Molecular Biology & Biochemistry - Biol 99

“Portfolio":  Biomolecules, pH, Amino Acids, Protein Structure


For all components of the “portfolio” assignment series:
•    hand drawing is required
•    any explanations longer than a sentence must be typed
•    labeling and math may be neatly handwritten, preferably in block print
•    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
•    nothing may be cut and pasted from hard copy sources or electronic sources

I.  Monomers, polymers, biomolecules                                                       due January 13, 2011
    For each category, follow the specific instructions preceded by ...

Draw and name:
•    a generic or generalized example of a monomer - if there is more than one type, draw an example of each
•    an example of a naturally occurring homopolymer (only draw a trimer or portion large enough to show the polymer nature).  If none exist in nature, so state.
•    an example of a naturally occurring heteropolymer (only draw a trimer or portion large enough to show the polymer nature).  If none exist in nature, so state.
 
A.  Carbohydrates
•    glyceraldehyde
•    dihydroxyacetone
•    a 6-carbon aldose highlighting its aldose characteristic component (how to identify it as an aldose)
•    a 6-carbon ketose highlighting its ketose characteristic component (how to identify it as a ketose)

B.  Proteins [more will follow]

C.  Nucleic Acids       
    •    each of the 4 nucleotides commonly found in DNA
    •    each of the 4 commonly found in RNA
    •    Draw at least one in each group as a
    •    nucleoside monophosphate
    •    nucleoside diphosphate
    •    nucleoside triphosphate

D.  Lipids
•    glycerol
•    saturated fatty acid 12C
•    mono-unsaturated fatty acid 12C
•    poly-unsaturated fatty acid 12C
•    neutral lipid
•    phospholipid
•    sphingolipid
•    cholesterol

II.  Draw the following pH titration curves showing clearly                            due January 18, 2011
•    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

III.  Protein Structure

A.  Amino Acids                                                                                         due January 20, 2011
•    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

B.  Peptide and Protein Structure                                                                due January 20, 2011

**  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  - - - -

**   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