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DNA Polymerase I
DNA
DNA
POLYMERASE I (or POL I) is an enzyme that participates in the process of prokaryotic DNA replication
DNA replication
. Discovered by Arthur Kornberg in 1956, it was the first known DNA polymerase
DNA polymerase
(and, indeed, the first known of any kind of polymerase ). It was initially characterized in E. coli and is ubiquitous in prokaryotes . In E. coli and many other bacteria, the gene that encodes Pol I is known as POLA. The E. coli form of the enzyme is composed of 928 amino acids, and is an example of a processive enzyme—it can sequentially catalyze multiple polymerisations without releasing the single-stranded template. The physiological function of Pol I is mainly to repair any damage with DNA, but it also serves to connect Okazaki fragments by deleting RNA
RNA
primers and replacing the strand with DNA
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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 letters G, U, A, and C to denote the nitrogenous bases guanine , uracil , adenine , and cytosine ) that directs synthesis of specific proteins. Many viruses encode their genetic information using an RNA
RNA
genome
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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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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
DNA
double helix, and contribute to the folded structure of both DNA and RNA
RNA
. Dictated by specific hydrogen bonding patterns, Watson-Crick base pairs (guanine -cytosine and adenine -thymine ) allow the DNA helix to maintain a regular helical structure that is subtly dependent on its nucleotide sequence . 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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UV Light
ULTRAVIOLET (UV) is an electromagnetic radiation with a wavelength from 10 nm to 400 nm, shorter than that of visible light but longer than X-rays . UV radiation constitutes about 10% of the total light output of the Sun, and is thus present in sunlight . It is also produced by electric arcs and specialized lights, such as mercury-vapor lamps , tanning lamps , and black lights . Although it is not considered an ionizing radiation because its photons lack the energy to ionize atoms , long-wavelength ultraviolet radiation can cause chemical reactions and causes many substances to glow or fluoresce . Consequently, the 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 , freckling and sunburn are familiar effects of over-exposure, along with higher risk of skin cancer
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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. When an incorrect base pair is recognized, DNA polymerase reverses its direction by one base pair of DNA and excises the mismatched base. Following base excision, the polymerase can re-insert the correct base and replication can continue. In eukaryotes only the polymerases that deal with the elongation (delta and epsilon) have proofreading ability (3’ → 5’ exonuclease activity)
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Ribonucleic Acid
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 letters G, U, A, and C to denote the nitrogenous bases guanine , uracil , adenine , and cytosine ) that directs synthesis of specific proteins. Many viruses encode their genetic information using an RNA
RNA
genome
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Deoxyribonucleic Acid
DEOXYRIBONUCLEIC ACID (/diˈɒksiˌraɪboʊnjʊˌkliːɪk, -ˌkleɪɪk/ ( listen ); DNA) is a molecule that carries the genetic instructions used in the growth, development, functioning and reproduction of all known living organisms and many viruses . 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 molecules consist of two biopolymer strands coiled around each other to form a double helix . The two DNA strands are called polynucleotides since they are composed of simpler monomer units called nucleotides . 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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Escherichia Coli
Bacillus coli communis Escherich 1885 ESCHERICHIA COLI (/ˌɛʃᵻˈrɪkiə ˈkoʊlaɪ/ ; also known as E. COLI) is a gram-negative , facultatively anaerobic , rod-shaped , coliform bacterium of the genus Escherichia that is commonly found in the lower intestine of warm-blooded organisms (endotherms). 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 . The harmless strains are part of the normal flora of the gut , and can benefit their hosts by producing vitamin K2 , and preventing colonization of the intestine with pathogenic bacteria , having a symbiotic relationship. E. coli is expelled into the environment within fecal matter. The bacterium grows massively in fresh fecal matter under aerobic conditions for 3 days, but its numbers decline slowly afterwards. E
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DNA
