Editing Protein biosynthesis (section)

==Transcription==
{{main|Transcription (biology)}}

Transcription occurs in the nucleus using [[DNA]] as a template to produce [[mRNA]]. In [[eukaryotes]], this mRNA molecule is known as [[pre-mRNA]] as it undergoes [[post-transcriptional modification]]s in the nucleus to produce a mature mRNA molecule. However, in prokaryotes post-transcriptional modifications are not required so the mature mRNA molecule is immediately produced by transcription.<ref name="Alberts 2015" />

{{multiple image
 | align = right
 | direction = horizontal
 | width = 200
 | image1 = Nucleotide structure within a polynucleotide chain.png
 | alt1 = A pentagon shaped 5 carbon sugar with a base and a phosphate group attached, joined via a phosphodiester bond to another nucleotide's phosphate group
 | caption1 = Illustrates the structure of a nucleotide with the 5 carbons labelled demonstrating the 5' nature of the phosphate group and 3' nature of hydroxyl group needed to form the connective phosphodiester bonds
 | image2 = Directionality of DNA molecule.png
 | alt2 = Shows the two polynucleotide strands within the DNA molecule joined by hydrogen bonds between complementary base pairs. One strand runs in the 5' to 3' direction and the complementary strands runs in the opposite direction 3' to 5' as it is antiparallel.
 | caption2 = Illustrates the intrinsic directionality of DNA molecule with the coding strand running 5' to 3' and the complimentary template strand running 3' to 5'
}}
Initially, an enzyme known as a [[helicase]] acts on the molecule of DNA. DNA has an [[Antiparallel (biochemistry)|antiparallel]], double helix structure composed of two, complementary [[polynucleotide]] strands, held together by [[hydrogen bond]]s between the base pairs. The helicase disrupts the hydrogen bonds causing a region of DNA{{Snd}}corresponding to a gene{{Snd}}to unwind, separating the two DNA strands and exposing a series of bases. Despite DNA being a double-stranded molecule, only one of the strands acts as a template for pre-mRNA synthesis; this strand is known as the template strand. The other DNA strand (which is [[Complementarity (molecular biology)|complementary]] to the template strand) is known as the coding strand.<ref name="Toole2015">{{Cite book |title=AQA biology A level. Student book |vauthors=Toole G, Toole S |date=2015 |publisher=Oxford University Press |isbn=9780198351771 |edition=Second |location=Great Clarendon Street, Oxford, OX2 6DP, UK}}</ref>

Both DNA and RNA have intrinsic [[Directionality (molecular biology)|directionality]], meaning there are two distinct ends of the molecule. This property of directionality is due to the asymmetrical underlying nucleotide subunits, with a phosphate group on one side of the pentose sugar and a base on the other. The five carbons in the pentose sugar are numbered from 1' (where ' means prime) to 5'. Therefore, the phosphodiester bonds connecting the nucleotides are formed by joining the [[hydroxyl]] group on the 3' carbon of one nucleotide to the phosphate group on the 5' carbon of another nucleotide. Hence, the coding strand of DNA runs in a 5' to 3' direction and the complementary, template DNA strand runs in the opposite direction from 3' to 5'.<ref name="Alberts 2015" />

[[File:Process of DNA transcription.png|upright=1.3|thumb|alt=Two strands of DNA separated with an RNA polymerase attached to one of the strands and an RNA molecule coming out of the RNA polymerase| Illustrates the conversion of the template strand of DNA to the pre-mRNA molecule by RNA polymerase.]]
The enzyme [[RNA polymerase]] binds to the exposed template strand and reads from the gene in the 3' to 5' direction. Simultaneously, the RNA polymerase synthesizes a single strand of pre-mRNA in the 5'-to-3' direction by catalysing the formation of [[phosphodiester bonds]] between activated nucleotides (free in the nucleus) that are capable of complementary [[base pair]]ing with the template strand. Behind the moving RNA polymerase the two strands of DNA rejoin, so only 12 base pairs of DNA are exposed at one time.<ref name="Toole2015" /> RNA polymerase builds the pre-mRNA molecule at a rate of 20 nucleotides per second enabling the production of thousands of pre-mRNA molecules from the same gene in an hour. Despite the fast rate of synthesis, the RNA polymerase enzyme contains its own proofreading mechanism. The proofreading mechanisms allows the RNA polymerase to remove incorrect nucleotides (which are not complementary to the template strand of DNA) from the growing pre-mRNA molecule through an excision reaction.<ref name="Alberts 2015" /> When RNA polymerases reaches a specific DNA sequence which [[stop codon|terminates]] transcription, RNA polymerase detaches and pre-mRNA synthesis is complete.<ref name="Toole2015" />

