The Satanic Bible

Biosynthesis of a Human Protein

Human Lineage
Scientific classification
Domain:	Eukaryota
Kingdom:	Animalia
Phylum:	Chordata
Subdivision:	Craniata
Subphylum:	Vertebrata
Infraphylum:	Euteleostomi
Class:	Mammalia
Infraclass:	Eutheria
Superorder:	Euarchontoglires
Order:	Primates
Suborder:	Haplorrhini
Infraorder:	Simiiformes
Parvorder:	Catarrhini É. Geoffroy, 1812
Family:	Hominidae
Subfamily:	Homininae
Tribe:	Hominini
Subtribe:	Hominina
Genus:	Homo Linnaeus, 1758
Species:	sapiens
Subspecies:	sapiens Homo sapiens sapiens

Consider starting with a specific gene. Assemble the transcription mechanism at the appropriate genome location. Transcribe the gene using nucleotide accountability.

Protein biosynthesis

A protein is a naturally occurring aliphatic compound, composed of amino acids (aa) and containing primarily at least the elements carbon (C), hydrogen (H), nitrogen (N), and oxygen (O). Many proteins also contain sulfur (S), occasionally phosphorus (P), and some iron (Fe).

Amino acids combine in a condensation reaction that releases water (dehydration reaction) to form a residue held together by a peptide bond. The digestion of dietary proteins produces dipeptides which are absorbed more rapidly than aa. Some tripeptides and tetrapeptides are synthesized in humans. Proteins are polypeptide molecules. Each protein is defined by a unique sequence of amino acid residues. This sequence is the primary structure of the protein.

In biosynthesis, precursors are activated often with nucleotides, generally in the presence of a catalyst, oxidizing or reducing agent, to interconvert biochemicals within living organisms.

Amino acid synthesis

Metabolic pathways) produce amino acids from other compounds. The substrates for these pathways are usually ingested or synthesized internally by intestinal microbiota or activation of the heterochromatin. Of the proteinogenic aa, humans are able to synthesise up to 12 at the level needed for normal growth. The remaining essential aa must be supplied with or from food.

Essential	Nonessential
Isoleucine	Alanine
Leucine	Asparagine
Lysine	Aspartate
Methionine	Cysteine*
Phenylalanine	Glutamate
Threonine	Glutamine*
Tryptophan	Glycine*
Valine	Proline*
	Serine*
	Tyrosine*
	Arginine*
	Histidine*

(*) Essential only in certain cases.

The situation is a more complicated since cysteine, tyrosine, histidine and arginine are semiessential aa in children. Their metabolic pathways are not fully developed. The aa amounts required depend on the age and health of the individual.

In the citric acid cycle glutamate dehydrogenase catalyzes the reductive amination of α-ketoglutarate to glutamate:

$\alpha -ketoglutarate+NH_{4}^{+}\rightleftarrows Glutamate$

At this step, the chirality of the amino acid is established. Afterwards, alanine and aspartate are synthesized by the transamination of glutamate, vis a vis the transamination of pyruvate and oxaloacetate, respectively. All of the remaining amino acids are constructed from glutamate or aspartate, by transamination of these two amino acids with one α-keto acid. Glutamine is synthesized from NH₄⁺ and glutamate, and asparagine is synthesized similarly. Proline and arginine are derived from glutamate. Serine formed from 3-phosphoglycerate, is the precursor of glycine and cysteine. Tyrosine is synthesized by the hydroxylation of phenylalanine, an essential amino acid.

Most of the pathways of amino acid biosynthesis are regulated by feedback inhibition, in which the committed step is allosterically inhibited by the final product. Branched pathways require extensive interaction among the branches that includes both negative and positive regulation. The regulation of glutamine synthetase from E. coli is a striking demonstration of cumulative feedback inhibition and of control by a cascade of reversible covalent modifications.

Nucleotide synthesis

De novo synthesis

Purine nucleotides

The synthesis of IMP.

