Question 1

The formation of open complex usually forms in GC rich regions of DNA due to the decreased number of hydrogen bonds.

Accepted Answer

The formation of open complexes typically occurs in AT-rich regions of DNA because AT pairs have two hydrogen bonds, which are easier to break compared to the three hydrogen bonds in GC pairs, making AT-rich regions more prone to unwinding.

Question 2

What is the correct order of elements that comprise a functional protein encoding gene in a prokaryote?

Accepted Answer

In a prokaryotic gene, the regulatory region comes first, followed by the promoter, the transcribed region, and finally the terminator. The regulatory region contains the binding sites for specific regulatory molecules that control the expression of the gene. The promoter is the site where RNA polymerase binds to initiate transcription. The transcribed region contains the DNA sequence that is transcribed into mRNA. The terminator signals the end of transcription. Choice B is the correct order of these elements.

Question 3

The Prinbow box contains a CACAAC consensus sequence located in the -100 region of the promoter.

Accepted Answer

There is no such thing as a "Prinbow box." Additionally, the CACAAC sequence is not a known consensus sequence for transcription factor binding.

Question 4

What do both the rho-dependent and rho-independent mechanisms of termination have in common?

Accepted Answer

Both the rho-dependent and rho-independent mechanisms of termination require the formation of a stem-loop structure to signal the end of transcription.

Question 5

The term ribozyme is given to catalytic RNA molecules.

Accepted Answer

This is correct. The term ribozyme is specifically used to describe RNA molecules that can catalyze chemical reactions.

Question 6

A main function of TFIID is

Accepted Answer

TFIID is a transcription factor that recognizes the TATA box, a DNA sequence commonly found in the promoter region of eukaryotic genes. TFIID binds to the TATA box and recruits other transcription factors and RNA polymerase II to the promoter to initiate transcription. Choices B, C, and D are not functions of TFIID.

Question 7

In eukaryotes, enhancers must be close to the promoter to have an effect

Accepted Answer

Enhancers can be located either upstream, downstream or even within introns of the gene they regulate. They can interact with the promoter region through DNA looping and protein-protein interactions, even if they are several kilobases away from the promoter.

Question 8

What structural motif is most commonly used by transcription factors in binding to DNA?

Accepted Answer

The helix-turn-helix motif is the most commonly used structural motif by transcription factors in binding to DNA. It consists of two α-helices separated by a turn, with the first helix inserting into the major groove of DNA to provide sequence specificity. Zinc fingers, leucine zipper, and homeodomain motifs can also be used for DNA binding, but they are less commonly used.

Question 9

In the process of RNA editing adenine or cytosine may be deaminated and the result is

Accepted Answer

In RNA editing, adenine can be deaminated to inosine, and cytosine can be deaminated to uracil (not thymidine as stated in option A, but the concept of change is correct). These changes can indeed result in new codons, which can alter the protein produced. Therefore, answers A and C are correct, making D the correct choice.

Question 10

The process of RNA editing can alter the base sequence of the mRNA following transcription.

Accepted Answer

RNA editing can change the base sequence of mRNA after transcription by adding, deleting, or changing nucleotides. This process can result in different protein products than what would be produced from the unedited mRNA sequence.

Question 11

What is the purpose of phosphorylating the carboxy terminal domain (CTD)?

Accepted Answer

Phosphorylation of the carboxy terminal domain (CTD) of RNA polymerase II allows for the transition from the initiation stage to the elongation stage of transcription.

Question 12

What occurs In both prokaryotic and eukaryotic tRNA maturation?

Accepted Answer

In both prokaryotic and eukaryotic tRNA maturation, the pre tRNA molecule is trimmed by exo and endonucleases to remove any extra nucleotides present at the ends of the molecule. This process is crucial for the formation of a mature and functional tRNA molecule. However, the other options listed (B, C, and D) are not common to both prokaryotic and eukaryotic tRNA maturation. Eukaryotic tRNA molecules are capped at the 5' end, but prokaryotic tRNA molecules are not. Splicing occurs in some eukaryotic tRNA molecules that contain introns, but this does not occur in prokaryotic tRNA molecules. RNA editing is a rare process that occurs in some eukaryotic tRNA molecules, but it is not found in prokaryotic tRNA molecules.

Question 13

What is a mechanism by which tRNA is processed in E. coli?

Accepted Answer

RNaseP is a ribonucleoprotein enzyme that cleaves the precursor tRNA at the 5' end, resulting in the correct mature tRNA. This processing is essential for the tRNA to be functional in translation.

Question 14

During the initiation phase of transcription the sigma (σ) factor, which is bound to RNA polymerase, binds into the major groove of DNA and recognizes sequence elements at the promoter. This process forms a closed complex

Accepted Answer

During the initiation phase of transcription, the sigma factor binds to RNA polymerase and recognizes sequence elements at the promoter, forming a closed complex.

Question 15

In bacterial RNA polymerase, the catalytic subunits are Beta and Beta'

Accepted Answer

The catalytic subunits of bacterial RNA polymerase are Beta and Beta'.

Question 16

In prokaryotes elongation requires the release of the sigma factor, while in eukaryotes the Mediator is involved.

Accepted Answer

In prokaryotes, the sigma factor is released after initiation to allow the RNA polymerase to proceed with elongation. In eukaryotes, the Mediator complex is involved in bridging the transcriptional machinery and gene-specific regulatory proteins, playing a crucial role in the regulation of transcription elongation.

Question 17

What is unusual about the 5' cap found on almost all eukaryotic mRNAs?

Accepted Answer

The 5' cap found on almost all eukaryotic mRNAs is unusual because the nucleotide added is a guanine methylated at N7 and the bond is created between the phosphate group on the guanine and the phosphate on the terminal nucleotide. This type of bond is not a typical phosphodiester bond.

Question 18

What snRNP holds the exons in place so that they can be connected after the intron is removed?

Accepted Answer

U5 snRNP holds the exons in place so they can be connected after the intron is removed. U1 snRNP is responsible for recognizing the 5' splice site, U2 snRNP recognizes the branch point, and U6 snRNP catalyzes the splicing reaction.

Question 19

What percentage of human pre-mRNA is alternatively spliced

Accepted Answer

It is estimated that about 70% of human pre-mRNA undergoes alternative splicing, allowing for a vast diversity of proteins to be produced from a limited number of genes.

Question 20

The RNA polymerase forms a closed complex during the process of elongation during transcription.

Accepted Answer

The RNA polymerase forms an open complex during the process of elongation, not a closed complex. A closed complex is formed during the initiation stage of transcription.

Quiz 12: Gene Transcription and Rna Modification