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BT301 Tutorial-2 Solutions

This document contains a tutorial on protein and nucleic acid structure. It includes questions about identifying secondary structure elements, characterizing α-helices and β-sheets, describing membrane protein topology, DNA and RNA structure, base pairing rules, and viral replication. The key concepts covered are protein folding, membrane protein structure-function relationships, DNA major and minor groove polarity, nucleic acid composition, and complementary base pairing.

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Shivaani Eswaran
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68 views17 pages

BT301 Tutorial-2 Solutions

This document contains a tutorial on protein and nucleic acid structure. It includes questions about identifying secondary structure elements, characterizing α-helices and β-sheets, describing membrane protein topology, DNA and RNA structure, base pairing rules, and viral replication. The key concepts covered are protein folding, membrane protein structure-function relationships, DNA major and minor groove polarity, nucleic acid composition, and complementary base pairing.

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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Session 6

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

Zero α-helices

One 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?

a. Right-handed if one considers the twist of the peptide planes, left-


handed if one considers the twist of strands along the sheet axis.

b. Steric clashes and the entropic contribution


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). 2
9
16 13
W K
K A
5 6
E K
12 K 17
T

V V 10

L A 3
8
A I
15 A V 14
A A
4 7
11 18
b. How are the polar and non-polar residues distributed around the helix
axis?

The polar and non-polar residues are roughly clustered on the opposite
faces of the helix.

Such a helix is called an amphipathic helix.

c. What is the net charge on the peptide at neutral pH?

There are 4 Lys (K) contributing +1 charge each, there is one Glu (E)
contributing -1 charge.

The net charge, therefore, is +3


d. How many aromatic amino acids are there?

One

Trp

e. How many amino acids with branched β-carbon are there?

Five

3 Val, 1 Ile, 1 Thr

f. What is the minimum integer number of residues that make a full


circle on a helical wheel?
There are 3.6 residues per turn

5 turns would place the Cα atoms on top of each other in the cross-
sectional view.

Therefore, 18 amino acids would make a full circle.


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?
The peptide bond is polar and it is not energetically favourable for the
polyamide to be in membrane core. In an, -helix , the polar peptide
backbone is involved in H-bonding and helix surface can be decorated by
hydrophobic residues.
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?
Left: 3ʹ→5ʹ Right: 5ʹ→3ʹ

b. What will be the polarity if you turn around and start walking
towards your starting point?
Same
e
c. Which direction would your hands go if you walk in the minor
groove?
Left: 5ʹ→3ʹ Right: 3ʹ→5ʹ
6. Given below are a few statements about nucleic acids. Identify the
correct ones and correct the incorrect ones.

a. DNA is the genetic material whereas RNA is not.


a. Both DNA and RNA are the genetic materials.

b. Only RNA contains thymine as the base


b. Only DNA contains thymine as the base
b. Only RNA contains uracil as the base
c. RNA and DNA both contain guanine and adenine as the pyrimidine
bases.
c. RNA and DNA both contain guanine and adenine as the purine bases.

d. DNA and RNA are the polymers of nucleosides.


d. DNA and RNA are the polymers of nucleotides.

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?

Yes
b. If so list them.

• The spacing between the bases is ~3.4 Å

• The termini of the molecule are wrongly


labelled: the 5’ and 3’ labelling is incorrect.
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.
Tertiary or secondary

b. What is the highest order (primary, secondary, tertiary, quaternary) of the


protein in its active state? Justify your answer.
Quaternary
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.
Dimerize
ii. The original pair A-M is changed to W-M. Justify your answer.
May not dimerize
9. Can you name a disease that is caused by a single amino acid
substitution in a protein?

Sickle-cell anaemia
E6V substitution in the β-globin chain
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.


Nucleic acid, phospholipids
ii. Which of the viral macromolecules be labelled with 35S.
Protein
iii. Which of the viral macromolecules be labelled with 15N.
Protein, Nucleic acid, possibly phospholipids as well
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?


It is a virus with single-stranded DNA as the genetic material.
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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