Molecular Biology & Biochemistry - Biol 99

pH, Amino Acids, and Protein Structure: “Portfolio” part I

For all components of the “portfolio” assignment series:
•    hand drawing is required
•    any explanations longer than a sentence must be typed
•    labeling and short explanations may be neatly handwritten
•    everything must be neat and legible
•    drawings should be sufficiently large and spread out that all components are easily distinguished and sufficient detail is included
•    no cut and paste from hard copy sources or electronic sources

I.  Draw the following pH titration curves showing clearly  due Jan 21, 2010
•    the molecule itself
•    list the pKa(s) for the molecule
•    which ionized/non-ionized form(s) are found under each distinct condition, e.g.
    •    every inflection point
    •    each region between inflection points
•    be sure that the boundaries of each region are clear - whether it is a point or a region -

        •    acetic acid (vinegar)
        •    NaHCO3 (baking soda) solution
        •    phosphate solution
        •    glycine
        •    glutamic acid

II.  Amino Acids        due Jan 21, 2010
•    Draw each amino acid using a modified skeletal format in which atoms are indicated.
•    Show molecules at neutral pH
•    Indicate charged structures
•    Label each molecule
•    Orient molecules with the backbone horizontal
•    Orient the molecules N–>C

•    Organize the drawings in correct categories (as per Schmeidler)
•    Within a category, list in more hydrophilic –> more hydrophobic order

III.  Peptide and Protein Structure        due Jan 26, 2010

A. Peptides
•    Draw the formation of a peptide bond, showing each step
•    Be sure to show each component of the reaction

•    Draw a dipeptide, indicating the R group simply as R1, etc.
    •    Highlight the planar portion of the structure
    •    Indicate the resonance structure by using  - - - -

B.  Polymers
•    Describe the primary, secondary, tertiary, and quaternary structure of a polymer
    •    be sure that this works for any biopolymer
•    Use a sketch to illustrate each structural level
•    Find an example of a monomer and a polymer for each main category of biomolecule
•    For each main category of biomolecule:
    •    Find an example of a homopolymer
    •    Find an example of a heteropolymer