The color scheme is as follows: enzymes, coenzymes, substrate names, metal ions, inorganic molecules

Pyrimidine nucleotides

The synthesis of UMP.

The color scheme is as follows: enzymes, coenzymes, substrate names, inorganic molecules

Adenosine triphosphate (ATP)

Anaerobic respiration

Glucose C₆H₁₂O₆ $\to$ 2 C₃H₆O₃ Lactic acid + 2 ATP.

Salvage synthesis

1. Adenine + Phosphoribosyl pyrophosphate PRPP <----> AMP + PP_i : Enzyme (Adenine phosphoribosyltransferase) APRT, GeneID: 353.

Cytidine triphosphate (CTP)

Uridine 5'-triphosphate (UTP) + Glutamine + ATP + H₂O => Cytidine 5'-triphosphate + Glutamate + ADP + Orthophosphate (P_i) : Enzyme (Cytidine 5' triphosphate synthetase) CTPS, GeneID: 1503.

Uridine triphosphate (UTP)

De novo synthesis of the pyrimidine ring and conversion to UMP:

1. L-Glutamine (Gln) + 2 ATP + HCO₃^- + H₂O => Carbamoyl phosphate + 2 ADP + Orthophosphate (P_i) + Glutamic acid (Glu) : Enzyme 1 (Carbomoyl-phosphate Synthetase 2, CPS II) CAD(E1), GeneID: 790.
2. Carbamoyl phosphate + L-Aspartate <=> N-carbamoyl L-aspartate + Orthophosphate (P_i) : Enzyme 2 (Aspartate transcarbamylase, ATCase) CAD(E2), GeneID: 790.
3. N-Carbamoyl L-Aspartate + H+ <=> (S)-Dihydroorotate + H₂O : Enzyme 3 (Dihydroorotase, DHO) CAD(E3), GeneID: 790.
4. (S)-Dihydroorotate + Ubiquinone => Orotate + Ubiquinol : Enzyme (Dihydroorotate dehydrogenase) DHODH, GeneID: 1723
5. Orotate + 5-Phospho-alpha-D-Ribose 1-Diphosphate (PRPP) <=> Orotidine 5'-monophosphate (OMP) + PP_i : Enzyme 1 (Uridine monophosphate synthetase) UMPS(E1), GeneID: 7372.
6. Orotidine 5'-monophosphate => Uridine 5'-monophosphate (UMP) + CO₂ : Enzyme 2 UMPS(E2), GeneID: 7372
7. Uridine 5'-monophosphate (UMP) + ATP <=> Uridine 5'-diphosphate (UDP) + ADP : Enzymes (Uridine monophosphate kinase) UMPK, GeneID: 51727; (uridine-cytidine kinase 2) UCK2, GeneID:7371.
8. Uridine 5'-diphosphate (UDP) + ADP <=> uridine 5'-triphosphate (UTP) + AMP : Enzymes (Nucleoside-diphosphate kinases A, B, C, D; NME6, NME7) NDKA-D, GeneIDs: 4830, 4831, 4832, 4833; NME6 GeneID: 10201, NME7 GeneID: 29922.

Transcription

A DNA sequence is enzymatically copied by RNA polymerase II to produce a complementary nucleotide RNA strand of messenger RNA (mRNA). mRNA is modified through RNA splicing, 5' end capping, and the addition of a polyA tail.

Transcriber

In human biochemistry a transcriber might be thought of as a tool assembled in the nucleus for the transcription of genetic information. It synthesizes (a nucleic acid, usually RNA) using an existing nucleic acid (DNA) as a template from which to copy.

Transcription factors

Transcription factors bind to specific sequences of DNA and are part of the system that controls the transcription of genetic information from DNA to RNA. Transcription factors occur in a complex, increase (as an activator), or prevent (as a repressor) the presence of RNA polymerase II.

Each transcription factor contains one or more DNA binding domains (DBDs) which attach to specific sequences of DNA adjacent to the gene that it regulates.

