Molecular genetics is the field of biology which studies the structure and function of genes at a molecular level. The field studies how the genes are transferred from generation to generation. Molecular genetics employs the methods of genetics and molecular biology. It is so-called to differentiate it from other sub fields of genetics such as ecological genetics and population genetics. An important area within molecular genetics is the use of molecular information to determine the patterns of descent, and therefore the correct scientific classification of organisms: this is called molecular systematics.
Along with determining the pattern of descendants, molecular genetics helps in understanding genetic mutations that can cause certain types of diseases. Through utilizing the methods of genetics and molecular biology, molecular genetics discovers the reasons why traits are carried on and how and why some may mutate.Friday, May 2, 2008
Ionizing R.adiation
Ionizing radiation refers to highly-energetic particles or waves that can detach (ionize) at least one electron from an atom or molecule. Ionizing ability is a function of the energy of individual particles or waves, and not a function of their number. A large flood of particles or waves will not, in the most-common situations, cause ionization if the individual particles or waves are insufficiently energetic.
Examples of ionizing radiation are energetic beta particles, neutrons, and alpha particles. The ability of light waves (photons) to ionize an atom or molecule varies across the electromagnetic spectrum. X-rays and gamma rays will ionize almost any molecule or atom; far ultraviolet light will ionize many atoms and molecules; near ultraviolet and visible light are ionizing to very few molecules; microwaves and radio waves are non-ionizing radiation. Visible light is so ubiquitous that molecules that are ionized by it will often react nearly spontaneously unless protected by materials that block the visible spectrum. Examples include photographic film and some molecules involved in photosynthesis.
If enough ionizations occur in a biological system, they can be destructive, such as by causing DNA damage in individual cells. Extensive doses of ionizing radiation have been shown to have a mutating effect on future generations arising from the individual receiving the dose.Mutation
In biology, mutations are changes to the nucleotide sequence of the genetic material of an organism. Mutations can be caused by copying errors in the genetic material during cell division, by exposure to ultraviolet or ionizing radiation, chemical mutagens, or viruses, or can occur deliberately under cellular control during processes such as hypermutation. In multicellular organisms, mutations can be subdivided into germ line mutations, which can be passed on to descendants, and somatic mutations, which are not transmitted to descendants in animals. Plants sometimes can transmit somatic mutations to their descendants asexually or sexually (in case when flower buds develop in somatically mutated part of plant). A new mutation that was not inherited from either parent is called a de novo mutation. The source of the mutation is unrelated to the consequence, although the consequences are related to which cells are affected.
Mutations create variations in the gene pool. Less favorable (or deleterious) mutations can be reduced in frequency in the gene pool by natural selection, while more favorable (beneficial or advantageous) mutations may accumulate and result in adaptive evolutionary changes. For example, a butterfly may produce offspring with new mutations. The majority of these mutations will have no effect; but one might change the color of one of the butterfly's offspring, making it harder (or easier) for predators to see. If this color change is advantageous, the chance of this butterfly surviving and producing its own offspring are a little better, and over time the number of butterflies with this mutation may form a larger percentage of the population.
Neutral mutations are defined as mutations whose effects do not influence the fitness of an individual. These can accumulate over time due to genetic drift. It is believed that the overwhelming majority of mutations have no significant effect on an organism's fitness. Also, DNA repair mechanisms are able to mend most changes before they become permanent mutations, and many organisms have mechanisms for eliminating otherwise permanently mutated somatic cells.
Mutation is generally accepted by the scientific community as the mechanism upon which natural selection acts, providing the advantageous new traits that survive and multiply in offspring or disadvantageous traits that die out with weaker organisms.
Biological classification
Biological classification or scientific classification in biology, is a method by which biologists group and categorize species of organisms. Biological classification is a form of scientific taxonomy, but should be distinguished from folk taxonomy, which lacks scientific basis. Modern biological classification has its root in the work of Carolus Linnaeus, who grouped species according to shared physical characteristics. These groupings since have been revised to improve consistency with the Darwinian principle of common descent. Molecular systematics, which uses DNA sequences as data, has driven many recent revisions and is likely to continue to do so. Biological classification belongs to the science of biological systematics.
Species
In biology, a species is one of the basic units of biological classification and a taxonomic rank. A species is often defined as a group of organisms capable of interbreeding and producing fertile offspring. While in many cases this definition is adequate, more precise or differing measures are often used, such as based on similarity of DNA or morphology. Presence of specific locally adapted traits may further subdivide species into subspecies.
The commonly used names for plant and animal taxa sometimes correspond to species: for example, "lion," "walrus," and "Camphor tree" – each refers to a species. In other cases common names do not: for example, "deer" refers to a family of 34 species, including Eld's Deer, Red Deer and Wapiti (Elk). The last two species were once considered a single species, illustrating how species boundaries may change with increased scientific knowledge.
Each species is placed within a single genus. This is a hypothesis that the species is more closely related to other species within its genus than to species of other genera. All species are given a binomial name consisting of the generic name and specific name (or specific epithet). For example, Pinus palustris (commonly known as the Longleaf Pine).
A usable definition of the word "species" and reliable methods of identifying particular species are essential for stating and testing biological theories and for measuring biodiversity. Traditionally, multiple examples of a proposed species must be studied for unifying characters before it can be regarded as a species. Extinct species known only from fossils are generally difficult to give precise taxonomic rankings to. A species which has been described scientifically can be referred to by its binomial names.
DNA replication
DNA replication is the process of copying a double-stranded DNA molecule to form two double-stranded molecule The process of DNA replication is a fundamental process used by all living organisms as it is the basis for biological inheritance. As each DNA strand holds the same genetic information, both strands can serve as templates for the reproduction of the opposite strand. The template strand is preserved in its entirety and the new strand is assembled from nucleotides. This process is called "semiconservative replication". The resulting double-stranded DNA molecules are identical; proofreading and error-checking mechanisms exist to ensure near perfect fidelity.
