Central Dogma of Life

The transmission of genetic information from DNA to protein via an RNA intermediary is described by the basic dogma of molecular biology, a concept that has remained unchanged for decades. Despite the fact that subsequent research has revealed numerous exceptions to the fundamental dogma, it remains a popular paradigm for describing and studying the link between genes and protein products.

The Central Dogma, written by Francis Crick in 1958, explains how DNA, mRNA, and proteins interact. Information can be transferred from DNA to DNA, DNA to mRNA, and mRNA to protein, according to the Central Dogma(Yockey, 2005).

Transcription in Prokaryotes: DNA to RNA
The goal of transcription is to create RNA molecules that can help in protein synthesis (translation). As a result, the complete genome is not transcribed at once; rather, specific DNA molecule sequences serve as templates as needed by the cell. The structural genes for metabolic processes in prokaryotes are generally physically contiguous, forming an operon, and are under the control of a single set of regulatory elements. The famous lac operon of E. coli, for example, has three regulatory elements (the repressor gene the promoter, and the operator) followed by three structural genes (the β-galactosidase, permease, and acetylase genes). 

RNA Polymerase
This enzyme has two significant differences from DNA polymerases: it can initiate RNA synthesis without a primer, and it does not proofread during transcription. In E. coli the RNA polymerase enzyme has five subunits (two of the α peptide and one each of the β and β' peptides and one σ peptide). This form is called the holoenzyme. The σ subunit may dissociate from the other subunits to leave a form known as the core enzyme.  

Important features of transcription include how the cell recognizes (1) where transcription is to begin (initiation), (2) where transcription is to end (termination), and (3) where a particularly of genes is to be expressed. The first two of these are functions of the prokaryotic RNA polymerase (Tsonis, 2003). 

INITIATION

In prokaryotes (and eukaryotes), transcription necessitates a partial unwinding of the DNA double helix in the mRNA synthesis region. The unwinding region is referred to as a transcription bubble. A promoter is a DNA sequence that the proteins and enzymes involved in transcription bind to start the process. Promoters are usually found upstream of the genes they control. The sequence of a promoter is crucial because it controls whether the related gene is transcribed all of the time, very occasionally, or not at all. A prokaryotic promoter's structure and function are straightforward. The TATA box, which is 10 bases before the transcription start site (-10) in the bacterial promoter, is an essential sequence.

The RNA polymerase holoenzyme assembles at the promoter to start transcription. The dissociation of permits the core enzyme to continue along the DNA template, manufacturing mRNA by adding RNA nucleotides according to base pairing principles, much like a new DNA molecule is created during DNA replication. Transcription occurs on only one of the two
DNA strands. Because it serves as a template for the creation of mRNA, the transcribed strand of DNA is referred to as the template strand. The mRNA result is complementary to the template strand and nearly identical to the other DNA strand, known as the non-template strand, with the exception that RNA contains uracil (U) instead of thymine (T). RNA polymerase, like DNA polymerase, attaches new nucleotides to the previous nucleotide's 3′- OH group. This indicates that the expanding mRNA strand is being produced from 5′ to 3′. Due to the anti-parallel nature of DNA, the RNA polymerase moves along the template strand in the 3′ to 5′ orientation(2).

ELONGATION
As the hydrogen bonds that bind the complementary base pairs in the DNA double helix are broken during elongation, the DNA is continually unraveled ahead of the core enzyme. As the hydrogen bonds are reestablished, the DNA is rewound behind the core enzyme. The base pairing between DNA and RNA isn't strong enough to keep the mRNA production components stable. Instead, the RNA polymerase serves as a stable linker between the DNA template and the newly formed RNA strand, preventing premature elongation(2). 

TERMINATION
After a gene has been transcribed, the RNA polymerase must be told to separate from the DNA template and release the freshly produced mRNA. There are two types of termination signals, depending on the gene being transcribed. The first is protein-based, while the second is RNA-based. Both termination signals are based on DNA sequences near the gene's end that cause the polymerase to release the mRNA, rho (p) and nusA peptides assist in recognition of termination sequences.

Because transcription and translation both take place in the cytoplasm of a prokaryotic cell, by the time transcription is finished, the transcript will have already been used to start manufacturing copies of the encoded protein. In eukaryotic cells, however, transcription and translation cannot occur at the same time because transcription takes place inside the nucleus and translation takes place outside in the cytoplasm.  

Specific regulatory proteins that bind to sequences linked with the promoter regions of operons are frequently used to time gene expression. Regulation can be both positive and negative. Repressor proteins bind to DNA to prevent RNA polymerase from moving from the promoter to the structural genes of the operon in negative regulation, whereas gene activator proteins help RNA polymerase attach to promoters in positive regulation. An operon can contain both types of control; the lac operon in E.coli is an example of this, as lactose causes derepression while the absence of glucose allows gene activation. 

Translation in prokaryotes: RNA to Protein
The product of most transcription in prokaryotes is a polycistronic mRNA molecule. This molecule contains the information coding for several proteins and does not have the 5’ "cap" or 3’ "tail" structures characteristic of eukaryotic mRNAs. As with transcription, translation requires identification of particular starting and stopping signals within the mRNA. An initiation codon (AUG), in association with other sequences for ribosome binding, marks the beginning of a protein-coding section of the mRNA, while any of three termination or "nonsense" codons (the amber triplet UAG, the ochre triplet UAA, and the opal triplet UGA) stop translation. Each initiation codon determines the reading frame, or groups of three bases to be translated, for that particular gene within the polycistronic mRNA(Tsonis, 2003).

References
1. Information Theory, Evolution, and the Origin of Life By Hubert P. Yockey
2. https://www.ncbi.nlm.nih.gov/books/NBK98 
3. Anatomy of Gene Regulation: A Three-Dimensional Structural Analysis By Panagiotis A. Tsonis

 By: Batool Murtaza