TRANSCRIPTION

• The production of RNA copies from a DNA template is known as transcription. 
• It is catalyzed by a specific enzyme RNA polymerase or transcriptase. 
• During this process, only one strand of DNA duplex is known as template strand or antisense strand. 
• This results in the production of m-RNA molecules having a base sequence complementary to the template DNA strand. 
• It should be noted here that the sense. strand or coding strand of DNA is now copied and has the same base sequence as the RNA produced by the antisense strand.

• The RNA polymerase is a complex enzyme and usually consists of a larger protein part (apoenzyme), which is known as core enzyme and a cofactor, which is known as sigma factor. 
• The two combine to produce the complete enzyme of holoenzyme. 
• Unless and until the two parts of RNA polymerase do not combine with each other, it is not functional. 
• As far as the nature of RNA polymerase in prokaryotes and eukaryotes is concerned, it shows much diversity. 
• While in prokaryotes like E.coli a single species of this enzyme is found, at least three distinct RNA polymerases have been reported in nuclei of most eukaryotes. 
• These have been named as : 

1.  RNA polymerase-I or A, 
2.  RNA polymerase-II or B and
3.  RNA Polymerase-III or C. 

• They have different functions as:

RNA polymerase-I or A: 

• It is located in the nucleolus and responsible for the synthesis of rRNA.

RNA polymerase-II or B: 

• It is found in the nucleoplasm and is responsible for the synthesis of hnRNA which is a precursor of mRNA.

RNA polymerase-III or C: 

• It is also found in the nucleoplasm. It is responsible for the production of 5s rRNA and tRNA.

Promoters for RNA Polymerase II The transcription unit 

• A transcription unit is a stretch of DNA that codes for an RNA molecule and the sequences necessary for its transcription. 
• Within a transcription unit are three critical regions: 
• a Promoter ,
• a RNA-coding Region, and
• a Transcription Termination Site. 

1. The promoter is a DNA sequence that the transcription apparatus recognizes and binds. 

• Transcription apparatus comprises RNA polymerase and certain proteins (known as Transcription Factors) which help transcription. 
• The promoter indicates which of the two DNA strands is to be read as the template and the direction of transcription.
•  It also determines the transcription start site, the first nucleotide that will be transcribed into RNA. 
• In most transcription units, the promoter is located next to the transcription start site but is not, itself, transcribed.

• 2. The second critical region of the transcription unit is the RNA-coding region, a sequence of DNA nucleotides that is copied into an RNA molecule.
• 3. The third component of the transcription unit is the Transcription 

• Termination Site, a sequence of nucleotides that signals where transcription is to end. 
• These sites are also called Terminators. 
• The Terminators are well defined in prokaryotic genomes but not so in Eukaryotes.

GENERAL FEATURES of TRANSCRIPTION

•  Broadly, the process appears to be similar to DNA replication, where one DNA strand acts as a template for the 5’3′ directed synthesis of a complementary strand.
•  However, a profound difference lies in the chemical nature of the complementary molecule.
•  In transcription, it is RNA. Hence, instead of deoxyribonucleotides, ribonucleotides are found. Moreover, Thymine is replaced by Uracil.
•  During Transcription in any given region, only one DNA strand is used as template, while in replication both the strands of parent DNA molecule act as template.
• RNA chain synthesis does not require any primer; it can start de novo.
• The reaction is catalyzed by enzymes called RNA polymerases.
• For the RNA synthesis, the polymerases need ribonucleotide triphosphates [rNTPs]. 
• This is a similarity with DNA polymerases.
• RNA Polymerases can initiate transcription only at specific nucleotide sequences. 
• Such nucleotide sequences are designated as promoter sequences. 
• Therefore, promoter sites are the locations on the DNA molecule where transcription begins.
• RNA polymerases are also capable of opening the DNA double helix locally. 
• Hence, there is no need for helicases. 
• Moreover, as transcription proceeds the same polymerase reseals the double strand too. By this mechanism, generation of torsion is avoided. 
• The locally unwound site of a DNA molecule is called a transcription bubble.
• The process of transcription can also be subdivided into three stages:
• A. Initiation
• B. Elongation
• C. Termination
• Molecular biologists often use the terms upstream and downstream to refer to the direction of transcription and the location of nucleotide sequences surrounding the RNA- coding sequence. 
• The transcription apparatus is said to move downstream during transcription; it binds to the promoter (which is usually upstream of the start site) and moves toward the terminator (which is downstream of the start site).

