Editing Protein biosynthesis

{{Short description|Assembly of proteins inside biological cells}}
{{Use dmy dates|date=February 2023}}
[[File:Summary of the protein biosynthesis process.png|thumb|upright=1.2|alt=A nucleus within a cell showing DNA, RNA and enzymes at the different stages of protein biosynthesis|Protein biosynthesis starting with transcription and post-transcriptional modifications in the nucleus. Then the mature mRNA is exported to the cytoplasm where it is translated. The polypeptide chain then folds and is post-translationally modified.]]

'''Protein biosynthesis''', or '''protein synthesis''', is a core biological process, occurring inside [[Cell (biology)|cells]], [[homeostasis|balancing]] the loss of cellular [[protein]]s (via [[Proteolysis|degradation]] or [[Protein targeting|export]]) through the production of new proteins. Proteins perform a number of critical functions as [[enzyme]]s, structural proteins or [[hormone]]s. Protein synthesis is a very similar process for both [[prokaryote]]s and [[eukaryote]]s but there are some distinct differences.<ref name="Alberts 2015">{{Cite book |title=Molecular biology of the cell |vauthors=Alberts B |date=2015 |publisher=Garland Science, Taylor and Francis Group |isbn=978-0815344643 |edition=Sixth |location=Abingdon, UK}}</ref>

Protein synthesis can be divided broadly into two phases: [[Transcription (biology)|transcription]] and [[Translation (biology)|translation]]. During transcription, a section of [[DNA]] encoding a protein, known as a [[gene]], is converted into a molecule called [[messenger RNA]] (mRNA). This conversion is carried out by enzymes, known as [[RNA polymerases]], in the [[cell nucleus|nucleus of the cell]].<ref name="O'Connor 2010">{{Cite book |url=https://www.nature.com/scitable/ebooks/essentials-of-cell-biology-14749010/ |title=Essentials of Cell Biology |vauthors=O'Connor C |date=2010 |publisher=Cambridge, MA |location=NPG Education |access-date=3 March 2020}}</ref> In eukaryotes, this mRNA is initially produced in a premature form ([[Primary transcript|pre-mRNA]]) which undergoes [[post-transcriptional modification]]s to produce [[Mature messenger RNA|mature mRNA]]. The mature mRNA is exported from the cell nucleus via [[nuclear pore]]s to the [[cytoplasm]] of the cell for translation to occur. During translation, the mRNA is read by [[ribosome]]s which use the [[nucleotide]] sequence of the mRNA to determine the sequence of [[amino acid]]s. The ribosomes catalyze the formation of [[covalent bond|covalent]] [[peptide bond]]s between the encoded amino acids to form a [[polypeptide chain]].{{cn|date=March 2024}}

Following translation the polypeptide chain must fold to form a functional protein; for example, to function as an enzyme the polypeptide chain must fold correctly to produce a functional [[active site]]. To adopt a functional three-dimensional shape, the polypeptide chain must first form a series of smaller underlying structures called [[protein secondary structure|secondary structures]]. The polypeptide chain in these secondary structures then folds to produce the overall 3D [[protein tertiary structure|tertiary structure]]. Once correctly folded, the protein can undergo further maturation through different [[post-translational modification]]s, which can alter the protein's ability to function, its location within the cell (e.g. cytoplasm or nucleus) and its ability to [[protein–protein interaction|interact with other proteins]].<ref name="Wang 2013">{{Cite journal |vauthors=Wang YC, Peterson SE, Loring JF |date=February 2014 |title=Protein post-translational modifications and regulation of pluripotency in human stem cells |journal=Cell Research |volume=24 |issue=2 |pages=143–160 |doi=10.1038/cr.2013.151 |pmc=3915910 |pmid=24217768 |doi-access=free}}</ref>

