Transcription in Prokaryotes and Eukaryotes: Mechanism, Regulation and Key Differences
Introduction
Transcription is a fundamental biological process in which genetic information from DNA is copied into RNA. This process is essential for gene expression and varies significantly between prokaryotes and eukaryotes. The differences arise due to variations in cellular complexity, transcription factors, and regulatory mechanisms. This study module explores the transcription mechanisms, regulatory strategies, and key distinctions between prokaryotic and eukaryotic transcription.
Prokaryotic transcription steps explained,
Eukaryotic transcription factors role,
Gene regulation in bacteria vs humans,
Transcription initiation process in cells,
Differences in transcription mechanisms.
Transcription in Prokaryotes
Prokaryotic transcription occurs in the cytoplasm and involves a simpler mechanism due to the absence of a nucleus. The key steps include initiation, elongation, and termination.
1. Mechanism of Transcription in Prokaryotes
Initiation
- RNA polymerase holoenzyme, consisting of a core enzyme and sigma factor (σ), binds to the promoter region of DNA.
- The promoter has two conserved sequences:
- -35 region (TTGACA)
- -10 region (Pribnow box, TATAAT)
- The sigma factor facilitates RNA polymerase binding and unwinding of DNA.
- Formation of the transcription bubble and the beginning of RNA synthesis.
Elongation
- Sigma factor dissociates after initiation, and RNA polymerase moves along the DNA template.
- Nucleotides are added complementary to the DNA strand in a 5’ to 3’ direction.
Termination
Two mechanisms exist for termination in prokaryotes:
- Rho-dependent termination: Rho protein binds to the nascent RNA, causing RNA polymerase to dissociate.
- Rho-independent termination: Formation of a GC-rich hairpin loop followed by a poly-U sequence causes transcription to end.
2. Regulation of Transcription in Prokaryotes
- Operon Model: Groups of genes regulated together.
- Example: Lac Operon (inducible) and Trp Operon (repressible).
- Regulatory Proteins: Activators and repressors control transcription.
- Sigma Factors: Different sigma factors recognize different promoters.
- Attenuation: A regulatory mechanism that affects elongation and termination.
Transcription in Eukaryotes
Eukaryotic transcription is more complex and occurs inside the nucleus. It involves multiple RNA polymerases, transcription factors, and post-transcriptional modifications.
1. Mechanism of Transcription in Eukaryotes
Initiation
- Three RNA polymerases play different roles:
- RNA Polymerase I: Transcribes rRNA genes.
- RNA Polymerase II: Transcribes mRNA and some snRNA genes.
- RNA Polymerase III: Transcribes tRNA and 5S rRNA genes.
- The promoter region contains TATA box (-25 region), GC box, and CAAT box.
- Transcription factors (TFs) like TFIID, TFIIA, and TFIIB help RNA polymerase II bind to the promoter.
- Formation of the pre-initiation complex (PIC) is essential for transcription initiation.
Elongation
- RNA polymerase moves along the DNA template, synthesizing RNA in a 5’ to 3’ direction.
- RNA processing occurs concurrently (e.g., capping, splicing).
Termination
- RNA Polymerase I: Uses a termination factor similar to rho-dependent termination.
- RNA Polymerase II: Transcription proceeds beyond the gene and then cleavage occurs.
- RNA Polymerase III: Uses a mechanism similar to rho-independent termination.
2. Regulation of Transcription in Eukaryotes
- Enhancers and Silencers: DNA sequences regulate transcription by interacting with activators or repressors.
- Chromatin Modifications:
- Histone Acetylation: Loosens chromatin and increases transcription.
- Histone Methylation: Can activate or repress transcription.
- DNA Methylation: Represses gene expression by preventing transcription factor binding.
- Transcription Factors: Examples include p53, NF-κB, and Myc, which regulate gene expression.
- Hormonal Regulation: Steroid hormones like cortisol influence transcription through receptor binding.
Key Differences Between Prokaryotic and Eukaryotic Transcription
| Feature | Prokaryotes | Eukaryotes |
|---|---|---|
| Location | Cytoplasm | Nucleus |
| RNA Polymerases | Single RNA polymerase | Three distinct RNA polymerases |
| Promoter Elements | -35 and -10 regions | TATA box, CAAT box, enhancers |
| Transcription Factors | Sigma factors | Multiple general transcription factors |
| Termination Mechanism | Rho-dependent/independent | Complex, includes polyadenylation signal |
| Post-Transcriptional Modifications | Absent | Capping, splicing, polyadenylation |
Conclusion
Transcription is a crucial process for gene expression in both prokaryotic and eukaryotic cells. While the basic principles remain the same, the mechanisms and regulatory elements differ significantly. Prokaryotic transcription is simpler and occurs quickly, whereas eukaryotic transcription is highly regulated and includes multiple post-transcriptional modifications.