In a cell, DNA replication must happen before cell division can occur. DNA synthesis begins at specific locations in the genome, called "origins", where the two strands of DNA are separated.RNA primers attach to single stranded DNA and the enzyme DNA polymerase extends the primers to form new strands of DNA, adding nucleotides matched to the template strand. The unwinding of DNA and synthesis of new strands forms a replication fork. In addition to DNA polymerase, a number of other proteins are associated with the fork and assist in the initiation and continuation of DNA synthesis.
DNA replication can also be performed artificially, using the same enzymes used within the cell. DNA polymerases and artificial DNA primers are used to initiate DNA synthesis at known sequences in a template molecule. The polymerase chain reaction (PCR), a common laboratory technique, employs artificial synthesis in a cyclic manner to rapidly and specifically amplify a target DNA fragment from a pool of DNA.
In a cell, DNA replication must happen before cell division can occur. DNA synthesis begins at specific locations in the genome, called "origins", where the two strands of DNA are separated.RNA primers attach to single stranded DNA and the enzyme DNA polymerase extends the primers to form new strands of DNA, adding nucleotides matched to the template strand. The unwinding of DNA and synthesis of new strands forms a replication fork. In addition to DNA polymerase, a number of other proteins are associated with the fork and assist in the initiation and continuation of DNA synthesis.
DNA replication can also be performed artificially, using the same enzymes used within the cell. DNA polymerases and artificial DNA primers are used to initiate DNA synthesis at known sequences in a template molecule. The polymerase chain reaction (PCR), a common laboratory technique, employs artificial synthesis in a cyclic manner to rapidly and specifically amplify a target DNA fragment from a pool of DNA.
Heredity
The ancients had a variety of ideas about heredity: Theophrastus proposed that male flowers caused female flowers to ripen; Hippocrates speculated that "seeds" were produced by various body parts and transmitted to offspring at the time of conception, and Aristotle thought that male and female semen mixed at conception. Aeschylus, in 458 BC, proposed the male as the parent, with the female as a "nurse for the young life sown within her".
Various hereditary mechanisms were envisaged without being properly tested or quantified. These included blending inheritance and the inheritance of acquired traits. Nevertheless, people were able to develop domestic breeds of animals as well as crops through artificial selection. The inheritance of acquired traits also formed a part of early Lamarckian ideas on evolution.
During the 1700s, Dutch microscopist Antonie van Leeuwenhoek (1632-1723) discovered "animalcules" in the sperm of humans and other animals. Some scientists speculated they saw a "little man" (homunculus) inside each sperm. These scientists formed a school of thought known as the "spermists". They contended the only contributions of the female to the next generation were the womb in which the homunculus grew, and prenatal influences of the womb. An opposing school of thought, the ovists, believed that the future human was in the egg, and that sperm merely stimulated the growth of the egg. Ovists thought women carried eggs containing boy and girl children, and that the gender of the offspring was determined well before conception.
Pangenesis was an idea that males and females formed "pangenes" in every organ. These pangenes subsequently moved through their blood to the genitals and then to the children. The concept originated with the ancient Greeks and influenced biology until little over 100 years ago. The terms "blood relative", "full-blooded", and "royal blood" are relicts of pangenesis. Francis Galton, Charles Darwin's cousin, experimentally tested and disproved pangenesis during the 1870s.
Various hereditary mechanisms were envisaged without being properly tested or quantified. These included blending inheritance and the inheritance of acquired traits. Nevertheless, people were able to develop domestic breeds of animals as well as crops through artificial selection. The inheritance of acquired traits also formed a part of early Lamarckian ideas on evolution.
During the 1700s, Dutch microscopist Antonie van Leeuwenhoek (1632-1723) discovered "animalcules" in the sperm of humans and other animals. Some scientists speculated they saw a "little man" (homunculus) inside each sperm. These scientists formed a school of thought known as the "spermists". They contended the only contributions of the female to the next generation were the womb in which the homunculus grew, and prenatal influences of the womb. An opposing school of thought, the ovists, believed that the future human was in the egg, and that sperm merely stimulated the growth of the egg. Ovists thought women carried eggs containing boy and girl children, and that the gender of the offspring was determined well before conception.
Pangenesis was an idea that males and females formed "pangenes" in every organ. These pangenes subsequently moved through their blood to the genitals and then to the children. The concept originated with the ancient Greeks and influenced biology until little over 100 years ago. The terms "blood relative", "full-blooded", and "royal blood" are relicts of pangenesis. Francis Galton, Charles Darwin's cousin, experimentally tested and disproved pangenesis during the 1870s.
RNA
Ribonucleic acid or RNA is a nucleic acid made from a long chain of nucleotide units. Each nucleotide consists of a nitrogenous base, a ribose sugar, and a phosphate. RNA is very similar to DNA, but differs in a few important structural details: in the cell RNA is usually single stranded, while DNA is usually double stranded. RNA nucleotides contain ribose while DNA contains deoxyribose (a type of ribose that lacks one oxygen atom), and RNA has the nucleotide uracil rather than thymine which is present in DNA.
RNA is transcribed from DNA by enzymes called RNA polymerases and is generally further processed by other enzymes. Some of these RNA-processing enzymes contain RNA as part of their structures. RNA is also central to the translation of some RNAs into proteins. In this process, a type of RNA called messenger RNA carries information from DNA to structures called ribosomes. These ribosomes are made from proteins and ribosomal RNAs, which come together to form a molecular machine that can read messenger RNAs and translate the information they carry into proteins. It has also been known since the 1990s that several types of RNA regulate which genes are active.
RNA is transcribed from DNA by enzymes called RNA polymerases and is generally further processed by other enzymes. Some of these RNA-processing enzymes contain RNA as part of their structures. RNA is also central to the translation of some RNAs into proteins. In this process, a type of RNA called messenger RNA carries information from DNA to structures called ribosomes. These ribosomes are made from proteins and ribosomal RNAs, which come together to form a molecular machine that can read messenger RNAs and translate the information they carry into proteins. It has also been known since the 1990s that several types of RNA regulate which genes are active.
