Assignments for the lecture material are in the text by Voet, Voet, and Pratt (vvp). Additional references are made to the book by Robyt and White (r&w) which provides supplementary background material for the topics discussed in class and for the experiments to be performed in the laboratory.

To view many of the structures in the links contained in this syllabus, download Chime as a plugin for Netscape and/or Rasmol to view molecular structures downloaded from the links or the Protein Data Bank.

I. Biochemistry -Setting the Stage (vvp, chapter 1)

  The early history of biochemistry
  The origin of life/living matter contains C, H, O, N, S, and P
  Biological macromolecules
  Organelles, cells, and organisms/cellular architecture/organismal evolution
  Thermodynamics

  Preparation and Properties of Solutions (r&w, chapter 2)

An interesting site with many links to the world of biochemistry and molecular biology is Pedro's BioMolecular Research Tools.

A novel educational tool was developed by the Experimental Study Group at MIT. It is called the MIT Biology Hypertextbook.

See the structure of many small biochemical compounds at Klotho: Biochemical Compounds Declarative Database. This is an interesting site in general but for the molecules just click on "compound listing."

II. Water, The Biological Solvent (vvp, chapter 2)

  Structure of water/Hydrogen bonding

An interesting molecular simulation of the structure of water: download and play with a movie player; watch carefully for the breaking and formation of hydrogen bonds.

  Physical properties
  Chemical properties
  Ionization of water, pH, pK, the Henderson-Hasselbalch equation

A novel educational tool was developed by the Experimental Study Group at MIT. It is called the MIT Biology Hypertextbook. See the Chemistry Review chapter for a discussion of chemical bonds, pH and basic organic functional groups.

III. Amino Acids (vvp, chapter 4)

  Amino acid structures
  Acidic and basic properties
  Stereochemistry of amino acids
  Reactions of the amino acid functional groups
  The nature of the peptide bond

Qualitative and Quantitative Methods for Determining Biological Molecules   Amino acids, peptides, and proteins (r&w, chapter 7.2)

Biological Preparations (r&w, chapter 8.1-8.5)

Good general site for Molecular Models for Biochemistry - check out the section on amino acid and peptide structures viewed as Chime-generated images.

A novel educational tool was developed by the Experimental Study Group at MIT. It is called the MIT Biology Hypertextbook. See the Large Molecules chapter for a discussion of amino acids and protein structure.

For an extensive amount of information on the amino acids see the PROWL site.

IV. Peptides, Polypeptides, and Proteins - Primary Structure (vvp, chapter 5)

  Protein function - structural proteins; enzymes; transport and storage;
    muscle contraction and motility; immunoproteins; regulatory and receptor proteins
  Protein purification
  Proteins can be purified and characterized by using:

  Solubility
  Chromatography
  Electrophoresis
  Ultracentrifugation
  Specific interactions

  Amino acid composition/sequence of proteins
  Protein Evolution

  Structural Analysis of Biological Molecules (r&w, chapter 10.2)

  Spectroscopic Methods (r&w, chapter 3.1-3.3)

  Chromatographic Techniques (r&w, chapter 4, part I; part II, section 4.11, 4.12)

  Electrophoretic Techniques (r&w, chapter 5)

V.Proteins - Three-Dimensional Structure (vvp, chapter 6)

  Secondary structure - a-helix, b-pleated sheet, and b-bends

Great illustrations and other material on secondary structure is presented here but requires Navigator 3.01.

  Analysis and prediction of secondary structure
  Fibrous proteins - keratin, collagen
  Supersecondary structures
  Tertiary structure and the presence of motifs and domains
  Subunit interaction and quaternary structure
  Forces that determine protein conformation
  Protein folding and stability

Good general site for Molecular Models for Biochemistry - check out the section on protein structure and protein architecture viewed as Chime-generated images.

A novel educational tool was developed by the Experimental Study Group at MIT. It is called the MIT Biology Hypertextbook. See the Large Molecules chapter for a discussion of amino acids and protein structure.

An excellent site for material on protein folding including the molecular chaperones can be found at "Unraveling the Mystery of Protein Folding."

Another excellent site for material on protein folding which specifically deals with molecular chaperones can be found at "The Chaperonin Home Page." At this site, be sure to check the The Chaperonin Structure Gallery.

VI. Protein Conformation, Dynamics and Function (vvp, chapter 7)

  Myoglobin and Hemoglobin

See the Protein Data Bank to obtain structures for these proteins.

