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DNA Polymerase I
DNA polymerase
DNA polymerase
I (or Pol I) is an enzyme that participates in the process of prokaryotic DNA
DNA
replication. Discovered by Arthur Kornberg in 1956,[1] it was the first known DNA polymerase
DNA polymerase
(and the first known of any kind of polymerase). It was initially characterized in E. coli and is ubiquitous in prokaryotes. In E. coli
E. coli
and many other bacteria, the gene that encodes Pol I is known as polA
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Escherichia Coli
Bacillus coli
Bacillus coli
communis Escherich 1885 Escherichia
Escherichia
coli (/ˌɛʃɪˈrɪkiə ˈkoʊlaɪ/;[1] also known as E. coli) is a Gram-negative, facultatively anaerobic, rod-shaped, coliform bacterium of the genus Escherichia
Escherichia
that is commonly found in the lower intestine of warm-blooded organisms (endotherms).[2][3] Most E. coli strains are harmless, but some serotypes can cause serious food poisoning in their hosts, and are occasionally responsible for product recalls due to food contamination.[4][5] The harmless strains are part of the normal flora of the gut, and can benefit their hosts by producing vitamin K2,[6] and preventing colonization of the intestine with pathogenic bacteria, having a symbiotic relationship.[7][8] E. coli is expelled into the environment within fecal matter
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Base Pair
A base pair (bp) is a unit consisting of two nucleobases bound to each other by hydrogen bonds. They form the building blocks of the DNA double helix, and contribute to the folded structure of both DNA
DNA
and RNA. Dictated by specific hydrogen bonding patterns, Watson-Crick base pairs (guanine-cytosine and adenine-thymine) allow the DNA
DNA
helix to maintain a regular helical structure that is subtly dependent on its nucleotide sequence.[1] The complementary nature of this based-paired structure provides a backup copy of all genetic information encoded within double-stranded DNA
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Primer (molecular Biology)
A primer is a short strand of RNA
RNA
or DNA
DNA
(generally about 18-22 bases) that serves as a starting point for DNA
DNA
synthesis. It is required for DNA
DNA
replication because the enzymes that catalyze this process, 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 vivo DNA
DNA
replication utilizes short strands of RNA
RNA
called RNA primers to initiate DNA
DNA
synthesis on both the leading and lagging strands – DNA
DNA
primers are not seen in vivo in humans
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Proofreading (biology)
The term proofreading is used in genetics to refer to the error-correcting processes, first proposed by John Hopfield and Jacques Ninio, involved in DNA replication, immune system specificity, enzyme-substrate recognition among many other processes that require enhanced specificity. The proofreading mechanisms of Hopfield and Ninio are non-equilibrium active processes that consume ATP to enhance specificity of various biochemical reactions. In bacteria, all three DNA polymerases (I, II and III) have the ability to proofread, using 3’ → 5’ exonuclease activity
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DNA Repair
DNA
DNA
repair is a collection of processes by which a cell identifies and corrects damage to the DNA
DNA
molecules that encode its genome. In human cells, both normal metabolic activities and environmental factors such as radiation can cause DNA
DNA
damage, resulting in as many as 1 million individual molecular lesions per cell per day.[1] Many of these lesions cause structural damage to the DNA
DNA
molecule and can alter or eliminate the cell's ability to transcribe the gene that the affected DNA
DNA
encodes. Other lesions induce potentially harmful mutations in the cell's genome, which affect the survival of its daughter cells after it undergoes mitosis. As a consequence, the DNA
DNA
repair process is constantly active as it responds to damage in the DNA
DNA
structure
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UV Light
Ultraviolet (UV) is an electromagnetic radiation with a wavelength from 100 nm to 400 nm, shorter than that of visible light but longer than X-rays. UV radiation is present in sunlight constituting about 10% of the total light output of the Sun. It is also produced by electric arcs and specialized lights, such as mercury-vapor lamps, tanning lamps, and black lights. Although long-wavelength ultraviolet is not considered an ionizing radiation because its photons lack the energy to ionize atoms, it can cause chemical reactions and causes many substances to glow or fluoresce. Consequently, the chemical and biological effects of UV are greater than simple heating effects, and many practical applications of UV radiation derive from its interactions with organic molecules. Suntan and sunburn are familiar effects of over-exposure of the skin to UV, along with higher risk of skin cancer
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RNase H
Ribonuclease
Ribonuclease
H (abbreviated RNase H
RNase H
or RNH) is a family of non-sequence-specific endonuclease enzymes that catalyze the cleavage of RNA
RNA
in an RNA/ DNA
DNA
substrate via a hydrolytic mechanism. Members of the RNase H
RNase H
family can be found in nearly all organisms, from bacteria to archaea to eukaryotes. The family is divided into evolutionarily related groups with slightly different substrate preferences, broadly designated ribonuclease H1 and H2.[2] The human genome encodes both H1 and H2
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RNA
Ribonucleic acid (RNA) is a polymeric molecule essential in various biological roles in coding, decoding, regulation, and expression of genes. RNA
RNA
and DNA
DNA
are nucleic acids, and, along with lipids, proteins and carbohydrates, constitute the four major macromolecules essential for all known forms of life. Like DNA, RNA
RNA