Spectroscopy
Spectroscopy was originally the study of the interaction between radiation and matter as a function of wavelength (λ). In fact, historically, spectroscopy referred to the use of visible light dispersed according to its wavelength, e.g. by a prism. Later the concept was expanded greatly to comprise any measurement of a quantity as function of either wavelength or frequency. Thus it also can refer to interactions with particle radiation or to a response to an alternating field or varying frequency (ν). A further extension of the scope of the definition added energy (E) as a variable, once the very close relationship E=hν for photons was realized. A plot of the response as a function of wavelength — or more commonly frequency — is referred to as a spectrum; see also spectral linewidth.
Spectrometry refers to when a spectroscopic technique is used to assess the concentration or amount of a given species. In those cases, the instrument that performs such measurements is a spectrometer or spectrograph.
Spectroscopy/spectrometry is often used in physical and analytical chemistry for the identification of substances through the spectrum emitted from or absorbed by them.
Spectroscopy/spectrometry is also heavily used in astronomy and remote sensing. Most large telescopes have spectrometers, which are used either to measure the chemical composition and physical properties of astronomical objects or to measure their velocities from the Doppler shift of their spectral lines.
Spectrometry refers to when a spectroscopic technique is used to assess the concentration or amount of a given species. In those cases, the instrument that performs such measurements is a spectrometer or spectrograph.
Spectroscopy/spectrometry is often used in physical and analytical chemistry for the identification of substances through the spectrum emitted from or absorbed by them.
Spectroscopy/spectrometry is also heavily used in astronomy and remote sensing. Most large telescopes have spectrometers, which are used either to measure the chemical composition and physical properties of astronomical objects or to measure their velocities from the Doppler shift of their spectral lines.
Hydrogen
Hydrogen is the chemical element with atomic number 1. It is represented by the symbol H. At standard temperature and pressure, hydrogen is a colorless, odorless, nonmetallic, tasteless, highly flammable diatomic gas with the molecular formula H2. With an atomic mass of 1.00794 amu, hydrogen is the lightest element.
Hydrogen is the most abundant of the chemical elements, constituting roughly 75% of the universe's elemental mass.Stars in the main sequence are mainly composed of hydrogen in its plasma state. Elemental hydrogen is relatively rare on Earth, and is industrially produced from hydrocarbons such as methane, after which most elemental hydrogen is used "captively" (meaning locally at the production site), with the largest markets about equally divided between fossil fuel upgrading (e.g., hydrocracking) and ammonia production (mostly for the fertilizer market). Hydrogen may be produced from water using the process of electrolysis, but this process is presently significantly more expensive commercially than hydrogen production from natural gas.
The most common naturally occurring isotope of hydrogen, known as protium, has a single proton and no neutrons. In ionic compounds it can take on either a positive charge (becoming a cation composed of a bare proton) or a negative charge (becoming an anion known as a hydride). Hydrogen can form compounds with most elements and is present in water and most organic compounds. It plays a particularly important role in acid-base chemistry, in which many reactions involve the exchange of protons between soluble molecules. As the only neutral atom for which the Schrödinger equation can be solved analytically, study of the energetics and bonding of the hydrogen atom has played a key role in the development of quantum mechanics.
Hydrogen is the most abundant of the chemical elements, constituting roughly 75% of the universe's elemental mass.Stars in the main sequence are mainly composed of hydrogen in its plasma state. Elemental hydrogen is relatively rare on Earth, and is industrially produced from hydrocarbons such as methane, after which most elemental hydrogen is used "captively" (meaning locally at the production site), with the largest markets about equally divided between fossil fuel upgrading (e.g., hydrocracking) and ammonia production (mostly for the fertilizer market). Hydrogen may be produced from water using the process of electrolysis, but this process is presently significantly more expensive commercially than hydrogen production from natural gas.
The most common naturally occurring isotope of hydrogen, known as protium, has a single proton and no neutrons. In ionic compounds it can take on either a positive charge (becoming a cation composed of a bare proton) or a negative charge (becoming an anion known as a hydride). Hydrogen can form compounds with most elements and is present in water and most organic compounds. It plays a particularly important role in acid-base chemistry, in which many reactions involve the exchange of protons between soluble molecules. As the only neutral atom for which the Schrödinger equation can be solved analytically, study of the energetics and bonding of the hydrogen atom has played a key role in the development of quantum mechanics.
Thursday, May 1, 2008
Microbiology
Microbiology is the study of microorganisms, which are unicellular or cell-cluster microscopic organisms.This includes eukaryotes such as fungi and protists, and prokaryotes such as bacteria and certain algae. Viruses, though not strictly classed as living organisms, are also studied.Microbiology is a broad term which includes many branches like virology, mycology, parasitology and others. A person who specializes in the area of microbiology is a microbiologist.
Although much is now known in the field of microbiology, advances are being made regularly. We have probably only studied about one percent of all of the microbe species on Earth. Thus, despite the fact that over three hundred years have passed since the discovery of microbes, the field of microbiology could be said to be in its infancy relative to other biological disciplines such as zoology, botany and entomology.
Although much is now known in the field of microbiology, advances are being made regularly. We have probably only studied about one percent of all of the microbe species on Earth. Thus, despite the fact that over three hundred years have passed since the discovery of microbes, the field of microbiology could be said to be in its infancy relative to other biological disciplines such as zoology, botany and entomology.
Eukaryote
Animals, plants, fungi, and protists are eukaryotes (IPA: /juːˈkærɪɒt/ or IPA: /-oʊt/), organisms whose cells are organized into complex structures enclosed within membranes. The defining membrane-bound structure which differentiates eukaryotic cells from prokaryotic cells is the nucleus. The presence of a nucleus gives these organisms their name, which comes from the Greek ευ, meaning "good/true", and κάρυον, "nut". Many eukaryotic cells contain other membrane-bound organelles such as mitochondria, chloroplasts and Golgi bodies. Eukaryotes often have unique flagella made of microtubules in a 9+2 arrangement.
