Transcription
Transcription is the process of copying genetic information from one strand of DNA into RNA. It is a crucial step in the flow of genetic information from DNA to proteins. Here are the key points about transcription:
Principle of Complementarity: Like DNA replication, transcription also follows the principle of complementarity, where the nucleotides in the RNA molecule are complementary to the nucleotides in the DNA template strand. However, in RNA, adenine (A) pairs with uracil (U), not thymine (T).
Selective Transcription: During transcription, only a specific segment of the DNA is transcribed, and only one of the DNA strands serves as the template. This segment of DNA is defined by regulatory regions that demarcate the boundaries of the gene. Transcription occurs in the 5′ to 3′ direction along the template strand.
Reason for Single-Strand Transcription: Only one DNA strand is transcribed to avoid complications in genetic information transfer and protein synthesis. If both DNA strands were transcribed, they would code for RNA molecules with different sequences. This, in turn, would lead to the coding of two different proteins, causing complexity in the genetic information transfer process.
Complementary RNA Strands: If both DNA strands were transcribed and produced RNA molecules simultaneously, these RNA molecules would be complementary to each other, forming double-stranded RNA. Double-stranded RNA is not suitable for protein translation, as it would inhibit the process. Transcription aims to produce single-stranded RNA molecules that can be translated into proteins.
A transcription unit in DNA is defined primarily by the three regions in the DNA:
(i) A Promoter
(ii) The Structural gene
(iii) A Terminator
Template Strand: The template strand is the DNA strand with a polarity of 3’→5′. During transcription, this strand serves as the template for RNA synthesis. The RNA polymerase reads the template strand and adds complementary nucleotides to synthesize the RNA molecule. The sequence of the RNA molecule will be complementary to the template strand, except that uracil (U) is used instead of thymine (T).
Coding Strand: The coding strand, also known as the non-template strand, has a polarity of 5’→3′. It has the same sequence as the RNA molecule being transcribed (except for the substitution of thymine with uracil). This strand does not serve as the template for RNA synthesis and is not directly involved in transcription.
The reference points for defining a transcription unit are made with respect to the coding strand. For example, the promoter, which is a DNA sequence providing the binding site for RNA polymerase, is considered to be located toward the 5′ end (upstream) of the structural gene when referencing the coding strand. Similarly, the terminator, which defines the end of the transcription process, is considered to be located toward the 3′ end (downstream) of the coding strand.
Transcription Unit and the Gene
Defining a gene in terms of a DNA sequence can be complex due to the diverse nature of genetic elements found within DNA. Here are some key points related to the concept of a gene:
Functional Unit of Inheritance: A gene is defined as the functional unit of inheritance. It carries the information necessary to produce a specific product, such as a protein, tRNA, rRNA, or other functional molecules.
Monocistronic and Polycistronic Genes: Genes can be categorized as monocistronic or polycistronic. In eukaryotes, most structural genes are monocistronic, meaning they code for a single polypeptide or functional product. In contrast, in prokaryotes (bacteria), genes are often organized in operons and are polycistronic, meaning they code for multiple polypeptides or products within a single transcription unit.
Exons and Introns: In eukaryotes, structural genes have a split-gene arrangement. They are composed of coding sequences called exons and non-coding sequences called introns. Exons are the sequences that appear in mature or processed RNA and are involved in protein synthesis. Introns, or intervening sequences, do not appear in mature RNA and are generally removed during RNA processing.
Regulatory Sequences: Genes also contain regulatory sequences, such as promoters and enhancers, that control gene expression. These regulatory sequences play a critical role in determining when and how a gene is transcribed and the level of gene expression.
Regulatory Genes: Some DNA sequences involved in gene regulation are loosely defined as regulatory genes. These sequences do not code for RNA or proteins themselves but are essential for controlling the expression of structural genes. They may include promoters, enhancers, silencers, and other elements that influence gene transcription.
Types of RNA and the process of Transcription
Types of RNA:
Messenger RNA (mRNA): mRNA carries the genetic information from the DNA in the cell nucleus to the ribosomes in the cytoplasm. It serves as a template for protein synthesis and contains the coding sequence for a specific protein.
Transfer RNA (tRNA): tRNA molecules are responsible for bringing amino acids to the ribosomes during protein synthesis. Each tRNA molecule carries a specific amino acid and has an anticodon region that can base-pair with the complementary codon on the mRNA.
Ribosomal RNA (rRNA): rRNA is a structural component of ribosomes, the cellular machinery where protein synthesis occurs. It helps in the assembly of ribosomes and plays a role in the catalytic functions of ribosomes during translation.