Protein biosynthesis has a key role in disease as changes and errors in this process, through underlying [[mutation|DNA mutations]] or [[protein misfolding]], are often the underlying causes of a disease. DNA mutations change the subsequent mRNA sequence, which then alters the mRNA encoded amino acid sequence. [[Nonsense mutation|Mutations can cause the polypeptide chain to be shorter]] by generating a [[stop codon|stop sequence]] which causes early termination of translation. Alternatively, a mutation in the mRNA sequence [[missense mutation|changes the specific amino acid encoded at that position]] in the polypeptide chain. This amino acid change can impact the protein's ability to function or to fold correctly.<ref name="Scheper 2008">{{Cite journal |vauthors=Scheper GC, van der Knaap MS, Proud CG |date=September 2007 |title=Translation matters: protein synthesis defects in inherited disease |journal=Nature Reviews. Genetics |volume=8 |issue=9 |pages=711–723 |doi=10.1038/nrg2142 |pmid=17680008 |s2cid=12153982}}</ref> Misfolded proteins have a tendency to form [[protein aggregation|dense protein clumps]], which are often implicated in diseases, particularly [[neurological disorder]]s including [[Alzheimer's]] and [[Parkinson's disease]].<ref name="Berg 2015">{{Cite book |title=Biochemistry |vauthors=Berg JM, Tymoczko JL, Gatto Jr GJ, Stryer L |date=2015 |publisher=W. H. Freeman and Company |isbn=9781464126109 |edition=Eighth |location=US}}</ref>

==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}}

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

[[File:Translation - cycle.png|upright=1.4|thumb|alt=Five strands of mRNA with all with a ribosome attached at different stages of translation. The first strand has a ribosome and one tRNA carrying its amino acid base pairing with the mRNA, the second strand has a ribosome and a second tRNA carrying an amino acid base pairing with the mRNA, the third strand has the ribosome catalysing a peptide bond between the two amino acids on the two tRNA's. The fourth strand has the first tRNA leaving the ribosome and a third tRNA with its amino acid arriving. The fifth strand has the ribosome catalysing a peptide bond between the amino acids on the second and third tRNA's with an arrowing indicating the cycle continues| Illustrates the translation process showing the cycle of tRNA codon-anti-codon pairing and amino acid incorporation into the growing polypeptide chain by the ribosome.]]
[[Image:Protein translation.gif|thumb|upright=1.2|right|A ribosome on a strand of mRNA with tRNA's arriving, performing codon-anti-codon base pairing, delivering their amino acid to the growing polypeptide chain and leaving. Demonstrates the action of the ribosome as a [[biological machine]] which functions on a [[Nanoscopic scale|nanoscale]] to perform translation. The ribosome moves along the mature mRNA molecule incorporating tRNA and producing a polypeptide chain.]]

During translation, ribosomes synthesize polypeptide chains from mRNA template molecules. In eukaryotes, translation occurs in the cytoplasm of the cell, where the ribosomes are located either free floating or attached to the [[endoplasmic reticulum]]. In prokaryotes, which lack a nucleus, the processes of both transcription and translation occur in the cytoplasm.<ref name="Khan Academy 2020">{{Cite web |title=Stages of translation (article) |url=https://www.khanacademy.org/science/biology/gene-expression-central-dogma/translation-polypeptides/a/the-stages-of-translation |access-date=10 March 2020 |website=Khan Academy |language=en}}</ref>