Cell division in eukaryotes is different from organisms without a nucleus (prokaryotes). It involves separating the duplicated chromosomes, through movements directed by microtubules. There are two types of division processes. In mitosis, one cell divides to produce two genetically-identical cells. In meiosis, which is required in sexual reproduction, one diploid cell (having two instances of each chromosome, one from each parent) undergoes recombination of each pair of parental chromosomes, and then two stages of cell division, resulting in four haploid cells (gametes). Each gamete has just one complement of chromosomes, each a unique mix of the corresponding pair of parental chromosomes.
Eukaryotes appear to be monophyletic, and so make up one of the three domains of life. The two other domains, bacteria and archaea, are prokaryotes, and have none of the above features. But eukaryotes do share some aspects of their biochemistry with archaea, and so are grouped with archaea in the clade Neomura.
Cell division in eukaryotes is different from organisms without a nucleus (prokaryotes). It involves separating the duplicated chromosomes, through movements directed by microtubules. There are two types of division processes. In mitosis, one cell divides to produce two genetically-identical cells. In meiosis, which is required in sexual reproduction, one diploid cell (having two instances of each chromosome, one from each parent) undergoes recombination of each pair of parental chromosomes, and then two stages of cell division, resulting in four haploid cells (gametes). Each gamete has just one complement of chromosomes, each a unique mix of the corresponding pair of parental chromosomes.
Eukaryotes appear to be monophyletic, and so make up one of the three domains of life. The two other domains, bacteria and archaea, are prokaryotes, and have none of the above features. But eukaryotes do share some aspects of their biochemistry with archaea, and so are grouped with archaea in the clade Neomura.
Genome
In biology the genome of an organism is its whole hereditary information and is encoded in the DNA (or, for some viruses, RNA). This includes both the genes and the non-coding sequences of the DNA. The term was coined in 1920 by Hans Winkler, Professor of Botany at the University of Hamburg, Germany. The Oxford English Dictionary suggests the name to be a portmanteau of the words gene and chromosome, however many related -ome words already existed, such as biome and rhizome, forming a vocabulary into which genome fit all too well.
More precisely, the genome of an organism is a complete genetic sequence on one set of chromosomes; for example, one of the two sets that a diploid individual carries in every somatic cell. The term genome can be applied specifically to mean that stored on a complete set of nuclear DNA (i.e., the "nuclear genome") but can also be applied to that stored within organelles that contain their own DNA, as with the mitochondrial genome or the chloroplast genome. When people say that the genome of a sexually reproducing species has been "sequenced," typically they are referring to a determination of the sequences of one set of autosomes and one of each type of sex chromosome, which together represent both of the possible sexes. Even in species that exist in only one sex, what is described as "a genome sequence" may be a composite read from the chromosomes of various individuals. In general use, the phrase "genetic makeup" is sometimes used conversationally to mean the genome of a particular individual or organism. The study of the global properties of genomes of related organisms is usually referred to as genomics, which distinguishes it from genetics which generally studies the properties of single genes or groups of genes.
More precisely, the genome of an organism is a complete genetic sequence on one set of chromosomes; for example, one of the two sets that a diploid individual carries in every somatic cell. The term genome can be applied specifically to mean that stored on a complete set of nuclear DNA (i.e., the "nuclear genome") but can also be applied to that stored within organelles that contain their own DNA, as with the mitochondrial genome or the chloroplast genome. When people say that the genome of a sexually reproducing species has been "sequenced," typically they are referring to a determination of the sequences of one set of autosomes and one of each type of sex chromosome, which together represent both of the possible sexes. Even in species that exist in only one sex, what is described as "a genome sequence" may be a composite read from the chromosomes of various individuals. In general use, the phrase "genetic makeup" is sometimes used conversationally to mean the genome of a particular individual or organism. The study of the global properties of genomes of related organisms is usually referred to as genomics, which distinguishes it from genetics which generally studies the properties of single genes or groups of genes.
Gene
A gene is a locatable region of genomic sequence, corresponding to a unit of inheritance, which is associated with regulatory regions, transcribed regions and/or other functional sequence regions. The physical development and phenotype of organisms can be thought of as a product of genes interacting with each other and with the environment. A concise definition of a gene, taking into account complex patterns of regulation and transcription, genic conservation and non-coding RNA genes, has been proposed by Gerstein et al. "A gene is a union of genomic sequences encoding a coherent set of potentially overlapping functional products".
Colloquially, the term gene is often used to refer to an inheritable trait which is usually accompanied by a phenotype as in ("tall genes" or "bad genes") -- the proper scientific term for this is allele.
In cells, genes consist of a long strand of DNA that contains a promoter, which controls the activity of a gene, and coding and non-coding sequence. Coding sequence determines what the gene produces, while non-coding sequence can regulate the conditions of gene expression. When a gene is active, the coding and non-coding sequence is copied in a process called transcription, producing an RNA copy of the gene's information. This RNA can then direct the synthesis of proteins via the genetic code. But some RNAs are used directly, for example as part of the ribosome. These molecules resulting from gene expression, whether RNA or protein, are known as gene products.
Colloquially, the term gene is often used to refer to an inheritable trait which is usually accompanied by a phenotype as in ("tall genes" or "bad genes") -- the proper scientific term for this is allele.
In cells, genes consist of a long strand of DNA that contains a promoter, which controls the activity of a gene, and coding and non-coding sequence. Coding sequence determines what the gene produces, while non-coding sequence can regulate the conditions of gene expression. When a gene is active, the coding and non-coding sequence is copied in a process called transcription, producing an RNA copy of the gene's information. This RNA can then direct the synthesis of proteins via the genetic code. But some RNAs are used directly, for example as part of the ribosome. These molecules resulting from gene expression, whether RNA or protein, are known as gene products.
Ecological genetics
Ecological genetics is the study of genetics in the context of the interactions among organisms and between the organisms and their environment. While molecular genetics studies the structure and function of genes at a molecular level, ecological genetics (and the related field of population genetics) studies phenotypic evolution in natural populations of organisms. Research in this field is of traits of ecological significance — that is, traits related to fitness, which affect an organism's survival and reproduction (e.g., flowering time, drought tolerance, sex ratio).
