International Rational Genome Design Contest

`Genome`

　In modern molecular biology, the genome is the entirety of an organism's hereditary information. It is encoded either in DNA or, for many types of virus, in RNA.
The genome includes both the genes and the non-coding sequences of the DNA. The term was adapted in 1920 by Hans Winkler, Professor of Botany at the University of Hamburg, Germany. The Oxford English Dictionary suggests the name to be a portmanteau of the words gene and chromosome. A few related -ome words already existed, such as biome and rhizome, forming a vocabulary into which genome fits systematically.
Some organisms have multiple copies of chromosomes, diploid, triploid, tetraploid and so on. In classical genetics, in a sexually reproducing organism (typically eukarya) the gamete has half of the number of chromosome of the somatic cell and the genome is a full set of chromosomes in a gamete. In haploid organisms, including cells of bacteria, archaea, and in organelles including mitochondria and chloroplasts, or viruses, that similarly contain genes, the single or set of circular and/or linear chains of DNA (or RNA for some viruses), likewise constitute the genome. The term genome can be applied specifically to mean that stored on a complete set of nuclear DNA (i.e., the "nuclear genome") but can also be applied to that stored within organelles that contain their own DNA, as with the "mitochondrial genome" or the "chloroplast genome". Additionally, the genome can comprise nonchromosomal genetic elements such as viruses, plasmids, and transposable elements. When people say that the genome of a sexually reproducing species has been "sequenced", typically they are referring to a determination of the sequences of one set of autosomes and one of each type of sex chromosome, which together represent both of the possible sexes. Even in species that exist in only one sex, what is described as "a genome sequence" may be a composite read from the chromosomes of various individuals. In general use, the phrase "genetic makeup" is sometimes used conversationally to mean the genome of a particular individual or organism. The study of the global properties of genomes of related organisms is usually referred to as genomics, which distinguishes it from genetics which generally studies the properties of single genes or groups of genes.

Both the number of base pairs and the number of genes vary widely from one species to another, and there is only a rough correlation between the two (an observation known as the C-value paradox). At present, the highest known number of genes is around 60,000, for the protozoan causing trichomoniasis (see List of sequenced eukaryotic genomes), almost three times as many as in the human genome.
An analogy to the human genome stored on DNA is that of instructions stored in a library:
* The library would contain 46 books (chromosomes)
* The books range in size from 400 to 3340 pages (genes)
* which is 48 to 250 million letters (A,C,G,T) per book.
* Hence the library contains over six billion letters total;
* The library fits into a cell nucleus the size of a pinpoint;
* A copy of the library (all 46 books) is contained in almost every cell of our body.
Genome. (2010, April 11). In Wikipedia, The Free Encyclopedia. Retrieved 03:11, April 19, 2010, from http://en.wikipedia.org/w/index.php?title=Genome&oldid=355380347

`Central dogma of molecular biology`

The central dogma of molecular biology was first enunciated by Francis Crick in 1958[1] and re-stated in a Nature paper published in 1970:
The central dogma of molecular biology deals with the detailed residue-by-residue transfer of sequential information. It states that information cannot be transferred back from protein to either protein or nucleic acid.
In other words, 'once information gets into protein, it can't flow back to nucleic acid.'

The dogma is a framework for understanding the transfer of sequence information between sequential information-carrying biopolymers, in the most common or general case, in living organisms. There are 3 major classes of such biopolymers: DNA and RNA (both nucleic acids), and protein. There are 3×3 = 9 conceivable direct transfers of information that can occur between these. The dogma classes these into 3 groups of 3: 3 general transfers (believed to occur normally in most cells), 3 special transfers (known to occur, but only under specific conditions in case of some viruses or in a laboratory), and 3 unknown transfers (believed to never occur). The general transfers describe the normal flow of biological information: DNA can be copied to DNA (DNA replication), DNA information can be copied into mRNA, (transcription), and proteins can be synthesized using the information in mRNA as a template (translation).
Central dogma of molecular biology. (2010, April 12). In Wikipedia, The Free Encyclopedia. Retrieved 03:19, April 19, 2010, fromhttp://en.wikipedia.org/w/index.php?title=Central_dogma_of_molecular_biology&oldid=355619972

`DNA`

Deoxyribonucleic acid (DNA) is a nucleic acid that contains the genetic instructions used in the development and functioning of all known living organisms and some viruses. The main role of DNA molecules is the long-term storage of information. DNA is often compared to a set of blueprints or a recipe, or a code, since it contains the instructions needed to construct other components of cells, such as proteins and RNA molecules. The DNA segments that carry this genetic information are called genes, but other DNA sequences have structural purposes, or are involved in regulating the use of this genetic information.
Chemically, DNA consists of two long polymers of simple units called nucleotides, with backbones made of sugars and phosphate groups joined by ester bonds. These two strands run in opposite directions to each other and are therefore anti-parallel. Attached to each sugar is one of four types of molecules called bases. It is the sequence of these four bases along the backbone that encodes information. This information is read using the genetic code, which specifies the sequence of the amino acids within proteins. The code is read by copying stretches of DNA into the related nucleic acid RNA, in a process called transcription.
Within cells, DNA is organized into long structures called chromosomes. These chromosomes are duplicated before cells divide, in a process called DNA replication. Eukaryotic organisms (animals, plants, fungi, and protists) store most of their DNA inside the cell nucleus and some of their DNA in organelles, such as mitochondria or chloroplasts. In contrast, prokaryotes (bacteria and archaea) store their DNA only in the cytoplasm. Within the chromosomes, chromatin proteins such as histones compact and organize DNA. These compact structures guide the interactions between DNA and other proteins, helping control which parts of the DNA are transcribed.
DNA. (2010, April 15). In Wikipedia, The Free Encyclopedia. Retrieved 03:22, April 19, 2010, from http://en.wikipedia.org/w/index.php?title=DNA&oldid=356243888

