Download LS1a Fall 2014 Lab 2 (PyMOL- Protein) question sheet Q1) (10 points)

Name: _______________
TF Name: __________________________
LS1a Fall 2014
Lab 2 (PyMOL- Protein) question sheet
Q1) (10 points) 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.
N-terminus
C-terminus
Q2) (9 points) 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.
The stick representation depicts every (non-hydrogen) atom with every bond connecting them to give
a detailed atomic map of a protein. The cartoon representation uses helix, sheet, or loop cartoons to
display a protein as an assembly of secondary structures. The surface representation demonstrates
how a protein looks while floating in a cell and interacting with other molecules. The stick
representation gives all the atomic detail, but it can be an overwhelming and unhelpful amount of
information.
The cartoon representation more easily displays secondary structure elements, such as alpha-helices
and beta-sheets, but you lose the chemical nature of the side chains. The surface representation
shows how all the levels of protein structure come together to form a macromolecule with a
particular global/overall structure, but you lose all interior detail.
Q3) (6 points) What is the difference between the tertiary- and quaternary-levels of protein structure?
How many polypeptide chains comprise a complete hemoglobin molecule?
“Tertiary” structure refers to the fold that one polypeptide chain assumes. “Quaternary” structure
refers to the manner in which multiple polypeptides fold together into one functional protein.
Hemoglobin is made of four polypeptide chains.
Q4) (5 points) How does the surface representation helps us predict where cofactors and other
molecules can bind the protein.
The surface representation indicates the internal cavity within hemoglobin where the porphyrin ring
and oxygen bind.
Q5) (10 points) 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
α-helix?
They point in opposite directions (towards each other allowing for the formation of hydrogen bonds
between peptide bonds that stabilizes the helix.
Q6) (10 points) 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?
Hydrogen atoms bound to the backbone nitrogens of the peptide bonds act as the H-bond donors (the
entire N-H group can also be considered the donor). Carbonyl oxygen atoms of the backbone peptide
bonds act as the acceptors. The H-bond donating residue is 4 residues away from the H-bond
accepting residue. (It should be 4 residues away, but sometimes it’s 3, so we accept that, too.)
Q7) (6 points) 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.
A proline within a peptide chain lacks a hydrogen atom bonded to its backbone nitrogen, and
therefore cannot donate a hydrogen bond unlike the other amino acids. (The backbone nitrogen of
proline only has one H to begin with, and that one is lost upon peptide bond formation.) Proline also
contorts or bends the helix due to its constrained bond angles.
Q8) (8 points) 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
Val Leu Ala/Asn
Glu Ala/Leu
Met
Asp Tyr
Ile
Acid
[Residues “R3” and “R5” appear in PyMOL as Ala, because of some computer glitch. However, if you
click on them, R3 is identified as Asn, and R5 is identified as Leu, so either answer is valid.]
Q9) (10 points) 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.
There are three polar/charged amino acid sidechains: Glu, Asp and Tyr. All of them tend to be
positioned along the same side of the helix. They are not distributed symmetrically along all faces of
the helix, as Leu, Met, and Ile are positioned on the opposite face of the helix.
If there are two identical copies of this alpha-helix, then they would interact along using other’s
hydrophobic side chains, thereby hiding them from solvent, and exposing the hydrophilic side chains.
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Q10) (5 points) 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?
The strands are antiparallel, as indicated by the orientation of the cartoon arrows.
Q11) (10 points) 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 betasheet strand. In addition, label the hydrophilic and hydrophobic faces of the beta sheet.
The amino-termini of the strands are where the cartoon arrow originates, and the carboxy-termini of
the strands are where the cartoon arrow ends with a pointy-end. The hydrophobic face has the cyclic
residues and is mostly populated by Ile and Val, and the hydrophilic face has the charged amino acids
along with threonine.
Q12) (5 points) Which side of the beta sheet (the polar or non-polar face) faces the alpha-helices?
The nonpolar face of the beta sheet faces the alpha helices.
Q13) (6 points) 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?
No, most do not form the maximum number of H-bonds (which is 4). We would not expect this in the
liquid state given the degree of movement of individual water molecules. The maximum number of Hbonds would be seen in the solid, crystalline state (namely, “ice”).
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