Molecular Structure & Behavior



Molecular Structures

Biophysics explains the biological functions of cells, tissues, and organisms in terms of the structure and behavior of biological molecules. Genes, the basic elements of biological information, reflect the molecular structures of the enormously large, linear DNA (deoxyribonucleic acid) molecules of which they are made. The behavior of enzymes, hormones, and antibodies reflects the molecular structures of proteins and the organic chemistry of the functional groups of the amino acid side chains.& The surface and barrier properties of biological membranes reflect the ability of lipids to aggregate into flexible two-dimensional bilayers with hydrophobic cores and polar surfaces.

Proteins

Structural Principles

  • The Protein Data Bank (PBD) provides a wealth of information on the structure, synthesis, and function of biological macromolecules at their education page. Content is suitable for students from middle school (advanced elementary) to college/university.
     
  • Primary Structure, Secondary Motifs, Tertiary Architecture And Quaternary Organization, Jannette Carey and Vanessa Hanley. Proteins are organized in a hierarchy of structures including primary structure (the amino acid sequence), secondary structure (a-helix and b-sheet), tertiary architecture (the specific atomic structure), and quaternary organization (arrangement of distinct polypeptide chains). Previously published in the Biophysics Textbook Online (BTOL).

Protein Sequences

Protein Structures

  • The Protein Data Bank (PDB) is “the single worldwide repository for the processing and distribution of 3-D biological macromolecular structure data”, providing access to images of 3-D structures and atomic coordinates for all published protein and nucleic acid X-ray crystal and NMR solution structures. It is operated and maintained by Rutgers, The State University of New Jersey, the San Diego Supercomputer Center of the University of California—San Diego, and the Center for Advanced Research in Biotechnology of the National Institute of Standards and Technology.
     
  • PDBsum is “a database of the 3D structures of known proteins and nucleic acids” maintained by the Department of Biochemistry and Molecular Biology, University College, London.
     
  • The Protein Information Resource is “an integrated public resource of protein informatics to support genomic and proteomic research and scientific discovery” maintained by the Georgetown University Medical Center.
     
  • The GenBank Entrez Proteinwebsite is a protein information search and retrieval system maintained by the National Center for Biotechnology Information (NCBI).
     
  • Jena Image Library of Biological Macromolecules

 

Structure of Membrane Proteins

 

Behavior of Proteins

  • Protein-Protein Interactions, Catherine Royer. Outline of the thermodynamic and structural principles governing the ways that proteins interact with other proteins. Previously published in the Biophysics Textbook Online (BTOL).
  • Structural Symmetry and Protein Function, David S. Goodsell and Arthur J. Olson. Many cellular proteins are composite structures consisting of two or more associated polypeptides. A description of the principles governing the symmetry of these complexes is described at the following site.
     

Nucleic Acids

Structural Principles

  • The Protein Data Bank (PDB) provides a wealth of information on the structure, synthesis, and function of biological macromolecules. Content is designed for students from middle school (advanced elementary) up to college/university level.

Nucleic Acid Sequences

  • Genbank is the NCBI database for gene sequences. “Established in 1988 as a national resource for molecular biology information, NCBI (the National Center for Biotechnology Information) creates public databases, conducts research in computational biology, develops software tools for analyzing genome data, and disseminates biomedical information - all for the better understanding of molecular processes affecting human health and disease.”
     
  • EMBL-Bank Nucleotide Sequence Database constitutes Europe's primary nucleotide sequence resource.

Nucleic Acid Structures

  • The Protein Data Bank (PDB) is “the single worldwide repository for the processing and distribution of 3-D biological macromolecular structure data”, providing access to images of 3-D structures and atomic coordinates for all published nucleic acid and protein X-ray crystal and NMR solution structures. It is operated and maintained by Rutgers, The State University of New Jersey, the San Diego Supercomputer Center of the University of California—San Diego, and the Center for Advanced Research in Biotechnology of the National Institute of Standards and Technology.

Behavior of Nucleic Acids

  • DNA Condensation, Victor Bloomfield. DNA molecules are often considerably longer than the largest dimension of the cell and must thus condense into compact structures within the chromosomes of cells. Previously published in the Biophysics Textbook Online (BTOL).
     
  • Circular DNA, Alexander Vologodskii. Some DNA molecules form closed circular structures that exhibit complex behavior related to variations in extent of internal twisting present in the molecules. Previously published in the Biophysics Textbook Online (BTOL).
     

Carbohydrates

  • The sugars and polysaccharides found in cells and organisms are complex and diverse. The structures of many carbohydrates are available at the following website. (This site is no longer updated regularly.)
     

Lipids & Membranes

Lipid Structures

  • The Lipid Data Bank provides information about the molecular structures, phases and phase transition temperatures, miscibility and phase diagrams, and critical micelle concentrations of biological lipids.
     
  • Data on the crystal structures of membrane lipids are available at a site hosted by the Department of Biochemistry, U of Missouri.
     
  • The Lipid Bank for the Web operated by the Japanese Conference on the Biochemistry of Lipids, provides information on the properties of biological lipids.


Membrane Structures


Membrane Proteins

The principles governing the assembly and energetics of proteins in biological membranes and the hydrophobicity of membrane proteins are outlined in a website maintained by the laboratory of Dr. Stephen White, University of California—Irvine.

Macromolecular Complexes

Proteins, nucleic acids, and other biological molecules can self-assemble into complex, often large macromolecular structures such as filaments, chromosomes, and ribosomes. Information on select macromolecular complexes is provided below.

  • Actin filaments (Paul Janmey) are major structural elements of cells and play essential roles in muscle contraction and cell motility. Previously published in the Biophysics Textbook Online (BTOL).
     

Metabolic Pathways

  • The International Union of Biochemistry and Molecular Biology supports a website that makes Nicholson Minimaps of the metabolic pathways available in a variety of file formats. These metabolic pathways charts were developed by Dr. Donald Nicholson, Department of Biochemistry and Molecular Biology, The University, Leeds, England.
     
  • KEGG Pathways Database – “Current knowledge on molecular interaction networks, including metabolic pathways, regulatory pathways, and molecular complexes.” Generated and maintained by the Kyoto Encyclopedia of Genes and Genomics.
     

Molecular Behavior

  • Molecules in Action, Christopher Miller. Previously published in the Biophysics Textbook Online (BTOL).