There are approximately 2600 proteins in the human genome that contain DNA-binding domains and most of these are presumed to function as transcription factors.

The combinatorial use of a subset of the approximately 2000 human transcription factors easily accounts for the unique regulation of each gene in the human genome during development.

General transcription factors (GTFs) are necessary for transcription to occur. GTFs are part of the large transcription preinitiation complex that interacts with RNA polymerase II directly. They are ubiquitous and interact with the core promoter region surrounding the transcription start site(s) of allclass II genes.

TFIIA TFIIB TFIID (see also TATA binding protein) TFIIE TFIIF TFIIH

Active transcription units (transcription factors) are clustered in the nucleus. There are ~10,000 factors in the nucleoplasm of a HeLa cell, among which are ~8,000 polymerase II factors and ~2,000 polymerase III factors. Each polymerase II factor contains ~8 polymerases. As most active transcription units are associated with only one polymerase, each factor will be associated with ~8 different transcription units. These units might be associated through promoters and/or enhancers, with loops forming a ‘cloud’ around the factor.

Additional proteins: coactivators chromatin remodelers histone acetylases deacetylases kinases methylases

play crucial roles in gene regulation.

The TATA binding protein (TBP, GeneID: 6908) is a transcription factor that binds specifically to a DNA sequence called the TATA box. This DNA sequence is found about 25-30 base pairs upstream of the transcription start site in some eukaryotic gene promoters. TBP, along with a variety of TBP-associated factors, make up the TFIID, a general transcription factor that in turn makes up part of the RNA polymerase II preinitiation complex. As one of the few proteins in the preinitation complex that binds DNA in a sequence-specific manner, it helps position RNA polymerase II over the transcription start site of the gene. However, it is estimated that only 10-20% of human promoters have TATA boxes. Therefore, TBP is probably not the only protein involved in positioning RNA polymerase II.

TBP is a subunit of the eukaryotic transcription factor TFIID. TFIID is the first protein to bind to DNA during the formation of the pre-initiation transcription complex of RNA polymerase II (RNA Pol II). Binding of TFIID to the TATA box in the promoter region of the gene initiates the recruitment of other factors required for RNA Pol II to begin transcription. Some of the other recruited transcription factors include TFIIA, TFIIB and TFIIF. Each of these transcription factors are formed from the interaction of many protein subunits, indicating that transcription is a heavily regulated process.

When TBP binds to a TATA box within the DNA, it distorts the DNA by inserting amino acid side chains between base pairs, partially unwinding the helix, and doubly kinking it. The distortion is accomplished through a great amount of surface contact between the protein and DNA. TBP binds with the negatively charged phosphates in the DNA backbone through positively charged lysine and arginine amino acid residues. The sharp bend in the DNA is produced through projection of four bulky phenylalanine residues into the minor groove. As the DNA bends, its contact with TBP increases, thus enhancing the DNA-protein interaction.

The strain imposed on the DNA through this interaction initiates melting, or separation, of the strands. Because this region of DNA is rich in adenine and thymine residues, which base pair through only two hydrogen bonds, the DNA strands are more easily separated. Separation of the two strands exposes the bases and allows RNA polymerase II to begin transcription of the gene.

RNA polymerase II

Each of the RNA polymerases transcribes different classes of proteins. Specifically, RNA polymerase I transcribes rRNA and RNA polymerase III transcribes various additional RNAs.

RNA polymerase II transcribes Class II genes to form proteins. It catalyzes the transcription of DNA to synthesize precursors of mRNA and most snRNA and microRNA.

It is a 550 kDa complex of 12 subunits:

Polymerase (RNA) II (DNA directed) polypeptide A, 220kDa (POLR2A), GeneID: 5430.

