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How was able to make a recombinant DNA?
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How was able to make a recombinant DNA?

Making Recombinant DNA

How does recombinant DNA technology work? The organism under study, which will be used to donate DNA for the analysis, is called the donor organism. The basic procedure is to extract and cut up DNA from a donor genome into fragments containing from one to several genes and allow these fragments to insert themselves individually into opened-up small autonomously replicating DNA molecules such as bacterial plasmids. These small circular molecules act as carriers, or vectors, for the DNA fragments. The vector molecules with their inserts are called recombinant DNA because they consist of novel combinations of DNA from the donor genome (which can be from any organism) with vector DNA from a completely different source (generally a bacterial plasmid or a virus). The recombinant DNA mixture is then used to transform bacterial cells, and it is common for single recombinant vector molecules to find their way into individual bacterial cells. Bacterial cells are plated and allowed to grow into colonies. An individual transformed cell with a single recombinant vector will divide into a colony with millions of cells, all carrying the same recombinant vector. Therefore an individual colony contains a very large population of identical DNA inserts, and this population is called a DNA clone. A great deal of the analysis of the cloned DNA fragment can be performed at the stage when it is in the bacterial host. Later, however, it is often desirable to reintroduce the cloned DNA back into cells of the original donor organism to carry out specific manipulations of genome structure and function. Hence the protocol is often as follows:

http://www.ncbi.nlm.nih.gov/books/bookres.fcgi/mga/ch10e1.gif


Inasmuch as the donor DNA was cut into many different fragments, most colonies will carry a different recombinant DNA (that is, a different cloned insert). Therefore, the next step is to find a way to select the clone with the insert containing the specific gene in which we are interested. When this clone has been obtained, the DNA is isolated in bulk and the cloned gene of interest can be subjected to a variety of analyses, which we shall consider later in the chapter. Notice that the cloning method works because individual recombinant DNA molecules enter individual bacterial host cells, and then these cells do the job of amplifying the single molecules into large populations of molecules that can be treated like chemical reagents. Figure 10-1 on the following page gives a general outline of the approach.

The term recombinant DNA must be distinguished from the natural DNA recombinants that result from crossing-over between homologous chromosomes in both eukaryotes and prokaryotes. Recombinant DNA in the sense being used in this chapter is an unnatural union of DNAs from nonhomologous sources, usually from different organisms. Some geneticists prefer the alternative name chimeric DNA, after the mythological Greek monster Chimera. Down through the ages, the Chimera has stood as the symbol of an impossible biological union, a combination of parts of different animals. Likewise, recombinant DNA is a DNA chimera and would be impossible without the experimental manipulation that we call recombinant DNA technology.
Isolating DNA

The first step in making recombinant DNA is to isolate donor and vector DNA. General protocols for DNA isolation were available many decades before the advent of recombinant DNA technology. With the use of such methods, the bulk of DNA extracted from the donor will be nuclear genomic DNA in eukaryotes or the main genomic DNA in prokaryotes; these types are generally the ones required for analysis. The procedure used for obtaining vector DNA depends on the nature of the vector. Bacterial plasmids are commonly used vectors, and these plasmids must be purified away from the bacterial genomic DNA. A protocol for extracting plasmid DNA by ultracentrifugation is summarized in Figure 10-2 on page 303. Plasmid DNA forms a distinct band after ultracentrifugation in a cesium chloride density gradient containing ethidium bromide. The plasmid band is collected by punching a hole in the plastic centrifuge tube. Another protocol relies on the observation that, at a specific alkaline pH, bacterial genomic DNA denatures but plasmids do not. Subsequent neutralization precipitates the genomic DNA, but plasmids stay in solution. Phages such as λ also can be used as vectors for cloning DNA in bacterial systems. Phage DNA is isolated from a pure suspension of phages recovered from a phage lysate.top link
Cutting DNA

The breakthrough that made recombinant DNA technology possible was the discovery and characterization of restriction enzymes. Restriction enzymes are produced by bacteria as a defense mechanism against phages. The enzymes act like scissors, cutting up the DNA of the phage and thereby inactivating it. Importantly, restriction enzymes do not cut randomly; rather, they cut at specific DNA target sequences, which is one of the key features that make them suitable for DNA manipulation. Any DNA molecule, from viruses to humans, contains restriction-enzyme target sites purely by chance and therefore may be cut into defined fragments of size suitable for cloning. Restriction sites are not relevant to the function of the organism, nor would they be cut in vivo, because most organisms do not have restriction enzymes.

