DNA structure
Main article: DNA
The chemical structure of DNA.
DNA usually exists in a double-stranded structure, with both strands coiled together to form the characteristic double-helix. Each single strand of DNA is a chain of four types of nucleotide: adenine, cytosine, guanine, and thymine. A nucleotide consists of a phosphate and a deoxyribose sugar forming the backbone of the DNA double helix plus a base that points inwards. Nucleotides are matched between strands through hydrogen bonds to form base pairs. Adenine pairs with thymine and cytosine pairs with guanine.
The physical pairing of bases in DNA means that the information contained within each strand is redundant. The nucleotides on a single strand can be used to reconstruct nucleotides on a newly synthesized partner strand.
DNA strands have a directionality, and the different ends of a single strand are called the "3' end" and the "5' end" (these refer to the carbon atom in ribose that the next phosphate in the chain attaches to). In addition to being complementary, the two strands of DNA are antiparallel: they are orientated in opposite directions. This directionality has consequences in DNA synthesis, because DNA polymerase can only synthesize DNA in one direction by adding nucleotides to the 3' end of a DNA strand
Main article: DNA
The chemical structure of DNA.
DNA usually exists in a double-stranded structure, with both strands coiled together to form the characteristic double-helix. Each single strand of DNA is a chain of four types of nucleotide: adenine, cytosine, guanine, and thymine. A nucleotide consists of a phosphate and a deoxyribose sugar forming the backbone of the DNA double helix plus a base that points inwards. Nucleotides are matched between strands through hydrogen bonds to form base pairs. Adenine pairs with thymine and cytosine pairs with guanine.
The physical pairing of bases in DNA means that the information contained within each strand is redundant. The nucleotides on a single strand can be used to reconstruct nucleotides on a newly synthesized partner strand.
DNA strands have a directionality, and the different ends of a single strand are called the "3' end" and the "5' end" (these refer to the carbon atom in ribose that the next phosphate in the chain attaches to). In addition to being complementary, the two strands of DNA are antiparallel: they are orientated in opposite directions. This directionality has consequences in DNA synthesis, because DNA polymerase can only synthesize DNA in one direction by adding nucleotides to the 3' end of a DNA strand
DNA polymerase
Main article: DNA polymerase
DNA polymerase adds nucleotides to the 3' end of a strand of DNA. If a mismatch is accidentally incorporated, the polymerase is inhibited from further extension. Proofreading removes the mismatched nucleotide and extension continues.
DNA polymerases are a family of enzymes critical for all forms of DNA replication.[4] A DNA polymerase synthesizes a new strand of DNA by extending the 3' end of an existing nucleotide chain, adding new nucleotides matched to the template strand one at a time. Some DNA polymerases may also have some proofreading ability, removing nucleotides from the end of a strand in order to remove any mismatched bases. DNA polymerases are generally extremely accurate, making less than one error for every 109 nucleotides added.
The energy for the process of DNA polymerization comes from the two additional phosphates attached to each of the unincorporated nucleotides. These free nucleotides, also known as nucleoside triphosphates, contain a total of three phosphates. When a nucleotide is being added to a growing DNA strand, two of the phosphates are removed and the energy produced is used to attach the remaining phosphate to the growing chain. The energetics of this process may also explain the directionality of synthesis - if DNA were synthesized in the 3' to 5' direction, the energy for the process would come from the 5' end of the growing strand rather than from free nucleotides. During proofreading, if the 5' nucleotide needed to be removed this triphosphate end would be lost, losing the energy source required to add a new nucleotide to the end.
DNA polymerase can only extend an existing DNA strand paired with a template strand, it cannot begin the synthesis of a new strand. To do this a short fragment of DNA or RNA, called a primer, must be created and paired with the template strand before DNA polymerase can synthesize new DNA.
[DNA replication within the cell
Main articles: Prokaryotic DNA replication and Eukaryotic DNA replication
Origins of replication
For a cell to divide, it must first replicate itself into newer ones DNA.
Main article: DNA polymerase
DNA polymerase adds nucleotides to the 3' end of a strand of DNA. If a mismatch is accidentally incorporated, the polymerase is inhibited from further extension. Proofreading removes the mismatched nucleotide and extension continues.
DNA polymerases are a family of enzymes critical for all forms of DNA replication.[4] A DNA polymerase synthesizes a new strand of DNA by extending the 3' end of an existing nucleotide chain, adding new nucleotides matched to the template strand one at a time. Some DNA polymerases may also have some proofreading ability, removing nucleotides from the end of a strand in order to remove any mismatched bases. DNA polymerases are generally extremely accurate, making less than one error for every 109 nucleotides added.
The energy for the process of DNA polymerization comes from the two additional phosphates attached to each of the unincorporated nucleotides. These free nucleotides, also known as nucleoside triphosphates, contain a total of three phosphates. When a nucleotide is being added to a growing DNA strand, two of the phosphates are removed and the energy produced is used to attach the remaining phosphate to the growing chain. The energetics of this process may also explain the directionality of synthesis - if DNA were synthesized in the 3' to 5' direction, the energy for the process would come from the 5' end of the growing strand rather than from free nucleotides. During proofreading, if the 5' nucleotide needed to be removed this triphosphate end would be lost, losing the energy source required to add a new nucleotide to the end.
DNA polymerase can only extend an existing DNA strand paired with a template strand, it cannot begin the synthesis of a new strand. To do this a short fragment of DNA or RNA, called a primer, must be created and paired with the template strand before DNA polymerase can synthesize new DNA.
[DNA replication within the cell
Main articles: Prokaryotic DNA replication and Eukaryotic DNA replication
Origins of replication
For a cell to divide, it must first replicate itself into newer ones DNA.
[5] This process is initiated at particular points within the DNA, known as "origins", which are targeted by proteins that separate the two strands and initiate DNA synthesis.
[3] Origins contain DNA sequences recognized by replication initiator proteins (eg. dnaA in E coli' and the Origin Recognition Complex in yeast).
[6] These initiator proteins recruit other proteins to separate the two strands and initiate replication forks.
Initiator proteins recruit other proteins to separate the DNA strands at the origin, forming a bubble. Origins tend to be "AT-rich" (rich in adenine and thymine bases) to assist this process because A-T base pairs have two hydrogen bonds (rather than the three formed in a C-G pair)—strands rich in these nucleotides are generally easier to separate.
Initiator proteins recruit other proteins to separate the DNA strands at the origin, forming a bubble. Origins tend to be "AT-rich" (rich in adenine and thymine bases) to assist this process because A-T base pairs have two hydrogen bonds (rather than the three formed in a C-G pair)—strands rich in these nucleotides are generally easier to separate.
[7] Once strands are separated, RNA primers are created on the template strands and DNA polymerase extends these to create newly synthesized DNA.
As DNA synthesis continues, the original DNA strands continue to unwind on each side of the bubble, forming replication forks. In bacteria, which have a single origin of replication on their circular chromosome, this process eventually creates a "theta structure" (resembling the Greek letter theta: θ).
As DNA synthesis continues, the original DNA strands continue to unwind on each side of the bubble, forming replication forks. In bacteria, which have a single origin of replication on their circular chromosome, this process eventually creates a "theta structure" (resembling the Greek letter theta: θ).
In contrast, eukaryotes have longer linear chromosomes and initiate replication at multiple origins within these.
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