`RNA`

Ribonucleic acid (RNA) is a biologically important type of molecule that consists of a long chain of nucleotide units. Each nucleotide consists of a nitrogenous base, a ribose sugar, and a phosphate. RNA is very similar to DNA, but differs in a few important structural details: in the cell, RNA is usually single-stranded, while DNA is usually double-stranded; RNA nucleotides contain ribose while DNA contains deoxyribose (a type of ribose that lacks one oxygen atom); and RNA has the base uracil rather than thymine that is present in DNA.

RNA is transcribed from DNA by enzymes called RNA polymerases and is generally further processed by other enzymes. RNA is central to protein synthesis. Here, a type of RNA called messenger RNA carries information from DNA to structures called ribosomes. These ribosomes are made from proteins and ribosomal RNAs, which come together to form a molecular machine that can read messenger RNAs and translate the information they carry into proteins. There are many RNAs with other roles – in particular regulating which genes are expressed, but also as the genomes of most viruses.
RNA. (2010, April 7). In Wikipedia, The Free Encyclopedia. Retrieved 03:23, April 19, 2010, from http://en.wikipedia.org/w/index.php?title=RNA&oldid=354593826

`Nucleotide`

Nucleotides are molecules that, when joined together, make up the structural units of RNA and DNA. In addition, nucleotides play central roles in metabolism. In that capacity, they serve as sources of chemical energy (adenosine triphosphate and guanosine triphosphate), participate in cellular signaling (cyclic guanosine monophosphate and cyclic adenosine monophosphate), and are incorporated into important cofactors of enzymatic reactions (coenzyme A, flavin adenine dinucleotide, flavin mononucleotide, and nicotinamide adenine dinucleotide phosphate).
Nucleotide. (2010, March 29). In Wikipedia, The Free Encyclopedia. Retrieved 03:25, April 19, 2010, from http://en.wikipedia.org/w/index.php?title=Nucleotide&oldid=352761757

`Ribosomes`

Ribosomes are molecular machines that make proteins out of amino acids. One of the central tenets of biology is that DNA makes RNA, which then makes protein. The DNA sequence in genes is copied into a messenger RNA (mRNA). Ribosomes then read the information in this RNA and use it to produce proteins. Ribosomes do this by binding to a messenger RNA and using it as a template for the correct sequence of amino acids in a particular protein. The amino acids are attached to transfer RNA (tRNA) molecules, which enter one part of the ribosome and bind to the messenger RNA sequence. The attached amino acids are then joined together by another part of the ribosome. The ribosome moves along the mRNA, "reading" its sequence and producing a chain of amino acids.

Ribosomes are made from complexes of RNA and protein. Ribosomes are divided into two subunits, one larger than the other. The smaller subunit binds to the mRNA, while the larger subunit binds to the tRNA and the amino acids. When a ribosome finishes reading a mRNA these two subunits split apart. Ribosomes have been classified as ribozymes, since the ribosomal RNA seems to be most important for the peptidyl transferase activity that links together amino acids.

Ribosomes from bacteria, archaea and eukaryotes (the three domains of life on Earth), have significantly different structure and RNA sequences. These differences in structure allow some antibiotics to kill bacteria by inhibiting their ribosomes, while leaving human ribosomes unaffected. The ribosomes in the mitochondria of eukaryotic cells resemble those in bacteria, reflecting the evolutionary origin of this organelle. The word ribosome comes from ribonucleic acid and the Greek: soma (meaning body).
Ribosome. (2010, April 18). In Wikipedia, The Free Encyclopedia. Retrieved 03:27, April 19, 2010, from http://en.wikipedia.org/w/index.php?title=Ribosome&oldid=356819821

`Protein`

Proteins (also known as polypeptides) are organic compounds made of amino acids arranged in a linear chain and folded into a globular form. The amino acids in a polymer chain are joined together by the peptide bonds between the carboxyl and amino groups of adjacent amino acid residues. The sequence of amino acids in a protein is defined by the sequence of a gene, which is encoded in the genetic code. In general, the genetic code specifies 20 standard amino acids; however, in certain organisms the genetic code can include selenocysteine — and in certain archaea — pyrrolysine. Shortly after or even during synthesis, the residues in a protein are often chemically modified by post-translational modification, which alters the physical and chemical properties, folding, stability, activity, and ultimately, the function of the proteins. Proteins can also work together to achieve a particular function, and they often associate to form stable complexes.

Like other biological macromolecules such as polysaccharides and nucleic acids, proteins are essential parts of organisms and participate in virtually every process within cells. Many proteins are enzymes that catalyze biochemical reactions and are vital to metabolism. Proteins also have structural or mechanical functions, such as actin and myosin in muscle and the proteins in the cytoskeleton, which form a system of scaffolding that maintains cell shape. Other proteins are important in cell signaling, immune responses, cell adhesion, and the cell cycle. Proteins are also necessary in animals' diets, since animals cannot synthesize all the amino acids they need and must obtain essential amino acids from food. Through the process of digestion, animals break down ingested protein into free amino acids that are then used in metabolism.