Promoter, enhancer and silencer sites for initiation of transcription in eukaryotes

• In eukaryotes there are three RNA polymerases:

 RNA polymerase I or RNAPI 

• for synthesis of pre-rRNA; 

RNA polymerase II or RNAPII 

• for synthesis of re-mRNA or hnRNA and several snRNAs, and 

RNA polymerase III or RNAPIII 

• for synthesis of 5S RNA, tRNA. 
• Different promoter sequences have been identified for different RNA polymerases.

RNA Polymerases

1. Which RNA polymerase synthesizes tRNA in eukaryotes?
   A. RNA Pol I
   B. RNA Pol II
   C. RNA Pol III
   Answer: C
2. RNA polymerase-I in eukaryotes is located in:
   A. Nucleoplasm
   B. Nucleolus
   C. Cytoplasm
   Answer: B
3. The sigma factor in prokaryotic RNA polymerase is a:
   A. Core enzyme
   B. Cofactor
   C. Terminator
   Answer: B
4. Which RNA polymerase transcribes hnRNA (pre-mRNA)?
   A. RNA Pol I
   B. RNA Pol II
   C. RNA Pol III
   Answer: B
5. 5S rRNA is synthesized by:
   A. RNA Pol I
   B. RNA Pol II
   C. RNA Pol III
   Answer: C
6. RNA polymerase-III is responsible for producing:
   A. mRNA
   B. tRNA
   C. rRNA
   Answer: B

Transcription Components

7. The promoter in a transcription unit is:
   A. Part of the RNA-coding region
   B. Located upstream of the transcription start site
   C. A termination signal
   Answer: B
8. Which component signals the end of transcription?
   A. Promoter
   B. Enhancer
   C. Terminator
   Answer: C
9. A transcription bubble refers to:
   A. A region of unwound DNA
   B. The RNA-DNA hybrid
   C. The terminator sequence
   Answer: A
10. The sense strand of DNA has the same sequence as:
    A. Template strand
    B. Newly synthesized RNA
    C. Antisense strand
    Answer: B
11. The RNA-coding region is:
    A. A promoter sequence
    B. Copied into RNA
    C. A termination signal
    Answer: B
12. Enhancers and silencers regulate transcription in:
    A. Prokaryotes
    B. Eukaryotes
    C. Both
    Answer: B

Transcription Process

13. RNA synthesis occurs in which direction?
    A. 3’→5’
    B. 5’→3’
    C. Both directions
    Answer: B
14. Transcription in eukaryotes requires:
    A. Sigma factors
    B. Transcription factors
    C. Primers
    Answer: B
15. Which nucleotide replaces thymine in RNA?
    A. Adenine
    B. Uracil
    C. Guanine
    Answer: B
16. Initiation of transcription begins with binding to the:
    A. Terminator
    B. Promoter
    C. Coding region
    Answer: B
17. During elongation, RNA polymerase:
    A. Adds nucleotides to the 5’ end
    B. Requires a primer
    C. Reseals the DNA double helix
    Answer: C
18. Termination in prokaryotes is signaled by:
    A. Promoters
    B. Well-defined terminators
    C. Enhancers
    Answer: B

Prokaryotes vs. Eukaryotes

19. A single RNA polymerase species is found in:
    A. Eukaryotes
    B. Prokaryotes
    C. Both
    Answer: B
20. Well-defined terminators are characteristic of:
    A. Prokaryotes
    B. Eukaryotes
    C. Both
    Answer: A
21. RNA polymerase holoenzyme in prokaryotes includes:
    A. Core enzyme + sigma factor
    B. RNA Pol I + II
    C. DNA ligase
    Answer: A
22. Eukaryotic RNA Pol II binds to the:
    A. TATA box
    B. CAAT box
    C. GC box
    Answer: A

