 to S phase.

Chromosomes and Cell Division
The first of three linked pages on the cell cycle, mitosis and meiosis.

Cell Division
Mitosis, meiosis and Mendelian inheritance.

Cell Division Tutorials
Self-paced tutorials, with quizzes, on mitosis and meiosis.

How Bacteria Grow
Factors that influence bacterial cell division.

Cell Division: Binary Fission and Mitosis
The cell cycle, phases of mitosis, and related links.

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Chapter 15: Cell Signaling: Communication between Cells and Their Environment

BIOL 445 - 1997 Lecture Notes on the WWW
How programmed cell death helps shape neuronal networks.

Cell Signaling
How cells respond to changes in their environment and to signals from other cells.

Lecture 2 2
How some toxins effect cells via cyclic AMP, a second messenger.

G-Protein Coupled Receptor Database
Receptor sequences, mutants, models and signalling mechanisms of over 2400 receptors.

Cell Signalling
Classes of cell-cell interactions, receptors, signal transduction and examples.

Apoptosis
Programmed cell death in neutrophils.

Prokaryotic Gene Regulation
An operon responsible for light production and "quorum sensing" in a marine bacterium.

Apoptosis on the Net
A review of Web sources on apoptosis, from the November issue of Nature Biotechnology.

Cell Death and Apoptosis
Current research, questions, and other cell death-related information.

Streptococcus
How a bacterium kills the cells that are supposed to kill it.

Signal Transduction Proteins
Images of some of the proteins involved in signal transduction.

Receptors
How environmental signals trigger actions within cells.

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Chapter 16: Cancer

Basset Healthcare Patient Advisory Group Education
Nontechnical descriptions of non-traditional treatments, hospice and biological factors of cancer.

Y-ME National Breast Cancer Organization
Information on breast cancer, including support resources and general breast cancer information.

Cancer Control and Prevention
Links to major research groups at the Memorial Sloan-Kettering Cancer Center.

Pathology 6311
Lecture slides on applications of molecular cytometry to cancer and gene therapy.

Breast Cancer Information Clearinghouse
Links to web sites, organizations and mailing lists about breast cancer.

Colon Connection
A long list of links about colon cancer: images, screening, heredity, literature, mailing lists, and a glossary.

The Prostate Cancer Infolink
Screening, treatments, support resources related to prostate cancer.

The Cell Cycle and Cancer
A summary of types and origins of cancer.

Cancer Examples
Some examples of cancer-producing mutations.

Cyberbotanica: Plant Compounds and Chemotherapy
Information about plant compounds used in cancer therapy and the plants that produce them.

Related Newsgroups:
sci.med.diseases.cancer
alt.support.cancer

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Chapter 17: The Immune Response

Regulation of Humoral Immunity
How major histocompatibility complexes (MHC) prevent autoimmune responses.

Some Biochemical Aspects of AIDS
Envelope structure, replication, method of infection, and drug therapies.

Biology 221a - 1997
An online course on the biology of infection and immunity.

Protease Inhibitors
Structures of several protease inhibitors used to treat individuals with AIDS.

Immunity an d Opportunism
Inherited and acquired immune system defects and some organisms take advantage of them.

Immunology
An overview of the vertebrate immune system, with links to detailed information on humoral and cellular immunity.

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Chapter 18: Techniques in Cell and Molecular Biology

Molecular Tools of Medicine
An overview of molecular techniques used in medicine, including Polymerase Chain Reaction, RFLP analysis, and gene therapy.

Partial Restriction Digestion
Annotated animation demonstrating the digestion of a plasmid with restriction endonucleases.

Cell Biology Laboratory Manual
Many protocols for cell biology techniques, including electrophoresis, fractionation, microscopy and histochemistry.

Biology 210 - GENETICS
A description of methods used for characterizing a sequence of DNA.

Comprehensive P rotocol Collection
Molecular biology and nematode research protocols.

Proto cols
Lab protocols and links to background information about yeast genetics, cell biology and biochemistry.

Tests
In vitro assays used by industrial toxicologists.

Mitchison Lab Protocols
Many protocols for microinjection, cytoskeleton immunofluorescence, antibody production, chromatin assays and microscopy, and microtubule isolation.

Table of Contents
A guide to different methods of sequence comparison, with links to the actual search engines.

REBASE - The Restriction Enzyme Database
comprehensive information on restriction enzymes, methylases, and the organisms from which they have been isolated.

Mike Serfas' lab protocols
Research methods for immunohistochemistry, in situ hybridization, and RNAse protection assays.

Molecu lar and Genetic Methods (Prof. Huberman)
Interactive exams on molecular and genetics methods, including hybridization, PCR, restriction enzymes, and cDNA cloning.

Microscopy: Yale Center for Cell Imaging
A manual of techniques associated with microscopy, including immunocytochemistry, cryosectioning, and specimen preparation for electron microscopy.

3-D Confocal Microscopy Home Page
An overview of 3-D laser scanning confocal microscopy.

Micrographs from the Yale Center for Cell Imaging
Light and electron micrographs of viruses, bacteria and infected cells.

Recombinant DNA Chapter Directory
Cloning, blots, PCR and DNA fingerprinting.

Basics of DNA Fingerprinting

A description of DNA fingerprinting, including applications and limitations.

sci.techniques.microscopy
The field of microscopy.

NanoWorld Gallery
The Center for Microimagery and Microanalysis, Queensland, Australia. Images, scientific papers, and other information about the study of organic and inorganic materials by the use of X-rays, ions, electrons and photons.

NWFSC Molecular Biology Protocols
Links to experimental techniques, journals and databases in molecular biology as well as a forum for posting questions.

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