Relevant Website Links
- Molecular Biology of the Cell – NCBI
- Transcription Mechanisms – Khan Academy
- Lac Operon Model – Nature
Further Reading
- RNA Polymerase Structure and Function
- Epigenetic Regulation of Transcription
- Gene Expression and Regulation
MCQs on “Transcription in Prokaryotes and Eukaryotes: Mechanism and Regulation”
1. Which enzyme is responsible for transcription in both prokaryotes and eukaryotes?
a) DNA polymerase
b) RNA polymerase ✅
c) Helicase
d) Ligase
Explanation: RNA polymerase catalyzes the synthesis of RNA from a DNA template. Prokaryotes have a single RNA polymerase, while eukaryotes have three major types (RNA Pol I, II, III).
2. In prokaryotic transcription, which subunit of RNA polymerase is responsible for recognizing the promoter?
a) α-subunit
b) β-subunit
c) σ-factor ✅
d) ω-subunit
Explanation: The sigma (σ) factor of prokaryotic RNA polymerase binds to the promoter and initiates transcription by recognizing the -10 and -35 consensus sequences.
3. What is the function of the promoter in transcription?
a) Terminate transcription
b) Initiate translation
c) Provide a binding site for RNA polymerase ✅
d) Degrade RNA
Explanation: The promoter is a DNA sequence that allows RNA polymerase to bind and start transcription. It contains conserved sequences such as the TATA box (-10 region in prokaryotes).
4. In eukaryotic transcription, which RNA polymerase is responsible for synthesizing mRNA?
a) RNA polymerase I
b) RNA polymerase II ✅
c) RNA polymerase III
d) Reverse transcriptase
Explanation: RNA polymerase II transcribes precursor mRNA (pre-mRNA) in eukaryotic cells, which is then processed to form mature mRNA.
5. Which of the following elements is found in the promoter region of eukaryotic genes transcribed by RNA polymerase II?
a) Pribnow box
b) TATA box ✅
c) Shine-Dalgarno sequence
d) Kozak sequence
Explanation: The TATA box is a conserved sequence found in eukaryotic promoters that helps RNA polymerase II bind and initiate transcription.
6. What is the role of rho protein in prokaryotic transcription?
a) It initiates transcription
b) It stabilizes the mRNA
c) It helps in transcription termination ✅
d) It enhances translation efficiency
Explanation: Rho protein is involved in rho-dependent transcription termination, where it binds to the RNA and disrupts the transcription complex.
7. Which modification occurs at the 5’ end of eukaryotic mRNA?
a) Polyadenylation
b) Splicing
c) 5’ capping ✅
d) Methylation of U residues
Explanation: A 7-methylguanosine (m7G) cap is added to the 5’ end of eukaryotic mRNA, aiding in stability and translation initiation.
8. Which of the following is NOT a component of the prokaryotic promoter?
a) -35 sequence
b) -10 sequence
c) TATA box ✅
d) UP element
Explanation: The TATA box is a characteristic of eukaryotic promoters, whereas prokaryotic promoters contain -10 and -35 sequences.
9. The poly-A tail in eukaryotic mRNA is added by:
a) RNA polymerase
b) Poly(A) polymerase ✅
c) DNA polymerase
d) Topoisomerase
Explanation: The poly(A) tail is added post-transcriptionally to the 3’ end of eukaryotic mRNA by poly(A) polymerase, increasing stability and aiding export from the nucleus.
10. Which transcription factor is essential for the binding of RNA polymerase II in eukaryotes?
a) TFIIA
b) TFIIB
c) TFIID ✅
d) TFIIF
Explanation: TFIID, which contains the TATA-binding protein (TBP), helps RNA polymerase II bind to the promoter.
11. The site of prokaryotic transcription occurs in the:
a) Nucleus
b) Cytoplasm ✅
c) Mitochondria
d) Nucleolus
Explanation: Since prokaryotes lack a nucleus, transcription occurs in the cytoplasm, allowing simultaneous translation.
12. Which process occurs only in eukaryotic transcription but not in prokaryotic transcription?
a) Splicing ✅
b) Initiation
c) Elongation
d) Termination
Explanation: Splicing removes introns from pre-mRNA and is unique to eukaryotes, as prokaryotic genes do not have introns.
13. What is the function of enhancers in transcription?
a) Promote transcription ✅
b) Inhibit translation
c) Bind ribosomes
d) Degrade mRNA
Explanation: Enhancers are DNA sequences that increase transcription efficiency by binding activator proteins.