Enzymes and Mechanisms

23. RNA polymerase can:
    A. Unwind DNA without helicase
    B. Require primers
    C. Synthesize DNA
    Answer: A
24. The core enzyme of RNA polymerase becomes functional only when combined with:
    A. Sigma factor
    B. Rho factor
    C. Transcription factors
    Answer: A
25. Transcription in eukaryotes is inhibited by:
    A. Enhancers
    B. Silencers
    C. Promoters
    Answer: B
26. RNA synthesis does NOT require:
    A. Ribonucleotides
    B. A primer
    C. DNA template
    Answer: B

RNA Types and Functions

27. hnRNA is a precursor to:
    A. tRNA
    B. mRNA
    C. rRNA
    Answer: B
28. The primary function of RNA Pol I is to synthesize:
    A. tRNA
    B. rRNA
    C. mRNA
    Answer: B
29. Which RNA is synthesized by RNA Pol II?
    A. 5S rRNA
    B. tRNA
    C. hnRNA
    Answer: C

DNA Strands and Templates

30. The template strand is also called the:
    A. Sense strand
    B. Antisense strand
    C. Coding strand
    Answer: B
31. The coding strand of DNA has a sequence identical to:
    A. The RNA transcript
    B. The template strand
    C. The terminator
    Answer: A
32. During transcription, only _____ strand of DNA is used.
    A. One
    B. Both
    C. Neither
    Answer: A

Transcription Stages

33. The first stage of transcription is:
    A. Elongation
    B. Termination
    C. Initiation
    Answer: C
34. During elongation, the transcription bubble:
    A. Moves with the polymerase
    B. Remains stationary
    C. Contains single-stranded DNA
    Answer: A
35. Termination in eukaryotes is less defined due to:
    A. Absence of terminators
    B. Post-transcriptional modifications
    C. Multiple RNA polymerases
    Answer: B

Molecular Features

36. Thymine in DNA is replaced by _____ in RNA.
    A. Adenine
    B. Uracil
    C. Cytosine
    Answer: B
37. RNA polymerase uses _____ for synthesis.
    A. dNTPs
    B. rNTPs
    C. ATP only
    Answer: B
38. The transcription apparatus moves:
    A. Upstream
    B. Downstream
    C. Randomly
    Answer: B

Regulatory Elements

39. The TATA box is part of the:
    A. Terminator
    B. Promoter
    C. Coding region
    Answer: B
40. Silencers in eukaryotes:
    A. Enhance transcription
    B. Repress transcription
    C. Bind RNA Pol III
    Answer: B
41. Promoters for RNA Pol II are recognized by:
    A. Sigma factors
    B. Transcription factors
    C. Ribosomes
    Answer: B

Comparative Analysis

42. In replication, both DNA strands act as templates, but in transcription:
    A. Only one strand is used
    B. Both strands are used
    C. No template is needed
    Answer: A
43. Unlike DNA replication, transcription:
    A. Uses uracil
    B. Requires helicase
    C. Synthesizes a double-stranded molecule
    Answer: A

Advanced Concepts

44. The term “upstream” in transcription refers to regions:
    A. After the start site
    B. Before the start site
    C. Within the coding region
    Answer: B
45. Transcription factors assist in:
    A. RNA splicing
    B. Binding RNA polymerase to DNA
    C. Terminating transcription
    Answer: B
46. Which is NOT a function of RNA polymerase?
    A. Unwinding DNA
    B. Adding nucleotides
    C. Proofreading RNA
    Answer: C

Miscellaneous

47. RNA synthesis starts _____ in transcription.
    A. At random sites
    B. Only at promoters
    C. Without a template
    Answer: B
48. The sigma factor’s role is to:
    A. Terminate transcription
    B. Help RNA polymerase recognize promoters
    C. Unwind DNA
    Answer: B
49. Eukaryotic RNA Pol I is primarily involved in synthesizing:
    A. mRNA
    B. rRNA
    C. tRNA
    Answer: B
50. Which statement is FALSE about transcription?
    A. It uses ribonucleotides
    B. It requires a primer
    C. It occurs 5’→3’
    Answer: B