Nucleic Acid Biochemistry Practice Questions

Q: Which enzyme polymerises Okazaki fragments?

DNA polymerase III. ***DNA polymerase III*** - **DNA polymerase III** is the primary replicative enzyme in **prokaryotes (bacteria)** responsible for synthesizing new DNA strands, including the **polymerization of Okazaki fragments** on the lagging strand. - It possesses high processivity (can add ~500 nucleotides without dissociating), essential for rapid and efficient DNA synthesis during replication, adding nucleotides in a **5' to 3' direction**. - In **eukaryotes**, DNA polymerase δ (delta) performs the analogous function of polymerizing Okazaki fragments. *DNA polymerase I* - **DNA polymerase I** in prokaryotes primarily functions in **removing RNA primers** left by primase and **filling the resulting gaps** with DNA nucleotides. - It has 5' to 3' exonuclease activity for primer removal and polymerase activity for gap filling, but is **not the main enzyme for elongating Okazaki fragments**. - Its role is in **DNA repair and finishing replication**, not the extensive synthesis of Okazaki fragments. *DNA polymerase II* - **DNA polymerase II** in prokaryotes is primarily involved in **DNA repair mechanisms**, particularly in **restarting stalled replication forks** and responding to DNA damage. - It is not the main enzyme responsible for the polymerization of **Okazaki fragments** during normal DNA replication. *RNA polymerase* - **RNA polymerase** (specifically **primase**, a specialized RNA polymerase) synthesizes short **RNA primers** (8-12 nucleotides) during DNA replication, which provide the 3'-OH group necessary to initiate DNA synthesis. - It does not synthesize DNA or polymerize **Okazaki fragments**; its function is to create RNA primers, not extend DNA strands.

Q: A frameshift mutation does not affect the complete amino acid sequence if it occurs in multiples of what number?

3. ***3*** - A **frameshift mutation** occurs when nucleotides are inserted or deleted in a number not divisible by three, altering the **reading frame** of the codons. - If insertions or deletions occur in multiples of **three**, the reading frame is restored after the mutation, largely preserving the downstream amino acid sequence. *1* - An insertion or deletion of a single nucleotide (1) definitively causes a **frameshift mutation**. - This alters all subsequent **codons**, leading to a completely different amino acid sequence downstream from the mutation. *2* - An insertion or deletion of two nucleotides (2) also results in a **frameshift mutation**. - This change shifts the **reading frame**, leading to the production of an altered protein or a premature stop codon. *None of the options* - This option is incorrect because a specific number, **three**, can allow for a frameshift mutation to not affect the complete amino acid sequence. - Multiples of three maintain the original **reading frame** (although potentially adding or removing a specific amino acid), whereas other numbers guarantee a frameshift.

Q: Which type of RNA is primarily involved in gene silencing?

miRNA. ***miRNA*** - **miRNA** (microRNA) is a small non-coding RNA molecule that plays a crucial role in **post-transcriptional regulation of gene expression**. - It functions by binding to complementary messenger RNA (mRNA) molecules, leading to **mRNA degradation** or **inhibition of translation**, thereby silencing genes. - miRNA is the primary RNA type involved in **gene silencing** through the RNA interference (RNAi) pathway. *rRNA* - **rRNA** (ribosomal RNA) is a primary component of **ribosomes**, the cellular machinery responsible for protein synthesis. - Its main function is to **catalyze peptide bond formation** and provide structural integrity to the ribosome, not gene silencing. *tRNA* - **tRNA** (transfer RNA) is responsible for carrying specific **amino acids** to the ribosome during protein synthesis. - It acts as an adapter molecule, translating the **genetic code** in mRNA into an amino acid sequence. *mRNA* - **mRNA** (messenger RNA) carries genetic information from **DNA to ribosomes** for protein synthesis. - While mRNA can be targeted by gene silencing mechanisms (like miRNA), it is not the RNA type that performs the silencing function itself.

Q: Which type of RNA is most commonly associated with pseudouridine?

transfer RNA (tRNA). ***Transfer RNA (tRNA)*** - **Pseudouridine (ψ)** is one of the most abundant modified nucleosides in RNA, and **tRNA contains the highest proportion** of pseudouridine modifications among all RNA types. - **tRNA molecules can contain up to 10-15% modified bases**, with pseudouridine being particularly abundant in the **TψC arm** (thymine-pseudouridine-cytosine loop). - These modifications are critical for **tRNA stability, proper folding, and accurate codon-anticodon recognition** during translation. - Pseudouridine enhances base stacking and stabilizes RNA structure through additional hydrogen bonding capability. *Ribosomal RNA (rRNA)* - While rRNA does contain pseudouridine modifications, they are present in **lower proportions compared to tRNA**. - rRNA pseudouridine modifications do play important roles in **ribosomal assembly and function**, but tRNA remains the RNA type most commonly associated with this modification. *Messenger RNA (mRNA)* - **mRNA is generally much less modified** than tRNA or rRNA. - Pseudouridine modifications in mRNA are relatively rare in prokaryotes and were only recently discovered to be more common in eukaryotic mRNA. - When present, they may affect **mRNA stability and translation efficiency**. *DNA* - **DNA does not contain pseudouridine** as this is an RNA-specific modification. - Pseudouridine is formed by **post-transcriptional isomerization** of uridine residues in RNA.