Studies are often done on insects and other organisms that have short generation times, and thus evolve at fast rates.
Studies are often done on insects and other organisms that have short generation times, and thus evolve at fast rates.
Carbohydrate
Carbohydrates (from 'hydrates of carbon') or saccharides (Greek σάκχαρον meaning "sugar") are the most abundant of the four major classes of biomolecules, which also include proteins, lipids and nucleic acids. They fill numerous roles in living things, such as the storage and transport of energy (starch, glycogen) and structural components (cellulose in plants, chitin in animals). Additionally, carbohydrates and their derivatives play major roles in the working process of the immune system, fertilization, pathogenesis, blood clotting, and development.
Chemically, carbohydrates are simple organic compounds that are aldehydes or ketones with many hydroxyl groups added, usually one on each carbon atom that is not part of the aldehyde or ketone functional group. The basic carbohydrate units are called monosaccharides, such as glucose, galactose, and fructose. The general stoichiometric formula of an unmodified monosaccharide is (C·H2O)n, where n is any number of three or greater; however, many molecules with formulae that differ slightly from this are still called carbohydrates and other compounds that possess formulae that agree with this general rule may not be in fact carbohydrates (eg formaldehyde).Despite the inexactness of the term, "carbohydrate" remains a useful descriptive name and with a little experience even a novice will soon become aware of what is, and is not, a carbohydrate. Monosaccharides can be linked together in almost limitless ways. Many carbohydrates contain one or more modified monosaccharide units that have had one or more groups replaced or removed. For example, deoxyribose, a component of DNA, is a modified version of ribose; chitin is composed of repeating units of N-acetylglucosamine, a nitrogen-containing form of glucose. The names of carbohydrates often end in the suffix -ose.
Chemically, carbohydrates are simple organic compounds that are aldehydes or ketones with many hydroxyl groups added, usually one on each carbon atom that is not part of the aldehyde or ketone functional group. The basic carbohydrate units are called monosaccharides, such as glucose, galactose, and fructose. The general stoichiometric formula of an unmodified monosaccharide is (C·H2O)n, where n is any number of three or greater; however, many molecules with formulae that differ slightly from this are still called carbohydrates and other compounds that possess formulae that agree with this general rule may not be in fact carbohydrates (eg formaldehyde).Despite the inexactness of the term, "carbohydrate" remains a useful descriptive name and with a little experience even a novice will soon become aware of what is, and is not, a carbohydrate. Monosaccharides can be linked together in almost limitless ways. Many carbohydrates contain one or more modified monosaccharide units that have had one or more groups replaced or removed. For example, deoxyribose, a component of DNA, is a modified version of ribose; chitin is composed of repeating units of N-acetylglucosamine, a nitrogen-containing form of glucose. The names of carbohydrates often end in the suffix -ose.
Macrocycle
The term macromolecule by definition implies "large molecule". In the context of biochemistry, the term may be applied to the four conventional biopolymers (nucleotides, proteins, carbohydrates, and lipids), as well as non-polymeric molecules with large molecular mass such as macrocycles.A macrocycle is, as defined by IUPAC, "a cyclic macromolecule or a macromolecular cyclic portion of a molecule.In the chemical literature, organic chemists may consider any molecule containing a ring of more than nine, or any arbitrarily large number of atoms (3 of them "donor atom") to be macrocyclic.Coordination chemists study macrocycle with three or more potential donor atoms in rings of greater than nine atoms as these compounds often have strong and specific binding with metals.This property of coordinating macrocyclic molecules is the macrocycle effect. It is in essence a specific case of the chelation effect: complexes of bidentate and polydentate ligands are more stable than those with unidentate ligands of similar strength (or similar donor atoms). A macrocycle has donor atoms arranged in more fixed positions and thus there is less of an entropic effect in the binding energy of macrocycles than monodentate or bidentate ligands with an equal number of donor atoms. Thus the macrocycle effect states that complexes of macrocyclic ligands are more stable than those with linear polydentate ligands of similar strength (or similar donor atoms). The same can be said for multicyclic macrocycles, or cryptates, being stronger complexing agents (a cryptate effect).
Protein
Proteins are large organic compounds made of amino acids arranged in a linear chain and joined together by peptide bonds between the carboxyl and amino groups of adjacent amino acid residues. The sequence of amino acids in a protein is defined by a gene and encoded in the genetic code. Although this genetic code specifies 20 "standard" amino acids plus selenocysteine and - in certain archaea - pyrrolysine, the residues in a protein are sometimes chemically altered in post-translational modification: either before the protein can function in the cell, or as part of control mechanisms. Proteins can also work together to achieve a particular function, and they often associate to form stable complexes.
Like other biological macromolecules such as polysaccharides and nucleic acids, proteins are essential parts of organisms and participate in every process within cells. Many proteins are enzymes that catalyze biochemical reactions and are vital to metabolism. Proteins also have structural or mechanical functions, such as actin and myosin in muscle and the proteins in the cytoskeleton, which form a system of scaffolding that maintains cell shape. Other proteins are important in cell signaling, immune responses, cell adhesion, and the cell cycle. Proteins are also necessary in animals' diets, since animals cannot synthesize all the amino acids they need and must obtain essential amino acids from food. Through the process of digestion, animals break down ingested protein into free amino acids that are then used in metabolism.
Like other biological macromolecules such as polysaccharides and nucleic acids, proteins are essential parts of organisms and participate in every process within cells. Many proteins are enzymes that catalyze biochemical reactions and are vital to metabolism. Proteins also have structural or mechanical functions, such as actin and myosin in muscle and the proteins in the cytoskeleton, which form a system of scaffolding that maintains cell shape. Other proteins are important in cell signaling, immune responses, cell adhesion, and the cell cycle. Proteins are also necessary in animals' diets, since animals cannot synthesize all the amino acids they need and must obtain essential amino acids from food. Through the process of digestion, animals break down ingested protein into free amino acids that are then used in metabolism.