This largest subunit contains a carboxy terminal domain composed of heptapeptide repeats that are essential for polymerase activity. These repeats contain serine and threonine residues that are phosphorylated in actively transcribing RNA polymerase. In addition, this subunit, in combination with several other polymerase subunits, forms the DNA binding domain of the polymerase, a groove in which the DNA template is transcribed into RNA.

Polymerase (RNA) II (DNA directed) polypeptide B, 140kDa (POLR2B), GeneID: 5431.

This second largest subunit, in combination with at least two other polymerase subunits, forms a structure within the polymerase that maintains contact in the active site of the enzyme between the DNA template and the newly synthesized RNA.

Polymerase (RNA) II (DNA directed) polypeptide C, 33kDa (POLR2C), GeneID: 5432.

This third largest subunit contains a cysteine rich region and exists as a heterodimer with another polymerase subunit, POLR2J. These two subunits form a core subassembly unit of the polymerase.

DNA-directed RNA polymerase II polypeptide D (or subunit B4) (POLR2D), GeneID: 5433.

This is the fourth largest subunit.

Polymerase (RNA) II (DNA directed) polypeptide E, 25kDa (POLR2E), GeneID: 5434.

This the fifth largest subunit is present in two-fold molar excess over the other polymerase subunits. An interaction may occur between transcriptional activators and the polymerase through this subunit.

Polymerase (RNA) II (DNA directed) polypeptide F (POLR2F), GeneID: 5435.

This sixth largest subunit, based on studies in yeast, in combination with at least two other subunits, may form a structure that stabilizes the transcribing polymerase on the DNA template.

Polymerase (RNA) II (DNA directed) polypeptide G (POLR2G), GeneID: 5436.

This seventh largest subunit, from studies in yeast, may play a role in regulating polymerase function.

Polymerase (RNA) II (DNA directed) polypeptide H (POLR2H), GeneID: 5437.

This is an essential subunit.

Polymerase (RNA) II (DNA directed) polypeptide I, 14.5kDa (POLR2I), GeneID: 5438.

This subunit in combination with two other polymerase subunits forms the DNA binding domain of the polymerase, a groove in which the DNA template is transcribed into RNA. The product of this gene has two zinc finger motifs with conserved cysteines and the subunit does possess zinc binding activity.

Polymerase (RNA) II (DNA directed) polypeptide J, 13.3kDa (POLR2J), GeneID: 5439.

This subunit exists as a heterodimer with another polymerase subunit; forming a core subassembly unit of the polymerase. Two similar genes are located nearby on chromosome 7q22.1.

DNA directed RNA polymerase II polypeptide J-related gene (POLR2J2), GeneID: 246721.

This gene is a member of the RNA polymerase II subunit 11 gene family, which includes three genes in a cluster on chromosome 7q22.1. The founding member of this family, DNA directed RNA polymerase II polypeptide J, encodes multiple, alternatively spliced transcripts that potentially express isoforms with distinct C-termini compared to DNA directed RNA polymerase II polypeptide J. Most or all variants are spliced to include additional non-coding exons at the 3' end which makes them candidates for nonsense-mediated decay (NMD). Consequently, it is not known if this locus expresses a protein or proteins in vivo.

DNA directed RNA polymerase II polypeptide J3 (POLR2J3), GeneID: 548644.

This gene is a member of the RNA polymerase II subunit 11 gene family, which includes three genes in a cluster on chromosome 7q22.1. This locus produces multiple, alternatively spliced transcripts that potentially express isoforms with distinct C-termini compared to DNA directed RNA polymerase II polypeptide J. Most or all variants are spliced to include additional non-coding exons at the 3' end which makes them candidates for nonsense-mediated decay (NMD). Consequently, it is not known if this locus expresses a protein or proteins in vivo.

DNA directed RNA polymerase II polypeptide J4, pseudogene (POLR2J4), GeneID: 84820.

Although now thought to be a pseudogene, model predictions suggests that a miscRNA from this gene of possible transcription function may be involved in DNA binding and DNA-directed RNA polymerase activity.

