Citizendia

Image:Molbio-Header.svg

This article is part of the series on:

Gene expression
a Molecular biology topic (portal)

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)

Translation is the first stage of protein biosynthesis (part of the overall process of gene expression). Gene expression is the process by which inheritable information from a Gene, such as the DNA sequence, is made into a functional Gene product, such Molecular biology is the study of Biology at a molecular level Genetics studies how living Organisms inherit many of the features of their ancestors &ndash for example children usually look and act like other people in their Deoxyribonucleic acid ( DNA) is a Nucleic acid that contains the genetic instructions used in the development and functioning of all known Messenger ribonucleic acid ( mRNA) is a molecule of RNA encoding a chemical "blueprint" for a Protein product Proteins are large Organic compounds made of Amino acids arranged in a linear chain and joined together by Peptide bonds between the Carboxyl The central dogma of molecular biology was first enunciated by Francis Crick in 1958 and re-stated in a Nature paper published in 1970 RNA-dependent RNA polymerase ( RDRP) or RNA replicase, is an Enzyme that catalyzes the replication of RNA from an RNA template Reverse transcription is the process of making a double stranded DNA (deoxyribonucleic acid molecule from a single stranded RNA (ribonucleic acid template A prion (ˈpriːɒn is thought to be an infectious agent that according to current scientific consensus is comprised entirely of a propagated, mis-folded The genetic code is the set of rules by which information encoded in genetic material ( DNA or RNA sequences is translated into Proteins Transcription is the synthesis of RNA under the direction of DNA In the field of Molecular biology, a transcription factor (sometimes called a sequence-specific DNA binding factor is a Protein that binds to specific sequences RNA polymerase ( RNAP or RNApol) is an Enzyme that produces RNA. In Biology, a promoter is a region of DNA that facilitates the transcription of a particular Gene. Post-transcriptional modification is a process in Cell biology by which in Eukaryotic cells, primary transcript RNA is converted into mature Precursor mRNA ( pre-mRNA) also termed heterogeneous nuclear RNA ( hnRNA) is an immature single strand of messenger ribonucleic acid ( MRNA Ribosomes ( from ribo nucleic acid and "Greek soma ( meaning body") are complexes of RNA and Protein that Transfer RNA (abbreviated tRNA) is a small RNA (usually about 74-95 nucleotides that transfers a specific Amino acid to a growing polypeptide chain at Posttranslational modification (PTM is the chemical modification of a Protein after its translation. Gene modulation redirects here For information on therapeutic regulation of gene expression see Therapeutic gene modulation. In Biology, the term epigenetics refers to changes in Gene expression caused by mechanisms other than changes in the underlying DNA sequence Homeotic genes specify the anterior-posterior axis and segment identity Genomic imprinting is a genetic phenomenon by which certain Genes are expressed in a Parent -of-origin-specific manner Transcriptional regulation is the change in gene expression levels by altering transcription rates Post-transcriptional regulation is the control of protein synthesis by Genes after synthesis of RNA has begun Processing bodies (also called GW or Dcp bodies are regions within the cytoplasm of the Eukaryotic cell consisting of many enzymes involved in MRNA turnover Alternative splicing is the RNA splicing variation mechanism in which the Exons of the primary gene transcript the Pre-mRNA, are separated and reconnected In Genetics, microRNAs ( miRNA) are single-stranded RNA molecules of about 21–23 Nucleotides in length which regulate Gene expression Post-translational regulation refers to the control of the levels of active protein either by means Phosphorylation is the addition of a Phosphate (PO4 group to a Protein molecule or a small molecule Proteolysis is the directed degradation ( digestion) of Proteins by cellular Enzymes called Proteases or by intramolecular digestion Protein biosynthesis (synthesis is the process in which cells build Proteins The term is sometimes used to refer only to protein translation but more Gene expression is the process by which inheritable information from a Gene, such as the DNA sequence, is made into a functional Gene product, such Translation occurs in the cytoplasm where the ribosomes are located. The cytoplasm is the contents of a cell that is enclosed within the Plasma membrane. Ribosomes ( from ribo nucleic acid and "Greek soma ( meaning body") are complexes of RNA and Protein that 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 genetic code. Messenger ribonucleic acid ( mRNA) is a molecule of RNA encoding a chemical "blueprint" for a Protein product Peptides (from the Greek πεπτίδια, "small digestibles" are short Polymers formed from the linking in a defined order of α- Amino The genetic code is the set of rules by which information encoded in genetic material ( DNA or RNA sequences is translated into Proteins This uses an mRNA sequence as a template to guide the synthesis of a chain of amino acids that form a protein. In Chemistry, an amino acid is a Molecule containing both Amine and Carboxyl Functional groups In Biochemistry, this 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). Peptides (from the Greek πεπτίδια, "small digestibles" are short Polymers formed from the linking in a defined order of α- Amino