Let's look at an example: the restriction enzyme EcoRI (from E. coli) recognizes the following sixnucleotide-pair sequence in the DNA of any organism:

more detail : http://www.ncbi.nlm.nih.gov/books/bv.fcgi?rid=mga.section.1549

Posted on: 2009/11/6 15:51
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Is There a 'Bad Driver' Gene?
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Is There a 'Bad Driver' Gene?


Is There a 'Bad Driver' Gene?
1 in 3 people have DNA that may make things tougher behind the wheel, researchers say

In a small study, researchers found that people with a gene variation performed 20 percent worse on simulated driving tests and did as poorly a few days later. Almost one in three Americans have the variation, the team said.

"These people make more errors from the get-go, and they forget more of what they learned after time away," said Dr. Steven Cramer, neurology associate professor at the University of California at Irvine and senior author of a study published recently in the journal Cerebral Cortex, in a statement.

The study authors say the gene variation lowers available levels of a protein that boosts memory by helping brain cells talk to one another and work properly.

Earlier research has suggested people with the variation engage smaller areas of the brain when they take on tasks.

"We wanted to study motor behavior, something more complex than finger-tapping," said Stephanie McHughen, a graduate student and lead author of the study in a statement. "Driving seemed like a good choice because it has a learning curve, and it's something most people know how to do."

Twenty-nine people took a driving test on a simulator, including seven with the gene variation. They had to learn to "drive" on a track that included tough-to-navigate curves and turns. They came back four days later to retake the test.

Those with the variant did worse and failed to remember as much the second time around as the others. "Behavior derives from dozens and dozens of neurophysiologic events, so it's somewhat surprising this exercise bore fruit," Cramer said.

But don't be alarmed if you think you have this gene variation -- it has it's good side. The researcher say the gene also slows mental decline for people with conditions such as Parkinson's disease, Huntington's disease or multiple sclerosis.

"It's as if nature is trying to determine the best approach," Cramer said. "If you want to learn a new skill or have had a stroke and need to regenerate brain cells, there's evidence that having the variant is not good. But if you've got a disease that affects cognitive function, there's evidence it can act in your favor. The variant brings a different balance between flexibility and stability."

Posted on: 2009/10/30 17:59
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FDA OKs New HPV Vaccine Cervarix
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FDA OKs New HPV Vaccine Cervarix


Cervarix targets two HPV strains, HPV 16 and HPV 18, which are leading causes of cervical cancer. Cervarix is approved to help prevent cervical precancers and cervical cancers associated with those two types of HPV.

HPV infection is common; the virus is sexually transmitted. Most women who get infected don't develop cervical cancer, and there are other causes of cervical cancer.

In clinical trials, Cervarix was shown to be 93% effective in preventing cervical precancers associated with HPV 16 or HPV18 in women with no evidence of current or previous infection with one of those two HPV types, according to GlaxoSmithKline, the drug company that makes Cervarix.

Cervarix is the second FDA-approved HPV vaccine. In June 2006, the FDA approved the first HPV vaccine, Gardasil, which targets four strains of HPV: HPV 6, HPV 11, HPV 16, and HPV 18.