Polymerase (RNA) II (DNA directed) polypeptide K, 7.0kDa (POLR2K), GeneID: 5540.

This is one of the smallest subunits.

RP11-90M2.3 novel protein similar to Polymerase (RNA) II (DNA directed) polypeptide K, 7.0kDa (RP11-90M2.3), GeneID: 100129174.

This maybe another small subunit.

Polymerase (RNA) II (DNA directed) polypeptide L, 7.6kDa (POLR2L), GeneID: 5441.

The subunit contains four conserved cysteines characteristic of an atypical zinc-binding domain.

RNA polymerase II holoenzyme

Initiation Regulation

Initiation is regulated by several mechanisms:

1. Protein interference.
2. Chromatin structure inhibition.
3. Phosphorylation.

Regulation by Protein interference

Protein interference is the process where some signaling protein interacts, either with the promoter or some stage of the partially constructed complex, to prevent further construction of the polymerase complex. This is generally a very rapid response and is used for fine level, individual gene control and for 'cascade' processes for a group of genes useful under a specific conditions (for example DNA repair genes or heat shock genes).

Regulation by Chromatin structure inhibition

Chromatin structure inhibition is the process where the promoter is hidden by chromatin structure. Chromatin structure is controlled by post-translational modification of the histones involved and leads to gross levels of high or low transcription levels. See: chromatin, histone and nucleosome.

These methods of control can be combined in a modular method, allowing very high specificity in transcription initiation control.

Regulation by Phosphorylation

POLR2A has a domain at its C-terminus, the CTD (C-terminal domain) which is the target of kinases and phosphatases. The phosphorylation of the CTD is an important regulation mechanism, as this allows attraction and rejection of factors that have a function in the transcription process. The CTD can be considered as a platform for transcription factors.

The CTD consists of repetitions of an amino acid motif, YSPTSPS, of which Serines and Threonines can be phosphorylated. The mammalian protein contains 52. There are many different combinations of phosphorylations possible on these repeats and these can change rapidly during transcription. The regulation of these phosphorylations and the consequences for the association of transcription factors plays a major role in the regulation of transcription.

During the transcription cycle, the CTD of POLR2A is reversibly phosphorylated. RNAP II containing unphosphorylated CTD is recruited to the promoter, whereas the hyperphosphorylated CTD form is involved in active transcription. Phosphorylation occurs at two sites within the heptapeptide repeat, at Serine 5 and Serine 2. Serine 5 phosphorylation is confined to promoter regions and is necessary for the initiation of transcription, whereas Serine 2 phosphorylation is important for mRNA elongation and 3'-end processing.

Messenger RNA

The "life cycle" of an mRNA in a eukaryotic cell. RNA is transcribed in the nucleus; once completely processed, it is transported to the cytoplasm and translated by the ribosome. At the end of its life, the mRNA is degraded.

In the ribosome, the nucleic acid polymer is translated into a polymer of amino acids: a protein.

File:Transcription label fromcommons.jpg

A micrograph of ongoing gene transcription of ribosomal RNA illustrating the growing primary transcripts. "Begin" indicates the 3' end of the DNA template strand, where new RNA synthesis begins; "end" indicates the 5' end, where the primary transcripts are almost complete.

Pre-Initiation

RNA polymerase II binds to the DNA and, along with other cofactors, unwinds the DNA to create an initiation bubble so that the polymerase has access to the single-stranded DNA template. RNA Polymerase II does require a promoter like sequence.

Proximal (core) Promoters: TATA promoters are found around -30 bp to the start site of transcription. Not all genes have TATA box promoters and there exists TATA-less promoters as well. The TATA promoter consensus sequence is TATA(A/T)A(A/T).

The following are the steps involved in TATA Promoter Complex formation:

1. General transcription factors bind

2. TFIID, TFIIA, TFIIB, TFIIF (w/RNA Polymerase II), TFIIH/E

From the beginning of complex formation, the pre-initiation complex is closed.