DEOXYRIBONUCLEIC ACID (/diˈɒksiˌraɪboʊnjʊˌkliːɪk, -ˌkleɪɪk/ ( listen ); 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 . Each nucleotide is composed of one of four nitrogen-containing nucleobases (cytosine , guanine , adenine or thymine ), 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 ANALYSISMany biophysical techniques such as crystallography , NMR
NMR
, electron paramagnetic resonance (EPR) using spin label techniques, circular dichroism (CD) , hydrogen exchange , and FRET can be used to study macromolecular conformational change. Dual polarisation interferometry is a benchtop technique capable of measuring conformational changes in biomolecules in real time at very high resolution
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Molecular Biology
MOLECULAR BIOLOGY /.əˈlɛkjʊlər/ concerns the molecular basis of biological activity between biomolecules in the various systems of a cell , including the interactions between DNA
DNA
, RNA
RNA
, and proteins and their biosynthesis , as well as the regulation of these interactions. Writing in Nature in 1961, William Astbury described molecular biology as: "...not so much a technique as an approach, an approach from the viewpoint of the so-called basic sciences with the leading idea of searching below the large-scale manifestations of classical biology for the corresponding molecular plan. It is concerned particularly with the forms of biological molecules and is predominantly three-dimensional and structural—which does not mean, however, that it is merely a refinement of morphology
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Polymerase Chain Reaction
POLYMERASE CHAIN REACTION (PCR) is a technique used in molecular biology to amplify a single copy or a few copies of a segment of DNA across several orders of magnitude, generating thousands to millions of copies of a particular DNA
DNA
sequence . It is an easy, cheap, and reliable way to repeatedly replicate a focused segment of DNA, a concept which is applicable to numerous fields in modern biology and related sciences. Developed in 1983 by Kary Mullis
Kary Mullis
, PCR is now a common and often indispensable technique used in clinical and research laboratories for a broad variety of applications
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Thermus Aquaticus
THERMUS AQUATICUS is a species of bacteria that can tolerate high temperatures, one of several thermophilic bacteria that belong to the Deinococcus–Thermus group. It is the source of the heat-resistant enzyme Taq DNA polymerase , one of the most important enzymes in molecular biology because of its use in the polymerase chain reaction (PCR) DNA amplification technique. CONTENTS * 1 History * 2 Biology * 3 Morphology * 4 Enzymes from T. aquaticus * 5 Controversy * 6 See also * 7 References * 8 Further reading * 9 External links HISTORY Hot springs with algae and bacteria in Yellowstone National Park When studies of biological organisms in hot springs began in the 1960s, scientists thought that the life of thermophilic bacteria could not be sustained in temperatures above about 55 °C (131 °F). Soon, however, it was discovered that many bacteria in different springs not only survived, but also thrived in higher temperatures. In 1969, Thomas D
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Mutant
In biology and especially genetics , a MUTANT is an organism or a new genetic character arising or resulting from an instance of mutation , which is an alteration of the DNA
DNA
sequence of a gene or chromosome of an organism . The natural occurrence of genetic mutations is integral to the process of evolution . The study of mutants is an integral part of biology; by understanding the effect that a mutation in a gene has, it is possible to establish the normal function of that gene. CONTENTS * 1 Etymology * 2 See also * 3 References * 4 External links ETYMOLOGYAlthough not all mutations have a noticeable phenotypic effect, the common usage of the word "mutant" is generally a pejorative term only used for noticeable mutations. Previously, people used the word "SPORT" (related to spurt) to refer to abnormal specimens. The scientific usage is broader, referring to any organism differing from the wild type
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John Cairns (biochemist)
(HUGH) JOHN FORSTER CAIRNS FRS (born 21 November 1922 ) is a British physician and molecular biologist who made significant contributions to molecular genetics , cancer research , and public health . Cairns received his M.D. from Oxford . He then worked as a virologist at the Walter and Eliza Hall Institute of Medical Research in Melbourne, Australia and at the Virus Research Institute at Entebbe , Uganda. He returned to Australia to work in the School of Microbiology at the John Curtin School of Medical Research . Cairns took a sabbatical to research at the Cold Spring Harbor Laboratory between 1960 and 1961, and returned there to serve as the director from 1963 to 1968. He remained a staff member at Cold Spring Harbor until 1972, when he was appointed head of the Mill Hill Laboratory of the Imperial Cancer Research Fund . After leaving Mill Hill in 1980 he took up a professorship at the Harvard School of Public Health . He retired in 1991
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