Molecule
In chemistry, a molecule is defined as a sufficiently stable electrically neutral group of at least two atoms in a definite arrangement held together by strong chemical bonds. In organic chemistry and biochemistry, the term molecule is used less strictly and also is applied to charged organic molecules and biomolecules. Molecules are distinguished from polyatomic ions in this strict sense.
This definition has evolved as knowledge of the structure of molecules has increased. Earlier definitions were less precise defining molecules as the smallest particles of pure chemical substances that still retain their composition and chemical properties.This definition often breaks down since many substances in ordinary experience, such as rocks, salts, and metals, are composed of atoms or ions, but are not made of molecules.
In the kinetic theory of gases the term molecule is often used for any gaseous particle regardless of their composition. According to this definition noble gases would also be considered molecules despite the fact that they are composed of a single non-bonded atom.
This definition has evolved as knowledge of the structure of molecules has increased. Earlier definitions were less precise defining molecules as the smallest particles of pure chemical substances that still retain their composition and chemical properties.This definition often breaks down since many substances in ordinary experience, such as rocks, salts, and metals, are composed of atoms or ions, but are not made of molecules.
In the kinetic theory of gases the term molecule is often used for any gaseous particle regardless of their composition. According to this definition noble gases would also be considered molecules despite the fact that they are composed of a single non-bonded atom.
Molecular phylogeny
Molecular phylogeny, also known as molecular systematics, is the use of the structure of molecules to gain information on an organism's evolutionary relationships. The result of a molecular phylogenetic analysis is expressed in a so-called phylogenetic tree.
A phylogenetic tree, also called an evolutionary tree, is a tree showing the evolutionary relationships among various biological species or other entities that are believed to have a common ancestor. In a phylogenetic tree, each node with descendants represents the most recent common ancestor of the descendants, and the edge lengths in some trees correspond to time estimates. Each node is called a taxonomic unit. Internal nodes are generally called hypothetical taxonomic units (HTUs) as they cannot be directly observed.
A phylogenetic tree, also called an evolutionary tree, is a tree showing the evolutionary relationships among various biological species or other entities that are believed to have a common ancestor. In a phylogenetic tree, each node with descendants represents the most recent common ancestor of the descendants, and the edge lengths in some trees correspond to time estimates. Each node is called a taxonomic unit. Internal nodes are generally called hypothetical taxonomic units (HTUs) as they cannot be directly observed.
Restriction enzyme
A restriction enzyme (or restriction endonuclease) is an enzyme that cuts double-stranded DNA. The enzyme makes two incisions, one through each of the sugar-phosphate backbones (i.e., each strand) of the double helix without damaging the nitrogenous bases. They work with cutting up foreign DNA, a process called restriction. Restriction enzymes therefore are believed to be a mechanism evolved by bacteria to resist attack from viruses called bacteriophages and to help in the removal of viral sequences. They are part of what is called the restriction modification system.
The chemical bonds that the enzymes cleave can be reformed by other enzymes known as ligases, so that restriction fragments carved from different chromosomes or genes can be spliced together, provided their ends are complementary (more below). Many of the procedures of molecular biology and genetic engineering rely on restriction enzymes.
The 1978 Nobel Prize in Medicine was awarded to Daniel Nathans, Werner Arber and Hamilton Smith for the discovery of restriction endonucleases, leading to the development of recombinant DNA technology. The first practical use of their work was the manipulation of E. coli bacteria to produce human insulin for diabetics.
The chemical bonds that the enzymes cleave can be reformed by other enzymes known as ligases, so that restriction fragments carved from different chromosomes or genes can be spliced together, provided their ends are complementary (more below). Many of the procedures of molecular biology and genetic engineering rely on restriction enzymes.
The 1978 Nobel Prize in Medicine was awarded to Daniel Nathans, Werner Arber and Hamilton Smith for the discovery of restriction endonucleases, leading to the development of recombinant DNA technology. The first practical use of their work was the manipulation of E. coli bacteria to produce human insulin for diabetics.
Cloning vector
A cloning vector is a small DNA vehicle into which a foreign DNA fragment can be inserted. The insertion of the fragment into the cloning vector is carried out by treating the vehicle and the foreign DNA with the same restriction enzyme, then ligating the fragments together. There are many types of cloning vectors. Genetically engineered plasmids and bacteriophages (such as phage λ) are perhaps most commonly used for this purpose. Other types of cloning vectors include bacterial artificial chromosomes (BACs) and yeast artificial chromosomes (YACs).
Molecular cloning
Molecular cloning refers to the procedure of isolating a defined DNA sequence and obtaining multiple copies of it in vivo. Cloning is frequently employed to amplify DNA fragments containing genes, but it can be used to amplify any DNA sequence such as promoters, non-coding sequences and randomly fragmented DNA. It is utilised in a wide array of biological experiments and practical applications such as large scale protein production. Occasionally, the term cloning is misleadingly used to refer to the identification of the chromosomal location of a gene associated with a particular phenotype of interest, such as in positional cloning. In practice, localization of the gene to a chromosome or genomic region does not necessarily enable one to isolate or amplify the relevant genomic sequence.
In essence, in order to amplify any DNA sequence in a living organism, that sequence must be linked to an origin of replication, a sequence element capable of directing the propagation of itself and any linked sequence. In practice, however, a number of other features are desired and a variety of specialised cloning vectors exist that allow protein expression, tagging, single stranded RNA and DNA production and a host of other manipulations.
Cloning of any DNA fragment essentially involves four steps: fragmentation, ligation, transfection, and screening/selection. Although these steps are invariable among cloning procedures a number of alternative routes can be selected, these are summarized as a ‘cloning strategy’.