[[Ribosome]]s are complex [[molecular machine]]s, made of a mixture of protein and [[ribosomal RNA]], arranged into two subunits (a large and a small subunit), which surround the mRNA molecule. The ribosome reads the mRNA molecule in a 5'-3' direction and uses it as a template to determine the order of amino acids in the polypeptide chain.<ref name="Khan Academy 2020 - 2">{{Cite web |title=Nucleus and ribosomes (article) |url=https://www.khanacademy.org/science/biology/structure-of-a-cell/prokaryotic-and-eukaryotic-cells/a/nucleus-and-ribosomes |access-date=10 March 2020 |website=Khan Academy |language=en}}</ref> To translate the mRNA molecule, the ribosome uses small molecules, known as [[transfer RNA]]s (tRNA), to deliver the correct amino acids to the ribosome. Each tRNA is composed of 70-80 nucleotides and adopts a characteristic cloverleaf structure due to the formation of hydrogen bonds between the nucleotides within the molecule. There are around 60 different types of tRNAs, each tRNA binds to a specific sequence of three nucleotides (known as a [[codon]]) within the mRNA molecule and delivers a specific amino acid.<ref name="Cooper 2000">{{Cite book |title=The cell : a molecular approach |vauthors=Cooper GM |date=2000 |publisher=Sinauer Associates |isbn=9780878931064 |edition=2nd |location=Sunderland (MA)}}</ref>

The ribosome initially attaches to the mRNA at the [[start codon]] (AUG) and begins to translate the molecule. The mRNA nucleotide sequence is read in [[genetic code|triplets]]; three adjacent nucleotides in the mRNA molecule correspond to a single codon. Each tRNA has an exposed sequence of three nucleotides, known as the anticodon, which are complementary in sequence to a specific codon that may be present in mRNA. For example, the first codon encountered is the start codon composed of the nucleotides AUG. The correct tRNA with the anticodon (complementary 3 nucleotide sequence UAC) binds to the mRNA using the ribosome. This tRNA delivers the correct amino acid corresponding to the mRNA codon, in the case of the start codon, this is the amino acid methionine. The next codon (adjacent to the start codon) is then bound by the correct tRNA with complementary anticodon, delivering the next amino acid to ribosome. The ribosome then uses its [[peptidyl transferase]] enzymatic activity to catalyze the formation of the covalent peptide bond between the two adjacent amino acids.<ref name="Toole2015" />

The ribosome then moves along the mRNA molecule to the third codon. The ribosome then releases the first tRNA molecule, as only two tRNA molecules can be brought together by a single ribosome at one time. The next complementary tRNA with the correct anticodon complementary to the third codon is selected, delivering the next amino acid to the ribosome which is covalently joined to the growing polypeptide chain. This process continues with the ribosome moving along the mRNA molecule adding up to 15 amino acids per second to the polypeptide chain. Behind the first ribosome, up to 50 additional ribosomes can bind to the mRNA molecule forming a [[polysome]], this enables simultaneous synthesis of multiple identical polypeptide chains.<ref name="Toole2015" /> Termination of the growing polypeptide chain occurs when the ribosome encounters a stop codon (UAA, UAG, or UGA) in the mRNA molecule. When this occurs, no tRNA can recognise it and a [[release factor]] induces the release of the complete polypeptide chain from the ribosome.<ref name="Cooper 2000" /> Dr. [[Har Gobind Khorana]], a scientist originating from India, decoded the RNA sequences for about 20 amino acids.{{Citation needed|date=January 2021|reason=List exact rather than approximate number and provide source.}} He was awarded the [[Nobel Prize]] in 1968, along with two other scientists, for his work.

==Protein folding==
{{Further|Protein folding}}[[File:Protein folding figure.png|300px|thumb|alt=three individual polypeptide chains at different levels of folding and a cluster of chains| Shows the process of a polypeptide chain folding from its initial primary structure through to the quaternary structure.]]