Posted on: 2009/10/23 15:31
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BioAnalyst Researcher
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BioAnalyst Researcher (m/f)

Job Description:

BioAnalysis Services team provides a customer-oriented working environment and dedicated services to BioScience R&D programs at competitive cost and time. The team actively participates to the definition of new approaches for the implementation of new technologies within research and frequently interact with bioinformatics competences and various researchers throughout the research departments of BioScience. In order to make competitive use of the complex in silico data coming from next-generation sequencing technologies, BioAnalysis Services will develop its competences in advanced areas such as systems biology and comparative genomics. Therefore we are looking for a BioAnalyst Researcher who will conduct the following tasks:
- Deliver genomic annotations for our crops of interest.
- Explore, test and evaluate existing tools to assemble NGS data
- Develop a quality control pipeline for this NGS data
- Develop tools/applications that will streamline our NGS platform
- Propose new strategies in order to extract information from the existing data
- Develop good relationships with the internal and external users/providers of NGS data
- Develop a good knowledge of the existing NGS platforms and keep up to date with this fast evolving area
Requirements:

You have got one of the following degrees:
- Master in bioinformatics
- Master in research fields related to biotechnology (molecular biology, genetics, genomics), but with a high interest in informatics
- Master in informatics/computer science or related research fields with a high interest in biotechnology/biology

Furtherone you have got a good knowledge of a programming language (Perl, JAVA, C#, etc) and databases. Knowledge of plant biology molecular genetics, marker technologies, protein biochemistry, genome engineering, plant breeding) and BioAnalysis (sequence analysis, genetic mapping, genome annotation, comparative genomics and systems biology).
Creative and flexible thinking, accuracy, autonomy and good communication skills for close relations with researchers and for the good understanding of the needs and a team player are also skills which you posses.

http://www.genomeweb.com/node/925295

Posted on: 2009/10/16 15:35
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Job -- Protein Chemist
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Protein Chemist

Description: We have an opportunity for an experienced protein chemist to participate in advancing Seattle Genetics’ industry-leading Antibody Drug Conjugate Technology in the Chemistry Department. We seek an individual who will enjoy working at the bench in a collaborative fashion alongside scientists with a variety of backgrounds and specialties. This position will allow a scientist to contribute to new antibody-drug conjugate programs from early discovery steps through IND submission.

RESPONSIBILITIES:

* Preparing antibody-drug conjugates (ADCs) at a variety of scales using established and experimental methodologies.
* Characterizing ADCs by a variety of techniques, including high resolution mass spectrometry and various chromatographic methods.
* Purifying antibodies and other recombinantly expressed proteins.
* Working with other scientists and departments in support of ADC discovery projects.
* Independent research to advance our understanding of ADC performance and improve future ADC programs.

Required Skills:

REQUIREMENTS:

* Ph.D. in Biochemistry, Chemistry, or a related field, or a B.S. degree with at least 8 years experience in the biopharmaceutical industry.
* Experience with chemical modification of proteins.
* Experience in the biochemical and biophysical characterization of purified proteins, including HPLC methods, SDS-PAGE, and spectroscopic methods.
* Good communication and organizational skills and the ability to interface constructively with other scientists.
* Desire to learn new techniques and expand one's skill set.

Please click on the following link to apply:
http://ats.staffxl.com/ATS/PortalViewRequirement.do?reqGK=43019

Posted on: 2009/10/9 13:59
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European Co-Ordination Of Antimalarial Drug Discovery
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European Co-Ordination Of Antimalarial Drug Discovery
The European Commission is funding a two year, €500,000 project to co-ordinate European and international research into the development of new drugs to treat malaria. The CRIMALDDI project (Coordination, Rationalisation and Integration of Antimalarial Drug Discovery and Development Initiatives) is being led by the Liverpool School of Tropical Medicine (LSTM) and brings together key players in ....

Posted on: 2009/10/2 14:38
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PPAR Inhibiors in Cancer Treatment
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PPAR Inhibiors in Cancer Treatment

Poly (ADP-Ribose) Polymerase (PARP) is a protein cells use to repair genetic injuries naturally. But cancer cells also use this protein to repair their own DNA damage. Inhibiting this action allows chemotherapy and radiation to do its job against cancers resulting from genetic mutation.

