Molecular Biology and Genomics Practice Questions

Q: Examine this pedigree chart carefully. What type of transmission does it depict?

Holandric Inheritance. ***Holandric Inheritance*** - **Holandric inheritance** (Y-linked) shows the trait appearing only in **males** and being transmitted from **father to all his sons**. - The pedigree demonstrates classic **father-to-son transmission** pattern where affected fathers (I-1 and II-3) pass the trait to all their male offspring. *AR Inheritance* - **Autosomal recessive** traits typically **skip generations** and affect both males and females equally. - Affected individuals usually have **unaffected carrier parents**, which is not consistently observed in this pedigree. *AD Inheritance* - **Autosomal dominant** traits affect both sexes equally and show **vertical transmission** through generations. - An affected father would pass the trait to approximately **50% of all children** regardless of sex, not exclusively to sons. *X-Linked Recessive* - **X-linked recessive** inheritance affects males predominantly, but **affected fathers cannot pass** the trait to their sons. - Sons receive the **Y chromosome from father** and X chromosome from mother, making father-to-son transmission impossible.

Q: The term restriction map primarily refers to the mapping of sites of

Cleavage of restriction enzymes. ***Correct Option: Cleavage of restriction enzymes*** - A **restriction map** is a diagram showing the positions of **restriction enzyme recognition and cleavage sites** along a DNA molecule - These maps are fundamental tools in **molecular biology** for DNA manipulation, gene cloning, and genetic engineering - The map indicates where specific restriction endonucleases cut the DNA sequence *Incorrect: DNA fingerprinting* - **DNA fingerprinting** utilizes restriction enzymes in the RFLP (restriction fragment length polymorphism) technique, but a restriction map itself is not a DNA fingerprint - DNA fingerprinting analyzes **variable number tandem repeats (VNTRs)** for identification purposes - A restriction map is a tool that may be used in fingerprinting, but the map specifically refers to enzyme cleavage sites *Incorrect: Mutational hotspot* - A **mutational hotspot** is a genomic region with high mutation frequency - While mutations can alter restriction sites, the primary purpose of a restriction map is to identify enzyme cleavage sites, not mutation hotspots - These are distinct concepts in molecular genetics *Incorrect: Action of bacteriophages* - **Bacteriophages** are viruses that infect bacteria - Restriction enzymes evolved as a bacterial defense mechanism against phage DNA - However, a "restriction map" specifically refers to the location of enzyme cleavage sites on DNA, not the action of bacteriophages themselves

Q: Apolipoprotein B-48 is made by which process?

RNA editing. ***RNA editing*** - Apolipoprotein B-48 is synthesized from ApoB-100 mRNA through a process called **RNA editing** (specifically ApoB mRNA editing) - This involves a **cytidine deaminase enzyme (APOBEC-1)** that converts cytidine to uridine at position 6666, changing a glutamine codon (CAA) to a premature stop codon (UAA) in the small intestine - This results in a truncated protein that is 48% the length of ApoB-100 - ApoB-48 is produced in the **intestine**, while ApoB-100 (unedited) is produced in the **liver** *DNA editing* - DNA editing refers to permanent modifications in the DNA sequence itself - The ApoB gene remains unchanged; only the mRNA transcript is edited in intestinal cells - This is not the mechanism for producing ApoB-48 *RNA alternate splicing* - Alternative splicing involves selecting different combinations of exons from pre-mRNA to produce multiple mRNA isoforms - This process creates different protein variants through exon inclusion/exclusion - ApoB-48 production does not involve alternative splicing but rather direct nucleotide modification (C to U) within the coding sequence *RNA interference* - RNA interference (RNAi) is a biological process involving small RNA molecules (siRNA, miRNA) that silence gene expression - RNAi typically degrades mRNA or blocks translation - This process is not involved in generating a truncated protein like ApoB-48 from the same mRNA transcript

Q: Mark the false statement regarding mitochondrial DNA:

Does not show heteroplasmy. ***Does not show heteroplasmy*** - This statement is false because **mitochondrial DNA (mtDNA)** commonly exhibits **heteroplasmy**, meaning the presence of more than one type of mitochondrial genome within a cell or individual. - **Heteroplasmy** arises due to the presence of both normal and mutated mtDNA, which can be passed down from the mother. *AGA and AGG are stop codons in mitochondrial DNA* - This statement is true; in the **universal genetic code**, AGA and AGG code for **arginine**, but in **human mitochondrial DNA**, they serve as **stop codons**. - This is an example of the **differences** in genetic code interpretation between the nuclear genome and the mitochondrial genome. *Kearns-Sayre Syndrome is a large deletion in mitochondrial DNA* - This statement is true; **Kearns-Sayre Syndrome** is a well-known mitochondrial disorder caused by a **large single deletion** in the mitochondrial DNA. - This deletion often leads to chronic progressive **external ophthalmoplegia**, **retinal pigmentary degeneration**, and **cardiac conduction defects**. *1% of cellular DNA, 13 proteins of respiratory chain* - This statement is true; **mitochondrial DNA constitutes** approximately **1% of the total cellular DNA** by mass. - It codes for **13 essential proteins** that are part of the **electron transport chain** (respiratory chain) complexes in the mitochondrion, along with ribosomal RNAs (rRNAs) and transfer RNAs (tRNAs).

Q: Klenow fragment is formed by loss of fragment having which activity?

5'- 3' exonuclease. ***5'- 3' exonuclease*** - The **Klenow fragment** is obtained by proteolytic cleavage of **DNA Polymerase I** from *E. coli*. - This process removes the domain responsible for the **5' → 3' exonuclease activity**, leaving the polymerase and 3' → 5' exonuclease activities intact. *5'- 3' polymerase* - The **Klenow fragment retains** the **5' → 3' polymerase activity**, which is essential for DNA synthesis. - This activity synthesizes new DNA strands in the **5' to 3' direction**. *3'- 5' polymerase* - **DNA Polymerase I** (and thus the Klenow fragment) does not possess **3' → 5' polymerase activity**. - DNA polymerases always synthesize DNA in the **5' to 3' direction**. *3'- 5' exonuclease* - The **Klenow fragment retains** the **3' → 5' exonuclease activity**, which is crucial for **proofreading**. - This activity removes incorrectly paired nucleotides from the **3' end** of the growing DNA strand.

Q: In CRISPR-Cas9 system, which repair mechanism is predominantly used for genome editing?

Non-Homologous End Joining (NHEJ). ***Non-Homologous End Joining (NHEJ)*** - **NHEJ** is the most common and error-prone repair pathway in mammalian cells, directly ligating the broken DNA ends created by **Cas9**. - This pathway often results in **insertions** or **deletions (indels)** at the cut site, leading to gene knockout by causing frameshifts. *Nucleotide excision repair* - **Nucleotide excision repair (NER)** is primarily involved in removing bulky DNA adducts and pyrimidine dimers caused by UV radiation. - It involves excising a segment of DNA around the damage, not repairing double-strand breaks induced by CRISPR-Cas9. *Homology-Directed Repair (HDR)* - **HDR** is a precise repair mechanism that uses a homologous DNA template to repair double-strand breaks, allowing for precise gene editing (e.g., specific base changes, gene insertion). - While it can be leveraged in **CRISPR-Cas9**, it is less efficient and less common than **NHEJ** in most mammalian cells, especially when no exogenous template is provided. *Mismatch repair* - **Mismatch repair (MMR)** systems correct base-pair mismatches and small insertion/deletion loops that arise during DNA replication. - This mechanism is not involved in repairing the double-strand breaks generated by the **CRISPR-Cas9** system.

Q: Which of the following doesn't occur in 5' to 3' direction?

RNA editing. ***RNA editing*** - **RNA editing** involves modifications to **RNA molecules** after transcription, such as base insertions, deletions, or substitutions. - This process does not follow a 5' to 3' synthesis direction, unlike DNA or RNA synthesis. *DNA repair* - **DNA repair mechanisms**, such as **excision repair**, involve synthesizing new DNA to replace damaged sections. - This synthesis occurs in the **5' to 3' direction** by **DNA polymerases**. *Transcription* - **Transcription** is the process where **RNA polymerase** synthesizes an **RNA molecule** from a **DNA template**. - This synthesis always occurs in the **5' to 3' direction**, adding nucleotides to the 3' end of the growing RNA strand. *DNA replication* - **DNA replication** involves the synthesis of new **DNA strands** from a **template strand**. - **DNA polymerase** adds nucleotides exclusively in the **5' to 3' direction**, requiring a primer for initiation.

Q: Which of the following binds mRNA with ribosome in prokaryotes?