Once synthesis of the polypeptide chain is complete, the polypeptide chain folds to adopt a specific structure which enables the protein to carry out its functions. The basic form of [[protein structure]] is known as the [[protein primary structure|primary structure]], which is simply the polypeptide chain i.e. a sequence of covalently bonded amino acids. The primary structure of a protein is encoded by a gene. Therefore, any changes to the sequence of the gene can alter the primary structure of the protein and all subsequent levels of protein structure, ultimately changing the overall structure and function.{{cn|date=April 2023}}

The primary structure of a protein (the polypeptide chain) can then fold or coil to form the secondary structure of the protein. The most common types of secondary structure are known as an [[alpha helix]] or [[beta sheet]], these are small structures produced by hydrogen bonds forming within the polypeptide chain. This secondary structure then folds to produce the tertiary structure of the protein. The tertiary structure is the proteins overall 3D structure which is made of different secondary structures folding together. In the tertiary structure, key protein features e.g. the active site, are folded and formed enabling the protein to function. Finally, some proteins may adopt a complex [[protein quaternary structure|quaternary structure]]. Most proteins are made of a single polypeptide chain, however, some proteins are composed of multiple polypeptide chains (known as subunits) which fold and interact to form the quaternary structure. Hence, the overall protein is a [[multi-subunit complex]] composed of multiple folded, polypeptide chain subunits e.g. [[haemoglobin]].<ref name="Khan proteins 2020">{{Cite web |title=Protein structure: Primary, secondary, tertiary & quaternary (article) |url=https://www.khanacademy.org/science/biology/macromolecules/proteins-and-amino-acids/a/orders-of-protein-structure |access-date=11 March 2020 |website=Khan Academy |language=en}}</ref>

== Post-translation events ==
There are events that follow protein biosynthesis such as '''proteolysis'''<ref>{{Cite web |title=proteolysis {{!}} chemistry {{!}} Britannica |url=https://www.britannica.com/science/proteolysis |access-date=17 May 2022 |website=Encyclopædia Britannica |language=en}}</ref> and protein-folding. Proteolysis refers to the cleavage of proteins by proteases and the breakdown of proteins into amino acids by the action of enzymes.

==Post-translational modifications==
When protein folding into the mature, functional 3D state is complete, it is not necessarily the end of the protein maturation pathway. A folded protein can still undergo further processing through post-translational modifications. There are over 200 known types of post-translational modification, these modifications can alter protein activity, the ability of the protein to interact with other proteins and where the protein is found within the cell e.g. in the cell nucleus or cytoplasm.<ref name="Duan 2015">{{Cite journal |vauthors=Duan G, Walther D |date=February 2015 |title=The roles of post-translational modifications in the context of protein interaction networks |journal=PLOS Computational Biology |volume=11 |issue=2 |pages=e1004049 |bibcode=2015PLSCB..11E4049D |doi=10.1371/journal.pcbi.1004049 |pmc=4333291 |pmid=25692714 |doi-access=free}}</ref> Through post-translational modifications, the diversity of proteins encoded by the genome is expanded by 2 to 3 [[Order of magnitude|orders of magnitude]].<ref name="Schubert 2015">{{Cite journal |vauthors=Schubert M, Walczak MJ, Aebi M, Wider G |date=June 2015 |title=Posttranslational modifications of intact proteins detected by NMR spectroscopy: application to glycosylation |journal=Angewandte Chemie |volume=54 |issue=24 |pages=7096–7100 |doi=10.1002/anie.201502093 |pmid=25924827 |doi-access=free}}</ref>

There are four key classes of post-translational modification:<ref name="Wang 2013" />
# Cleavage
# Addition of chemical groups
# Addition of complex molecules
# Formation of intramolecular bonds

===Cleavage===
[[File:Post-translational modification by cleavage.png|400px|thumb|alt= Two polypeptide chain, one chain is intact with three arrows indicating sites of protease cleavage on the chain and intermolecular disulphide bonds. The second chain is in three pieces connected by disulphide bonds.| Shows a post-translational modification of the protein by protease cleavage, illustrating that pre-existing bonds are retained even if when the polypeptide chain is cleaved.]]
[[Proteolysis|Cleavage]] of proteins is an irreversible post-translational modification carried out by enzymes known as [[proteases]]. These proteases are often highly specific and cause [[hydrolysis]] of a limited number of peptide bonds within the target protein. The resulting shortened protein has an altered polypeptide chain with different amino acids at the start and end of the chain. This post-translational modification often alters the proteins function, the protein can be inactivated or activated by the cleavage and can display new biological activities.<ref name="Ciechanover 2005">{{Cite journal |vauthors=Ciechanover A |date=January 2005 |title=Proteolysis: from the lysosome to ubiquitin and the proteasome |journal=Nature Reviews. Molecular Cell Biology |volume=6 |issue=1 |pages=79–87 |doi=10.1038/nrm1552 |pmid=15688069 |s2cid=8953615}}</ref>