Posted on: 2009/9/17 13:43
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molecular tools restriction enzyme for recombinant DNA in a biotechnology revolution
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molecular tools restriction enzyme for recombinant DNA in a biotechnology revolution



Introduction
Watson and Crick's description, in 1953, of the double helical structure of the DNA molecule (See Classic Collection- The Structure of DNA) opened the door to a new era in biological understanding and research. Scientists, now knowing the molecular structure of the hereditary molecule, could begin both to elucidate and to manipulate its function. These new studies were, however, dependent on the discovery and use of the many enzymes that are able to modify or join existing DNA molecules, or to aid in the synthesis of new DNA molecules.
DNA enzymology
The late 1950's and the decade of the 60's saw enormous breakthroughs in DNA enzymology. For example, it was during this time that Arthur Kornberg and colleagues isolated DNA polymerase (1955), B. Weiss and C.C. Richardson isolated DNA ligase (1966), and H.O. Smith, K.W. Wilcox, and T.J. Kelley isolated and characterized the first sequence specific restriction nuclease (1968). These enzymes, respectively, play roles in the synthesis of DNA molecules, the attachment of two or more DNA molecules to one another, and the breaking of DNA molecules into fragments. Importantly, these enzymes make it possible to create entirely new kinds of DNA molecules and, equally important, to manipulate the functioning of the genes located on these new molecules.
Phage growth restriction
It had been known since the 1950's that phage particles that grow well and efficiently infect one strain of bacteria are often unable to grow well and infect other strains of the same bacterial species. In addition, phage particles that do succeed in infecting a second strain often show the opposite pattern: they are able to efficiently infect the second strain while growing only poorly in the original strain. A series of studies showed that phage particles that efficiently grow and infect host cells have DNA molecules that have been chemically modified by the addition of methyl groups to some of their adenine and/or cytosine bases, while the DNA of poorly infecting phage particles does not show this pattern of chemical modification or "methylation." Phage particles with unmethylated DNA do not grow and infect efficiently because their DNA molecules are cleaved and degraded by enzymes of the host cell, while methylated DNA is protected from this degradation. This phenomenon of degrading unmethylated DNA destroys the growth ability of the phage, and is responsible for the pattern of growth restriction described above.
Methylase and nuclease
In the late 1960's, scientists Stewart Linn and Werner Arber isolated examples of the two types of enzymes responsible for phage growth restriction in Escherichia coli (E. coli) bacteria. One of these enzymes methylated DNA, while the other cleaved unmethylated DNA at a wide variety of locations along the length of the molecule. The first type of enzyme was called a "methylase" while the other was called a "restriction nuclease." These enzymatic tools were important to scientists who were gathering the tools needed to "cut and paste" DNA molecules. What was needed now was a tool that would cut DNA at specific sites, rather than at random sites along the length of the molecule, so that scientists could cut DNA molecules in a predictable and reproducible way.
Site-specific nuclease
This important development came when H.O. Smith, K.W. Wilcox, and T.J. Kelley, working at Johns Hopkins University in 1968, isolated and characterized the first restriction nuclease whose functioning depended on a specific DNA nucleotide sequence. Working with Haemophilus influenzae bacteria, this group isolated an enzyme, called HindII, that always cut DNA molecules at a particular point within a specific sequence of six base pairs. This sequence is:

5' G T ( pyrimidine: T or C) ( purine: A or G) A C 3'
3' C A ( purine: A or G) ( pyrimidine: T or C) T G 5'

They found that the HindII enzyme always cuts directly in the center of this sequence. Wherever this particular sequence of six base pairs occurs unmodified in a DNA molecule, HindII will cleave both DNA backbones between the 3rd and 4th base pairs of the sequence. Moreover, HindII will only cleave a DNA molecule at this particular site. For this reason, this specific base sequence is known as the "recognition sequence" for HindII.