Initially, the DNA of interest needs to be isolated to provide a DNA segment of suitable size. Subsequently, a ligation procedure is used where the amplified fragment is inserted into a vector. The vector (which is frequently circular) is linearised using restriction enzymes, and incubated with the fragment of interest under appropriate conditions with an enzyme called DNA ligase. Following ligation the vector with the insert of interest is transfected into cells. A number of alternative techniques are available, such as chemical sensitivation of cells, electroporation and biolistics. Finally, the transfected cells are cultured. As the aforementioned procedures are of particularly low efficiency, there is a need to identify the cells that have been successfully transfected with the vector construct containing the desired insertion sequence in the required orientation. Modern cloning vectors include selectable antibiotic resistance markers, which allow only cells in which the vector has been transfected, to grow. Additionally, the cloning vectors may contain colour selection markers which provide blue/white screening (α-factor complementation) on X-gal medium. Nevertheless, these selection steps do not absolutely guarantee that the DNA insert is present in the cells obtained. Further investigation of the resulting colonies is required to confirm that cloning was successful. This may be accomplished by means of PCR, restriction fragment analysis and/or DNA sequencing.
In essence, in order to amplify any DNA sequence in a living organism, that sequence must be linked to an origin of replication, a sequence element capable of directing the propagation of itself and any linked sequence. In practice, however, a number of other features are desired and a variety of specialised cloning vectors exist that allow protein expression, tagging, single stranded RNA and DNA production and a host of other manipulations.
Cloning of any DNA fragment essentially involves four steps: fragmentation, ligation, transfection, and screening/selection. Although these steps are invariable among cloning procedures a number of alternative routes can be selected, these are summarized as a ‘cloning strategy’.
Initially, the DNA of interest needs to be isolated to provide a DNA segment of suitable size. Subsequently, a ligation procedure is used where the amplified fragment is inserted into a vector. The vector (which is frequently circular) is linearised using restriction enzymes, and incubated with the fragment of interest under appropriate conditions with an enzyme called DNA ligase. Following ligation the vector with the insert of interest is transfected into cells. A number of alternative techniques are available, such as chemical sensitivation of cells, electroporation and biolistics. Finally, the transfected cells are cultured. As the aforementioned procedures are of particularly low efficiency, there is a need to identify the cells that have been successfully transfected with the vector construct containing the desired insertion sequence in the required orientation. Modern cloning vectors include selectable antibiotic resistance markers, which allow only cells in which the vector has been transfected, to grow. Additionally, the cloning vectors may contain colour selection markers which provide blue/white screening (α-factor complementation) on X-gal medium. Nevertheless, these selection steps do not absolutely guarantee that the DNA insert is present in the cells obtained. Further investigation of the resulting colonies is required to confirm that cloning was successful. This may be accomplished by means of PCR, restriction fragment analysis and/or DNA sequencing.
DNA methylation
DNA methylation is a type of chemical modification of DNA that can be inherited and subsequently removed without changing the original DNA sequence. As such, it is part of the epigenetic code and is also the most well characterized epigenetic mechanism.
DNA methylation involves the addition of a methyl group to DNA — for example, to the number 5 carbon of the cytosine pyrimidine ring — with the effect of reducing gene expression. DNA methylation at the N5 position of cytosine has been found in every vertebrate examined. In humans, approximately 1% of DNA bases undergo DNA methylation. In adult somatic tissues, DNA methylation typically occurs in a CpG dinucleotide context; non-CpG methylation is prevalent in embryonic stem cells.
In plants, cytosines are methylated both symmetrically (CpG or CpNpG) and asymmetrically (CpNpNp), where N can be any nucleotide. Some organisms, such as fruit flies, exhibit virtually no DNA methylation.
DNA methylation involves the addition of a methyl group to DNA — for example, to the number 5 carbon of the cytosine pyrimidine ring — with the effect of reducing gene expression. DNA methylation at the N5 position of cytosine has been found in every vertebrate examined. In humans, approximately 1% of DNA bases undergo DNA methylation. In adult somatic tissues, DNA methylation typically occurs in a CpG dinucleotide context; non-CpG methylation is prevalent in embryonic stem cells.
In plants, cytosines are methylated both symmetrically (CpG or CpNpG) and asymmetrically (CpNpNp), where N can be any nucleotide. Some organisms, such as fruit flies, exhibit virtually no DNA methylation.
RNA interference
RNA interference (RNAi) is a mechanism that inhibits gene expression at the stage of translation or by hindering the transcription of specific genes. RNAi targets include RNA from viruses and transposons (significant for some forms of innate immune response), and also plays a role in regulating development and genome maintenance. Small interfering RNA strands (siRNA) are key to the RNAi process, and have complementary nucleotide sequences to the targeted RNA strand. Specific RNAi pathway proteins are guided by the siRNA to the targeted messenger RNA (mRNA), where they "cleave" the target, breaking it down into smaller portions that can no longer be translated into protein. A type of RNA transcribed from the genome itself, microRNA (miRNA), works in the same way.
The RNAi pathway is initiated by the enzyme dicer, which cleaves long, dsRNA molecules into short fragments of 20–25 base pairs. One of the two strands of each fragment, known as the guide strand, is then incorporated into the RNA-induced silencing complex (RISC) and pairs with complementary sequences. The most well-studied outcome of this recognition event is post-transcriptional gene silencing. This occurs when the guide strand specifically pairs with an mRNA molecule and induces the degradation by argonaute, the catalytic component of the RISC complex. Another outcome is epigenetic changes to a gene – histone modification and DNA methylation – affecting the degree the gene is transcribed
The RNAi pathway is initiated by the enzyme dicer, which cleaves long, dsRNA molecules into short fragments of 20–25 base pairs. One of the two strands of each fragment, known as the guide strand, is then incorporated into the RNA-induced silencing complex (RISC) and pairs with complementary sequences. The most well-studied outcome of this recognition event is post-transcriptional gene silencing. This occurs when the guide strand specifically pairs with an mRNA molecule and induces the degradation by argonaute, the catalytic component of the RISC complex. Another outcome is epigenetic changes to a gene – histone modification and DNA methylation – affecting the degree the gene is transcribed
Phylogenetics
In biology, phylogenetics (Greek: phyle = tribe, race and genetikos = relative to birth, from genesis = birth) is the study of evolutionary relatedness among various groups of organisms (e.g., species, populations). Also known as phylogenetic systematics or cladistics, phylogenetics treats each species as a group of lineage-connected individuals. Taxonomy, the classification of organisms according to similarity, has been richly informed by phylogenetics but remains methodologically and logically distinct.
