This set of Bioinformatics Multiple Choice Questions & Answers (MCQs) focuses on “Promoter and Regulatory Elements in Prokaryotes & Eukaryotes”.
1. In bacteria, transcription is initiated by DNA polymerase.
a) True
b) False
View Answer
Explanation: In bacteria, transcription is initiated by RNA polymerase, which is a multi-subunit enzyme. The σ subunit (e.g., σ70) of the RNA polymerase is the protein that recognizes specific sequences upstream of a gene and allows the rest of the enzyme complex to bind.
2. The upstream sequence where the σ protein binds constitutes the promoter sequence.
a) True
b) False
View Answer
Explanation: This includes the sequence segments located 35 and 10 base pairs (bp) upstream from the transcription start site. They are also referred to as the −35 and −10 boxes. For the σ70 subunit in Escherichia coli, for example, the −35 box has a consensus sequence of TTGACA. The –10 box has a consensus of TATAAT.
3. The promoter sequence may determine the expression of one gene or a number of linked genes downstream.
a) True
b) False
View Answer
Explanation: In the latter case, the linked genes form an operon. It is controlled by the promoter.
4. In addition to the RNA polymerase, there are also a number of DNA-binding proteins that facilitate the process of transcription.
a) True
b) False
View Answer
Explanation: These proteins are called transcription factors. They bind to specific DNA sequences to either enhance or inhibit the function of the RNA polymerase.
5. The specific DNA sequences to which the transcription factors bind are referred to as _____
a) replication elements
b) blocking factors
c) transcription factors
d) regulatory elements
View Answer
Explanation: The regulatory elements may bind in the vicinity of the promoter or bind to a site several hundred bases away from the promoter. The reason that the binding of the regulatory protein at long distance can still exert their effect is because of the flexible structure of DNA, which is able to bend and exert its effect by bringing the transcription factors in close contact with the RNA polymerase complex.
6. In eukaryotes, gene expression is not regulated by a protein complex formed between transcription factors and RNA polymerase.
a) True
b) False
View Answer
Explanation: Here, the gene expression is also regulated by a protein complex formed between transcription factors and RNA polymerase. However, eukaryotic transcription has an added layer of complexity in that there are three different types of RNA polymerase complexes, namely RNA polymerases I, II, and III.
7. Which of the following is untrue?
a) RNA polymerases I is responsible for the transcription of ribosomal RNA
b) RNA polymerases III is responsible for the transcription of tRNA
c) RNA polymerase II is exclusively responsible for transcribing protein-encoding genes
d) Synthesis of mRNAs is carried out by RNA polymerase I
View Answer
Explanation: Ach polymerase transcribes different sets of genes. RNA polymerase II is exclusively responsible for transcribing protein-encoding genes or synthesis of mRNAs.
8. In eukaryotes, genes often form an operon with a shared promoter.
a) True
b) False
View Answer
Explanation: Unlike in prokaryotes, where genes often form an operon with a shared promoter, each eukaryotic gene has its own promoter. The eukaryotic transcription machinery also requires many more transcription factors than its prokaryotic counterpart to help initiate transcription.
9. Eukaryotic RNA polymerase II does not directly bind to the promoter, but relies on a dozen or more transcription factors to recognize and bind to the promoter in a specific order before its own binding around the promoter.
a) True
b) False
View Answer
Explanation: The core of many eukaryotic promoters is a so-called TATA box, located 30 bps upstream from the transcription start site, having a consensus motif TATA (A/T) A (A/T). However, not all eukaryotic promoters contain the TATA box. Many genes such as housekeeping genes do not have the TATA box in their promoters.
10. The TATA box is often used as an indicator of the presence of a promoter.
a) True
b) False
View Answer
Explanation: In addition, many genes have a unique initiator sequence (Inr), which is a pyrimidine rich sequence with a consensus (C/T)(C/T)CA(C/T)(C/T). This site coincides with the transcription start site. Most of the transcription factor binding sites are located within 500 bp upstream of the transcription start site.
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