Download Representative Quiz Questions_Key

The quiz that will take place in section on Monday, February 8 th, will contain no more than
three questions similar in style to the ones below.
1. Draw valine and proline as their most abundant form at physiological pH.
2. Given the conformation of the DNA in the protein-DNA complex above, identify which of
the following base pairs could come from this structure.
(a) Name each of the standard bases shown below in the space provided.
(b) Place an “X” over all non-standard bases.
(c) Write “WC” beside the names of all Watson-Crick base pairs
(d) Circle the base pair(s) that could be found in B-form DNA.
(e) Label the major and minor grooves on a Watson-Crick base pair of your choosing.
Guanine-Cytosine WC
Adenine-Uracil WC
Guanine – X WC
Guanine-Cytosine WC
Guanine-Uracil
Guanine-Cytosine WC
3.
Trypsin is a serine protease: a protein that uses a serine residue to catalyze the hydrolysis of
a peptide bond.
(a) Two views of the peptide substrate are shown below. The view on the left and right are
related by a 90° rotation as indicated. Provide the amino acid sequence of the peptide
substrate in single-letter code. N-terminus – GPCKAR – C-terminus
0 cis peptide bond(s), and ________
5
(b) The peptide has _______
trans peptide bond(s).
(c) Below are two views of trypsin in grey, with the active site serine side chain in orange sticks,
and the peptide substrate in cyan. The inset is a zoomed-in view of the substrate bound to
trypsin. Trypsin cleaves peptide bonds C-terminal to positively charged residues. Circle in the
zoomed-in view the peptide bond that will be cleaved by trypsin. (Tip: the views are oriented
the same as the peptide images above.)
(d) Below is an illustration of the three residues (orange, cyan, and orange) that form the
catalytic triad. The backbone (grey) of adjacent residues is provided for context. The central
cyan residue’s side chain lacks the proper coloring by atom type. On the drawing, identify
the atoms around the ring.
(e) The protease works best when the central cyan residue is neutral. Illustrate on the above
drawing: (1) The protonation state of all three catalytic residues; (2) hydrogen bonds between
the catalytic residue side chains; and (3) the name of each catalytic residue.
4. President Obama recruits you to work for the top-secret Center for Routine Biochemistry. Once
you get to work, you learn that they have evidence that aliens have recently crash-landed on
earth, but did not survive the impact. You are charged with studying the evidence suggesting
alien genetic material. You decide to first extract nucleobases from a tissue sample and are
surprised to isolate only the following molecules:
A
B
C
D
(a) You realize that one of these bases is found in earth DNA: circle this base. You hypothesize
that these four bases together support a genetic system analogous to your familiar WatsonCrick DNA. Write down the letter combination for the basepair that would form between the
earth base and a non-earth base.
A:D
(b) To test your hypothesis you synthesize DNA containing the bases shown above. You
discover that the alien duplex has a significantly higher melting temperature than earth DNA.
What interaction would contribute most significantly to this effect?
Since the alien DNA is all purines with two rings, you would get more base stacking energy.
5. mRNA structures affect protein translation by causing a ribosome to “slip” over a stop codon,
thereby extending the amino acid sequence. For example, the structure of the murine leukemia
virus RNA caused the ribosome to slip with a precise frequency. This enables the virus to
maintain a critical ratio between two proteins: Gag, a structural protein, and Gag-Pol, an
extended form of Gag with catalytic activity.
This ratio is maintained by a pseudoknot immediately downstream of the Gag stop codon. The
pseudoknot is in equilibrium between its active state (which causes the ribosome to slip over
the stop codon) and its inactive state. In its active state, A17 is protonated, and forms a triplebase interaction with G53 and C23 (see diagram below). Because the pKa of this particular
Adenine is 6.2, only 6% of pseudoknot molecules are in the active conformation, yielding ~6
Gag-Pol for every 94 Gag molecules.
A17
+
C23
G53
Houck-Loomis B et al. Nature. 2011 Nov 27; 480 (7378):561-4.
On the triple base diagram above (on the right):
(a) label the three bases (A17, G53 and C23)
(b) indicate the protonated atom that allows for the active pseudoknot to form with a “+” sign
(c) circle the Watson-Crick basepair within the base triplet.