The Process of Transcription:
Transcription is the process by which RNA is synthesized from a DNA template. It involves several key steps:
Initiation:
- Transcription begins with the recognition of a specific DNA sequence, known as the promoter, by RNA polymerase, the enzyme responsible for transcription.
- In prokaryotes, a single RNA polymerase enzyme is involved in transcription, while in eukaryotes, multiple types of RNA polymerase are used for different classes of RNA (e.g., RNA polymerase II for mRNA).
- The promoter region typically includes a sequence called the TATA box in eukaryotes and a -35 and -10 sequence in prokaryotes.
- RNA polymerase binds to the promoter, and the DNA helix is unwound in the transcription initiation complex. The sigma factor is responsible for recognizing the promoter sequences.
Elongation:
- During elongation, RNA polymerase moves along the DNA template strand, unwinding the DNA ahead of it.
- As RNA polymerase progresses, it adds complementary ribonucleotides (rNTPs) to the growing RNA strand, following the base-pairing rules: adenine (A) in DNA pairs with uracil (U) in RNA, and guanine (G) in DNA pairs with cytosine (C) in RNA.
- The RNA strand is synthesized in the 5′ to 3′ direction, and the complementary RNA sequence is created.
Termination:
- Transcription continues until a termination signal is reached.
- In prokaryotes, there are two common termination mechanisms:
- Rho-independent termination: A terminator sequence in the DNA forms a hairpin loop in the RNA, causing RNA polymerase to pause and eventually dissociate from the DNA.
- Rho-dependent termination: The Rho protein binds to the growing RNA strand and causes RNA polymerase to release from the DNA.
- In eukaryotes, termination is more complex and often involves the recognition of specific termination sequences and the cleavage of the pre-mRNA.
Post Transcriptional Modification
In eukaryotes, processing of the initial transcript, known as pre-mRNA (pre-messenger RNA), is a crucial step in gene expression. Pre-mRNA undergoes several modifications to become mature mRNA, which can then be transported to the cytoplasm for translation into proteins. Here are the key steps involved in processing pre-mRNA in eukaryotes:
Capping (5′ Cap):
- The 5′ end of the pre-mRNA is modified by the addition of a 5′ cap. The 5′ cap consists of a modified guanosine nucleotide linked to the initial nucleotide of the mRNA.
- The 5′ cap serves several important functions:
- It protects the mRNA from degradation by exonucleases.
- It helps in the efficient transport of mRNA from the nucleus to the cytoplasm.
- It is involved in the initiation of translation by facilitating ribosome binding to the mRNA.
Splicing:
- Pre-mRNA often contains non-coding regions called introns and coding regions called exons.
- Introns are removed from the pre-mRNA through a process called splicing, and the exons are joined together to form the mature mRNA.
- Splicing is carried out by a complex called the spliceosome, which consists of small nuclear ribonucleoproteins (snRNPs) and other protein factors.
- Alternative splicing can result in different combinations of exons being included or excluded in the mature mRNA, leading to multiple protein isoforms from a single gene.
Polyadenylation (3′ Poly-A Tail):
- The 3′ end of the pre-mRNA is modified by the addition of a polyadenylate tail, known as the poly-A tail. This tail consists of multiple adenine (A) nucleotides.
- The poly-A tail serves several functions:
- It protects the mRNA from degradation by exonucleases.
- It plays a role in regulating mRNA stability and turnover.
- It is involved in the efficient translation of the mRNA.
In eukaryotic cells, there are multiple RNA polymerases that are responsible for transcribing different types of RNA. Here’s a brief summary of their functions:
RNA Polymerase I (Pol I):
- RNA Polymerase I is responsible for transcribing ribosomal RNA (rRNA) genes.
- It synthesizes the 28S, 18S, and 5.8S rRNA components, which are essential for ribosome formation and protein synthesis.
RNA Polymerase II (Pol II):
- RNA Polymerase II transcribes a wide range of genes, primarily those that encode messenger RNA (mRNA) and some small nuclear RNAs (snRNAs).
- It produces precursor mRNA molecules (hnRNA) that undergo post-transcriptional modifications and splicing to become mature mRNA.
- Pol II plays a central role in gene expression by transcribing protein-coding genes.
RNA Polymerase III (Pol III):
- RNA Polymerase III is responsible for transcribing genes that produce small RNA molecules, including transfer RNA (tRNA), 5S ribosomal RNA (5S rRNA), and various small nuclear RNAs (snRNAs).
- tRNAs are crucial for protein synthesis, while snRNAs are involved in processes such as splicing of mRNA.
Each of these RNA polymerases has a specific set of genes it transcribes, and they play distinct roles in the cell. This division of labor allows for the precise and coordinated transcription of various types of RNA essential for different cellular functions.