Initiation

Simple diagram of transcription initiation. RNAP = RNA polymerase II

A collection of transcription factors mediate the binding of RNA polymerase II and the initiation of transcription. Only after certain transcription factors are attached to the promoter does the polymerase bind to it. The completed assembly of transcription factors and RNA polymerase II (transcription initiation complex) bind to the promoter.

Once the complex is opened by TFIIH initiation starts and the first phosphodiester bond is formed.

Promoter Clearance

During the formation of the first nucleotide bond the RNA polymerase begins to clear the promoter. There is a tendency to release the RNA transcript and produce truncated transcripts (abortive initiation). Once the transcript reaches approximately 23 nucleotides it no longer slips and Elongation can occur. This is an ATP dependent process. The short-lived, unprocessed or partially processed, product is termed pre-mRNA.

Promoter clearance also coincides with Phosphorylation of serine 5 on the carboxy terminal domain which is phosphorylated by TFIIH.

Eukaryotic pre-mRNA processing

Main article: Post-transcriptional modification

Pre-mRNA requires extensive processing.

5' cap addition

Main article: 5' cap

A 5' cap (also termed an RNA cap, an RNA 7-methylguanosine cap or an RNA m⁷G cap) is a modified guanine nucleotide that is added to the "front" or 5' end of a the pre-mRNA using a 5',5-Triphosphate linkage shortly after the start of transcription. The 5' cap consists of a terminal 7-methylguanosine residue which is linked through a 5'-5'-triphosphate bond to the first transcribed nucleotide. Its presence is critical for recognition and proper attachment of mRNA by the ribosome and protection from 5' exonucleases RNases.

Cap addition is coupled to transcription, and occurs co-transcriptionally, such that each influences the other. Shortly after the start of transcription, the 5' end of the mRNA being synthesized is bound by a cap-synthesizing complex associated with RNA polymerase. This enzymatic complex catalyzes the chemical reactions that are required for mRNA capping. Synthesis proceeds as a multi-step biochemical reaction.

Coding regions

Main article: Coding region

Coding regions are composed of codons, which are decoded and translated into one protein by the ribosome. Coding regions begin with the start codon and end with the a stop codons. Generally, the start codon is an AUG triplet and the stop codon is UAA, UAG, or UGA. The coding regions tend to be stabilised by internal base pairs, this impedes degradation. In addition to being protein-coding, portions of coding regions may serve as regulatory sequences in the pre-mRNA as exonic splicing enhancers or exonic splicing silencers.

Untranslated regions

Main articles: 5' UTR and 3' UTR

Untranslated regions (UTRs) are sections of the mRNA before the start codon and after the stop codon that are not translated, termed the five prime untranslated region (5' UTR) and three prime untranslated region (3' UTR), respectively. These regions are transcribed with the coding region and thus are exonic as they are present in the mature mRNA. Several roles in gene expression have been attributed to the untranslated regions, including mRNA stability, mRNA localization, and translational efficiency. The ability of a UTR to perform these functions depends on the sequence of the UTR and can differ between mRNAs.

The stability of mRNAs may be controlled by the 5' UTR and/or 3' UTR due to varying affinity for RNA degrading enzymes called ribonucleases and for ancillary proteins that can promote or inhibit RNA degradation.

Translational efficiency, including sometimes the complete inhibition of translation, can be controlled by UTRs. Proteins that bind to either the 3' or 5' UTR may affect translation by influencing the ribosome's ability to bind to the mRNA. MicroRNAs bound to the 3' UTR also may affect translational efficiency or mRNA stability.

Cytoplasmic localization of mRNA is thought to be a function of the 3' UTR. Proteins that are needed in a particular region of the cell can actually be translated there; in such a case, the 3' UTR may contain sequences that allow the transcript to be localized to this region for translation.

