Difference between revisions of "Translation (biology)" - New World Encyclopedia

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A [[protein]] is a complex, high-molecular mass organic compound comprising [[amino acid]]s joined together in chains. The ultimate template for construction of a protein is the DNA of the organisms. However, the site of protein synthesis is the [[ribosome]] and it is [[messenger RNA]]'s (mRNA) that  provide the code or chemical blueprint for linking amino acids together to form new proteins. Messenger RNAs are synthesized from the DNA template in the process known as DNA transcription and then carry this coding information to the ribosomes, where the transcription into proteins takes place.
 
A [[protein]] is a complex, high-molecular mass organic compound comprising [[amino acid]]s joined together in chains. The ultimate template for construction of a protein is the DNA of the organisms. However, the site of protein synthesis is the [[ribosome]] and it is [[messenger RNA]]'s (mRNA) that  provide the code or chemical blueprint for linking amino acids together to form new proteins. Messenger RNAs are synthesized from the DNA template in the process known as DNA transcription and then carry this coding information to the ribosomes, where the transcription into proteins takes place.
  
In mRNA, as in DNA, genetic information is encoded in the sequence of four [[nucleotides]] arranged into [[codon]]s of three bases each. Each codon encodes for a specific [[amino acid]], except the [[stop codon]]s that terminate protein synthesis. At the site of protein synthesis, transfer RNAs (tRNAs) bind on one end to specific codons (three-base region) in the mRNA and bind on the other end to the amino acids specified by that codon, and thus place the amino acids in the correct sequence in the growing polypeptide according to the template (sequence of nucleotides) provided by the mRNA (Alberts et al. 1989). That is, the nucleic acid polymer is translated into a protein.  
+
In mRNA, as in DNA, genetic information is encoded in the sequence of four [[nucleotides]] arranged into [[codon]]s of three bases each. Each codon encodes for a specific [[amino acid]], except the [[stop codon]]s that terminate protein synthesis. At the site of protein synthesis, transfer RNAs (tRNAs) bind on one end to specific codons (three-base region) in the mRNA and bind on the other end to the amino acids specified by that codon, and thus place the amino acids in the correct sequence in the growing polypeptide according to the template (sequence of nucleotides) provided by the mRNA, as derived from the DNA gene (Alberts et al. 1989). That is, the nucleic acid polymer is translated into a protein. Each tRNA transports only one particular amino acid.  
  
 +
Translation proceeds in four phases: activation, initiation, elongation, and termination. In '''activation''', the correct amino acid is [[Covalent_bond| covalently bonded]] to the correct [[tRNA| transfer RNA (tRNA)]]. While this is not technically a step in translation, it is required for translation to proceed. The amino acid 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). '''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 a [[release factor|releasing factor]] can recognize [[Stop_codon| nonsense codons]] and causes the release of the polypeptide chain.
  
'''Transfer RNA''' '''(tRNA)''' is a class of short-chain, non-coding ribonucleic acid ([[RNA]]) molecules in which each variety attaches to and transfers a specific [[amino acid]] to a polypeptide chain at the [[ribosome|ribosomal]] site of [[protein]] synthesis during [[translation (biology)|translation]]. As non-coding RNA, tRNA itself is not translated into a protein, but it does serve to transport amino acids for incorporation into proteins, using the chemical blueprint for the protein product provided by messenger RNA (mRNA), as derived from the [[DNA]] [[gene]]s. Transfer RNA often is small, only about 74-79 nucleotides.
 
 
Each tRNA transports only one particular amino acid.
 
 
the first stage of [[protein biosynthesis]] (part of the overall process of [[gene expression]]).  Translation is the production of proteins by decoding mRNA produced in [[Transcription (genetics)|transcription]]. Translation occurs in the [[cytoplasm]] where the [[ribosome]]s are located. Ribosomes are made of a small and large subunit which surrounds the mRNA. In translation, [[mRNA|messenger RNA (mRNA)]] is decoded to produce a specific [[polypeptide]] according to the rules specified by the [[genetic code]]. This uses an mRNA sequence as a template to guide the synthesis of  a chain of [[amino acid]]s that form a protein. Many types of transcribed RNA, such as transfer RNA, ribosomal RNA, and small nuclear RNA are not necessarily translated into an amino acid sequence. 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). Amino acids are brought to ribosomes and assembled into proteins.
 
