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BT 301 Biophysics Tutorial Sheet-II

The document is a tutorial sheet containing 11 questions about biophysics concepts. It covers topics like protein secondary structure, DNA structure, membrane proteins, and viral replication. Specifically, it asks about: 1) The number of alpha helices and beta sheets in a protein structure. 2) The handedness and origin of twist in beta sheets. 3) Assigning residues to a helical wheel diagram and analyzing properties of an alpha helical peptide. 4) Why alpha helices but not beta strands can serve as transmembrane domains. 5) Polarity and direction of hands sliding in DNA grooves. 6) Correcting statements about nucleic acids. 7) Identifying mistakes in a B-DNA diagram. 8) Analyzing structural properties

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Shivaani Eswaran
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52 views3 pages

BT 301 Biophysics Tutorial Sheet-II

The document is a tutorial sheet containing 11 questions about biophysics concepts. It covers topics like protein secondary structure, DNA structure, membrane proteins, and viral replication. Specifically, it asks about: 1) The number of alpha helices and beta sheets in a protein structure. 2) The handedness and origin of twist in beta sheets. 3) Assigning residues to a helical wheel diagram and analyzing properties of an alpha helical peptide. 4) Why alpha helices but not beta strands can serve as transmembrane domains. 5) Polarity and direction of hands sliding in DNA grooves. 6) Correcting statements about nucleic acids. 7) Identifying mistakes in a B-DNA diagram. 8) Analyzing structural properties

Uploaded by

Shivaani Eswaran
Copyright
© © All Rights Reserved
We take content rights seriously. If you suspect this is your content, claim it here.
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Download as PDF, TXT or read online on Scribd
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BT 301 Biophysics

Tutorial Sheet-II

1. Look at the protein structure below and write down the number of α-helices and
β-sheets?

2. The β-sheets found in proteins are not flat but mostly twisted?
a. What is the handedness of twist?
b. What is the origin of such a twist?

3. For an ideal α-helix, there are 3.6 residues per turn. An α-helix can be
represented as a helical wheel as shown below. The helix axis is perpendicular to
the plane of paper and side chains are displayed as circles.
a. Write down the peptide sequence: VKAAEKVLWVAKAIAKTA on the
helical wheel (start form the circle labelled 1 and label the other
residues similarly).

b. How are the polar and non-polar residues distributed around the helix
axis?
c. What is the net charge on the peptide at neutral pH?
d. How many aromatic amino acids are there?
e. How many amino acids with branched β-carbon are there?
f. What is the minimum integer number of residues that make a full
circle on a helical wheel?

4. The transmembrane region of a single-pass transmembrane protein, i.e. a protein


that passes through the membrane exactly once, is mostly an α-helix. Why do
think that the α-helix is suitable, but a β-strand unsuitable, as a transmembrane
domain?

5. Suppose you can walk inside the DNA grooves from left to right with your hands
sliding on DNA backbone.
a. Which direction (5ʹ→3ʹ or 3ʹ→5ʹ) would your left and right hand go if you
walk in the major groove?
b. What will be the polarity if you turn around and start walking towards
your starting point?
c. Which direction would your hands go if you walk in the minor groove?

6. Given below are statements about nucleic acids. Identify the correct ones and
correct the incorrect ones.
a. DNA is the genetic material whereas RNA is not.
b. Only RNA contains thymine as the base
c. RNA and DNA both contain guanine and adenine as the pyrimidine bases.
d. DNA and RNA are the polymers of nucleosides.
e. The term “acid” in nucleic acids is indicative of the acidic nature of the
phosphate group.

7. Have a look at the diagrammatic representation of a B-DNA molecule below:

a. Is there any mistake?


b. If so, list them.

8. Take a look at the schematic representation of a membrane protein that acts as a


growth factor receptor. Binding of the ligand (the growth factor) to the protein
causes its dimerization, that is essential for its activity.
a. What is the highest order (primary, secondary, tertiary, quaternary) of the
protein in its inactive state? Justify your answer.
b. What is the highest order (primary, secondary, tertiary, quaternary) of the
protein in its active state? Justify your answer.
c. From the list of amino acids given below, circle those that could be part of
the extracellular domain of the protein and could form hydrogen bonds
with water through their side-chain.
K W D Q F
d. Circle the amino acids that could lies in the transmembrane domain and
interact with the acyl chains of lipids.
K W D Q F
e. Dimerization of the receptor is mediated by specific intermolecular
interactions. Which of the following interactions do you think is
strongest?
D-K W-Q A-M
f. Substitution of single amino acid can have dramatic effect on the
dimerization and consequently on the function. Predict for the following
cases if the protein could dimerize or not.
i. The original pair D-K is changed to D-R. Justify your answer.
ii. The original pair A-M is changed to W-M. Justify your answer.

9. Can you name a disease that is caused by a single amino acid substitution in a
protein?

10. You discover a novel virus that is spreading in a population. You discover that the
virus contains lipid, nucleic acid, and protein, and lipid. It became easy for you to
study when you found that the virus could infect e. coli cells and grow in it.
a. You grow the bacteria in medium containing 32P, 35S or 15N.
i. Which of the viral macromolecules be labelled with 32P.
ii. Which of the viral macromolecules be labelled with 35S.
iii. Which of the viral macromolecules be labelled with 15N.
b. You analyse the nucleic acid composition and find the following:

Percentage

A G T C U

28.2 22.3 17.0 16.2 0.8

What can you conclude about the virus?

11. The sequence of one of the DNA strands is 5ʹ-GTCGATCAGC-3ʹ. Which of the
following is the sequence of its complementary strand?
a. 5ʹ-GCTGATCGAC-3ʹ
b. 5ʹ-CAGCTAGTCG-3ʹ
c. 5ʹ-GCUGAUCGAC-3ʹ
d. 5ʹ-CAGCUAGUCG-3ʹ

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