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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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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? --- Transcription of DNA

The majority of genes are expressed as the proteins they encode. The process occurs in two steps:

* Transcription = DNA → RNA
* Translation = RNA → protein

Taken together, they make up the "central dogma" of biology: DNA → RNA → protein.


More detail: http://users.rcn.com/jkimball.ma.ultr ... ages/T/Transcription.html

Posted on: 2009/8/10 14:45
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How does DNA replicate? - Polymerase chain reaction in a biotechnology revolution
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How does DNA replicate? - Polymerase chain reaction in a biotechnology revolution

Researchers commonly replicate DNA in vitro using the polymerase chain reaction (PCR). PCR uses a pair of primers to span a target region in template DNA, and then polymerizes partner strands in each direction from these primers using a thermostable DNA polymerase. Repeating this process through multiple cycles produces amplification of the targeted DNA region. At the start of each cycle, the mixture of template and primers is heated, separating the newly synthesized molecule and template. Then, as the mixture cools, both of these become templates for annealing of new primers, and the polymerase extends from these. As a result, the number of copies of the target region doubles each round, increasing exponentially

Posted on: 2009/8/3 14:54
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How does DNA replicate? - Rolling circle replication in a biotechnology revolution
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How does DNA replicate? - Rolling circle replication in a biotechnology revolution


Another method of copying DNA, sometimes used in vivo by bacteria and viruses, is the process of rolling circle replication.[16] In this form of replication, a single replication fork progresses around a circular molecule to form multiple linear copies of the DNA sequence. In cells, this process can be used to rapidly synthesize multiple copies of plasmids or viral genomes.

In the cell, rolling circle replication is initiated by an initiator protein encoded by the plasmid or virus DNA. This protein is able to nick one strand of the double-stranded, circular DNA molecule at a site called the double-strand origin (DSO) and remains bound to the 5' phosphate end of the nicked strand. The free 3' hydroxyl end is released and can serve as a primer for DNA synthesis. Using the unnicked strand as a template, replication proceeds around the circular DNA molecule, displacing the nicked strand as single-stranded DNA. Continued DNA synthesis produces multiple single-stranded linear copies of the original DNA in a continuous head-to-tail series. In vivo these linear copies are subsequently converted to double-stranded circular molecules.

Rolling circle replication can also be performed in vitro and has found wide uses in academic research and biotechnology, often used for amplification of DNA from very small amounts of starting material. Replication can be initiated by nicking a double-stranded circular DNA molecule or by hybridizing a primer to a single-stranded circle of DNA. The use of a reverse primer (or random primers) produces hyperbranched rolling circle amplification, resulting in exponential rather than linear growth of the DNA molecule.


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Posted on: 2009/7/27 14:55
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How does DNA replicate? - DNA replication within the cell in a biotechnology revolution - Terminat
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How does DNA replicate? - DNA replication within the cell in a biotechnology revolution - Termination of replication

Termination of replication

Because bacteria have circular chromosomes, termination of replication occurs when the two replication forks meet each other on the opposite end of the parental chromosome. E coli regulate this process through the use of termination sequences which, when bound by the Tus protein, enable only one direction of replication fork to pass through. As a result, the replication forks are constrained to always meet within the termination region of the chromosome.[15]

Eukaryotes initiate DNA replication at multiple points in the chromosome, so replication forks meet and terminate at many points in the chromosome; these are not known to be regulated in any particular manner. Because eukaryotes have linear chromosomes, DNA replication often fails to synthesize to the very end of the chromosomes (telomeres), resulting in telomere shortening. This is a normal process in somatic cells cells are only able to divide a certain number of times before the DNA loss prevents further division. (This is known as the Hayflick limit.) Within the germ cell line, which passes DNA to the next generation, the enzyme telomerase extends the repetitive sequences of the telomere region to prevent degradation. Telomerase can become mistakenly active in somatic cells, sometimes leading to cancer formation.

Posted on: 2009/7/20 14:39
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How does DNA replicate? - DNA replication within the cell in a biotechnology revolution - Bacteria
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How does DNA replicate? - DNA replication within the cell in a biotechnology revolution - Bacteria

Bacteria

Most bacteria do not go through a well-defined cell cycle and instead continuously copy their DNA; during rapid growth this can result in multiple rounds of replication occurring concurrently.[13] Within E coli, the most well-characterized bacteria, regulation of DNA replication can be achieved through several mechanisms, including: the hemimethylation and sequestering of the origin sequence, the ratio of ATP to ADP, and the levels of protein DnaA. These all control the process of initiator proteins binding to the origin sequences.

