If you'd like a review of pH, Buffers, etc.
you might like to look at my Chem
109 notes for these topics
Know how to draw, fully label, and interpret titration curves!(See Chemistry Supplements )
A fun, if a bit off-the-wall look at proteins uses sequences as a basis for musical expression. You might like to check out A Musical Introduction to Protein Structure at http://www.whozoo.org/mac/Music/Primer/Primer_index.htm
From the Exam 1 Study Guide:
Amino Acids - Know:
- Know general formula for aa's.
- Why are they called "alpha amino acids"?
- General acid/base properties.
- Appearance of titration curve for a general amino acid
(keep in mind that each buffer region will be of the same length
for each titratable group, and that these regions are additive).
- how will the curve differ for an acidic side chain e.g. asp,
- Note that if the alpha and side chain acid have overlapping
buffer regions you will just see an longer buffer region (how
much longer?). Similar considerations apply below.
- However, if the pKa's of the side chains and end
groups are significanlty different, then one will see another,
distinct, buffer region.
- how will the curve differ for a basic side chain (e.g. lys,
cys, tyr) aa?
- how will the curve differ for a neutral side chain (e.g.
- Approximate values of pKa's and ionic forms
predominating at any pH.
- Note that the side chains have pKa's very similar
to what we expect for organic acids and bases (e.g. pKa
for acids about 4, for bases around 10).
- Note that the pKa's of the a-carboxyl
groups are about pH 2, significantly different than the normal
values expected for an organic acid (why? think of counter
charge stabilization and induction).
- With these considerations in mind, what should the pKa's
of the a-carboxyl groups be when they
are incorporated as the carboxy terminus of a peptide?
- Should the pKa's of peptide/protein carboxy-terminii
differ significantly from the pKa's of asp and glu
side chains? Why or why not?
- Similarly the pKa's of the a-amino
groups differ from expectations, in this case because the electron
withdrawing effect of the carboxyl group (induction) makes
it more difficult for the nitrogen to keep a proton (its made
more positive, so it tends to lose the positive proton).
- Know hydrophobic charecter of aa side chains (note
that these categories overlap, and some change with pH):
- hydrophobic (ala - trp)
- neutral (gly & ala)
- acidic (asp, glu, his)
- basic (lys, arg)
- polar, un-charged (ser. thr, asn, gln, cys, tyr).
- What's special about proline?
- Chirality of aa's.
- Why is this significant?
- D & L vs. R & S.
- How many aa's are used to synthesize proteins?
- Others are found in proteins - what's happening?
Memorize structures for: gly, ala, asp, lys,
cys, ser, leu, met, glu, phe.
- Peptide bond (= amide bond)
- stability in aqueous solution
- planar nature of bond (resonance)
- amino acid minus water lost in peptide bond formation.
- Rotation angles - many are forbidden.
Protein 3-D Structure
- What is a globular protein?
- Hierarchy of Protein Folding Description:
- Based on percieved differences in organization: e.g. periodicity,
- Broken into four "classical" levels, with two
sub-levels added within the tertiary level:
- Primary: Sequence of covalently (peptide) bonded aa residues
- Secondary: Steric relations of residues nearby in the primary structure (interactions due to peptide backbone).
Classically repetitive, highly ordered structures.
- "Random" structure. "Random" folding
- Alpha helices and beta strands
- Tertiary: Steric relations of residues distant in the primary structure (interactions largely due to side-chain interactions).
- Super secondary structures (motifs and folds)
- What are the characteristics of each level
- Steric relations of residues
- Charecteristic bonding types.
© R. A. Paselk 2010;
Last modified 23 February 2011