For an excellent site dealing with many aspects of hemoglobin structure see Hemoglobin. Check out the section on Hydrophobicity, Polarity, & Charge.

  Structure
  Mechanism of oxygen binding and transport
  Ligand binding
  Factors that influence oxygen binding

The compound 2,3 bisphosphoglycerate (2,3 BPG) influences oxygen binding - see its structure and that of many other small biochemical compounds at Klotho: Biochemical Compounds Declarative Database.

  Myosin and actin

Mechanism of muscle contraction

A neat site called the Cell Movement Home Page has a link to the Contractile Systems Proteins

  Immunoglobulins

  Structure and function of antibodies
  Antigen-antibody binding

Another terrific site from UMASS and Eric Martz illustrates the Antibodies.

  Structural features of DNA binding proteins (vvp, chapter 23-4)

VII. Enzymes - Catalysis (vvp, chapter 11)

  Enzyme specificity/cofactors and coenzymes
  Mechanism of action - acid-base catalysis; covalent catalysis; metal ion catalysis; 
       electrostatic catalysis; catalysis through proximity and orientation effects; 
       and catalysis by preferential transition state binding
  Active sites
  The mechanism of specific enzymes

  Lysozyme
  Serine proteases - chymotrypsin, trypsin, and elastase
  Ribonuclease A
  Carboxypeptidase A
  Digestive enzymes and coagulation factors

A novel educational tool was developed by the Experimental Study Group at MIT. It is called the MIT Biology Hypertextbook. See the Enzyme Biochemistry chapter for a discussion of enzyme mechanisms.

For information on the nomenclature of enzymes, see the Enzyme Nomenclature Database

VIII. Enzymes - Kinetics (vvp, chapter 12)

  Chemical kinetics
  Enzyme kinetics
  Michaelis-Menten kinetic analysis - equilibrium
  Briggs-Haldane kinetic analysis - steady state
  Multisubstrate enzyme kinetics
  Enzyme inhibition

  Irreversible
  Competitive
  Noncompetitive
  Uncompetitive

  Regulation of Enzyme Activity
  Allosteric regulation
  Aspartate transcarbamoylase
  Reversible covalent modification
  Enzyme stimulation and inhibition by control proteins

  Enzymology (r&w, chapter 9)

A novel educational tool was developed by the Experimental Study Group at MIT. It is called the MIT Biology Hypertextbook. See the Enzyme Biochemistry chapter for a discussion of enzyme kinetics.

A site from the United Kingdom that provides "An Introduction to Enzyme Kinetics" deals with: (a) the effect of substrate concentration; (b) determination of kinetic parameters; (c) kinetics of enzyme inhibitors; (d) kinetics of multisubstrate systems; (e) kinetics of allosteric enzymes.

IX. Nucleic Acids (vvp, chapter 3 and 23)

Nucleotide - structure and function   Basic nucleic acid composition and structure   Nucleic acid sequencing   Recombinant DNA technology   DNA   DNA helix   Forces stabilizing nucleic acid structures   RNA   Structure   Fractionation and characterization of nucleic acids   Nucleic acid-protein interactions Higher orders of nucleic acid structure

  Structural Analysis of Biological Molecules (r&w, chapter 10.3)

Good general site for Molecular Models for Biochemistry - check out the section on an overview of DNA and RNA structure viewed as Chime-generated images. ALSO check the section on Structures for Molecular Biology.

An excellent Primer on Molecular Genetics from the U. S. Department of Energy.

Two excellent nucleic acid sites are the Nucleic Acid Database at the Biological Structure Resource and the Atlas of Nucleic Acid Containing Structures.

X. DNA Replication, Repair, and Recombination (vvp, chapter 24)

  Replication
  Mechanism of action of DNA polymerase
  Repair
  Direct repair
  Excision repair
  SOS response and recombination repair
  Recombination

XI. The Flow of Genetic Information (vvp, chapter 25 and 26)

  Transcription (vvp, chapter 25)
  Mechanism of action of RNA polymerase
  Posttranscriptional processing of RNA
  Self-splicing RNA
  Translation (vvp, chapter 26)
  The genetic code
  Transfer RNA
  Ribosome
  Polypeptide synthesis

See the course description for Chem/Biol/BIMO 321

See the laboratory schedule for Chem/Biol/BIMO 321

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