6. Below are two triple-base interactions.
(a) Label each of the bases by their full name.
(b) Which of the nucleotides (from 1-6) could be part of a DNA molecule? None (ribose)
(c) Which of the bases (from 1-6) have a syn conformation? ____None____________
(d) On each drawing, circle any Watson-Crick basepair.
(e) Which base (from 1-6), if any could be in the minor groove of a double helix? ___#3_____
Cytosine
1
2
Guanine
Adenine
3
Adenine
5
Uracil
Uracil
4
6
7. Direct recognition of ligands by mRNA riboswitches is a unique way of regulating gene
expression. An example is the “purine riboswitch” class of riboswitches that selectively
recognizes either a G or A base and turns translation “on” or “off” depending on the
concentration of the respective base in the cell. In the example given below, a purine base (in
blue) is recognized by its riboswitch. One of the reasons for specificity comes from the direct
interaction of the purine base with two residues (a and b) in the binding pocket.
Hoogsteen face
W-C face
(a) In diagram (1), identify the ligand base and the nucleotide residues (a and b) in the binding
pocket.
The ligand base is Adenine and both residues a and b are Uridine
(b) Label both the Watson-Crick and Hoogsteen faces of the ligand base in diagram (1)
(c) While residue (a) is conserved, the specificity for the ligand base is determined by residue (b),
which is always a pyrimidine. Complete diagram (2) to show the triple base interaction that
would specify the alternative purine base. The conserved residue (a) is already drawn.
8. Draw a purine base. Clearly label the name and where ribose would attach. Draw an amino
acid forming at least two hydrogen bonds to the Watson-Crick face of the base via its side
chain with an appropriate stereochemistry at the α-carbon. Clearly label the name of the
amino acid.
9. A peptide has the following sequence:
D-E-N-S-I-T-Y
(a) Rewrite the peptide sequence using three-letter names:
Asp-Glu-Asn-Ser-Ile-Thr-Tyr
(b) How many positive and negative charges are there in this peptide at physiological pH?
Briefly justify your answer.
One positive and three negative charges. The N-terminus is positively charged, and D, E and the
C-terminus are negatively charged.
(c) If this peptide was completely -helical, how many main chain hydrogen bonds would be
formed? Briefly explain your reasoning.
3 hydrogen bonds – one between n and n+4 (D and I), n+1 and n+5 (E and T) and n+2 and n+6
(N and Y).
10. Draw a Watson-Crick base pair of your choice. Identify which base pair you have drawn.
Then draw (and label) one amino acid side chain that could recognize chemical groups in the
minor groove of that base pair, and draw in the interactions that facilitate recognition.
Sample answer:
Uracil also accepted instead of thymine.
11. Draw the tripeptide Leu-Asp-Arg at pH 7.
12(a) Invent a sequence for the peptide illustrated below so that it generates an amphipathic
structure. Provide the resulting sequence (of length corresponding to the number of C positions
in the illustration) in single-letter code. Briefly justify your answer.
10 residues, down, up, or loop
D-U-D-U-L-L-U-D-U-D
Pick one side as hydrophobic (A,C,F,I,L,M,V,W) the other as hydrophilic
(D,E,H,K,N,Q,R,S,T)
Loop – G,P,S,N are most common, but anything goes
Nice touch: include a number of -branched or aromatic residues
Figure source: TMOL
(b) Draw a the chemical structure of a dipeptide segment of your choice from your sequence above,
and circle the corresponding sequence region in your sequence above.
Answer: any side chains are appropriate, as long as they represent the part of the sequence that
was circled.
13. (4 points) You are working for a scientific press that is putting the final touches on a textbook
on macromolecules. Here are a few figures that were proposed for the chapter on nucleic acids.
Indicate whether each figure is correct or not. If you think a figure is incorrect, explain very briefly
why.
(A) Correct? Yes No If not, why? Helix is left-handed.
(B) Correct? Yes No If not, why?
(C) Correct? Yes No If not, why? It’s DNA because the sugars are deoxyriboses.
(D) Correct? Yes No If not, why? There are no Ts in mRNA.