Proteins were first described by the Dutch chemist Gerhardus Johannes Mulder and named by the Swedish chemist Jöns Jakob Berzelius in 1838. The central role of proteins in living organisms was however not fully appreciated until 1926, when James B. Sumner showed that the enzyme urease was a protein. The first protein to be sequenced was insulin, by Frederick Sanger, who won the Nobel Prize for this achievement in 1958. The first protein structures to be solved were hemoglobin and myoglobin, by Max Perutz and Sir John Cowdery Kendrew, respectively, in 1958. The three-dimensional structures of both proteins were first determined by x-ray diffraction analysis; Perutz and Kendrew shared the 1962 Nobel Prize in Chemistry for these discoveries. Proteins may be purified from other cellular components using a variety of techniques such as ultracentrifugation, precipitation, electrophoresis, and chromatography; the advent of genetic engineering has made possible a number of methods to facilitate purification. Methods commonly used to study protein structure and function include immunohistochemistry, site-directed mutagenesis, and mass spectrometry.
Protein. (2010, April 18). In Wikipedia, The Free Encyclopedia. Retrieved 03:30, April 19, 2010, from http://en.wikipedia.org/w/index.php?title=Protein&oldid=356760096

`Amino acid`

Amino acids are molecules containing an amine group, a carboxylic acid group and one of the twenty R-groups. These molecules are particularly important in biochemistry, where this term refers to alpha-amino acids with the general formula H2NCHRCOOH, where R is an organic substituent. In the alpha amino acids, the amino and carboxylate groups are attached to the same carbon atom, which is called the α–carbon. The various alpha amino acids differ in which side chain (R group) is attached to their alpha carbon. They can vary in size from just a hydrogen atom in glycine through a methyl group in alanine to a large heterocyclic group in tryptophan.

Amino acids are critical to life, and have a variety of roles in metabolism. One particularly important function is as the building blocks of proteins, which are linear chains of amino acids. Every protein is chemically defined by this primary structure, its unique sequence of amino acid residues, which in turn define the three-dimensional structure of the protein. Just as the letters of the alphabet can be combined to form an almost endless variety of words, amino acids can be linked together in varying sequences to form a vast variety of proteins. Amino acids are also important in many other biological molecules, such as forming parts of coenzymes, as in S-adenosylmethionine, or as precursors for the biosynthesis of molecules such as heme. Due to this central role in biochemistry, amino acids are very important in nutrition.

Amino acids are commonly used in food technology and industry. For example, monosodium glutamate is a common flavor enhancer that gives foods the taste called umami. Beyond the amino acids that are found in all forms of life, amino acids are also used in industry. Applications include the production of biodegradable plastics, drugs and chiral catalysts.
Amino acid. (2010, April 16). In Wikipedia, The Free Encyclopedia. Retrieved 03:40, April 19, 2010, from http://en.wikipedia.org/w/index.php?title=Amino_acid&oldid=356414982

`DNA replication`

DNA replication, the basis for biological inheritance, is a fundamental process occurring in all living organisms to copy their DNA. This process is "semiconservative" in that each strand of the original double-stranded DNA molecule serves as template for the reproduction of the complementary strand. Hence, following DNA replication, two identical DNA molecules have been produced from a single double-stranded DNA molecule. Cellular proofreading and error-checking mechanisms ensure near perfect fidelity for DNA replication.

In a cell, DNA replication begins at specific locations in the genome, called "origins". Unwinding of DNA at the origin, and synthesis of new strands, forms a replication fork. In addition to DNA polymerase, the enzyme that synthesizes the new DNA by adding nucleotides matched to the template strand, a number of other proteins are associated with the fork and assist in the initiation and continuation of DNA synthesis.

DNA replication can also be performed in vitro (outside a cell). DNA polymerases, isolated from cells, and artificial DNA primers are used to initiate DNA synthesis at known sequences in a template molecule. The polymerase chain reaction (PCR), a common laboratory technique, employs such artificial synthesis in a cyclic manner to amplify a specific target DNA fragment from a pool of DNA.
DNA replication. (2010, April 15). In Wikipedia, The Free Encyclopedia. Retrieved 03:42, April 19, 2010, from http://en.wikipedia.org/w/index.php?title=DNA_replication&oldid=356075480

`Transcription`

Transcription, or RNA synthesis, is the process of creating an equivalent RNA copy of a sequence of DNA. Both RNA and DNA are nucleic acids, which use base pairs of nucleotides as a complementary language that can be converted back and forth from DNA to RNA in the presence of the correct enzymes. During transcription, a DNA sequence is read by RNA polymerase, which produces a complementary, antiparallel RNA strand. As opposed to DNA replication, transcription results in an RNA compliment that includes uracil (U) in all instances where thymine (T) would have occurred in a DNA compliment.

Transcription is the first step leading to gene expression. The stretch of DNA transcribed into an RNA molecule is called a transcription unit and encodes at least one gene. If the gene transcribed encodes for a protein, the result of transcription is messenger RNA (mRNA), which will then be used to create that protein via the process of translation. Alternatively, the transcribed gene may encode for either ribosomal RNA (rRNA) or transfer RNA (tRNA), other components of the protein-assembly process, or other ribozymes.

