🔬biological chemistry i review
13.1 Transcription initiation, elongation, and termination
Last Updated on August 7, 2024
RNA transcription is a crucial process in gene expression. It involves copying DNA into RNA using RNA polymerase. The process has three main stages: initiation, elongation, and termination.
Initiation starts when RNA polymerase binds to a promoter region. Elongation continues as the enzyme adds nucleotides to the growing RNA chain. Termination occurs when the polymerase stops and releases the completed RNA transcript.
Transcription Initiation
RNA Polymerase and Promoter Recognition
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- RNA polymerase is the enzyme responsible for synthesizing RNA from a DNA template
- Promoter is a specific DNA sequence located upstream of a gene that signals the starting point for transcription
- RNA polymerase recognizes and binds to the promoter region to initiate transcription
- TATA box is a conserved DNA sequence (TATAAA) found in many eukaryotic promoters approximately 25-30 base pairs upstream of the transcription start site
Transcription Factors and Initiation Complex Formation
- Transcription factors are proteins that help regulate gene expression by binding to specific DNA sequences and promoting or inhibiting transcription
- General transcription factors (GTFs) are required for the initiation of transcription by RNA polymerase II in eukaryotes
- GTFs and RNA polymerase assemble at the promoter to form the initiation complex (also known as the preinitiation complex)
- The initiation complex unwinds the double-stranded DNA, allowing RNA polymerase to access the template strand and begin transcription
Transcription Elongation
RNA Synthesis and Strand Terminology
- Elongation is the process by which RNA polymerase extends the growing RNA chain by adding nucleotides complementary to the template strand
- Template strand (also known as the antisense strand) is the DNA strand that serves as a template for RNA synthesis, with the RNA being synthesized in the 5' to 3' direction
- Coding strand (also known as the sense strand) is the DNA strand that has the same sequence as the transcribed RNA, except for the substitution of uracil (U) for thymine (T)
- RNA polymerase uses the template strand to synthesize the complementary RNA molecule, which is identical in sequence to the coding strand except for the U-T substitution
5' Cap Addition
- 5' cap is a modified guanine nucleotide added to the 5' end of the growing RNA transcript during elongation
- The 5' cap protects the nascent RNA from degradation and plays a role in nuclear export and translation initiation
- Cap addition occurs when the RNA transcript is approximately 20-30 nucleotides long and is catalyzed by the enzyme guanylyltransferase
Transcription Termination
Termination Mechanisms
- Termination is the process by which RNA polymerase stops synthesizing RNA and dissociates from the DNA template
- Rho-dependent termination involves the Rho protein, which is an ATP-dependent helicase that binds to specific sequences on the nascent RNA and causes RNA polymerase to pause and dissociate from the DNA template
- Rho-independent termination (also known as intrinsic termination) relies on specific DNA sequences that form stable stem-loop structures in the nascent RNA, causing RNA polymerase to pause and dissociate without the need for additional factors
Poly-A Tail Addition
- Poly-A tail is a long sequence of adenine (A) nucleotides added to the 3' end of the RNA transcript after termination
- The poly-A tail is added by the enzyme poly(A) polymerase (PAP) and typically consists of 100-250 adenine residues in eukaryotes
- The poly-A tail protects the mRNA from degradation, facilitates nuclear export, and enhances translation efficiency by interacting with translation initiation factors (eIF4E and eIF4G)
Key Terms to Review (22)
Gene expression: Gene expression is the process by which information from a gene is used to synthesize functional gene products, usually proteins, which then carry out various functions in the cell. This process is fundamental to all cellular activities, affecting how cells respond to their environment, differentiate, and maintain homeostasis. It is closely linked to biochemical processes, the role of biomolecules in cellular functions, signaling pathways, and the steps of transcription and translation.
Initiation: Initiation is the first step in the processes of DNA replication, transcription, and translation, where the molecular machinery assembles at the start site of a gene or a DNA strand. This process is critical because it ensures that the correct sequence of nucleotides or amino acids is synthesized, setting the stage for accurate replication, expression, or protein synthesis. Successful initiation is essential for the proper functioning of all cellular processes that involve genetic information.
Rho-dependent termination: Rho-dependent termination is a mechanism in prokaryotic transcription where the Rho protein facilitates the release of the RNA polymerase from the DNA template at specific termination sites. This process occurs after the RNA chain has been synthesized and involves the Rho factor binding to the nascent RNA, moving along it, and ultimately causing the RNA polymerase to dissociate, ending transcription. This termination method is crucial for regulating gene expression and ensuring proper RNA processing.
Poly-A tail: A poly-A tail is a stretch of adenine nucleotides added to the 3' end of a newly synthesized messenger RNA (mRNA) molecule during the post-transcriptional modification process. This modification plays a crucial role in mRNA stability, nuclear export, and translation efficiency, linking it to essential steps in gene expression regulation.
Rho-independent termination: Rho-independent termination is a mechanism of transcription termination in prokaryotes that does not require the protein rho. This process relies on the formation of a stable hairpin loop in the RNA transcript, followed by a stretch of uracil residues. The hairpin structure causes the RNA polymerase to pause, which ultimately leads to the release of the newly synthesized RNA strand.
TATA box: The TATA box is a DNA sequence found in the promoter region of genes in eukaryotes, recognized by transcription factors and RNA polymerase II to initiate transcription. It typically consists of a consensus sequence that includes thymine (T) and adenine (A) nucleotides, usually located about 25 to 30 base pairs upstream from the transcription start site. This element plays a critical role in the assembly of the transcription machinery, marking the beginning of the transcription process.