Shine Dalgarno sequence. ***Shine Dalgarno sequence*** - The **Shine-Dalgarno sequence** is a **ribosome binding site** in prokaryotic mRNA, typically located 3-9 nucleotides upstream of the start codon (AUG). - It base-pairs with a complementary sequence in the **16S rRNA** of the 30S ribosomal subunit, correctly positioning the ribosome for translation initiation. *7 methyl guanosine capping* - **7-methylguanosine capping** occurs at the 5' end of **eukaryotic mRNA** and is crucial for ribosome binding, protection from degradation, and export from the nucleus. - This modification is **absent in prokaryotic mRNA**, which does not require nuclear export or 5' capping for translation. *tRNA* - **tRNA (transfer RNA)** molecules are responsible for carrying specific **amino acids** to the ribosome and recognizing corresponding codons on the mRNA. - While essential for protein synthesis, tRNA itself **does not bind mRNA to the ribosome**; instead, it mediates the amino acid incorporation based on the mRNA sequence once the ribosome is bound. *Poly A tail* - The **poly-A tail** is a long stretch of adenine nucleotides added to the **3' end of eukaryotic mRNA**, important for stability and translation efficiency. - It is **largely absent in prokaryotic mRNA** and does not play a role in ribosome binding in prokaryotes.

Q: In DNA replication, which enzyme fills gaps left by RNA primer removal?

DNA polymerase I. ***DNA polymerase I*** - This enzyme possesses **5' to 3' exonuclease activity** which is used to remove the RNA primers - It also has **5' to 3' polymerase activity** to synthesize DNA and fill the gaps left by primer removal - This dual function makes it uniquely suited for **"nick translation"** - the process of removing primers and filling gaps in Okazaki fragments *Primase* - **Synthesizes short RNA primers** (8-12 nucleotides) that provide a free 3'-OH group for DNA polymerase to initiate DNA synthesis - It does not fill gaps or remove primers during replication - Functions only at the initiation phase of DNA synthesis *DNA polymerase III* - The **primary replicative enzyme** responsible for synthesizing the bulk of new DNA in both the leading and lagging strands - It lacks the 5' to 3' exonuclease activity needed for primer removal and gap filling - Extends RNA primers but cannot remove them *Helicase* - Responsible for **unwinding the DNA double helix** at the replication fork by breaking hydrogen bonds between complementary base pairs - Creates the replication bubble but does not participate in primer processing or gap filling - Works ahead of the DNA polymerases

Question 1

Examine this pedigree chart carefully. What type of transmission does it depict?

Accepted Answer

Holandric Inheritance

Answer

AR Inheritance

Answer

AD Inheritance

Answer

X-Linked Recessive

Question 2

The term restriction map primarily refers to the mapping of sites of

Accepted Answer

Cleavage of restriction enzymes

Answer

DNA fingerprinting

Answer

Mutational hotspot

Answer

Action of bacteriophages

Question 3

Apolipoprotein B-48 is made by which process?

Accepted Answer

RNA editing

Answer

DNA editing

Answer

RNA alternate splicing

Answer

RNA interference

Question 4

Mark the false statement regarding mitochondrial DNA:

Accepted Answer

Does not show heteroplasmy

Answer

AGA and AGG are stop codons in mitochondrial DNA

Answer

Kearns-Sayre Syndrome is a large deletion in mitochondrial DNA

Answer

1% of cellular DNA, 13 proteins of respiratory chain

Question 5

Klenow fragment is formed by loss of fragment having which activity?

Accepted Answer

5'- 3' exonuclease

Answer

5'- 3' polymerase

Answer

3'- 5' polymerase

Answer

3'- 5' exonuclease

Question 6

In CRISPR-Cas9 system, which repair mechanism is predominantly used for genome editing?

Accepted Answer

Non-Homologous End Joining (NHEJ)

Answer

Nucleotide excision repair

Answer

Mismatch repair

Answer

Homology-Directed Repair (HDR)

Question 7

Which of the following doesn't occur in 5' to 3' direction?

Accepted Answer

RNA editing

Answer

DNA repair

Answer

Transcription

Answer

DNA replication

Question 8

Which of the following binds mRNA with ribosome in prokaryotes?

Accepted Answer

Shine Dalgarno sequence

Answer

7 methyl guanosine capping

Answer

tRNA

Answer

Poly A tail

Question 9

Assertion: DNA methylation leads to gene silencing. Reason: Methylation prevents binding of transcription factors to promoter regions.

Accepted Answer

Both assertion and reason are true and reason is the correct explanation.

Answer

Assertion is true but reason is false.

Answer

Both assertion and reason are true but reason is not the correct explanation.

Answer

Both assertion and reason are false.

Question 10

In DNA replication, which enzyme fills gaps left by RNA primer removal?

Accepted Answer

DNA polymerase I

Answer

Primase

Answer

DNA polymerase III

Answer

Helicase

Molecular Biology and Genomics — MCQs

Molecular Biology and Genomics — MCQs

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