===Addition of chemical groups===
[[File:Post-translational modification through the addition of small chemical groups.png|400px|thumb|alt= Three polypeptide chains with one amino acid side chain showing, two have a lysine and one has a serine. Three arrows indicating different post-translational modifications with the new chemical group added to each side chain. The first is methylation then acetylation followed by phosphorylation.| Shows the post-translational modification of protein by methylation, acetylation and phosphorylation]]
Following translation, small chemical groups can be added onto amino acids within the mature protein structure.<ref name="Brenner 2001">{{Cite book |title=Encyclopedia of genetics |vauthors=Brenner S, Miller JH |date=2001 |publisher=Elsevier Science Inc |isbn=978-0-12-227080-2 |pages=2800}}</ref> Examples of processes which add chemical groups to the target protein include methylation, [[Protein acetylation|acetylation]] and [[Protein phosphorylation|phosphorylation]].<ref>{{Cite journal |last=Zhong |first=Qian |last2=Xiao |first2=Xina |last3=Qiu |first3=Yijie |last4=Xu |first4=Zhiqiang |last5=Chen |first5=Chunyu |last6=Chong |first6=Baochen |last7=Zhao |first7=Xinjun |last8=Hai |first8=Shan |last9=Li |first9=Shuangqing |last10=An |first10=Zhenmei |last11=Dai |first11=Lunzhi |date=2023-05-02 |title=Protein posttranslational modifications in health and diseases: Functions, regulatory mechanisms, and therapeutic implications |url=https://pmc.ncbi.nlm.nih.gov/articles/PMC10152985/ |journal=MedComm |language=en |volume=4 |issue=3 |doi=10.1002/mco2.261 |issn=2688-2663 |archive-url=http://web.archive.org/web/20250211232904/https://pmc.ncbi.nlm.nih.gov/articles/PMC10152985/ |archive-date=2025-02-11|pmc=10152985 }}</ref>

Methylation is the reversible addition of a [[methyl group]] onto an amino acid catalyzed by [[methyltransferase]] enzymes. Methylation occurs on at least 9 of the 20 common amino acids, however, it mainly occurs on the amino acids [[lysine]] and [[arginine]]. One example of a protein which is commonly methylated is a [[histone]]. Histones are proteins found in the nucleus of the cell. DNA is tightly wrapped round histones and held in place by other proteins and interactions between negative charges in the DNA and positive charges on the histone. A highly specific pattern of [[histone methylation|amino acid methylation]] on the histone proteins is used to determine which regions of DNA are tightly wound and unable to be transcribed and which regions are loosely wound and able to be transcribed.<ref name="Murn 2017">{{Cite journal |vauthors=Murn J, Shi Y |date=August 2017 |title=The winding path of protein methylation research: milestones and new frontiers |journal=Nature Reviews. Molecular Cell Biology |volume=18 |issue=8 |pages=517–527 |doi=10.1038/nrm.2017.35 |pmid=28512349 |s2cid=3917753}}</ref>

