Bio/CS 251 Bioinformatics
Homework 2 KEY
1/27/06
20 points
Due Date: Tuesday, 1/31/06 at 5 pm to Dr. James, 255 SC
1.
1.4, K & R:
Organic molecules that contain hydroxyl groups (-OH) are called alcohols.
Would you expect such molecules to be hydrophobic or hydrophilic? Why?
Hydrophilic.
The Oxygen atom attracts electrons much more forcefully than does a Hydrogen atom.
In this way, oxygen is a strongly electronegative atom. As a result the O-H bond is
said to be polarized, such that one of the atoms has a partial negative charge, and the
other a partial positive charge. Molecules, such at water, that have an asymmetric
distribution of charge are said to be polar. Polar molecules of biological importance
contain one or more electronegative atoms, usually O, N, S, and/or P.
2.
1.5, K & R:
Examine the chemical structures of the amino acid R groups shown in Figure 1.5B.
What atom(s) is/are found in the R groups that are in the hydrophilic amino acids that
generally is/are absent in the nonpolar group of amino acids?
(List all polar chemical groups found in hydrophilic amino acids)
-C=O
- SH
- NH3+
- C = NH2+
- NH2
-C=O
|
O-
- OH
-C=O
|
NH2
3.
The following amino acids are internal residues in a polypeptide chain and are located
such that they can interact as indicated.
Which amino acid pairs in (a) could produce ionic interactions?
Which amino acid pairs in (b) could form H-bonds?
Which amino acid pairs in (c) could produce hydrophobic interactions?
For each of your answer choices in (a), (b), and (c), draw the interactions
that would occur between the appropriate atoms.
(a)
(b)
(c)
1.
Leu…..His
Cys…..Cys
Arg…..Thr
2.
Asn….Gln
Ala…..Pro
Ile…..Ile
3.
Arg….Asp
Tyr….Glu
Val….Leu
4.
Cys….Met
Gly…Ala
Pro….Phe
An –helical segment consists of 180 amino acid residues. How many turns are there
in this segment, and how long is it?
4.
At 3.6 aa per turn, 180/3.6 = 50 turns x 0.54 nm per turn = 27 nm long =
(pitch)
2.7 x 10-8 meters
(1 nanometer = 1 x 10-9 meters)
5.
Examine the following two peptide sequences, each of which is part of a larger protein,
and answer the questions that follow.
A - Val – Gly – Ile – Met – Ile – Leu – Leu – Phe – Ala – Gly – Val – Met – Ile – Cys – Val – Ile – Leu – Trp B
– Glu – Ala – Tyr – Leu – Thr – Phe – Gln – Val – Asp – Met – Asn – Ile – Ser -
(a) Which peptide is likely to be found in the interior of a protein? Why?
Peptide A is likely to be found in a protein’s interior, shielded from water molecules,
because this peptide is uniformly hydrophobic. This hydrophobic peptide could also
be found in a lipid bilayer, e.g., the cell membrane.
(b) Which peptide could form an amphipathic -sheet? Why?
Where in the protein would this peptide most likely be found. Why?
Peptide B could form an amphipathic -sheet, because the peptide alternates
hydrophilic with hydrophobic aa’s every other residue. This could easily form one
strand of a -sheet in which all of the hydrophilic residues would be on one face of the
sheet, with all of the hydrophobic residues on the other face.
An amphipathic -sheet would most likely be found on the surface of a protein, with
the hydrophilic residues facing outward into the aqueous environment, and the
hydrophobic residues facing inward away from water.
(c) Draw the -sheet structure (actually, the -strand structure) formed by this
peptide, showing the peptide backbone, with correct orientation of peptide bonds,
and showing each of the R-groups
Glu
Tyr
Ala
Thr
Leu
Gln
Phe
Asp
Val
Asn
Met
Ser
Ile
…compact image courtesy of Chris Husko, ’06 (thanks, Chris!)
(d) Which peptide is most likely to span a membrane? Why?
Is this membrane-spanning peptide most likely to form an -helix or -sheet?
Explain.
Peptide A is hydrophobic and therefore would be more stable within the hydrophobic
interior of a lipid bilayer than Peptide B. Although it could form a -sheet, it is very
common for hydrophobic membrane-spanning domains to fold into an -helix.