 
In activation, the correct amino acid is [[Covalent_bond| covalently bonded]] to the correct [[tRNA| transfer RNA (tRNA)]]. While this is not technically a step in translation, it is required for translation to proceed. The amino acid 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). 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 a [[release factor|releasing factor]] can recognize [[Stop_codon| nonsense codons]] and causes the release of the polypeptide chain.
 
 
The 5' end of the mRNA gives rise to the proteins N-terminal and the direction of translation can therefore be stated as N->C.
 
The 5' end of the mRNA gives rise to the proteins N-terminal and the direction of translation can therefore be stated as N->C.
  
The capacity of disabling or inhibiting translation in protein biosynthesis is used by [[antibiotic]]s such as: [[anisomycin]], [[cycloheximide]], [[chloramphenicol]], [[tetracycline]], [[streptomycin]], [[erythromycin]], [[puromycin]] etc.
+
The capacity of disabling or inhibiting translation in protein biosynthesis is used by [[antibiotic]]s such as: [[anisomycin]], [[cycloheximide]], [[chloramphenicol]], [[tetracycline]], [[streptomycin]], [[erythromycin]], [[puromycin]], and so forth.
  
 
==Basic mechanisms==
 
==Basic mechanisms==

Revision as of 15:24, 19 February 2009

Molbio-Header.svg

This article is part of the series on:

Gene expression
a Molecular biology topic (portal)
(Glossary)

Introduction to Genetics
General flow: DNA > RNA > Protein
special transfers (RNA > RNA,
RNA > DNA, Protein > Protein)
Genetic code
Transcription
Transcription (Transcription factors,
RNA Polymerase,promoter)
post-transcriptional modification
(hnRNA,Splicing)
Translation
Translation (Ribosome,tRNA)
post-translational modification
(functional groups, peptides,
structural changes
)
gene regulation
epigenetic regulation (Hox genes,
Genomic imprinting)
transcriptional regulation
post-transcriptional regulation
(sequestration,
alternative splicing,miRNA)
post-translational regulation
(reversible,irrevesible)

In genetics, translation is the cellular process in which proteins are produced by decoding, or translating, particular genetic information of the DNA using a messenger RNA (mRNA) intermediate as the template. Also known as protein synthesis or protein biosynthesis, translation occurs in the cytoplasm where the ribosomes are located and utilizes transfer RNAs (tRNAs) for attaching the specific amino acids that make up the protein. Translation is the second of two basic steps in the process of converting genes to proteins, with the first step being the transcription of a portion of the DNA into the mRNA. Then during translation, the mRNA guides the assembly of the amino acids into the particular sequence.

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.


Overview

The conversion of genes to proteins is essentially a two-step process: transcription and translation. Sometimes the term "protein synthesis" is used to refer only to protein translation, since this is the first stage in actually building the protein, but the entire process of expressing the gene into a protein requires transcription as well.

A protein is a complex, high-molecular mass organic compound comprising amino acids joined together in chains. The ultimate template for construction of a protein is the DNA of the organisms. However, the site of protein synthesis is the ribosome and it is messenger RNA's (mRNA) that provide the code or chemical blueprint for linking amino acids together to form new proteins. Messenger RNAs are synthesized from the DNA template in the process known as DNA transcription and then carry this coding information to the ribosomes, where the transcription into proteins takes place.

In mRNA, as in DNA, genetic information is encoded in the sequence of four nucleotides arranged into codons of three bases each. Each codon encodes for a specific amino acid, except the stop codons that terminate protein synthesis. At the site of protein synthesis, transfer RNAs (tRNAs) bind on one end to specific codons (three-base region) in the mRNA and bind on the other end to the amino acids specified by that codon, and thus place the amino acids in the correct sequence in the growing polypeptide according to the template (sequence of nucleotides) provided by the mRNA, as derived from the DNA gene (Alberts et al. 1989). That is, the nucleic acid polymer is translated into a protein. Each tRNA transports only one particular amino acid.

Translation proceeds in four phases: activation, initiation, elongation, and termination. In activation, the correct amino acid is covalently bonded to the correct transfer RNA (tRNA). While this is not technically a step in translation, it is required for translation to proceed. The amino acid 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). 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 a releasing factor can recognize nonsense codons and causes the release of the polypeptide chain.