Because E coli methylates GATC DNA sequences, DNA synthesis results in hemimethylated sequences. This hemimethylated DNA is recognized by a protein (SeqA) which binds and sequesters the origin sequence; in addition, dnaA (required for initiation of replication) binds less well to hemimethylated DNA. As a result, newly replicated origins are prevented from immediately initiating another round of DNA replication.[14]

ATP builds up when the cell is in a rich medium, triggering DNA replication once the cell has reached a specific size. ATP competes with ADP to bind to DnaA, and the DnaA-ATP complex is able to initiate replication. A certain number of DnaA proteins are also required for DNA replication each time the origin is copied the number of binding sites for DnaA doubles, requiring the synthesis of more DnaA to enable another initiation of replication.

Posted on: 2009/7/13 14:40
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How does DNA replicate? - DNA replication within the cell in a biotechnology revolution - Regulati
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How does DNA replicate? - DNA replication within the cell in a biotechnology revolution - Regulation of replication

Regulation of replication

Eukaryotes

Within eukaryotes, DNA replication is controlled within the context of the cell cycle. As the cell grows and divides, it progresses through stages in the cell cycle; DNA replication occurs during the S phase (Synthesis phase). The progress of the eukaryotic cell through the cycle is controlled by cell cycle checkpoints. Progression through checkpoints is controlled through complex interactions between various proteins, including cyclins and cyclin-dependent kinases.[12]

The G1/S checkpoint (or restriction checkpoint) regulates whether eukaryotic cells enter the process of DNA replication and subsequent division. Cells which do not proceed through this checkpoint are quiescent in the "G0" stage and do not replicate their DNA.

Replication of chloroplast and mitochondrial genomes occurs independent of the cell cycle, through the process of D-loop replication.

Posted on: 2009/7/2 13:26
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How does DNA replicate? - DNA replication within the cell in a biotechnology revolution - Dynamics
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How does DNA replicate? - DNA replication within the cell in a biotechnology revolution - Dynamics at the replication fork


Dynamics at the replication fork

As helicase unwinds DNA at the replication fork, the DNA ahead is forced to rotate. This process results in a build-up of twists in the DNA ahead.[10] This build-up would form a resistance that would eventually halt the progress of the replication fork. DNA topoisomerases are enzymes that solve these physical problems in the coiling of DNA. Topoisomerase I cuts a single backbone on the DNA, enabling the strands to swivel around each other to remove the build-up of twists. Topoisomerase II cuts both backbones, enabling one double-stranded DNA to pass through another, thereby removing knots and entanglements that can form within and between DNA molecules.

Bare single-stranded DNA has a tendency to fold back upon itself and form secondary structures; these structures can interfere with the movement of DNA polymerase. To prevent this, single-strand binding proteins bind to the DNA until a second strand is synthesized, preventing secondary structure formation.[11]

Clamp proteins form a sliding clamp around DNA, helping the DNA polymerase maintain contact with its template and thereby assisting with processivity. The inner face of the clamp enables DNA to be threaded through it. Once the polymerase reaches the end of the template or detects double stranded DNA, the sliding clamp undergoes a conformational change which releases the DNA polymerase. Clamp-loading proteins are used to initially load the clamp, recognizing the junction between template and RNA primers.

Posted on: 2009/6/15 18:19
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How does DNA replicate? - DNA replication within the cell in a biotechnology revolution - Lagging
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How does DNA replicate? - DNA replication within the cell in a biotechnology revolution - Lagging strand synthesis

Lagging strand synthesis

The lagging strand is the DNA strand at the opposite side of the replication fork from the leading strand, running in the 3' to 5' direction. Because DNA polymerase III cannot synthesize in the 3'→5' direction, the lagging strand is synthesized in short segments known as Okazaki fragments. Along the lagging strand's template, primase builds RNA primers in short bursts. DNA polymerases are then able to use the free 3' OH groups on the RNA primers to synthesize DNA in the 5'→3' direction. The RNA fragments are then removed by DNA polymerase I for prokaryotes or DNA polymerase δ for eukaryotes (different mechanisms are used in eukaryotes and prokaryotes) and new deoxyribonucleotides are added to fill the gaps where the RNA was present. DNA ligase then joins the deoxyribonucleotides together, completing the synthesis of the lagging strand.


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Posted on: 2009/6/8 16:50
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How does DNA replicate? - DNA replication within the cell in a biotechnology revolution -Leading s
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How does DNA replicate? - DNA replication within the cell in a biotechnology revolution -Leading strand synthesis

Leading strand synthesis

In DNA replication, the leading strand is defined as the new DNA strand at the replication fork that is synthesized in the 5'→3' direction in a continuous manner. When the enzyme topoisomerase unwinds DNA, two single stranded regions of DNA (the "replication fork") are formed by the enzyme helicase. On the leading strand DNA polymerase III is able to synthesize DNA using the free 3' OH group donated by a single RNA primer and continuous synthesis occurs in the direction in which the replication fork is moving.

Posted on: 2009/6/1 17:26
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