HindII is only one example of the class of enzymes known as restriction nucleases. In fact, more than 900 restriction enzymes, some sequence specific and some not, have been isolated from over 230 strains of bacteria since the initial discovery of HindII. These restriction enzymes generally have names that reflect their origin--The first letter of the name comes from the genus and the second two letters come from the species of the prokaryotic cell from which they were isolated. For example EcoRI comes from Escherichia coli RY13 bacteria, while HindII comes from Haemophilus influenzae strain Rd. Numbers following the nuclease names indicate the order in which the enzymes were isolated from single strains of bacteria. Nucleases are further described by addition of the prefix "endo" or "exo" to the name: The term "endonuclease" applies to sequence specific nucleases that break nucleic acid chains somewhere in the interior, rather than at the ends, of the molecule. Nucleases that function by removing nucleotides from the ends of the molecule are called "exonucleases."
Endonucleases and DNA fragments
A restriction endonuclease functions by "scanning" the length of a DNA molecule. Once it encounters its particular specific recognition sequence, it will bond to the DNA molecule and makes one cut in each of the two sugar-phosphate backbones of the double helix. The positions of these two cuts, both in relation to each other, and to the recognition sequence itself, are determined by the identity of the restriction endonuclease used to cleave the molecule in the first place. Different endonucleases yield different sets of cuts, but one endonuclease will always cut a particular base sequence the same way, no matter what DNA molecule it is acting on. Once the cuts have been made, the DNA molecule will break into fragments.
Endonucleases and sticky ends
Not all restriction endonucleases cut symmetrically and leave blunt ends like HindII described above. Many endonucleases cleave the DNA backbones in positions that are not directly opposite each other. For example, the nuclease EcoRI has the following recognition sequence:

5' G A A T T C 3'
3' C T T A A G 5'

When the enzyme encounters this sequence, it cleaves each backbone between the G and the closest A base residues. Once the cuts have been made, the resulting fragments are held together only by the relatively weak hydrogen bonds that hold the complementary bases to each other. The weakness of these bonds allows the DNA fragments to separate from one each other. Each resulting fragment has a protruding 5' end composed of unpaired bases. Other enzymes create cuts in the DNA backbone which result in protruding 3' ends. Protruding ends--both 3' and 5'-- are sometimes called "sticky ends" because they tend to bond with complementary sequences of bases. In other words, if an unpaired length of bases (5' A A T T 3') encounters another unpaired length with the sequence (3' T T A A5') they will bond to each other--they are "sticky" for each other. Ligase enzyme is then used to join the phosphate backbones of the two molecules. The cellular origin, or even the species origin, of the sticky ends does not affect their stickiness. Any pair of complementary sequences will tend to bond, even if one of the sequences comes from a length of human DNA, and the other comes from a length of bacterial DNA. In fact, it is this quality of stickiness that allows production of recombinant DNA molecules, molecules which are composed of DNA from different sources, and which has given birth to an industry!

Posted on: 2009/9/9 13:41
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molecular tools: plasmids for recombinant DNA in a biotechnology revolution
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molecular tools: plasmids for recombinant DNA in a biotechnology revolution

Plasmids

A plasmid is an independent, circular, self-replicating DNA molecule that carries only a few genes. The number of plasmids in a cell generally remains constant from generation to generation. Plasmids are autonomous molecules and exist in cells as extrachromosomal genomes, although some plasmids can be inserted into a bacterial chromosome, where they become a permanent part of the bacterial genome. It is here that they provide great functionality in molecular science.

Plasmids are easy to manipulate and isolate using bacteria (see also alkaline lysis) They can be integrated into mammalian genomes, thereby conferring to mammalian cells whatever genetic functionality they carry. Thus, this gives you the ability to introduce genes into a given organism by using bacteria to amplify the hybrid genes that are created in vitro. This tiny but mighty plasmid molecule is the basis of recombinant DNA technology.

There are two categories of plasmids. Stringent plasmids replicate only when the chromosome replicates. This is good if you are working with a protein that is lethal to the cell. Relaxed plasmids replicate on their own. This gives you a higher ratio of plasmids to chromosome.

So how do we manipulate these plasmids?

1. Mutate them using restriction enzymes, ligation enzymes, and PCR. Mutagenesis is easily accomplished by using restriction enzymes to cut out portions of one genome and insert them into a plasmid. PCR can also be used to facilitate mutagenesis. Plasmids are mapped out indicating the locations of their origins of replication and restriction enzyme sites.

2. Select them using genetic markers. Some bacteria are antibiotic resistant. While this is a serious health problem, it is a godsend to molecular scientists. The gene that confers antibiotic resistance can be added (ligated) to the gene you are inserting into the plasmid. So every plasmid that contains your target gene will not be killed by antibiotics. After you transfect your bacterial cells with your engineered plasmid (the one with the target gene and the antibiotic resistant marker), you incubate them in a nutrient broth that also contains antibiotic (usually ampecillin). Any cells that were not transfected (this means they do not have your target gene in them) are killed by the antibiotic. The ones that do have the gene also have the antibiotic resistant gene, and therefore survive the selection process.