Histone-based regulation of DNA transcription is also modified by acetylation. Acetylation is the reversible covalent addition of an [[acetyl group]] onto a lysine amino acid by the enzyme [[acetyltransferase]]. The acetyl group is removed from a donor molecule known as [[Acetyl-CoA|acetyl coenzyme A]] and transferred onto the target protein.<ref name="Drazic 2016">{{Cite journal |vauthors=Drazic A, Myklebust LM, Ree R, Arnesen T |date=October 2016 |title=The world of protein acetylation |journal=Biochimica et Biophysica Acta (BBA) - Proteins and Proteomics |volume=1864 |issue=10 |pages=1372–1401 |doi=10.1016/j.bbapap.2016.06.007 |pmid=27296530 |doi-access=free}}</ref> [[Histone acetylation and deacetylation|Histones undergo acetylation]] on their lysine residues by enzymes known as [[histone acetyltransferase]]. The effect of acetylation is to weaken the charge interactions between the histone and DNA, thereby making more genes in the DNA accessible for transcription.<ref name="Bannister 2011">{{Cite journal |vauthors=Bannister AJ, Kouzarides T |date=March 2011 |title=Regulation of chromatin by histone modifications |journal=Cell Research |volume=21 |issue=3 |pages=381–395 |doi=10.1038/cr.2011.22 |pmc=3193420 |pmid=21321607 |doi-access=free}}</ref>

The final, prevalent post-translational chemical group modification is phosphorylation. Phosphorylation is the reversible, covalent addition of a [[phosphate]] group to specific amino acids ([[serine]], [[threonine]] and [[tyrosine]]) within the protein. The phosphate group is removed from the donor molecule [[Adenosine triphosphate|ATP]] by a protein [[kinase]] and transferred onto the [[hydroxyl]] group of the target amino acid, this produces [[adenosine diphosphate]] as a byproduct. This process can be reversed and the phosphate group removed by the enzyme protein [[phosphatase]]. Phosphorylation can create a binding site on the phosphorylated protein which enables it to interact with other proteins and generate large, multi-protein complexes. Alternatively, phosphorylation can change the level of protein activity by altering the ability of the protein to bind its substrate.<ref name="Alberts 2015" />

===Addition of complex molecules===
[[File:Glycosylation of a polypeptide.png|400px|thumb|alt=Two polypeptide chains, one with an asparagine side chain exposed and a polysaccharide attached to the nitrogen atom within asparagine. The other polypeptide has a serine side chain exposed and the core of a polysaccharide attached to the oxygen atom within serine.| Illustrates the difference in structure between N-linked and O-linked glycosylation on a polypeptide chain.]]
Post-translational modifications can incorporate more complex, large molecules into the folded protein structure. One common example of this is [[glycosylation]], the addition of a polysaccharide molecule, which is widely considered to be most common post-translational modification.<ref name="Schubert 2015" />

In glycosylation, a [[polysaccharide]] molecule (known as a [[glycan]]) is covalently added to the target protein by [[glycosyltransferases]] enzymes and modified by [[glycoside hydrolases|glycosidases]] in the [[endoplasmic reticulum]] and [[Golgi apparatus]]. Glycosylation can have a critical role in determining the final, folded 3D structure of the target protein. In some cases glycosylation is necessary for correct folding. N-linked glycosylation promotes protein folding by increasing [[solubility]] and mediates the protein binding to [[chaperone (protein)|protein chaperones]]. Chaperones are proteins responsible for folding and maintaining the structure of other proteins.<ref name="Alberts 2015" />

There are broadly two types of glycosylation, [[N-linked glycosylation]] and [[O-linked glycosylation]]. N-linked glycosylation starts in the endoplasmic reticulum with the addition of a precursor glycan. The precursor glycan is modified in the Golgi apparatus to produce complex glycan bound covalently to the nitrogen in an [[asparagine]] amino acid. In contrast, O-linked glycosylation is the sequential covalent addition of [[Monosaccharide|individual sugars]] onto the oxygen in the amino acids serine and threonine within the mature protein structure.<ref name="Alberts 2015" />

