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Q.1 (Compulsory): Give short answers
a. Differentiate between DNA circular and superhelical DNA
Feature Circular DNA Superhelical DNA
Covalently closed DNA forming a Circular DNA that is further twisted or coiled
Structure
simple circle upon itself
Twisted, underwound or overwound forming
Topology Relaxed circular structure
supercoils
Common in plasmids, bacterial Often found in bacteria and plasmids under
Occurrence
chromosomes physiological conditions
Helps in compacting DNA and regulating
Function Stable storage of genetic material
replication/transcription
Visual Smooth circle under electron Appears as twisted coils or loops under electron
Appearance microscopy microscopy
b. What is renaturation?
Renaturation is the process by which single-stranded nucleic acids (DNA or RNA) reform a
double-stranded structure after being denatured (separated) by heat or chemicals.
Complementary base pairing allows the strands to reassociate and regain their native helical
structure.
c. Differentiate between alpha helix and beta pleated sheet of protein
Feature Alpha Helix Beta Pleated Sheet
Shape Spiral or helical Sheet-like, zigzag pattern
Hydrogen Hydrogen bonds between every 4th Hydrogen bonds between adjacent
Bonding amino acid along the backbone strands (parallel or antiparallel)
Stability More flexible and elastic Rigid and strong
Examples Found in keratin, myoglobin Found in silk fibroin, beta-keratin
d. Write at least four functions of proteins
1. Structural support: Proteins like collagen and keratin provide support to tissues.
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2. Catalysis: Enzymes accelerate biochemical reactions.
3. Transport: Hemoglobin transports oxygen; membrane proteins transport ions and
molecules.
4. Signaling: Hormones and receptor proteins mediate communication between cells.
5. Defense: Antibodies protect against pathogens.
Q.2: Discuss synthesis of DNA briefly
DNA synthesis, or DNA replication, is a semi-conservative process that occurs during the S-
phase of the cell cycle. Each new DNA molecule contains one parental strand and one newly
synthesized strand. The main steps include:
1. Initiation:
Replication begins at specific sites called origins of replication.
Helicase unwinds the double helix, creating a replication fork.
Single-strand binding proteins (SSBs) stabilize unwound DNA.
2. Primer synthesis:
Primase synthesizes short RNA primers complementary to the template strand.
3. Elongation:
DNA polymerase adds nucleotides to the 3’ end of the primer in a 5’ → 3’ direction.
The leading strand is synthesized continuously, while the lagging strand is
synthesized in fragments (Okazaki fragments).
4. Primer removal and ligation:
RNA primers are removed by RNase H or DNA polymerase I.
DNA ligase joins the Okazaki fragments to form a continuous strand.
5. Proofreading:
DNA polymerases have 3’→5’ exonuclease activity to correct errors.
Q.3: Define sequencing. Discuss any method used to sequence nucleic acid
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Definition:
Sequencing is the process of determining the exact order of nucleotides (A, T, G, C) in a DNA or
RNA molecule. It allows us to identify genes, mutations, and regulatory regions.
Sanger (Dideoxy) Sequencing Method:
This is a classical method for DNA sequencing.
Principle: DNA polymerase synthesizes a complementary strand using a DNA template, but
incorporation of dideoxynucleotides (ddNTPs) terminates synthesis at specific bases.
Steps:
1. DNA template is denatured into single strands.
2. A primer is annealed to the template.
3. DNA polymerase extends the primer in the presence of normal deoxynucleotides (dNTPs)
and small amounts of labeled ddNTPs (ddATP, ddTTP, ddGTP, ddCTP).
4. Incorporation of ddNTP terminates elongation, producing fragments of different lengths.
5. Fragments are separated by gel electrophoresis, and the sequence is read based on the
labeled ddNTPs.
Applications: Mutation detection, genome sequencing, and gene analysis.
Q.4: Explain general mechanism of transcription
Transcription is the process of synthesizing RNA from a DNA template. It occurs in the nucleus
of eukaryotes and cytoplasm in prokaryotes.
Steps of Transcription:
1. Initiation:
RNA polymerase binds to a promoter region on DNA.
In eukaryotes, transcription factors help RNA polymerase locate the promoter.
The DNA strands are unwound to expose the template strand.
2. Elongation:
RNA polymerase moves along the DNA template, synthesizing RNA in the 5’ → 3’
direction by adding ribonucleotides complementary to the DNA template.
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The RNA strand grows continuously.
3. Termination:
RNA polymerase reaches a termination signal on DNA.
In prokaryotes, termination may occur via rho-dependent or rho-independent
mechanisms.
In eukaryotes, transcription continues beyond the coding sequence and RNA is
processed (capping, polyadenylation, splicing).
4. Post-transcriptional modifications (eukaryotes only):
Addition of 5’ cap and poly-A tail.
Splicing removes introns to form mature mRNA ready for translation.
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