A DNA transcription unit encoding for a protein contains not only the sequence that will eventually be directly translated into the protein (the coding sequence) but also regulatory sequences that direct and regulate the synthesis of that protein. The regulatory sequence before (upstream from) the coding sequence is called the five prime untranslated region (5'UTR), and the sequence following (downstream from) the coding sequence is called the three prime untranslated region (3'UTR).

Transcription has some proofreading mechanisms, but they are fewer and less effective than the controls for copying DNA; therefore, transcription has a lower copying fidelity than DNA replication.

As in DNA replication, DNA is read from 3' → 5' during transcription. Meanwhile, the complementary RNA is created from the 5' → 3' direction. Although DNA is arranged as two antiparallel strands in a double helix, only one of the two DNA strands, called the template strand, is used for transcription. This is because RNA is only single-stranded, as opposed to double-stranded DNA. The other DNA strand is called the coding strand, because its sequence is the same as the newly created RNA transcript (except for the substitution of uracil for thymine). The use of only the 3' → 5' strand eliminates the need for the Okazaki fragments seen in DNA replication.

Transcription is divided into 5 stages: pre-initiation, initiation, promoter clearance, elongation and termination.

Transcription (genetics). (2010, April 18). In Wikipedia, The Free Encyclopedia. Retrieved 03:46, April 19, 2010, from http://en.wikipedia.org/w/index.php?title=Transcription_(genetics)&oldid=356869701

`Translation`

Translation is 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. 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 genetic code. This uses an mRNA sequence as a template to guide the synthesis of a chain of amino acids 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 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 protein's N-terminus, and the direction of translation can therefore be stated as N->C.

A number of antibiotics act by inhibiting translation; these include anisomycin, cycloheximide, chloramphenicol, tetracycline, streptomycin, erythromycin, and puromycin, among others. Prokaryotic ribosomes have a different structure from that of eukaryotic ribosomes, and thus antibiotics can specifically target bacterial infections without any detriment to a eukaryotic host's cells.
Translation (genetics). (2010, April 14). In Wikipedia, The Free Encyclopedia. Retrieved 03:54, April 19, 2010, from http://en.wikipedia.org/w/index.php?title=Translation_(genetics)&oldid=355963714

`RNA splicing`

In molecular biology, splicing is a modification of an RNA after transcription, in which introns are removed and exons are joined. This is needed for the typical eukaryotic messenger RNA before it can be used to produce a correct protein through translation. For many eukaryotic introns, splicing is done in a series of reactions which are catalyzed by the spliceosome, a complex of small nuclear ribonucleoproteins (snRNPs), but there are also self-splicing introns.
RNA splicing. (2010, April 9). In Wikipedia, The Free Encyclopedia. Retrieved 03:57, April 19, 2010, from http://en.wikipedia.org/w/index.php?title=RNA_splicing&oldid=355000369

`Messenger RNA`

Messenger ribonucleic acid (mRNA) is a molecule of RNA encoding a chemical "blueprint" for a protein product. mRNA is transcribed from a DNA template, and carries coding information to the sites of protein synthesis: the ribosomes. Here, the nucleic acid polymer is translated into a polymer of amino acids: a protein. In mRNA as in DNA, genetic information is encoded in the sequence of nucleotides arranged into codons consisting of three bases each. Each codon encodes for a specific amino acid, except the stop codons that terminate protein synthesis. This process requires two other types of RNA: transfer RNA (tRNA) mediates recognition of the codon and provides the corresponding amino acid, while ribosomal RNA (rRNA) is the central component of the ribosome's protein manufacturing machinery.
Messenger RNA. (2010, April 16). In Wikipedia, The Free Encyclopedia. Retrieved 04:03, April 19, 2010, from http://en.wikipedia.org/w/index.php?title=Messenger_RNA&oldid=356361397

`Exon`

An exon is a nucleic acid sequence that is represented in the mature form of an RNA molecule after either portions of a precursor RNA (introns) have been removed by cis-splicing or by two or more precursor RNA molecules have been ligated by trans-splicing. The mature RNA molecule can be a messenger RNA or a functional form of a non-coding RNA such as rRNA or tRNA. Depending on the context, exon can refer to the sequence in the DNA or its RNA transcript.
Exon. (2010, March 16). In Wikipedia, The Free Encyclopedia. Retrieved 04:57, April 19, 2010, from http://en.wikipedia.org/w/index.php?title=Exon&oldid=350155520

`Intron`

An intron is a DNA region within a gene that is not translated into protein. These non-coding sections are transcribed to precursor mRNA (pre-mRNA) and some other RNAs (such as long noncoding RNAs), and subsequently removed by a process called splicing during the processing to mature RNA. After intron splicing (ie. removal), the mRNA consists only of exon derived sequences, which are translated into a protein.