Some of the elements contained in untranslated regions form a characteristic secondary structure when transcribed into RNA. These structural mRNA elements are involved in regulating the mRNA. Some, such as the SECIS element, are targets for proteins to bind. One class of mRNA element, the riboswitches, directly bind small molecules, changing their fold to modify levels of transcription or translation. In these cases, the mRNA regulates itself.

Splicing

Main article: Splicing (genetics)

Splicing is the process by which pre-mRNA is modified to remove certain stretches of non-coding sequences called introns; the stretches that remain include protein-coding sequences and are called exons. Sometimes pre-mRNA messages may be spliced in several different ways, allowing a single gene to encode multiple proteins. This process is called alternative splicing. Splicing is usually performed by an RNA-protein complex called the spliceosome, but some RNA molecules are also capable of catalyzing their own splicing (see ribozymes).

Editing

In some instances, an mRNA will be edited, changing the nucleotide composition of that mRNA. In humans is the apolipoprotein B mRNA, which is edited in some tissues, but not others. The editing creates an early stop codon, which upon translation, produces a shorter protein.

Polyadenylation

Main article: Polyadenylation

Polyadenylation is the covalent linkage of a polyadenylyl moiety to a messenger RNA molecule. Most messenger RNA (mRNA) molecules are polyadenylated at the 3' end. The poly(A) tail and the protein bound to it aid in protecting mRNA from degradation by exonucleases. Polyadenylation is also important for transcription termination, export of the mRNA from the nucleus, and translation. mRNA can also be polyadenylated in prokaryotic organisms, where poly(A) tails act to facilitate, rather than impede, exonucleolytic degradation. The 3' poly(A) tail is a long sequence of adenine nucleotides (often several hundred) at the 3' end of the pre-mRNA. This tail promotes export from the nucleus and translation, and protects the mRNA from degradation.

Monocistronic versus polycistronic mRNA

An mRNA molecule is said to be monocistronic when it contains the genetic information to translate only a single protein. This is the case for most of the eukaryotic mRNAs.

Elongation

Simple diagram of transcription elongation

One strand of DNA, the template strand (or non-coding strand), is used as a template for RNA synthesis. As transcription proceeds, RNA polymerase II traverses the template strand and uses base pairing complementarity with the DNA template to create an RNA copy. Although polymerase traverses the template strand from 3' → 5', the coding (non-template) strand is usually used as the reference point, so transcription is said to go from 5' → 3'. This produces an RNA molecule from 5' → 3', an exact copy of the coding strand (except that thymines are replaced with uracils, and the nucleotides are composed of a ribose (5-carbon) sugar where DNA has deoxyribose (one less oxygen atom) in its sugar-phosphate backbone).

mRNA transcription can involve multiple RNA polymerases on a single DNA template and multiple rounds of transcription (amplification of particular mRNA), so many mRNA molecules can be produced from a single copy of a gene. This step also involves a proofreading mechanism that can replace incorrectly incorporated bases.

The polymerase can experience pauses. These pauses may be intrinsic to RNA polymerase II or due to chromatin structure. Often the polymerase pauses to allow appropriate RNA editing factors to bind.

Termination

Simple diagram of transcription termination

Transcription termination in eukaryotes is less well understood, but involves cleavage of the new transcript, followed by template-independent addition of As at its new 3' end, in a process called polyadenylation.

Polyadenylation occurs during and immediately after transcription of DNA into RNA. After transcription has been terminated, the mRNA chain is cleaved through the action of an endonuclease complex associated with RNA polymerase II. After the mRNA has been cleaved, around 250 adenosine residues are added to the free 3' end at the cleavage site. This reaction is catalyzed by polyadenylate polymerase. Just as in alternative splicing, there can be more than one polyadenylation variant of a mRNA.

Once completely processed, the mRNA is termed mature mRNA.

Structure

The structure of a mature eukaryotic mRNA. A fully processed mRNA includes a 5' cap, 5' UTR, coding region, 3' UTR, and poly(A) tail.