14. In eukaryotic transcription, termination of mRNA transcription involves:
a) Rho protein
b) Hairpin loop formation
c) Polyadenylation signal (AAUAAA) ✅
d) Sigma factor
Explanation: The polyadenylation signal (AAUAAA) leads to cleavage and addition of a poly(A) tail, signaling termination.
15. Which type of RNA polymerase transcribes rRNA genes in eukaryotes?
a) RNA polymerase I ✅
b) RNA polymerase II
c) RNA polymerase III
d) Reverse transcriptase
Explanation: RNA polymerase I transcribes large rRNA genes (28S, 18S, and 5.8S rRNA).
16. In prokaryotes, transcription and translation are:
a) Separate processes
b) Occur simultaneously ✅
c) Take place in different compartments
d) Regulated by the nuclear membrane
Explanation: Prokaryotic transcription and translation occur simultaneously in the cytoplasm due to the absence of a nucleus.
17. Which protein is responsible for opening the DNA double helix during transcription?
a) DNA polymerase
b) RNA polymerase ✅
c) Helicase
d) Topoisomerase
Explanation: RNA polymerase itself unwinds the DNA to create a transcription bubble during initiation.
18. Which of the following acts as a transcriptional repressor in prokaryotes?
a) RNA polymerase
b) Sigma factor
c) Lac repressor ✅
d) Enhancer
Explanation: The Lac repressor binds to the operator of the lac operon to inhibit transcription when lactose is absent.
19. In the lac operon, which molecule functions as an inducer?
a) Glucose
b) Lactose ✅
c) ATP
d) cAMP
Explanation: Lactose (or allolactose) binds to the Lac repressor, removing it from the operator and allowing transcription.
20. The termination of transcription in prokaryotes by the formation of a hairpin loop is called:
a) Rho-dependent termination
b) Rho-independent termination ✅
c) Polyadenylation
d) 5’ capping
Explanation: In rho-independent termination, a GC-rich hairpin loop forms, causing RNA polymerase to detach from DNA.
21. The transcription of the tryptophan operon is regulated by:
a) Inducer binding
b) Riboswitches
c) Attenuation ✅
d) Enhancers
Explanation: The trp operon is regulated by attenuation, where a leader sequence controls termination based on tryptophan levels.
22. Which eukaryotic RNA polymerase transcribes tRNA?
a) RNA polymerase I
b) RNA polymerase II
c) RNA polymerase III ✅
d) Reverse transcriptase
Explanation: RNA polymerase III transcribes tRNA and 5S rRNA genes.
23. Which of the following is a coactivator in eukaryotic transcription?
a) Histone deacetylase
b) Mediator complex ✅
c) Lac repressor
d) Rho factor
Explanation: The Mediator complex bridges activator proteins and RNA polymerase II, enhancing transcription.
24. In eukaryotic cells, which histone modification promotes transcription?
a) Methylation
b) Acetylation ✅
c) Ubiquitination
d) Phosphorylation
Explanation: Histone acetylation reduces DNA-histone interaction, making chromatin more accessible for transcription.
25. Which of the following RNA polymerases is sensitive to α-amanitin?
a) RNA polymerase I
b) RNA polymerase II ✅
c) RNA polymerase III
d) Prokaryotic RNA polymerase
Explanation: RNA polymerase II is highly sensitive to α-amanitin, a toxin that inhibits transcription.
26. Which regulatory sequence is found upstream of eukaryotic genes and binds general transcription factors?
a) Enhancer
b) Promoter ✅
c) Operator
d) Silencer
Explanation: The promoter, including the TATA box, allows binding of general transcription factors for initiation.
27. In eukaryotic cells, which transcription factor recruits RNA polymerase II to the promoter?
a) TFIIA
b) TFIIB
c) TFIID
d) TFIIF ✅
Explanation: TFIIF helps RNA polymerase II bind the promoter along with TFIID and TFIIB.
28. Which of the following is NOT involved in eukaryotic transcription initiation?
a) RNA polymerase II
b) TATA-binding protein
c) Shine-Dalgarno sequence ✅
d) General transcription factors
Explanation: The Shine-Dalgarno sequence is involved in bacterial translation, not transcription.
29. Which enzyme removes introns from eukaryotic pre-mRNA?
a) DNA polymerase
b) RNA polymerase
c) Spliceosome ✅
d) Helicase
Explanation: The spliceosome removes introns from pre-mRNA and joins exons to form mature mRNA.
30. Which of the following best describes transcription in mitochondria?
a) Uses nuclear RNA polymerase
b) Uses mitochondrial RNA polymerase ✅
c) Occurs in the cytoplasm
d) Does not require a promoter
Explanation: Mitochondria have their own RNA polymerase and transcription system, independent of nuclear transcription.