The word intron is derived from the term intragenic region and also called intervening sequence (IVS)
Intron. (2010, April 5). In Wikipedia, The Free Encyclopedia. Retrieved 05:01, April 19, 2010, from http://en.wikipedia.org/w/index.php?title=Intron&oldid=354000554

`Transfer RNA`

Transfer RNA (abbreviated tRNA) is a small RNA molecule (usually about 74-95 nucleotides) that transfers a specific active amino acid to a growing polypeptide chain at the ribosomal site of protein synthesis during translation. It has a 3' terminal site for amino acid attachment. This covalent linkage is catalyzed by an aminoacyl tRNA synthetase. It also contains a three base region called the anticodon that can base pair to the corresponding three base codon region on mRNA. Each type of tRNA molecule can be attached to only one type of amino acid, but because the genetic code contains multiple codons that specify the same amino acid, tRNA molecules bearing different anticodons may also carry the same amino acid. Transfer RNA. (2010, April 16). In Wikipedia, The Free Encyclopedia. Retrieved 05:06, April 19, 2010, from "http://en.wikipedia.org/w/index.php?title=Transfer_RNA&oldid=356361902

`Ribosomal RNA`

Ribosomal RNA (rRNA) is the central component of the ribosome, the protein manufacturing machinery of all living cells. The function of the rRNA is to provide a mechanism for decoding mRNA into amino acids and to interact with the tRNAs during translation by providing peptidyl transferase activity.The tRNA then brings the necessary amino acids corresponding to the appropriate mRNA codon.
Ribosomal RNA. (2010, April 14). In Wikipedia, The Free Encyclopedia. Retrieved 05:09, April 19, 2010, from http://en.wikipedia.org/w/index.php?title=Ribosomal_RNA&oldid=356053357

`DNA polymerase`

A DNA polymerase is an enzyme that catalyzes the polymerization of deoxyribonucleotides into a DNA strand. DNA polymerases are best-known for their role in DNA replication, in which the polymerase "reads" an intact DNA strand as a template and uses it to synthesize the new strand. The newly-polymerized molecule is complementary to the template strand and identical to the template's original partner strand. DNA polymerases use a magnesium ion for catalytic activity.
DNA polymerase. (2010, April 13). In Wikipedia, The Free Encyclopedia. Retrieved 05:11, April 19, 2010, from http://en.wikipedia.org/w/index.php?title=DNA_polymerase&oldid=355807933

`RNA polymerase`

RNA polymerase (RNAP or RNApol) is an enzyme that produces RNA. In cells, RNAP is needed for constructing RNA chains from DNA genes as templates, a process called transcription. RNA polymerase enzymes are essential to life and are found in all organisms and many viruses. In chemical terms, RNAP is a nucleotidyl transferase that polymerizes ribonucleotides at the 3' end of an RNA transcript.
RNA polymerase. (2010, April 16). In Wikipedia, The Free Encyclopedia. Retrieved 05:15, April 19, 2010, from http://en.wikipedia.org/w/index.php?title=RNA_polymerase&oldid=356301938

`Promoter`

In genetics, a promoter is a region of DNA that facilitates the transcription of a particular gene. Promoters are typically located near the genes they regulate, on the same strand and upstream (towards the 5' region of the sense strand).
Promoter. (2010, March 16). In Wikipedia, The Free Encyclopedia. Retrieved 05:19, April 19, 2010, from http://en.wikipedia.org/w/index.php?title=Promoter&oldid=350139623

`Terminator`

In genetics, a terminator, or transcription terminator is a section of genetic sequence that marks the end of gene or operon on genomic DNA for transcription. In eukaryotes, terminators are recognized by protein factors that co-transcriptionally cleave the nascent RNA at a polyadenylation signal, halting further elongation of the transcript by RNA polymerase. The subsequent addition of the poly-A tail at this site stabilizes the mRNA and allows it to be exported outside the nucleus. Terminator sequences are distinct from termination codons that occur in the mRNA and are the stopping signal for translation, which may also be called nonsense codons.
Terminator (genetics). (2010, April 11). In Wikipedia, The Free Encyclopedia. Retrieved 02:39, April 19, 2010, from http://en.wikipedia.org/w/index.php?title=Terminator_(genetics)&oldid=355406763

`Shine-Dalgarno sequence`

The Shine-Delgarno sequence (or Shine-Dalgerno box), proposed by Australian scientists John Shine and Lynn Dalgerno, is a ribosomal binding site in the mRNA, generally located 16 nucleotides upstream of the start codon AUG. The Shine-Dalgarno sequence exists only in prokaryotes. The six-base consensus sequence is AGGAGG; in E. coli, for example, the sequence is AGGAGGU. This sequence helps recruit the ribosome to the mRNA to initiate protein synthesis by aligning it with the start codon. The complementary sequence (CCUCCU), is called the anti-Shine-Dalgarno sequence and is located at the 3' end of the 16S rRNA in the ribosome. The eukaryotic equivalent of the Shine-Dalgarno sequence is called the Kozak sequence.

Mutations in the Shine-Dalgarno sequence can reduce translation. This reduction is due to a reduced mRNA-ribosome pairing efficiency, as evidenced by the fact that complementary mutations in the anti-Shine-Dalgarno sequence can restore translation.

When the Shine-Dalgarno sequence and the anti-Shine-Dalgarno sequence pair, the translation initiation factors IF2-GTP, IF1, IF3, as well as the initiator tRNA fMet-tRNA(fmet) are recruited to the ribosome.