===Formation of covalent bonds===
[[File:Formation of disulphide covalent bonds.png|400px|thumb|alt=Formation of a disulfide bond between two cysteine amino acids within a single polypeptide chain and formation of a disulphide bond between two cysteine amino acids on different polypeptide chains, thereby joining the two chains.|Shows the formation of disulphide covalent bonds as a post-translational modification. Disulphide bonds can either form within a single polypeptide chain (left) or between polypeptide chains in a multi-subunit protein complex (right).]]
Many proteins produced within the cell are secreted outside the cell to function as [[extracellular]] proteins. Extracellular proteins are exposed to a wide variety of conditions. To stabilize the 3D protein structure, covalent bonds are formed either within the protein or between the different polypeptide chains in the quaternary structure. The most prevalent type is a [[disulfide|disulfide bond]] (also known as a disulfide bridge). A disulfide bond is formed between two [[cysteine]] amino acids using their side chain chemical groups containing a Sulphur atom, these chemical groups are known as [[thiol]] functional groups. Disulfide bonds act to stabilize the [[protein structure|pre-existing structure]] of the protein. Disulfide bonds are formed in an [[redox|oxidation reaction]] between two thiol groups and therefore, need an oxidizing environment to react. As a result, disulfide bonds are typically formed in the oxidizing environment of the endoplasmic reticulum catalyzed by enzymes called protein disulfide isomerases. Disulfide bonds are rarely formed in the cytoplasm as it is a reducing environment.<ref name="Alberts 2015" />

==Role of protein synthesis in disease==
Many diseases are caused by mutations in genes, due to the direct connection between the DNA nucleotide sequence and the amino acid sequence of the encoded protein. Changes to the primary structure of the protein can result in the protein mis-folding or malfunctioning. Mutations within a single gene have been identified as a cause of multiple diseases, including [[sickle cell disease]], known as single gene disorders.{{cn|date=December 2024}}

===Sickle cell disease===
[[File:Sickle Cell Anaemia red blood cells in blood vessels.png|450px|thumb|alt=two blood curved vessels are shown, on the left one blood vessel contain normal red blood cells throughout the vessel. On the right, the red blood cells have a dish shape due to being sickled, a blockage composed of these distorted red blood cells is present at the curve in the blood vessel.| A comparison between an unaffected individual and an individual with sickle cell anaemia illustrating the different red blood cell shapes and differing blood flow within blood vessels.]]

Sickle cell disease is a group of diseases caused by a mutation in a subunit of hemoglobin, a protein found in red blood cells responsible for transporting oxygen. The most dangerous of the sickle cell diseases is known as sickle cell anemia. Sickle cell anemia is the most common [[genetic disorder|homozygous recessive single gene disorder]], meaning the affected individual must carry a mutation in both copies of the affected gene (one inherited from each parent) to experience the disease. Hemoglobin has a complex quaternary structure and is composed of four polypeptide subunits{{Snd}}two A subunits and two B subunits.<ref name="Steinberg 2016">{{Cite journal |vauthors=Habara A, Steinberg MH |date=April 2016 |title=Minireview: Genetic basis of heterogeneity and severity in sickle cell disease |journal=Experimental Biology and Medicine |volume=241 |issue=7 |pages=689–696 |doi=10.1177/1535370216636726 |pmc=4950383 |pmid=26936084}}</ref> Patients with sickle cell anemia have a missense or substitution mutation in the gene encoding the hemoglobin B subunit polypeptide chain. A missense mutation means the nucleotide mutation alters the overall codon triplet such that a different amino acid is paired with the new codon. In the case of sickle cell anemia, the most common missense mutation is a single nucleotide mutation from thymine to adenine in the hemoglobin B subunit gene.<ref name="StatPearls 2020">{{Cite journal |last=Mangla |first=A. |last2=Ehsan |first2=M. |last3=Agarwal |first3=N. |last4=Maruvada |first4=S. |year=2020 |title=Sickle Cell Anemia |url=https://www.ncbi.nlm.nih.gov/books/NBK482164/ |publisher=StatPearls Publishing |pmid=29489205 |access-date=12 March 2020 |website=StatPearls}}</ref> This changes codon 6 from encoding the amino acid glutamic acid to encoding valine.<ref name="Steinberg 2016" />