In activation, the correct amino acid is covalently bonded to the correct transfer RNA (tRNA). Transfer RNA (abbreviated tRNA) is a small RNA (usually about 74-95 nucleotides that transfers a specific Amino acid to a growing polypeptide chain at 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). Initiation factors are proteins that bind to the small subunit of the Ribosome during the initiation of translation, a part of Protein biosynthesis. 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 release factor is a Protein that recognizes the Termination codon or stop Codon in a MRNA sequence on the ribosome The capacity of disabling or inhibiting translation in protein biosynthesis is used by antibiotics such as: anisomycin, cycloheximide, chloramphenicol, tetracycline, streptomycin, erythromycin, puromycin etc. In modern usage an antibiotic is a Chemotherapeutic agent with activity against Microorganisms such as Bacteria, fungi or Protozoa Anisomycin, also known as flagecidin is an Antibiotic produced by Streptomyces griseolus which inhibits protein synthesis. Cycloheximide is an inhibitor of Protein biosynthesis in eukaryotic organisms produced by the bacterium Streptomyces griseus Chloramphenicol is a Bacteriostatic Antimicrobial originally derived from the Bacterium Streptomyces venezuelae, isolated by This article deals with the specific antibiotic called tetracycline Streptomycin is an Antibiotic drug the first of a class of drugs called Aminoglycosides to be discovered and was the first antibiotic remedy for Tuberculosis Erythromycin is a Macrolide Antibiotic that has an antimicrobial spectrum similar to or slightly wider than that of Penicillin, and is often used for people Puromycin is an Antibiotic that is a potent inhibitor of translation.

Contents

Basic mechanisms

See main articles at prokaryotic translation and eukaryotic translation

The mRNA carries genetic information encoded as a ribonucleotide sequence from the chromosomes to the ribosomes. Prokaryotic translation is the process by which Messenger RNA is translated into Proteins in Prokaryotes. Eukaryotic translation is the process by which Messenger RNA is translated into Proteins in Eukaryotes. Messenger ribonucleic acid ( mRNA) is a molecule of RNA encoding a chemical "blueprint" for a Protein product The genetic code is the set of rules by which information encoded in genetic material ( DNA or RNA sequences is translated into Proteins The ribonucleotides are "read" by translational machinery in a sequence of nucleotide triplets called codons. Nucleotides are Organic compounds that consist of three joined structures a nitrogenous base a Sugar, and a Phosphate group Each of those triplets codes for a specific amino acid. In Chemistry, an amino acid is a Molecule containing both Amine and Carboxyl Functional groups In Biochemistry, this

The ribosome and tRNA molecules translate this code to a specific sequence of amino acids. Ribosomes ( from ribo nucleic acid and "Greek soma ( meaning body") are complexes of RNA and Protein that The ribosome is a multisubunit structure containing rRNA and proteins. Ribosomal RNA ( rRNA) is the central component of the Ribosome, the protein manufacturing machinery of all living cells. 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. In Chemistry, an amino acid is a Molecule containing both Amine and Carboxyl Functional groups In Biochemistry, this

Aminoacyl tRNA synthetase (an enzyme) catalyzes the bonding between specific tRNAs and the amino acids that their anticodons sequences call for. An aminoacyl tRNA synthetase ( aaRS) is an Enzyme that catalyzes the Esterification of a specific Amino acid or its precursor to one of all its compatible Enzymes are Biomolecules that catalyze ( ie increase the rates of Chemical reactions Almost all enzymes are Proteins Transfer RNA (abbreviated tRNA) is a small RNA (usually about 74-95 nucleotides that transfers a specific Amino acid to a growing polypeptide chain at In Chemistry, an amino acid is a Molecule containing both Amine and Carboxyl Functional groups In Biochemistry, this 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. In Molecular biology, two Nucleotides on opposite complementary DNA or RNA strands that are connected via Hydrogen bonds are called Transfer RNA (abbreviated tRNA) is a small RNA (usually about 74-95 nucleotides that transfers a specific Amino acid to a growing polypeptide chain at 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.