Shine-Dalgarno sequence. (2010, February 4). In Wikipedia, The Free Encyclopedia. Retrieved 05:37, April 19, 2010, from http://en.wikipedia.org/w/index.php?title=Shine-Dalgarno_sequence&oldid=341939443

`Polymerase chain reaction`

In molecular biology, the polymerase chain reaction (PCR) is a technique to amplify a single or few copies of a piece of DNA across several orders of magnitude, generating thousands to millions of copies of a particular DNA sequence. The method relies on thermal cycling, consisting of cycles of repeated heating and cooling of the reaction for DNA melting and enzymatic replication of the DNA. Primers (short DNA fragments) containing sequences complementary to the target region along with a DNA polymerase (after which the method is named) are key components to enable selective and repeated amplification. As PCR progresses, the DNA generated is itself used as a template for replication, setting in motion a chain reaction in which the DNA template is exponentially amplified. PCR can be extensively modified to perform a wide array of genetic manipulations.

Almost all PCR applications employ a heat-stable DNA polymerase, such as Taq polymerase, an enzyme originally isolated from the bacterium Thermus aquaticus. This DNA polymerase enzymatically assembles a new DNA strand from DNA building blocks, the nucleotides, by using single-stranded DNA as a template and DNA oligonucleotides (also called DNA primers), which are required for initiation of DNA synthesis. The vast majority of PCR methods use thermal cycling, i.e., alternately heating and cooling the PCR sample to a defined series of temperature steps. These thermal cycling steps are necessary first to physically separate the two strands in a DNA double helix at a high temperature in a process called DNA melting. At a lower temperature, each strand is then used as the template in DNA synthesis by the DNA polymerase to selectively amplify the target DNA. The selectivity of PCR results from the use of primers that are complementary to the DNA region targeted for amplification under specific thermal cycling conditions.

Developed in 1984 by Kary Mullis, PCR is now a common and often indispensable technique used in medical and biological research labs for a variety of applications. These include DNA cloning for sequencing, DNA-based phylogeny, or functional analysis of genes; the diagnosis of hereditary diseases; the identification of genetic fingerprints (used in forensic sciences and paternity testing); and the detection and diagnosis of infectious diseases. In 1993 Mullis was awarded the Nobel Prize in Chemistry for his work on PCR.
Polymerase chain reaction. (2010, April 16). In Wikipedia, The Free Encyclopedia. Retrieved 05:39, April 19, 2010, from http://en.wikipedia.org/w/index.php?title=Polymerase_chain_reaction&oldid=356308744

`Genetic engineering`

Genetic engineering, recombinant DNA technology, genetic modification/manipulation (GM) and gene splicing are terms that apply to the direct manipulation of an organism's genes. Genetic engineering is different from traditional breeding, where the organism's genes are manipulated indirectly. Genetic engineering uses the techniques of molecular cloning and transformation to alter the structure and characteristics of genes directly. Genetic engineering techniques have found some successes in numerous applications. Some examples are in improving crop technology, the manufacture of synthetic human insulin through the use of modified bacteria, the manufacture of erythropoietin in hamster ovary cells, and the production of new types of experimental mice such as the oncomouse (cancer mouse) for research.

The term "genetic engineering" was coined in Jack Williamson's science fiction novel Dragon's Island, published in 1951, two years before James Watson and Francis Crick showed that DNA could be the medium of transmission of genetic information.
Genetic engineering. (2010, April 2). In Wikipedia, The Free Encyclopedia. Retrieved 05:44, April 19, 2010, from http://en.wikipedia.org/w/index.php?title=Genetic_engineering&oldid=353566426

`Primer`

A primer is a strand of nucleic acid that serves as a starting point for DNA replication. They are required because the enzymes that catalyze replication, DNA polymerases, can only add new nucleotides to an existing strand of DNA. The polymerase starts replication at the 3'-end of the primer, and copies the opposite strand.

In most cases of natural DNA replication, the primer for DNA synthesis and replication is a short strand of RNA (which can be made de novo). This RNA is produced by primase, and is later removed and replaced with DNA by a repair polymerase.

Many of the laboratory techniques of biochemistry and molecular biology that involve DNA polymerase, such as DNA sequencing and the polymerase chain reaction (PCR), require DNA primers. These primers are usually short, chemically synthesized oligonucleotides, with a length of about twenty bases. They are hybridized to a target DNA, which is then copied by the polymerase.
Primer (molecular biology). (2010, April 11). In Wikipedia, The Free Encyclopedia. Retrieved 05:45, April 19, 2010, from http://en.wikipedia.org/w/index.php?title=Primer_(molecular_biology)&oldid=355413542

`Restriction enzyme`

A restriction enzyme (or restriction endonuclease) is an enzyme that cuts double-stranded or single stranded DNA at specific recognition nucleotide sequences known as restriction sites. Such enzymes, found in bacteria and archaea, are thought to have evolved to provide a defense mechanism against invading viruses. Inside a bacterial host, the restriction enzymes selectively cut up foreign DNA in a process called restriction; host DNA is methylated by a modification enzyme (a methylase) to protect it from the restriction enzyme’s activity. Collectively, these two processes form the restriction modification system. To cut the DNA, a restriction enzyme makes two incisions, once through each sugar-phosphate backbone (i.e. each strand) of the DNA double helix.