This change in the primary structure of the hemoglobin B subunit polypeptide chain alters the functionality of the hemoglobin multi-subunit complex in low oxygen conditions. When red blood cells unload oxygen into the tissues of the body, the mutated haemoglobin protein starts to stick together to form a semi-solid structure within the red blood cell. This distorts the shape of the red blood cell, resulting in the characteristic "sickle" shape, and reduces cell flexibility. This rigid, distorted red blood cell can accumulate in blood vessels creating a blockage. The blockage prevents blood flow to tissues and can lead to [[necrosis|tissue death]] which causes great pain to the individual.<ref name="Ilesanmi 2010">{{Cite journal |vauthors=Ilesanmi OO |date=January 2010 |title=Pathological basis of symptoms and crises in sickle cell disorder: implications for counseling and psychotherapy |journal=Hematology Reports |volume=2 |issue=1 |pages=e2 |doi=10.4081/hr.2010.e2 |pmc=3222266 |pmid=22184515 |doi-access=free}}</ref>

=== Cancer ===
[[File:Cancer requires multiple mutations from NIHen.png|thumb|300x300px|Formation of cancerous genes due to malfunction of suppressor genes.]]
Cancers form as a result of gene mutations as well as improper protein translation. In addition to cancer cells proliferating abnormally, they suppress the [[Gene expression|expression]] of anti-apoptotic or pro-apoptotic genes or proteins. Most cancer cells see a mutation in the signaling protein Ras, which functions as an on/off signal transductor in cells. In cancer cells, the RAS protein becomes persistently active, thus promoting the proliferation of the cell due to the absence of any regulation.<ref name=":0">{{Cite web |title=Cell Division, Cancer {{!}} Learn Science at Scitable |url=https://www.nature.com/scitable/topicpage/cell-division-and-cancer-14046590/ |access-date=30 November 2021 |website=Nature |language=en}}</ref> Additionally, most cancer cells carry two mutant copies of the regulator gene p53, which acts as a gatekeeper for damaged genes and initiates apoptosis in malignant cells. In its absence, the cell cannot initiate apoptosis or signal for other cells to destroy it.<ref>{{Cite web |title=p53, Cancer {{!}} Learn Science at Scitable |url=https://www.nature.com/scitable/topicpage/p53-the-most-frequently-altered-gene-in-14192717/ |access-date=30 November 2021 |website=Nature |language=en}}</ref>

As the tumor cells proliferate, they either remain confined to one area and are called benign, or become malignant cells that migrate to other areas of the body. Oftentimes, these malignant cells secrete proteases that break apart the extracellular matrix of tissues. This then allows the cancer to enter its terminal stage called Metastasis, in which the cells enter the bloodstream or the lymphatic system to travel to a new part of the body.<ref name=":0" />

== See also ==
* [[Central dogma of molecular biology]]
* [[Genetic code]]
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== References ==
{{Reflist}}

== External links ==
* [https://www.youtube.com/watch?v=K2bGjTaNsnM A more advanced video detailing the different types of post-translational modifications and their chemical structures]
* [https://www.youtube.com/watch?v=gG7uCskUOrA A useful video visualising the process of converting DNA to protein via transcription and translation]
* [https://www.youtube.com/watch?v=hok2hyED9go Video visualising the process of protein folding from the non-functional primary structure to a mature, folded 3D protein structure with reference to the role of mutations and protein mis-folding in disease]

{{Protein primary structure}}
{{protein biosynthesis}}{{Protein topics}}

{{Authority control}}

[[Category:Protein biosynthesis| ]]
[[Category:Gene expression]]
[[Category:Proteins]]
[[Category:Biosynthesis]]
[[Category:Metabolism]]