The pre-mRNA molecule synthesized is complementary to the template DNA strand and shares the same nucleotide sequence as the coding DNA strand. However, there is one crucial difference in the nucleotide composition of DNA and mRNA molecules. DNA is composed of the bases: [[guanine]], [[cytosine]], [[adenine]] and [[thymine]] (G, C, A and T). RNA is also composed of four bases: guanine, cytosine, adenine and [[uracil]]. In RNA molecules, the DNA base thymine is replaced by uracil which is able to base pair with adenine. Therefore, in the pre-mRNA molecule, all complementary bases which would be thymine in the coding DNA strand are replaced by uracil.<ref name="Berk2000">{{Cite book |title=Molecular cell biology |vauthors=Berk A, Lodish H, Darnell JE |date=2000 |publisher=W.H. Freeman |isbn=9780716737063 |edition=4th |location=New York}}</ref>

===Post-transcriptional modifications===
[[File:Post-transcriptional modification of pre-mRNA.png|upright=1.2|thumb|alt=three strands of RNA at different stages of maturation, the first strand contains introns and exons only, the second strand has gained a 5' cap and 3' tail and contains still introns and exons, the third strand has the cap and tail but the introns have been removed| Outlines the process of post-transcriptionally modifying pre-mRNA through capping, polyadenylation and splicing to produce a mature mRNA molecule ready for export from the nucleus.]]

Once transcription is complete, the pre-mRNA molecule undergoes post-transcriptional modifications to produce a mature mRNA molecule.{{cn|date=December 2024}}

There are 3 key steps within post-transcriptional modifications:{{cn|date=April 2023}}
# Addition of a [[Five-prime cap|5' cap]] to the 5' end of the pre-mRNA molecule
# Addition of a 3' [[polyadenylation|poly(A) tail]] is added to the 3' end pre-mRNA molecule
# Removal of [[intron]]s via [[RNA splicing]]
The 5' cap is added to the 5' end of the pre-mRNA molecule and is composed of a guanine nucleotide modified through [[Protein methylation|methylation]]. The purpose of the 5' cap is to prevent break down of mature mRNA molecules before translation, the cap also aids binding of the ribosome to the mRNA to start translation<ref name="Khan2020">{{Cite web |title=Eukaryotic pre-mRNA processing |url=https://www.khanacademy.org/science/biology/gene-expression-central-dogma/transcription-of-dna-into-rna/a/eukaryotic-pre-mrna-processing |access-date=9 March 2020 |website=Khan Academy}}</ref> and enables mRNA to be differentiated from other RNAs in the cell.<ref name="Alberts 2015" /> In contrast, the 3' Poly(A) tail is added to the 3' end of the mRNA molecule and is composed of 100-200 adenine bases.<ref name="Khan2020" /> These distinct mRNA modifications enable the cell to detect that the full mRNA message is intact if both the 5' cap and 3' tail are present.<ref name="Alberts 2015" />

This modified pre-mRNA molecule then undergoes the process of RNA splicing. Genes are composed of a series of introns and [[exon]]s, introns are nucleotide sequences which do not encode a protein while, exons are nucleotide sequences that directly encode a protein. Introns and exons are present in both the underlying DNA sequence and the pre-mRNA molecule, therefore, to produce a mature mRNA molecule encoding a protein, splicing must occur.<ref name="Toole2015" /> During splicing, the intervening introns are removed from the pre-mRNA molecule by a multi-protein complex known as a [[spliceosome]] (composed of over 150 proteins and RNA).<ref name="Jo2015">{{Cite journal |vauthors=Jo BS, Choi SS |date=December 2015 |title=Introns: The Functional Benefits of Introns in Genomes |journal=Genomics & Informatics |volume=13 |issue=4 |pages=112–118 |doi=10.5808/GI.2015.13.4.112 |pmc=4742320 |pmid=26865841}}</ref> This mature mRNA molecule is then exported into the cytoplasm through nuclear pores in the envelope of the nucleus.{{cn|date=December 2024}}