After isolating the first restriction enzyme, HindII, in 1970, and the subsequent discovery and characterization of numerous restriction endonucleases, the 1978 Nobel Prize for Physiology or Medicine was awarded to Daniel Nathans, Werner Arber, and Hamilton Smith. Their discovery led to the development of recombinant DNA technology that allowed, for example, the large scale production of human insulin for diabetics using E. coli bacteria. Over 3000 restriction enzymes have been studied in detail, and more than 600 of these are available commercially and are routinely used for DNA modification and manipulation in laboratories.
Restriction enzyme. (2010, April 15). In Wikipedia, The Free Encyclopedia. Retrieved 05:48, April 19, 2010, from http://en.wikipedia.org/w/index.php?title=Restriction_enzyme&oldid=356093175

`DNA ligase`

In molecular biology, DNA ligase is a special type of ligase (EC 6.5.1.1) that can link together two DNA strands that have double-strand break (a break in both complementary strands of DNA). The alternative, a single-strand break, is fixed by a different type of DNA ligase using the complementary strand as a template but still requires DNA ligase to create the final phosphodiester bond to fully repair the DNA.

DNA ligase has applications in both DNA repair and DNA replication (see Mammalian ligases). In addition, DNA ligase has extensive use in molecular biology laboratories for Genetic recombination experiments
DNA ligase. (2010, April 17). In Wikipedia, The Free Encyclopedia. Retrieved 05:50, April 19, 2010, from http://en.wikipedia.org/w/index.php?title=DNA_ligase&oldid=356622202

`Codon usage bias`

Codon usage bias refers to differences in the frequency of occurrence of synonymous codons in genomic DNA. A codon is a series of three nucleotides (triplets) that encodes a specific amino acid residue in a polypeptide chain.

Because there are four nucleotides in DNA, adenine (A), guanine (G), cytosine (C) and thymine (T), there are 64 possible triplets encoding 20 amino acids, and three translation termination (nonsense) codons. Because of this degeneracy, all but two amino acids are encoded by more than one triplet. Different organisms often show particular preferences for one of the several codons that encode the same amino acid. How these preferences arise is a much debated area of molecular evolution.

It is generally acknowledged that codon preferences reflect a balance between mutational biases and natural selection for translational optimization. Optimal codons in fast-growing microorganisms, like Escherichia coli or Saccharomyces cerevisiae (baker's yeast), reflect the composition of their respective genomic tRNA pool. It is thought that optimal codons help to achieve faster translation rates and high accuracy. As a result of these factors, translational selection is expected to be stronger in highly expressed genes, as is indeed the case for the above-mentioned organisms. In other organisms that do not show high growing rates or that present small genomes, codon usage optimization is normally absent, and codon preferences are determined by the characteristic mutational biases seen in that particular genome. Examples of this are Homo sapiens (human) and Helicobacter pylori. Organisms that show an intermediate level of codon usage optimization include Drosophila melanogaster (fruit fly), Caenorhabditis elegans (nematode worm) or Arabidopsis thaliana (wall cress).

The nature of the codon usage-tRNA optimization has been fiercely debated. It is not clear whether codon usage drives tRNA evolution or vice versa. At least one mathematical model has been developed where both codon-usage and tRNA-expression co-evolve in feedback fashion (i.e., codons already present in high frequencies drive up the expression of their corresponding tRNAs, and tRNAs normally expressed at high levels drive up the frequency of their corresponding codons!), however this model does not seem to yet have experimental confirmation. Another problem is that the evolution of tRNA genes has been a very inactive area of research.
Codon usage bias. (2009, September 18). In Wikipedia, The Free Encyclopedia. Retrieved 06:39, April 19, 2010, from http://en.wikipedia.org/w/index.php?title=Codon_usage_bias&oldid=314777262

`GC-content`

GC-content (or guanine-cytosine content), in molecular biology, is the percentage of nitrogenous bases on a DNA molecule which are either guanine or cytosine (from a possibility of four different ones, also including adenine and thymine). This may refer to a specific fragment of DNA or RNA, or that of the whole genome. When it refers to a fragment of the genetic material, it may denote the GC-content of part of a gene (domain), single gene, group of genes (or gene clusters) or even a non-coding region. G (guanine) and C (cytosine) undergo a specific hydrogen bonding whereas A (adenine) bonds specifically with T (thymine).

The GC pair is bound by three hydrogen bonds, while AT pairs are bound by two hydrogen bonds. DNA with high GC-content is more stable than DNA with low GC-content, but contrary to popular belief, the hydrogen bonds do not stabilize the DNA significantly and stabilization is mainly due to stacking interactions. In spite of the higher thermostability conferred to the genetic material, it is envisaged that cells with DNA with high GC-content undergo autolysis, thereby reducing the longevity of the cell per se. Due to the robustness endowed to the genetic materials in high GC organisms it was commonly believed that the GC content played a vital part in adaptation temperatures, a hypothesis which has recently been refuted.

In PCR experiments, the GC-content of primers are used to predict their annealing temperature to the template DNA. A higher GC-content level indicates a higher melting temperature.

GC-content. (2010, April 18). In Wikipedia, The Free Encyclopedia. Retrieved 05:56, April 19, 2010, from http://en.wikipedia.org/w/index.php?title=GC-content&oldid=356818564

`Life Science `

The life sciences comprise all fields of science that involve the scientific study of living organisms, like plants, animals, and human beings. However, the study of behavior of organisms, such as practiced in ethnology and psychology, is only included inasmuch as it involves a clearly biological aspect.