is assembled as a chain of nucleotides, but unlike DNA
DNA
it is more often found in nature as a single-strand folded onto itself, rather than a paired double-strand. Cellular organisms use messenger RNA
RNA
(mRNA) to convey genetic information (using the nitrogenous bases guanine, uracil, adenine, and cytosine, denoted by the letters G, U, A, and C) that directs synthesis of specific proteins
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Primase
DNA primase is an enzyme involved in the replication of DNA and is a type of RNA polymerase. Primase catalyzes the synthesis of a short RNA (or DNA in some organisms [1]) segment called a primer complementary to a ssDNA template. Primase is of key importance in DNA replication because no known replicative DNA polymerases can initiate the synthesis of a DNA strand without an initial RNA or DNA primer (for temporary DNA elongation). After this elongation the RNA piece is removed by a 5' to 3' exonuclease and refilled with DNA.Contents1 Function 2 Multifunctional primases2.1 In eukaryotes 2.2 In archaea 2.3 In bacteria3 Types 4 References 5 External linksFunction[edit] In bacteria, primase binds to the DNA helicase forming a complex called the primosome
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Lagging Strand
In molecular biology, DNA replication is the biological process of producing two identical replicas of DNA from one original DNA molecule. This process occurs in all living organisms and is the basis for biological inheritance. The cell possesses the distinctive property of division, which makes replication of DNA essential. DNA is made up of a double helix of two complementary strands. During replication, these strands are separated
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Nucleotides
Nucleotides are organic molecules that serve as the monomer units for forming the nucleic acid polymers deoxyribonucleic acid (DNA) and ribonucleic acid (RNA), both of which are essential biomolecules in all life-forms on Earth. Nucleotides are the building blocks of nucleic acids; they are composed of three subunit molecules: a nitrogenous base, a five-carbon sugar (ribose or deoxyribose), and at least one phosphate group. They are also known as phosphate nucleotides. A nucleoside is a nitrogenous base and a 5-carbon sugar. Thus a nucleoside plus a phosphate group yields a nucleotide. Nucleotides also play a central role in life-form metabolism at the fundamental, cellular level
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DNA Ligase
DNA
DNA
ligase is a specific type of enzyme, a ligase, (EC 6.5.1.1) that facilitates the joining of DNA
DNA
strands together by catalyzing the formation of a phosphodiester bond. It plays a role in repairing single-strand breaks in duplex DNA
DNA
in living organisms, but some forms (such as DNA
DNA
ligase IV) may specifically repair double-strand breaks (i.e. a break in both complementary strands of DNA). Single-strand breaks are repaired by DNA
DNA
ligase using the complementary strand of the double helix as a template,[1] with DNA
DNA
ligase creating the final phosphodiester bond to fully repair the DNA. DNA
DNA
ligase is used in both DNA
DNA
repair and DNA
DNA
replication (see Mammalian ligases)
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RNA Primer
A primer is a short strand of RNA or DNA (generally about 18-22 bases) that serves as a starting point for DNA synthesis. It is required for DNA replication because the enzymes that catalyze this process, 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 vivo DNA replication utilizes short strands of RNA called RNA primers to initiate DNA synthesis on both the leading and lagging strands – DNA primers are not seen in vivo in humans. These RNA primers can be made de novo. On the other hand, many of the in vitro laboratory techniques that involve DNA polymerase in biochemistry and molecular biology (such as DNA sequencing and the polymerase chain reaction), use DNA primers because they are more temperature stable. In experiments, it is often important to use a primer with a similar Tm (melting temperature) to the template strand it will be hybridizing to
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DNA
Deoxyribonucleic acid (/diˈɒksiˌraɪboʊnjʊˈkliːɪk, -ˈkleɪ.ɪk/ ( listen);[1] DNA) is a thread-like chain of nucleotides carrying the genetic instructions used in the growth, development, functioning and reproduction of all known living organisms and many viruses. DNA
DNA
and ribonucleic acid (RNA) are nucleic acids; alongside proteins, lipids and complex carbohydrates (polysaccharides), they are one of the four major types of macromolecules that are essential for all known forms of life. Most DNA
DNA
molecules consist of two biopolymer strands coiled around each other to form a double helix. The two DNA
DNA
strands are called polynucleotides since they are composed of simpler monomer units called nucleotides.[2][3] Each nucleotide is composed of one of four nitrogen-containing nucleobases (cytosine [C], guanine [G], adenine [A] or thymine [T]), a sugar called deoxyribose, and a phosphate group
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Conformational Change
In biochemistry, a conformational change is a change in the shape of a macromolecule, often induced by environmental factors. A macromolecule is usually flexible and dynamic. It can change its shape in response to changes in its environment or other factors; each possible shape is called a conformation, and a transition between them is called a conformational change. Factors that may induce such changes include:temperature, pH, voltage, ion concentration, phosphorylation, or the binding of a ligand.Laboratory analysis[edit] Many biophysical techniques such as crystallography, NMR, electron paramagnetic resonance (EPR) using spin label techniques, circular dichroism (CD), hydrogen exchange, and FRET can be used to study macromolecular conformational change
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