Q: What does salvage purine synthesis refer to?

Synthesis of purine nucleotides from purine bases. ***Synthesis of purine nucleotides from purine bases*** - **Salvage pathways** recycle pre-existing purine or pyrimidine bases (from nucleic acid degradation) by re-attaching them to a **ribose phosphate** to form a new nucleotide. - This process is energy-efficient as it bypasses several steps of the de novo synthesis pathway, utilizing enzymes like **adenine phosphoribosyltransferase (APRT)** and **hypoxanthine-guanine phosphoribosyltransferase (HGPRT)**. *Synthesis of purine nucleotides from ribose-5-phosphate.* - While **ribose-5-phosphate** is a precursor, the complete synthesis from this molecule is part of the **de novo pathway**, which starts with PRPP (phosphoribosyl pyrophosphate) formation from ribose-5-phosphate. - This option does not specify the direct reuse of a pre-formed purine base, which is the hallmark of salvage. *Synthesis of purine nucleotides from simple precursors (de novo synthesis).* - **De novo synthesis** is the creation of nucleotides from scratch using simple metabolic precursors like amino acids (glycine, aspartate, glutamine), CO2, and THF derivatives. - This contrasts with salvage pathways, which recycle existing bases. *Synthesis of purine nucleotides from degraded RNA.* - Degraded RNA breaks down into **nucleotides**, which can then be further broken down into **purine bases** and ribose phosphates. - The direct synthesis of purine nucleotides from *degraded RNA* involves recovering the individual bases or nucleosides, then converting them to nucleotides via salvage, not directly using the entire degraded RNA.

Q: Which type of DNA polymerase is responsible for the replication of mitochondrial DNA?

DNA polymerase gamma. ***DNA polymerase gamma*** - **DNA polymerase gamma** is the sole DNA polymerase responsible for replicating and repairing the mitochondrial DNA in eukaryotic cells. - It consists of a large catalytic subunit and two smaller accessory subunits that provide **proofreading** and processivity functions. *DNA polymerase alpha* - **DNA polymerase alpha** is primarily involved in initiating DNA replication on both the leading and lagging strands of nuclear DNA. - It forms a complex with **primase** to synthesize short RNA primers followed by a short stretch of DNA. *DNA polymerase delta* - **DNA polymerase delta** is a key enzyme in nuclear DNA replication, primarily responsible for the **elongation of the lagging strand**. - It also plays a significant role in various DNA repair pathways, including **nucleotide excision repair**. *DNA polymerase beta* - **DNA polymerase beta** is mainly involved in **DNA repair processes**, specifically **base excision repair (BER)** in the nucleus. - It has a low processivity and lacks **proofreading activity**, making it unsuitable for bulk DNA replication.

Q: Which of the following molecular interactions are found in the structure of DNA?

All of the options. ***All of the options*** - All three types of molecular interactions listed are present in DNA structure, making this the correct answer. - **Hydrogen bonds** hold together the two strands of the DNA double helix, forming between complementary base pairs (A-T with 2 hydrogen bonds, G-C with 3 hydrogen bonds). - **Glycosidic bonds** (N-glycosidic bonds) link the nitrogenous bases to the C1' carbon of the deoxyribose sugar in each nucleotide. - **Covalent interactions** (phosphodiester bonds) form the strong, stable sugar-phosphate backbone by linking the 3' hydroxyl group of one sugar to the 5' phosphate group of the next. *Hydrogen bond* - This is a **true statement** - hydrogen bonds are essential structural components of DNA. - However, this option alone is **incomplete** as DNA structure also contains glycosidic bonds and covalent phosphodiester bonds. - If only hydrogen bonds were present, there would be no nucleotides or backbone structure. *Glycosidic bond* - This is a **true statement** - glycosidic bonds are present in every nucleotide of DNA. - However, this option alone is **incomplete** as DNA also requires hydrogen bonds for base pairing and phosphodiester bonds for the backbone. - Without other bonds, individual nucleotides could not form a functional double helix. *Covalent interactions* - This is a **true statement** - covalent phosphodiester bonds form the DNA backbone within each strand. - However, this option alone is **incomplete** as it doesn't account for glycosidic bonds (nucleotide formation) or hydrogen bonds (strand pairing). - While the strongest bonds in DNA, they alone cannot create the complete double helix structure.

Q: Which of the following is NOT a characteristic of the genetic code?