The 5' end of the mRNA gives rise to the proteins N-terminal and the direction of translation can therefore be stated as N->C.

The capacity of disabling or inhibiting translation in protein biosynthesis is used by antibiotics such as: anisomycin, cycloheximide, chloramphenicol, tetracycline, streptomycin, erythromycin, puromycin, and so forth.

Basic mechanisms

See articles at prokaryotic translation and eukaryotic translation
Diagram showing the translation of mRNA and the synthesis of proteins by a ribosome

The mRNA carries genetic information encoded as a ribonucleotide sequence from the chromosomes to the ribosomes. The ribonucleotides are "read" by translational machinery in a sequence of nucleotide triplets called codons. Each of those triplets codes for a specific amino acid.

The ribosome and tRNA molecules translate this code to a specific sequence of amino acids. The ribosome is a multisubunit structure containing rRNA and proteins. It is the "factory" where amino acids are assembled into proteins. tRNAs are small noncoding RNA chains (74-93 nucleotides) that transport amino acids to the ribosome. tRNAs have a site for amino acid attachment, and a site called an anticodon. The anticodon is an RNA triplet complementary to the mRNA triplet that codes for their cargo amino acid.

Aminoacyl tRNA synthetase (an enzyme) catalyzes the bonding between specific tRNAs and the amino acids that their anticodons sequences call for. The product of this reaction is an aminoacyl-tRNA molecule. This aminoacyl-tRNA travels inside the ribosome, where mRNA codons are matched through complementary base pairing to specific tRNA anticodons. The amino acids that the tRNAs carry are then used to assemble a protein. The energy required for translation of proteins is significant. For a protein containing n amino acids, the number of high-energy Phosphate bonds required to translate it is 4n-1. The rate of translation varies; it is significantly higher in prokaryotic cells (up to 17-21 amino acid residues per second) than in eukaryotic cells (up to 6-7 amino acid residues per second) [1]

Translation by hand

It is also possible to translate either by hand (for short sequences) or by computer (after first programming one appropriately, see section below); this allows biologists and chemists to draw out the chemical structure of the encoded protein on paper.

First, convert each template DNA base to its RNA complement (note that the complement of A is now U), as shown below. Note that the template strand of the DNA is the one the RNA is polymerized against; the other DNA strand would be the same as the RNA, but with thymine instead of uracil.

DNA -> RNA
 A  ->  U
 T  ->  A
 G  ->  C
 C  ->  G

Then split the RNA into triplets (groups of three bases). Note that there are 3 translation "windows", or reading frames, depending on where you start reading the code. Finally, use the table at Genetic code to translate the above into a structural formula as used in chemistry.

This will give you the primary structure of the protein. However, proteins tend to fold, depending in part on hydrophilic and hydrophobic segments along the chain. Secondary structure can often still be guessed at, but the proper tertiary structure is often very hard to determine.

This approach may not give the correct amino acid composition of the protein, in particular if unconventional amino acids such as selenocysteine are incorporated into the protein, which is coded for by a conventional stop codon in combination with a downstream hairpin (SElenoCysteine Insertion Sequence, or SECIS).

Translation by computer

Many computer programs capable of translating a DNA/RNA sequence into protein sequence exist. Normally this is performed using the Standard Genetic Code; many bioinformaticians have written at least one such program at some point in their education. However, few programs can handle all the "special" cases, such as the use of the alternative initiation codons. For example, the rare alternative start codon CTG codes for Methionine when used as a start codon, and for Leucine in all other positions.

Example: Condensed translation table for the Standard Genetic Code (from the NCBI Taxonomy webpage).

