Protein biosynthesis: Wikis

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RNA is transcribed in the nucleus; once completely processed, it is transported to the cytoplasm and translated by the ribosome (not shown).

Protein synthesis is the process in which cells build proteins. The term is sometimes used to refer only to protein translation but more often it refers to a multi-step process, beginning with amino acid synthesis and transcription of nuclear DNA into messenger RNA which is then used as input to translation.

The cistron DNA is transcribed into a variety of RNA intermediates. The last version is used as a template in synthesis of a polypeptide chain. Proteins can often be synthesized directly from genes by translating mRNA. When a protein is harmful and needs to be available on short notice or in large quantities, a protein precursor is produced. A proprotein is an inactive protein containing one or more inhibitory peptides that can be activated when the inhibitory sequence is removed by proteolysis during posttranslational modification. A preprotein is a form that contains a signal sequence (an N-terminal signal peptide) that specifies its insertion into or through membranes; i.e., targets them for secretion.[1] The signal peptide is cleaved off in the endoplasmic reticulum.[1] Preproproteins have both sequences (inhibitory and signal) still present.

For synthesis of protein, a succession of tRNA molecules charged with appropriate amino acids have to be brought together with an mRNA molecule and matched up by base-pairing through their anti-codons with each of its successive codons. The amino acids then have to be linked together to extend the growing protein chain, and the tRNAs, relieved of their burdens, have to be released. This whole complex of processes is carried out by a giant multimolecular machine, the ribosome, formed of two main chains of RNA, called ribosomal RNA (rRNA), and more than 50 different proteins. This molecular juggernaut latches onto the end of an mRNA molecule and then trundles along it, capturing loaded tRNA molecules and stitching together the amino acids they carry to form a new protein chain.[2]

Protein biosynthesis, although very similar, is different for prokaryotes and eukaryotes.

Contents

Amino acid synthesis

Amino acids are the monomers which are polymerized to produce proteins. Amino acid synthesis is the set of biochemical processes (metabolic pathways) which build the amino acids from carbon sources like glucose.

Many organisms have the ability to synthesize only a subset of the amino acids they need. Adult humans, for example, need to obtain 10 of the 20 amino acids from their food.

Transcription

Simple diagram of transcription elongation

In transcription an mRNA chain is generated, with one strand of the DNA double helix in the genome as template. This strand is called the template strand. Transcription can be divided into 3 stages: Initiation, Elongation and Termination, each regulated by a large number of proteins such as transcription factors and coactivators that ensure the correct gene is transcribed.

The DNA strand is read in the 3' to 5' direction and the mRNA is transcribed in the 5' to 3' direction by the RNA polymerase.

Transcription occurs in the cell nucleus, where the DNA is held. The DNA structure is two helixes made up of sugar and phosphate held together by the bases. The sugar and the phosphate are joined together by covalent bond. The DNA is "unzipped" by the enzyme helicase, leaving the single nucleotide chain open to be copied. RNA polymerase reads the DNA strand from 3 prime (3') end to the 5 prime (5') end, while it synthesizes a single strand of messenger RNA in the 5' to 3' direction. The general RNA structure is very similar to the DNA structure, but in RNA the nucleotide uracil takes the place that thymine occupies in DNA. The single strand of mRNA leaves the nucleus through nuclear pores, and migrates into the cytoplasm.

The first product of transcription differs in prokaryotic cells from that of eukaryotic cells, as in prokaryotic cells the product is mRNA, which needs no post-transcriptional modification, while in eukaryotic cells, the first product is called primary transcript, that needs post-transcriptional modification (capping with 7 methyl guanosine, tailing with a poly A tail) to give hnRNA (heterophil nuclear RNA). hnRNA then undergoes splicing of introns (non coding parts of the gene) via spliceosomes to produce the final mRNA.

Translation

Diagram showing the translation of mRNA and the synthesis of proteins by a ribosome

The synthesis of proteins is known as translation. Translation occurs in the cytoplasm where the ribosomes are located. Ribosomes are made of a small and large subunit which surrounds the mRNA. In translation, messenger RNA (mRNA) is decoded to produce a specific polypeptide according to the rules specified by the trinucleotide genetic code. This uses an mRNA sequence as a template to guide the synthesis of a chain of amino acids that form a protein. Translation proceeds in four phases: activation, initiation, elongation and termination (all describing the growth of the amino acid chain, or polypeptide that is the product of translation).

In activation, the correct amino acid (AA) is joined to the correct transfer RNA (tRNA). While this is not technically a step in translation, it is required for translation to proceed. The AA is joined by its carboxyl group to the 3' OH of the tRNA by an ester bond. When the tRNA has an amino acid linked to it, it is termed "charged". Initiation involves the small subunit of the ribosome binding to 5' end of mRNA with the help of initiation factors (IF), other proteins that assist the process. Elongation occurs when the next aminoacyl-tRNA (charged tRNA) in line binds to the ribosome along with GTP and an elongation factor. Termination of the polypeptide happens when the A site of the ribosome faces a stop codon (UAA, UAG, or UGA). When this happens, no tRNA can recognize it, but releasing factor can recognize nonsense codons and causes the release of the polypeptide chain. The capacity of disabling or inhibiting translation in protein biosynthesis is used by antibiotics such as: anisomycin, cycloheximide, chloramphenicol, tetracycline, streptomycin, erythromycin, puromycin etc.

Translation is the process of converting the mRNA codon sequences into an amino acid polypeptide chain. 1.Aminoacid activation

2.Initiation - A ribosome attaches to the mRNA and starts to code at the FMet codon (usually AUG, sometimes GUG or UUG). 3.Elongation - tRNA brings the corresponding amino acid (which has an anticodon that identifies the amino acid as the corresponding molecule to a codon) to each codon as the ribosome moves down the mRNA strand. 4.Termination - Reading of the final mRNA codon (aka the STOP codon), which ends the synthesis of the peptide chain and releases it.