While biology and medicine remain centerpieces of the life sciences, technological advances in molecular biology and biotechnology have led to a burgeoning of specializations and new, often interdisciplinary, fields. Life sciences. (2010, February 27). In Wikipedia, The Free Encyclopedia. Retrieved 05:58, April 19, 2010, from http://en.wikipedia.org/w/index.php?title=Life_sciences&oldid=346609797

`Genetic Codes`

The genetic code is the set of rules by which information encoded in genetic material (DNA or mRNA sequences) is translated into proteins (amino acid sequences) by living cells. The code defines a mapping between tri-nucleotide sequences, called codons, and amino acids. With some exceptions, a triplet codon in a nucleic acid sequence usually specifies a single amino acid. Because the vast majority of genes are encoded with exactly the same code (see the RNA codon table), this particular code is often referred to as the canonical or standard genetic code, or simply the genetic code, though in fact there are many variant codes. Thus the canonical genetic code is not universal. In humans, for example, protein synthesis in mitochondria relies on a genetic code that varies from the standard genetic code.

Not all genetic information is stored using the genetic code. All organisms' DNA contains regulatory sequences, intergenic segments, and chromosomal structural areas that can contribute greatly to phenotype. Those higher-level or epigenetic elements operate under sets of rules that are distinct from the codon-to-amino acid paradigm underlying the genetic code.
Genetic code. (2010, April 14). In Wikipedia, The Free Encyclopedia. Retrieved 06:01, April 19, 2010, from http://en.wikipedia.org/w/index.php?title=Genetic_code&oldid=355938020

`Vector (Molecular Biology)`

In molecular biology, a vector is a DNA molecule used as a vehicle to transfer foreign genetic material into another cell. The four major types of vectors are plasmids, bacteriophages and other viruses, cosmids, and artificial chromosomes. Common to all engineered vectors are an origin of replication, a multicloning site, and a selectable marker.

The vector itself is generally a DNA sequence that consists of an insert (transgene) and a larger sequence that serves as the "backbone" of the vector. The purpose of a vector which transfers genetic information to another cell is typically to isolate, multiply, or express the insert in the target cell. Vectors called expression vectors (expression constructs) specifically are for the expression of the transgene in the target cell, and generally have a promoter sequence that drives expression of the transgene. Simpler vectors called transcription vectors are only capable of being transcribed but not translated: they can be replicated in a target cell but not expressed, unlike expression vectors. Transcription vectors are used to amplify their insert.

Insertion of a vector into the target cell is generally called transfection, although insertion of a viral vector is often called transduction. Vector (molecular biology). (2010, January 7). In Wikipedia, The Free Encyclopedia. Retrieved 06:02, April 19, 2010, from http://en.wikipedia.org/w/index.php?title=Vector_(molecular_biology)&oldid=336392637

`IRES`

An internal ribosome entry site, abbreviated IRES, is a nucleotide sequence that allows for translation initiation in the middle of a messenger RNA (mRNA) sequence as part of the greater process of protein synthesis. Usually, in eukaryotes, translation can be initiated only at the 5' end of the mRNA molecule, since 5' cap recognition is required for the assembly of the initiation complex. Internal ribosome entry site. (2010, April 5). In Wikipedia, The Free Encyclopedia. Retrieved 06:04, April 19, 2010, from http://en.wikipedia.org/w/index.php?title=Internal_ribosome_entry_site&oldid=354001633

`Arabidopsis thaliana`

　Arabidopsis thaliana (A-ra-bi-dóp-sis tha-li-á-na; thale cress, mouse-ear cress or Arabidopsis), is a small flowering plant native to Europe, Asia, and northwestern Africa. A spring annual with a relatively short life cycle, Arabidopsis is popular as a model organism in plant biology and genetics. Its genome is one of the smallest plant genomes and was the first plant genome to be sequenced. Arabidopsis is a popular tool for understanding the molecular biology of many plant traits, including flower development and light sensing. Arabidopsis thaliana. (2010, April 12). In Wikipedia, The Free Encyclopedia. Retrieved 02:47, April 19, 2010, from http://en.wikipedia.org/w/index.php?title=Arabidopsis_thaliana&oldid=355633591

【JavaScript】

　JavaScript is an object-oriented scripting language used to enable programmatic access to objects within both the client application and other applications. It is primarily used in the form of client-side JavaScript, implemented as an integrated component of the web browser, allowing the development of enhanced user interfaces and dynamic websites. JavaScript is a dialect of the ECMAScript standard and is characterized as a dynamic, weakly typed, prototype-based language with first-class functions. JavaScript was influenced by many languages and was designed to look like Java, but to be easier for non-programmers to work with.
JavaScript. (2010, April 18). In Wikipedia, The Free Encyclopedia. Retrieved 06:07, April 19, 2010, from http://en.wikipedia.org/w/index.php?title=JavaScript&oldid=356687793

【JavaScript@SciNetS】

　JavaScript@SciNetS is a library which enables JavaScript users to utilize the clusters of databases integrated by RIKEN SciNeS.

【JavaScript@SciNetS Editor】

　JavaScript@SciNetS Editor is an editor for creating and executing JavaScript programs on RIKEN SciNeS and a unique system where JavaScript@SciNeS can be used. In GenoCon, participants are able to use the editor after their registrations for the contest.

Adapted from Wikipedia, the free encyclopedia