Genes and Gene Expression

General

• Biochemistry Online: An Approach Based on Chemical Logic - Biochemistry within the framework of chemical principles and logic. (Henry Jakubowski, College of St. Benedict/St. John's University)
  • Binding and the Control of Gene Expression
  • The Central Dogma of Biology
  • Human Genome Review
  • The Language of DNA
  • The Structure of DNA

• BodyMap - An anatomical expression database of human genes.
• Cell Biology Web Pages - Text- and image-based overviews of cell and organelle structure and function. (Gwen V. Childs, University of Arkansas for Medical Sciences) (Just above Beginner's Level)
  • The Cell Nucleus I: Nuclear Organization
    • Nuclear Envelope
    • Nucleolar Structure
  • The Cell Nucleus II: Chromosomes
  • The Ribosome
• cellnucleus.com - This site "aims to be a major portal for the field of nuclear organization and higher-order chromatin structure. Here you will find teaching materials for lectures, study materials for students, and advanced research material for professionals." Excellent comprehensive site on nuclear structure and function with movies, lectures and descriptions of current research and methods in the field.
• Genetics Tutorials - Definitions of terms, animations and test crosses for learning basic genetics. (North Harris College) (Beginner's Level)
• The Interactive Fly: Evolutionarily Conserved Pathways (Society for Developmental Biology), with sections on:
  • Chromatin Assembly and Gene Activation - "Acetylation, histone escorts, and chromatin assembly factors and histone deacetylase."
  • Dorsal-Ventral Patterning and the Immune Response - "A common pathway activates Dorsal and NF-κB, two conserved c-Rel homologs."
  • Endodermal and Ectodermal Portions of the Digestive System - "Transcription factors required for development of the gut."
  • General Gene Activation Machines - "NURF and SWI/SNF."
  • Hindbrain and the Spinal Cord - "Conserved role for Antennapedia class homeobox proteins."
  • Neural, Ectodermal and Mesodermal Patterning - "A conserved role for Drosophila pair rule genes."
  • Neural Patterning and Epidermal-Mesenchymal Interactions - "Conserved function of muscle segment homeobox. Neural patterning is carried out cooperatively with ventral nervous system defective/NK2 in a similar pattern to vertebrate msh and vnd homologs."
  • Neuron Differentiation - "Involvement of POU domain protein in the terminal differetiation of neurons."
  • Molting and the Response to Small Hydrophobic Hormones - "The steroid receptor superfamily."
  • Muscle Induction Pathways - "Conserved factors involved in determination of cardiac and somatic muscle."
  • Segmentation and Segment Polarity - "A conserved role for Engrailed."
  • Subdivision of Anterior-Posterior Axis - "A function of Homeobox cluster genes."
  • Subdivision of the Brain - "Role of orthodenticle and empty spiracles and other transcription factors and signaling proteins."
• Kimball's Biology Pages - Mini-essays on a number of biological topics, with a lot of cell biology. (Beginner's Level)
  • The Double Helix - Basic DNA structure.
  • DNA Replication - Introduction to DNA replication in prokaryotes and eukaryotes.
• MIT Biology Hypertextbook - A general tutorial on biochemistry, genetics and molecular and cell biology. (Beginner's Level)
  • Central Dogma - DNA to RNA to protein for beginners.
  • Prokaryotic Genetics and Gene Expression - Tutorial on the genetics of prokaryotes and their gene expression.
• On-Line Biology Book - Comprehensive introduction to biology at the "college freshman" level by M.J. Farabee. (Beginner's Level)
  • Control of Gene Expression
  • DNA and Molecular Genetics
  • Gene Interactions
  • Human Genetics
  • Introduction to Genetics
• Wikipedia - Free online encyclopedia with basic overviews. (Beginner's Level)
• DNA
• DNA Replication
• Gene
• Gene Expression
• Genetics
• Genomics
• Messenger RNA (mRNA)
• RNA
• Transcription
• Translation
• WWW Virtual Library of Genetics

DNA and Chromatin

• Chromatin Structure and Function - Information on chromatin structure, proteins that modify chromatin structure and the effects that these modifications have on cell function.
• Euchromatin Network - The site is "designed to help researchers and others interested in the latest developments in our studies of this most active part of the genome within the cell nucleus." (John H. Frenster, Physicians' Educational Series)
• Histone Acetyltransferase Page - Information on proteins that acetylate the core histones of nucleosomes.
• Human DNA Repair Genes - " This is the supplement to the paper by Wood RD, Mitchell M, Sgouros J, Lindahl T published in Science." (Computational Genome Analysis Laboratory, Cancer Research UK)
• The Medical Biochemistry Page: DNA Synthesis - Chromatin structure, DNA replication, DNA recombination and DNA transposition and DNA repair. (Michael W. King, Terre Haute Center for Medical Education, Indiana University School of Medicine)
• Virtual Tour of the Nucleosome - Diagrams of and information on DNA, histones, nucleosomes, higher-order chromatin structure and histone acetylation. (Dmitry Pruss)
• Waterborg's Chromatin Home Page - Information on chromatin, including nucleosome structure and function, histone acetylation and deacetylation. (Jakob Waterborg, University of Missouri, Kansas City)