Transcriptional activation: Transcriptional activation is the process by which specific proteins, known as transcription factors, increase the likelihood of transcription of a particular gene by binding to nearby DNA. This mechanism is crucial for regulating gene expression, allowing cells to respond to various signals and environmental changes. It plays a key role in transcription initiation, where RNA polymerase is recruited to the promoter region of the gene, facilitating the start of RNA synthesis.
Non-coding RNA: Non-coding RNA (ncRNA) refers to RNA molecules that do not translate into proteins but play critical roles in regulating gene expression and maintaining cellular functions. These molecules are essential for various biological processes, including transcription regulation, RNA splicing, and chromatin remodeling, making them vital players in the overall genetic landscape of organisms.
Messenger RNA (mRNA): Messenger RNA (mRNA) is a single-stranded molecule that carries genetic information from DNA to the ribosome, where proteins are synthesized. This process involves several key stages, including transcription, where mRNA is produced from a DNA template, and translation, where the information in mRNA is used to assemble amino acids into proteins. mRNA plays a crucial role in gene expression and regulation.
Silencers: Silencers are regulatory DNA sequences that can suppress the transcription of specific genes, playing a crucial role in gene expression control. These elements work by binding repressor proteins, which can block the assembly of the transcription machinery or interfere with the promoter region's ability to initiate transcription. By modulating transcription initiation, silencers contribute significantly to maintaining appropriate levels of gene expression during cellular processes.
Enhancers: Enhancers are regulatory DNA sequences that increase the likelihood of transcription of a particular gene by binding transcription factors. They play a critical role in controlling gene expression, often working from a distance to enhance the assembly of the transcription machinery at the promoter region, which is essential for initiating transcription.
Promoter: A promoter is a specific DNA sequence located upstream of a gene that serves as the binding site for RNA polymerase and transcription factors, initiating the process of transcription. The promoter plays a crucial role in determining when and where a gene is expressed, influencing both the efficiency and specificity of gene transcription.
Dna-rna hybrid: A dna-rna hybrid refers to a double-stranded structure formed when a single strand of RNA pairs with a complementary single strand of DNA. This hybridization plays a crucial role in the processes of transcription, where genetic information from DNA is copied into RNA, facilitating the transfer of information needed for protein synthesis.
Template strand: The template strand is the single strand of DNA that serves as a guide for synthesizing RNA during transcription. This strand contains the specific sequence of nucleotides that will be transcribed into messenger RNA (mRNA), which ultimately carries the genetic information required for protein synthesis. Understanding the role of the template strand is crucial for grasping how genetic information is expressed through the processes of initiation, elongation, and termination in transcription.
Termination: Termination is the final step in both transcription and translation processes, where the synthesis of RNA or protein is concluded. During termination, specific signals indicate to the cellular machinery that the process should stop, leading to the release of the newly formed molecule. This process ensures that genes are expressed accurately and that proteins are produced correctly, playing a crucial role in gene regulation and cellular function.
Terminator: In the context of transcription, a terminator is a specific sequence of nucleotides in DNA that signals the end of transcription. This sequence plays a crucial role in ensuring that RNA polymerase knows when to stop synthesizing RNA, allowing for the proper processing and release of the newly formed RNA molecule. The termination process is vital for gene expression, as it helps maintain the integrity and functionality of the RNA produced.
Elongation: Elongation is the process in which a polypeptide chain is extended during protein synthesis and RNA strand is extended during transcription. It is a critical phase in both transcription and translation, where nucleotides or amino acids are sequentially added to form a longer RNA molecule or protein, respectively. This phase involves specific enzymatic activities that facilitate the incorporation of building blocks into the growing chain, ensuring accurate synthesis according to the genetic template.
RNA polymerase: RNA polymerase is an enzyme responsible for synthesizing RNA from a DNA template during the process of transcription. This enzyme plays a critical role in gene expression, facilitating the conversion of genetic information stored in DNA into functional RNA molecules, which can be further processed into proteins or serve other cellular functions.
Polyadenylation: Polyadenylation is the addition of a poly(A) tail, a long chain of adenine nucleotides, to the 3' end of an mRNA molecule. This process plays a crucial role in the stability, transport, and translation of mRNA, ultimately influencing gene expression and protein synthesis.
5' cap: The 5' cap is a modified guanine nucleotide added to the beginning of eukaryotic mRNA transcripts during RNA processing. This structure protects the mRNA from degradation, assists in ribosome binding during translation, and plays a role in RNA splicing and export from the nucleus.
Pre-initiation complex: The pre-initiation complex (PIC) is a crucial assembly of proteins that forms on the promoter region of a gene before the transcription process begins. It includes RNA polymerase II and various transcription factors that help to position the polymerase correctly at the start site of transcription. The formation of the PIC is a key regulatory step that influences gene expression by determining whether transcription will proceed or not.
Transcription factors: Transcription factors are proteins that bind to specific DNA sequences, playing a crucial role in regulating the transcription of genes from DNA to RNA. They act as molecular switches that can enhance or repress the expression of particular genes, thus influencing various biological processes and cellular functions. By interacting with the promoter and enhancer regions of DNA, transcription factors help determine when and how much of a gene is expressed.