The DNA contains the code for making all proteins. In order for proteins to be synthesized, the code on the DNA for making the protein of interest must be transcribed. Imagine trying to make a cake (the protein) that you have never made before. Consider that the book with the recipe is in a rare book that cannot leave the library. However, copies of various sections of the book can be made, which could then leave the library. Once you have the copy of the recipe you want, you can take it home and make the cake in your kitchen. In molecular biology you could consider the nucleus of the cell to be the library and the DNA to be the books in the library. The DNA cannot leave the nucleus but parts of it may be copied and sent to the cytosol where the message can be translated and protein made. The copying of the DNA is called transcription and the reading and interpretation of the transcript is called translation.
Parts of the DNA Involved In Transcription
The DNA to be transcribed consists of the following main parts,
- Activator or Repressor Region: Part of the DNA to which proteins bind, activating or hindering activity of RNA polymerase, and thereby activating or promoting transcription
- Promoter Region (also called the TATA box): Part of the DNA located between 25 and 35 base pairs upstream from the coding region
- Coding Region: Part of the DNA where genes get transcribed
Steps in DNA Transcription
DNA transcription consists of the following major steps, i.e., initiation, elongation, termination, and splicing.
Initiation: RNA polymerase binds to the promotor site and the DNA unwinds to make ready for copying
Elongation: RNA polymerase reads the template strand from the 3′ to 5′ end and writes down new nucleotides from 5′ to 3′ (Remember: “Read up and write down rule”). The new template is called pre mRNA. Remember that RNA does not have thymine but uracil instead. Therefore, during transcription, wherever there is an A on the template, U will be “typed” instead of T. As soon as transcription begins, the 5′ end is capped by the addition of methyl guanosine. This process, along with polyadenylation that will come later, helps in preventing degradation of the mRNA before it can be transcribed.
Once RNA polymerase reaches a termination sequence (AAUAAA), terminator proteins bind to the pre mRNA and cleaves it away from the DNA. RNA polymerase II continues to transcribe beyond the end of the transcription site. However, the overhanging template is degraded by a 5′-exonuclease. When the 5′-exonuclease “bumps into” RNA polymerase, it disengages it from the strand and ultimately ends transcription.
After release of the pre mRNA, cleavage factors bind to the termination sequence (the AAUUAAA signal) and cleaves pre mRNA at the 3’end. Poly-A polymerase then adds adenine to form a poly-A tail.
The new pre mRNA is also referred to as heterogenous nuclear RNA (hnRNA). This is because it consists of RNA that will be eventually expressed to make proteins (exons) and others that are considered as “junk” and will be thrown out (introns). Processing involves getting rid of the introns via splicing.
Mechanism of Splicing
In general, a complex biological machine consisting of proteins and small nuclear RNA (snRNA) called a spliceosome, cuts away the introns and join the exons together.
Three parts of an intron are important to remember, i.e., its start, end, and branch point. The start and end of an intron are characterized by GU and AG respectively. The branch point is an adenine (A) nucleotide. During the excision process, the spliceosome cuts off the intron at GU. The GU sequence then binds to the branch point (A) forming a lariat (rope with a loop). The lariat is then gets cut out and the exons joined together. The mRNA is now ready for translation.