Events following protein translation

The events following biosynthesis include post-translational modification and protein folding. During and after synthesis, polypeptide chains often fold to assume, so called, native secondary and tertiary structures. This is known as protein folding.

Many proteins undergo 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.

In general , protein molecules are believed to be modified by small chemical groups, post-translationally. Chemical modifications such as, phosphorylation of serine / threonine, acetylation or methylation of lysine, hydroxylation of proline / lysine, formylation of glycine , glycosylation of serine / threonine / asparagine, acylation of cysteine , myristoylation of glycine , biotinylation of lysine, ubiquitination , etc. on proteins is a very important issue in relation to properly understand the biological functions of a given protein. These post- translational modifications are studied hard and well-established with the discovery of the respective enzymes (kinases for phosphorylation, acetylases for acetylation, methyl transferases for methylation, etc. ) which carry on the chemical modifications on the specific amino acid residues . All of these modifications are still believed to be happened as post-translational events ; There is no study yet on when actually one particular modification occurs on a given amino acid residue in a given protein . Does it happen when the protein is already formed, or, when the amino acid chain is being synthesized, or before the translation of the primary chain has begun?

Since these chemical modifications are related to the biological functions of a protein, it is easy to think that these chemical modifications are happened to the whole protein molecule , after the protein primary chain is fully synthesized ; but , if that is the case, we have to consider the fact that the primary chains get folded instantly, (in a similar way as the newly synthesized DNA strands form helixes), to attain its compact-globular conformation ; As most of the primary chains are fairly long [a 5Kd protein may have 40-45 amino acid residues in its primary chain], it is likely that the newly formed amino acid chain tries to remain intact by folding thereby avoiding its breakdown via lots of proteases present within the cytoplasm. And, no capping event to protect the N-terminal end of the primary sequence (similar to 5' m-RNA capping to protect m-RNAs) is ever discovered for protein primary structure .So, by folding mechanism the primary chain perhaps avoids the protease attacks . However, once it gets folded, it may be very difficult for the respective enzyme molecule to find out the particular aa residue from the complexity of that compactly folded conformation . In addition, it can be clearly imagined that this enzymatic modification/reaction on a given amino acid requires presence and association of the appropriate enzyme, necessary cofactors, etc ; This association is much easier to occur when the amino acid residues in the primary structure are readily available for binding ; in other words , it is much difficult for the enzyme molecules to find and to bind to its substrate amino acid residue in a mature protein molecule after its three-dimentional conformation been attained .

So one can think that the modifications can happen while the primary chain of the protein is being synthesized during the translation process on the m-RNA strand ; the amino acid residues on the primary chain can be modified instantly and enzymatically by kinases , acetylases , hydroxylases, methyltransferases, etc. (a) to initiate proper folding for protection , in order to (b) avoid degradation by proteases and (c) thereby, gaining the globular form .

Also, the reader can imagine of another scenario in which, while the free amino acid molecules are formed within a cell and get available , they[in that free state] may be modified enzymatically before taking the ride to the translational event ; this means, while the primary chain is being synthesized , the pre-modified amino acid molecules are already there to take the ride on. But it is hard to imagine that an enzyme , a big protein molecule itself , plus the cofactors , can bind to a single amino acid (usually a small molecule) ; However, if the particular amino acid is bound to its t-RNA and can stop , as a whole [t-RNA + aa] molecule , at the appropriate enzymatic factory-parlor to modify itself appropriately, getting ready for the m-RNA machinery to take the final translational ride . This way , as the primary chain is getting synthesized , it does not have to be modified by the modifying enzymes anymore , and can fold itself instantaneously without thinking of its degradation . This also arises new thoughts that (i) phosphate,acetyl, methyl, biotinyl , acyl , etc. groups may have the ability to inhibit protease actions on the primary chains; (ii) most or all of the amino acid residues get modified by small chemical groups [ so far, only some chemical groups are known]

It is still not fully known , exactly when and how, the actual modification of a given amino acid residue occurs, at which stage of synthesis, within a protein molecule .

Once the chemically-modified , protease-insensitive, intact protein molecule is generated , it has to do its biological function; for this it has to be activated . The activation is probably done by a second set of enzymatic reactions when these chemical groups are removed from the aa residues ( or added back again) . So,the second type of post-translational modifications are the opposite reactions of the described type (above) : those are dephosphorylation by phosphatases or phosphoryl transferases, deacetylation by deacetylases or acetyltransferases , demethylation by demethylases or methyl-transferases, ubiquitination , SuMoylation, glycosylation, biotinylation , etc. These are taking place on the whole protein molecule towards generating its activated form to execute a particular function or towards its deactivation followed by its total degradation . As the chemical groups are removed (or added) , it is quite clear that the proteins can go through different states of structural / conformational change. Thus , post-translationally , a protein can change its conformation dynamically while the chemical groups are removed or added enzymatically ; these conformational changes in the protein structure help the protein to proceed through its life cycle , until it is ubiquitinated for its total degradation .

See also

External links

References

  1. ^ a b Alberts, Bruce (2002). Molecular biology of the cell. New York: Garland Science. pp. 760. ISBN 0-8153-3218-1. 
  2. ^ Alberts, Bruce. Molecular Biology of the Cell, 5e. New York: Garland Science, 2008.
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Simple English

Protein biosynthesis (synthesis) is when cells build proteins. The term is sometimes used to refer only to protein translation but more often it refers to a multi-step process, beginning with amino acid synthesis and transcription which are then used for translation. Protein biosynthesis, differs between prokaryotes and eukaryotes, though several parts of the process are the same in both.

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