Transcriptional Regulation

• Kimball's Biology Pages - Mini-essays on a number of biological topics, with a lot of cell biology. (Beginner's Level)
  • The Operon - Introduction to the concept of the operon in prokaryotes and positive and negative control of gene expression in the lac operon.
  • Gene Expression: Transcription - Basic information on transcription of DNA to RNA.
• The Medical Biochemistry Page - An excellent biochemistry tutorial with information on a broad range of biochemical pathways. (Michael W. King, Terre Haute Center for Medical Education, Indiana University School of Medicine)
  • Control of Gene Expression - Transcriptional control of gene expression in prokaryotes (the lac and trp operons are used as examples) and eukaryotes.
  • RNA Synthesis - RNA polymerases, post-transcriptional processing and RNA splicing .
• The Nuclear Receptor Resource - A collection of individual databases on members of the steroid and thyroid hormone receptor superfamily (such as glucocorticoid, androgen, thyroid hormone and mineralocorticoid receptors).
• NURSA - Nuclear Receptor Signaling Atlas - "The primary directive of our NURSA program is to gather and organize information relating to key aspects of orphan nuclear receptor biology, with the aim of extending this blueprint to the wider discipline of nuclear receptor signaling." (Co-Directors: Bert W. O'Malley, Baylor College of Medicine; Ronald M. Evans, Salk Institute for Biological Studies
• Transcription Regulatory Regions Database - Links to gene databases and information on extended regulatory regions of eukaryotic genes, the regulatory elements they contain, such as transcription factor binding sites, promoters, enhancers and silencers, and expression patterns of the genes. (Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences)

Translation and Protein Synthesis

• Kimball's Biology Pages - Mini-essays on a number of biological topics, with a lot of cell biology. (Beginner's Level)
  • The Genetic Code - Codons and the genetic code.
  • Translation: RNA → Protein - Basic information on translation (synthesis of proteins from RNA).
• The Medical Biochemistry Page: Protein Synthesis - Translation of RNA to protein, the genetic code, amino acid activation, the "wobble" hypothesis, regulation of translation and antibiotic inhibitors of protein synthesis. (Michael W. King, Terre Haute Center for Medical Education, Indiana University School of Medicine)
• On-Line Biology Book: Protein Synthesis - Introduction to protein synthesis by M.J. Farabee. (Beginner's Level)
• Protein Synthesis - An introduction to protein synthesis. (Terre Haute Center for Medical Education)

See also the Proteins: Biogenesis to Degradation page.

Nucleic Acid, Gene and Genomics Databases

Discussion Groups

• BioChemWeb.org Discussion Board - Discussions and questions/answers for scientists and students.

• Usenet newsgroup archives from BIOSCI/bionet (can also be accessed through Google Groups: bionet):
  • ARRAYS/bionet.molbio.genearrays - Gene array and microarray technology.
  • AUTOSEQ/bionet.genome.autosequencing - Research and support on automated DNA sequencing.
  • BIOCHROM/bionet.genome.chromosomes - Mapping and sequencing of eukaryotic chromosomes.
  • GEN-LINK/bionet.molbio.gene-linkage - Discussions about genetic linkage analysis.
  • GENSTRUC/bionet.genome.gene-structure - Genome and chromatin structure and function.
  • GNOMEPR/bionet.molbio.genome-program - Discussions regarding the international Human Genome Project.
  • MARKERS/bionet.genomes.markers - Molecular markers, microsatellites and Amplified Fragment Length Polymorphisms (AFLPs).
  • MOLREPS/bionet.molecules.repertoires - Generation and use of libraries of molecules.
  • MOL-EVOL/bionet.molbio.evolution - Discussions about research in molecular evolution.
  • MOLLUSCS/bionet.molbio.molluscs - Discussions about research on mollusc DNA.
  • MUTATION/prototype - Discussions on any aspect of environmental mutagenesis and mechanisms of mutation.
  • RAPD/bionet.molbio.rapd - Research on Randomly Amplified Polymorphic DNA (RAPD).
  • RECOM/bionet.molbio.recombination - Research on the recombination of DNA or RNA.
  • RNA/Prototype - Discussions about RNA editing, RNA splicing, and ribozyme activities of RNA.

Labs Studying Genes or Gene Expression