3. Isolate them (such as with alkaline lysis)

4. Transform them into cells where they become vectors to transport foreign genes into a recipient organism.

There are some minimum requirements for plasmids that are useful for recombination techniques:

1. Origin of replication (ORI). They must be able to replicate themselves or they are of no practical use as a vector.

2. Selectable marker. They must have a marker so you can select for cells that have your plasmids.

3. Restriction enzyme sites in non-essential regions. You don't want to be cutting your plasmid in necessary regions such as the ORI.

In addition to these necessary requirements, there are some factors that make plasmids either more useful or easier to work with.

1. Small. If they are small, they are easier to isolate (you get more), handle (less shearing), and transform.

2. Multiple restriction enzyme sites. More sites give you greater flexibility in cloning, perhaps even allowing for directional cloning.

3. Multiple ORIs. It is important to note that two genes must have different ORIs if they are going to be inserted in the same plasmid.

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Posted on: 2009/8/27 14:04
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The "central dogma" in biology can be briefly described as follows: "DNA is transcribed to RNA and R
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The "central dogma" in biology can be briefly described as follows: "DNA is transcribed to RNA and RNA is translated to a protein." What happens during transcription? What happens during translation? --- Translation of DNA


DNA Translation

Deoxyribonucleic acid (DNA) is composed of a sequence of nucleotide bases paired together to form a double-stranded helix structure. Through a series of complex biochemical processes the nucleotide sequences in an organism's DNA are translated into the proteins it requires for life. The object of this problem is to write a computer program which accepts a DNA strand and reports the protein generated, if any, from the DNA strand.

The nucleotide bases from which DNA is built are adenine, cytosine, guanine, and thymine (hereafter referred to as A, C, G, and T, respectively). These bases bond together in a chain to form half of a DNA strand. The other half of the DNA strand is a similar chain, but each nucleotide is replaced by its complementary base. The bases A and T are complementary, as are the bases C and G. These two ``half-strands'' of DNA are then bonded by the pairing of the complementary bases to form a strand of DNA.

Typically a DNA strand is listed by simply writing down the bases which form the primary strand (the complementary strand can always be created by writing the complements of the bases in the primary strand). For example, the sequence TACTCGTAATTCACT represents a DNA strand whose complement would be ATGAGCATTAAGTGA. Note that A is always paired with T, and C is always paired with G.

From a primary strand of DNA, a strand of ribonucleic acid (RNA) known as messenger RNA (mRNA for short) is produced in a process known as transcription. The transcribed mRNA is identical to the complementary DNA strand with the exception that thymine is replaced by a nucleotide known as uracil (hereafter referred to as U). For example, the mRNA strand for the DNA in the previous paragraph would be AUGAGCAUUAAGUGA.

It is the sequence of bases in the mRNA which determines the protein that will be synthesized. The bases in the mRNA can be viewed as a collection of codons, each codon having exactly three bases. The codon AUG marks the start of a protein sequence, and any of the codons UAA, UAG, or UGA marks the end of the sequence. The one or more codons between the start and termination codons represent the sequence of amino acids to be synthesized to form a protein. For example, the mRNA codon AGC corresponds to the amino acid serine (Ser), AUU corresponds to isoleucine (Ile), and AAG corresponds to lysine (Lys). So, the protein formed from the example mRNA in the previous paragraph is, in its abbreviated form, Ser-Ile-Lys.

The complete genetic code from which codons are translated into amino acids is shown in the table below (note that only the amino acid abbreviations are shown). It should also be noted that the sequence AUG, which has already been identified as the start sequence, can also correspond to the amino acid methionine (Met). So, the first AUG in a mRNA strand is the start sequence, but subsequent AUG codons are translated normally into the Met amino acid.


http://acm.uva.es/p/v3/385.html

Posted on: 2009/8/17 15:37
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