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" 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. The genetic code is the set of rules by which information encoded in genetic material ( DNA or RNA sequences is translated into Proteins The genetic code is the set of rules by which information encoded in genetic material ( DNA or RNA sequences is translated into Proteins The structural formula of a Chemical compound is a graphical representation of the molecular structure showing how the atoms are arranged

This will give you the primary structure of the protein. In Biochemistry, the primary structure of a biological molecule is the exact specification of its atomic composition and the chemical bonds connecting those atoms (including However, proteins tend to fold, depending in part on hydrophilic and hydrophobic segments along the chain. Protein folding is the physical process by which a Polypeptide folds into its characteristic and functional three-dimensional structure. Hydrophile, from the Greek (hydros "water" and φιλια (philia "friendship" refers to a physical property of a Molecule In Chemistry, hydrophobicity (from the combining form of water in Attic Greek hydro- and for fear phobos) refers to the physical property of Secondary structure can often still be guessed at, but the proper tertiary structure is often very hard to determine. In Biochemistry and Structural biology, secondary structure is the general three-dimensional form of local segments of Biopolymers such as In Biochemistry and Chemistry, the tertiary structure of a Protein or any other Macromolecule is its three-dimensional structure as defined

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). In Chemistry, an amino acid is a Molecule containing both Amine and Carboxyl Functional groups In Biochemistry, this Selenocysteine is an Amino acid that is present in several Enzymes (for example Glutathione peroxidases tetraiodothyronine 5' deiodinases

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. Bioinformatics is the application of information technology to the field of molecular biology 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 TTG codes for Methionine when used as a start codon, and for Leucine in all other positions. Methionine ( abbreviated as Met or M) is an α- Amino acid with the Chemical formula HO2CCH(NH2CH2CH2SCH3 Leucine (abbreviated as Leu or L) is an α- Amino acid with the Chemical formula HO2CCH(NH2CH2CH(CH32

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. Animals Plants fungi, and Protists are eukaryotes (juːˈkærɪɒt or -oʊt Organisms whose cells are organized into complex Yeasts are a growth form of eukaryotic Microorganisms classified in the kingdom Fungi, with about 1500 Species currently described 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 Code10: 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 >Seq1Reading 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   >>>. The GenBank Sequence database is an Open access, annotated collection of all publicly available Nucleotide sequences and their Protein translations In Cell biology, a mitochondrion (plural mitochondria) is a membrane-enclosed Organelle found in most eukaryotic cells. Yeasts are a growth form of eukaryotic Microorganisms classified in the kingdom Fungi, with about 1500 Species currently described WikipediaManual_of_Style#National_varieties_of_English --> Molds (or  Protozoa (in Greek πρῶτον proton "first" and ζῷα zoia "animals" are unicellular Eukaryotes (singular Coelenterata is an obsolete long term encompassing two animal phyla, the Ctenophora (comb jellies and the Cnidaria ( Coral animals true Mycoplasma is a Genus of bacteria which lack a Cell wall. Without a cell wall they are unaffected by many common Antibiotics such Spiroplasma is a genus of Mollicutes, a group of small Bacteria without Cell walls Spiroplasma shares the simple Metabolism  An invertebrate is an Animal lacking a Vertebral column. The group includes 98% of all animal Species — all animals except those in the Chordate The ciliates are one of the most important groups of Protists common almost everywhere there is water — lakes ponds oceans rivers and soils with many ectosymbiotic Hole in the Head Disease, also known as Head and Lateral Line Erosion or HLLE is a Fish disease that affects both freshwater and marine fish in captivity Echinoderms (Phylum Echinodermata) are a phylum of marine Animals (including Sea stars) The flatworms (Phylum Platyhelminthes from the Greek πλατύ platy, meaning "flat" and ἕλμινς (root ἑλμινθ- helminth- Plastids are major Organelles found in plants and algae Plastids often contain pigments used in photosynthesis and the types of pigments present can change Ascidiacea (commonly known as the ascidians or Sea squirts is a class in the Tunicata Subphylum of sac-like marine Filter feeders Blepharisma is a Genius of The weirdo family Ciliates (a type of Protista which contains many species The Trematoda is a class within the phylum Platyhelminthes that contains two groups of parasitic Worms commonly referred to as flukes . . ))). . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . )))     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

© 2009 citizendia.org; parts available under the terms of GNU Free Documentation License, from http://en.wikipedia.org
 Dapyx Software network: MP3 Explorer | Ebook Manager | Zenithic