   AAs  = FFLLSSSSYY**CC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG
 Starts = ---M---------------M---------------M----------------------------
 Base1  = TTTTTTTTTTTTTTTTCCCCCCCCCCCCCCCCAAAAAAAAAAAAAAAAGGGGGGGGGGGGGGGG
 Base2  = TTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGG
 Base3  = TCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAG

Translation tables

Even when working with ordinary Eukaryotic sequences such as the Yeast genome, it is often desired to be able to use alternative translation tables — namely for translation of the mitochondrial genes. Currently the following translation tables are defined by the NCBI Taxonomy Group for the translation of the sequences in GenBank:

 1: The Standard 
 2: The Vertebrate Mitochondrial Code 
 3: The Yeast Mitochondrial Code 
 4: The Mold, Protozoan, and Coelenterate Mitochondrial Code  and the Mycoplasma/Spiroplasma Code 
 5: The Invertebrate Mitochondrial Code 
 6: The Ciliate, Dasycladacean and Hexamita Nuclear Code 
 9: The Echinoderm and Flatworm Mitochondrial Code
10: The Euplotid Nuclear Code 
11: The Bacterial and Plant Plastid Code 
12: The Alternative Yeast Nuclear Code 
13: The Ascidian Mitochondrial Code 
14: The Alternative Flatworm Mitochondrial Code 
15: Blepharisma Nuclear Code 
16: Chlorophycean Mitochondrial Code 
21: Trematode Mitochondrial Code 
22: Scenedesmus obliquus mitochondrial Code 
23: Thraustochytrium Mitochondrial Code

Software examples

Example of computational translation - notice the indication of (alternative) start-codons:

VIRTUAL RIBOSOME
----
Translation table: Standard SGC0 

>Seq1
Reading frame: 1

    M  V  L  S  A  A  D  K  G  N  V  K  A  A  W  G  K  V  G  G  H  A  A  E  Y  G  A  E  A  L  
5' ATGGTGCTGTCTGCCGCCGACAAGGGCAATGTCAAGGCCGCCTGGGGCAAGGTTGGCGGCCACGCTGCAGAGTATGGCGCAGAGGCCCTG 90
   >>>...)))..............................................................................))) 

    E  R  M  F  L  S  F  P  T  T  K  T  Y  F  P  H  F  D  L  S  H  G  S  A  Q  V  K  G  H  G  
5' GAGAGGATGTTCCTGAGCTTCCCCACCACCAAGACCTACTTCCCCCACTTCGACCTGAGCCACGGCTCCGCGCAGGTCAAGGGCCACGGC 180
   ......>>>...))).......................................)))................................. 

    A  K  V  A  A  A  L  T  K  A  V  E  H  L  D  D  L  P  G  A  L  S  E  L  S  D  L  H  A  H  
5' GCGAAGGTGGCCGCCGCGCTGACCAAAGCGGTGGAACACCTGGACGACCTGCCCGGTGCCCTGTCTGAACTGAGTGACCTGCACGCTCAC 270
   ..................)))..................)))......))).........)))......)))......)))......... 

    K  L  R  V  D  P  V  N  F  K  L  L  S  H  S  L  L  V  T  L  A  S  H  L  P  S  D  F  T  P  
5' AAGCTGCGTGTGGACCCGGTCAACTTCAAGCTTCTGAGCCACTCCCTGCTGGTGACCCTGGCCTCCCACCTCCCCAGTGATTTCACCCCC 360
   ...)))...........................))).........))))))......))).............................. 

    A  V  H  A  S  L  D  K  F  L  A  N  V  S  T  V  L  T  S  K  Y  R  *  
5' GCGGTCCACGCCTCCCTGGACAAGTTCTTGGCCAACGTGAGCACCGTGCTGACCTCCAAATACCGTTAA 429
   ...............))).........)))..................)))...............*** 

Annotation key:
>>> : START codon (strict)
))) : START codon (alternative)
*** : STOP

References
ISBN links support NWE through referral fees

alberts et al. 1989

  1. J F Ross and M Orlowski, Growth-rate-dependent adjustment of ribosome function in chemostat-grown cells of the fungus Mucor racemosus., J Bacteriol. 1982 February; 149(2): 650–653., PMCID: PMC216554
  • Pamela C Champe, Richard A Harvey and Denise R Ferrier (2005). Lippincott's Illustrated Reviews: Biochemistry (3rd ed.). Lippincott Williams & Wilkins. ISBN 0-7817-2265-9.
  • David L. Nelson and Michael M. Cox (2005). Lehninger Principles of Biochemistry (4th ed.). W.H. Freeman. ISBN 0-7167-4339-6.
  • Zengel, J. 2003. Translation. In R. Robinson, Genetics. New York: Macmillan Reference USA. OCLC 55983868.


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