Transport

Because eukaryotic transcription and translation is compartmentally separated, eukaryotic mRNAs are exported from the nucleus to the cytoplasm. Mature mRNAs are recognized by their processed modifications and then exported through the nuclear pore.

Translation

Main article: Translation (genetics)

Eukaryotic mRNA that has been processed and transported to the cytoplasm (i.e. mature mRNA) can then be translated by the ribosome. Translation may occur at ribosomes free-floating in the cytoplasm, or directed to the endoplasmic reticulum by the signal recognition particle.

Post-translational modification

This may include the formation of disulfide bridges or attachment of any of a number of biochemical functional groups, such as acetate, phosphate, various lipids and carbohydrates. Enzymes may also remove one or more amino acids from the leading (amino) end of the polypeptide chain, leaving a protein consisting of two polypeptide chains connected by disulfide bonds.

Protein folding

During and after synthesis, polypeptide chains often fold to assume, so called, native secondary and tertiary structures.

Degradation

After a certain amount of time, the message is degraded by RNases. The limited lifetime of mRNA enables a cell to alter protein synthesis rapidly in response to its changing needs.

Different mRNAs within the same cell have distinct lifetimes (stabilities). In mammalian cells, mRNA lifetimes range from several minutes to days. The greater the stability of an mRNA, the more protein may be produced from that mRNA. The presence of AU-rich elements in some mammalian mRNAs tends to destabilize those transcripts through the action of cellular proteins that bind these motifs. Rapid mRNA degradation via AU-rich elements is a critical mechanism for preventing the overproduction of potent cytokines such as tumor necrosis factor (TNF) and granulocyte-macrophage colony stimulating factor (GM-CSF). Base pairing with a small interfering RNA (siRNA) or microRNA (miRNA) can also accelerate mRNA degradation.

Further reading

• Doolittle, R.F. (1989) Redundancies in protein sequences. In Predictions of Protein Structure and the Principles of Protein Conformation (Fasman, G.D. ed) Plenum Press, New York, pp. 599-623
• David L. Nelson and Michael M. Cox, Lehninger Principles of Biochemistry, 3rd edition, 2000, Worth Publishers, ISBN 1-57259-153-6
• Uwe Meierhenrich, Amino acids and the asymmetry of life, Springer-Verlag, 2008, ISBN 978-3-540-76885-2

See also

• Genetic code
• Cistron
• Operon
• lac operon

External links

Amino Acids

• Protein isoelectric point according amino acids charge
• Learn the 20 proteinogenic amino acids online
• The PDF List of Standard Amino Acids
• Molecular Expressions: The Amino Acid Collection - Has detailed information and microscopy photographs of each amino acid.
• Nomenclature and Symbolism for Amino Acids and Peptides International Union of Pure and Applied Chemistry and The International Union of Biochemistry and Molecular Biology. IUPAC-IUB Joint Commission on Biochemical Nomenclature (JCBN)
• Amino acids overview at Peptide Guide
• Amino acid properties - Properties of the amino acids (a tool aimed mostly at molecular geneticists trying to understand the meaning of mutations)
• Right-handed amino acids were left behind
• Amino acid solutions pH, titration curves and distribution diagrams - freeware
• Synthesis of Amino Acids and Derivatives
• 22nd amino acid - Press release from Ohio State describing the discovery of pyrrolysine as a 22nd amino acid.
• NCBI Bookshelf Free Textbook Access

Nucleotide synthesis

• Overview at Queen Mary, University of London

Protein synthesis

• Protein Synthesis
• Protein Synthesis Animation Wesleyan University Learning Objects animation of protein synthesis.
• Science aid:Protein synthesis For high school

Transcription

• Transcription
• Interactive Java simulation of transcription initiation. From Center for Models of Life at the Niels Bohr Institute.
• From RNA to Protein Synthesis hypervideo.

Translation

• Translation

• Translation of mRNA Section of The Cell: A Molecular Approach by Geoffrey M. Cooper