Name: _______________

TF Name: __________________________

LS1a Fall 2014 Lab 2 (PyMOL- Protein) question sheet

Q1) Draw this tripeptide (Lys-Val-Ala) as it would predominately exist at pH 7 in the space provided on
your answer sheet. Label the amino- and carboxy-termini.










Q2) How do the stick, cartoon, and surface representations convey structural and chemical information
differently? Give one strength and one weakness for each type of representation.










Q3) What is the difference between the tertiary- and quaternary-levels of protein structure? How many
polypeptide chains comprise a complete hemoglobin molecule?





Q4) How does the surface representation helps us predict where cofactors and other molecules can bind
the protein.




Q5) Take a close look at the directions in which the white hydrogen atoms and the red
oxygen atoms face. Do the hydrogen atoms generally point in the same direction as the
oxygen atoms, in opposite directions, or neither? How does this orientation explain the stability of the
-helix?






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Q6) Which atoms form the H-bond donors? Which form the H-bond acceptors? The amino acid that
donates the hydrogen forms a hydrogen bond with the acceptor amino acid how many residues away?






Q7) The presence of the amino acid proline within an alpha helix can often disrupt the structure of the
helix by interrupting the regular pattern of hydrogen bonds within the helix. What is different about
proline that does not allow it to form stabilizing H-bonds in the same way as other amino acids? Think
about the specific atoms involved in H-bond formation in a helix.







Q8) Use the helical wheel diagram to label the relative positions of the amino acid side chains along the
Top_Down_Helix shown on your screen. Carbons are shown in blue, Oxygen in red, and Sulfur in yellow.
The first amino acid at position R1 is Valine. Fill in the correct amino acids for positions R2 through R9 in
the table provided below. Use the three-letter code for each amino acid. Consult your online lecture
notes to find the structures.

Position R1 R2 R3 R4 R5 R6 R7 R8 R9
Amino
Acid
Val

















Q9) Take a look at how the polar and charged amino acid side chains that are positioned along the face
of the helix. For this helix, do polar and charged side chains tend to occupy the same side of the helix, or
are they distributed rather symmetrically along all sides? If there were two copies of this same helix,
predict how they would interact with one another in an aqueous environment.







Q10) Do the beta-strands shown in the PyMOL structure run parallel or anti-parallel to each other? How
is this information conveyed in the cartoon representation?






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Q11) Capture two high-resolution images of the beta sheets with both the Sheet_Sticks and B_Sheet
both turned on by following the instructions below. Note how the side chains on one face of the beta
sheet are mostly non-polar whereas the other face has residues that are mostly either charged or polar.
Play around with the orientations and capture two images, one that you feel best show the each of the
two faces of the beta sheet.
To take a picture of this image:
Go to the top menu bar on the control panel, and select Display.
Scroll down the drop-down menu and select Background, and then unselect Opaque.
Type ray in the command line (either one).
Click on File, and scroll down to Save Image As, and select PNG Title and save your image to the
Documents folder so that you can email it to yourself as an attachment.

For next week, print and annotate your two images. Label the amino- and carboxy-termini of each beta-
sheet strand. In addition, label the hydrophilic and hydrophobic faces of the beta sheet.

Q12) Which side of the beta sheet (the polar or non-polar face) faces the alpha-helices?



Q13) Do most of the molecules in this structure form the maximum number of bonds? Would you
expect them to? If not, in what state would you expect to see water forming the maximum number of H-
bonds?