Overlapping. ***Overlapping*** - The genetic code is generally **non-overlapping**, meaning each nucleotide is part of only one codon, and codons are read sequentially. - An overlapping code would mean that a single nucleotide could be part of multiple codons, which is not how protein synthesis typically occurs. *Nonambiguous* - This statement IS a characteristic; each codon specifies **only one amino acid**, meaning there is no ambiguity about which amino acid will be added. - While multiple codons can specify the same amino acid, a single codon never specifies more than one different amino acid. *Universal* - This statement IS a characteristic; the genetic code is largely **universal** across almost all organisms, from bacteria to humans. - The same codons typically specify the same amino acids in different species, which supports the idea of common ancestry. *Degeneracy* - This statement IS a characteristic; the genetic code is **degenerate**, meaning that most amino acids are specified by more than one codon. - This redundancy helps protect against the effects of single-nucleotide mutations.

Q: What is attached to the 3' end of mRNA after transcription?

Poly-A tail. ***Poly-A tail*** - A **poly-A tail**, consisting of multiple adenosine monophosphates, is added to the **3' end of mRNA** after transcription to protect it from degradation. - This modification aids in the **transport of mRNA from the nucleus to the cytoplasm** and in its translation. *CCA* - The **CCA sequence** is found at the **3' end of tRNA**, not mRNA, and is critical for amino acid attachment. - It is added post-transcriptionally to tRNA molecules by the enzyme **tRNA nucleotidyltransferase**. *Intron* - **Introns** are non-coding regions within a gene that are transcribed into mRNA but are subsequently removed during **RNA splicing**, not added to the 3' end. - Their removal ensures that only the **coding regions (exons)** are translated into protein. *7-methylguanosine* - **7-methylguanosine** forms the **5' cap** of mRNA, which is added to the 5' end, not the 3' end. - This cap is important for **mRNA stability**, ribosome binding, and protection against degradation.

Q: What does Chargaff's rule state regarding the base pairing in DNA?

A=T, G=C. ***A=T, G=C*** - **Chargaff's rules** state that in any double-stranded DNA, the amount of **adenine (A)** is approximately equal to the amount of **thymine (T)**, and the amount of **guanine (G)** is approximately equal to the amount of **cytosine (C)**. - This equivalency reflects the specific **base pairing** in the DNA double helix, where A always pairs with T, and G always pairs with C. *A=G, T=C* - This statement is incorrect as it proposes an atypical and biologically inaccurate pairing between a **purine (A)** and another **purine (G)**, and a **pyrimidine (T)** with a **pyrimidine (C)**. - This combination would disrupt the uniform diameter of the DNA double helix required for its structural stability. *A=C, G=T* - This option is incorrect because it suggests pairing a purine (A) with a pyrimidine (C) and a purine (G) with a pyrimidine (T) in a way that is not observed in natural DNA. - Such pairings would also lead to an irregular width of the DNA molecule, destabilizing its structure. *Any combination possible* - This statement is false; base pairing in DNA is **highly specific** and not random due to chemical and structural constraints. - The specific pairing rules (**A with T, G with C**) are crucial for maintaining the consistent structure of the DNA double helix and for accurate DNA replication and transcription.

Question 1

Which enzyme polymerises Okazaki fragments?

Accepted Answer

DNA polymerase III

Answer

DNA polymerase I

Answer

DNA polymerase II

Answer

RNA polymerase

Question 2

A frameshift mutation does not affect the complete amino acid sequence if it occurs in multiples of what number?

Accepted Answer

3

Answer

1

Answer

2

Answer

None of the options

Question 3

Which type of RNA is primarily involved in gene silencing?

Accepted Answer

miRNA

Answer

rRNA

Answer

tRNA

Answer

mRNA

Question 4

Which type of RNA is most commonly associated with pseudouridine?

Accepted Answer

transfer RNA (tRNA)

Answer

messenger RNA (mRNA)

Answer

ribosomal RNA (rRNA)

Answer

DNA

Question 5

What does salvage purine synthesis refer to?

Accepted Answer

Synthesis of purine nucleotides from purine bases

Answer

Synthesis of purine nucleotides from ribose-5-phosphate

Answer

Synthesis of purine nucleotides from simple precursors (de novo synthesis)

Answer

Synthesis of purine nucleotides from degraded RNA

Question 6

Which type of DNA polymerase is responsible for the replication of mitochondrial DNA?

Accepted Answer

DNA polymerase gamma

Answer

DNA polymerase delta

Answer

DNA polymerase alpha

Answer

DNA polymerase beta

Question 7

Which of the following molecular interactions are found in the structure of DNA?

Accepted Answer

All of the options

Answer

Hydrogen bond

Answer

Glycosidic bond

Answer

Covalent interactions

Question 8

Which of the following is NOT a characteristic of the genetic code?

Accepted Answer

Overlapping

Answer

Universal

Answer

Degeneracy

Answer

Nonambiguous

Question 9

What is attached to the 3' end of mRNA after transcription?

Accepted Answer

Poly-A tail

Answer

CCA

Answer

Intron

Answer

7-methylguanosine

Question 10

What does Chargaff's rule state regarding the base pairing in DNA?

Accepted Answer

A=T, G=C

Answer

A=G, T=C

Answer

A=C, G=T

Answer

Any combination possible

Nucleic Acid Biochemistry — MCQs

Nucleic Acid Biochemistry — MCQs

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