Evolution is regarded as a branching process, whereby populations are altered over time and may speciate into separate branches, hybridize together, or terminate by extinction. This may be visualized as a multidimensional character-space that a population moves through over time. The problem posed by phylogenetics is that genetic data are only available for the present, and fossil records (osteometric data) are sporadic and less reliable. Our knowledge of how evolution operates is used to reconstruct the full tree.
Evolution is regarded as a branching process, whereby populations are altered over time and may speciate into separate branches, hybridize together, or terminate by extinction. This may be visualized as a multidimensional character-space that a population moves through over time. The problem posed by phylogenetics is that genetic data are only available for the present, and fossil records (osteometric data) are sporadic and less reliable. Our knowledge of how evolution operates is used to reconstruct the full tree.
Phenotype
A phenotype is any observed quality of an organism, such as its morphology, development, or behavior, as opposed to its genotype - the inherited instructions it carries, which may or may not be expressed. This genotype-phenotype distinction was proposed by Wilhelm Johannsen in 1911 to make clear the difference between an organism's heredity and what that heredity produces. The distinction is similar to that proposed by August Weismann, who distinguished between germ plasm (heredity) and somatic cells (the body). A more modern version is Francis Crick's Central dogma of molecular biology.
Despite its seemingly straightforward definition, the concept of the phenotype has some hidden subtleties. First, most of the molecules and structures coded by the genetic material are not visible in the appearance of an organism, yet are part of the phenotype. Human blood groups are an example. So, by extension, the term phenotype must include characteristics that can be made visible by some technical procedure. A further, and more radical, extension would add inherited behaviour to the phenotype.
Despite its seemingly straightforward definition, the concept of the phenotype has some hidden subtleties. First, most of the molecules and structures coded by the genetic material are not visible in the appearance of an organism, yet are part of the phenotype. Human blood groups are an example. So, by extension, the term phenotype must include characteristics that can be made visible by some technical procedure. A further, and more radical, extension would add inherited behaviour to the phenotype.
Gene therapy
Gene therapy is the insertion of genes into an individual's cells and tissues to treat a disease, and hereditary diseases in which a defective mutant allele is replaced with a functional one. Although the technology is still in its infancy, it has been used with some success. Antisense therapy is not strictly a form of gene therapy, but is a genetically-mediated therapy and is often on other menthod . On September 14, 1990 at the U.S. National Institutes of Health W. French Anderson, M.D., and his colleagues R. Michael Blaese, M.D., C. Bouzaid, M.D., and Kenneth Culver, M.D., performed the first approved gene therapy procedure on four-year old Ashanthi DeSilva. Born with a rare genetic disease called severe combined immunodeficiency (SCID), she lacked a healthy immune system, and was vulnerable to every passing germ or infection. Children with this illness usually develop overwhelming infections and rarely survive to adulthood; a common childhood illness like chickenpox is life-threatening. Ashanthi led a cloistered existence -- avoiding contact with people outside her family, remaining in the sterile environment of her home, and battling frequent illnesses with massive amounts of antibiotics.
In Ashanthi's gene therapy procedure, doctors removed white blood cells from the child's body, let the cells grow in the lab, inserted the missing gene into the cells, and then infused the genetically modified blood cells back into the patient's bloodstream. Laboratory tests have shown that the therapy strengthened Ashanthi's immune system by 40%; she no longer has recurrent colds, she has been allowed to attend school, and she was immunized against whooping cough. This procedure was not a cure; the white blood cells treated genetically only work for a few months, after which the process must be repeated (VII, Thompson [First] 1993). As of early 2007, she was still in good health, and she was attending college. However, there is no consensus on what portion of her improvement should be attributed to gene therapy versus other treatments. Some would state that the case is of great importance despite its indefinite results, if only because it demonstrated that gene therapy could be practically attempted without adverse consequencessidered together with other methods.
In Ashanthi's gene therapy procedure, doctors removed white blood cells from the child's body, let the cells grow in the lab, inserted the missing gene into the cells, and then infused the genetically modified blood cells back into the patient's bloodstream. Laboratory tests have shown that the therapy strengthened Ashanthi's immune system by 40%; she no longer has recurrent colds, she has been allowed to attend school, and she was immunized against whooping cough. This procedure was not a cure; the white blood cells treated genetically only work for a few months, after which the process must be repeated (VII, Thompson [First] 1993). As of early 2007, she was still in good health, and she was attending college. However, there is no consensus on what portion of her improvement should be attributed to gene therapy versus other treatments. Some would state that the case is of great importance despite its indefinite results, if only because it demonstrated that gene therapy could be practically attempted without adverse consequencessidered together with other methods.
Microorganism
A microorganism (also can be spelled as micro organism) or microbe is an organism that is microscopic (too small to be seen by the naked human eye). The study of microorganisms is called microbiology, a subject that began with Anton van Leeuwenhoek's discovery of microorganisms in 1675, using a microscope of his own design.
Microorganisms are incredibly diverse and include bacteria, fungi, archaea, and protists, as well as some microscopic plants and animals. They do not include viruses and prions, which are generally classified as non-living. Most microorganisms are single-celled, or unicellular, but some multicellular organisms are microscopic, while some unicellular protists, and a bacteria called Thiomargarita namibiensis are visible to the naked eye.
Microorganisms live in all parts of the biosphere where there is liquid water, including hot springs, on the ocean floor, high in the atmosphere and deep inside rocks within the Earth's crust. Microorganisms are critical to nutrient recycling in ecosystems as they act as decomposers. As some microorganisms can fix nitrogen, they are a vital part of the nitrogen cycle, and recent studies indicate that airborne microbes may play a role in precipitation and weather.Single-celled microorganisms were the first forms of life to develop on earth, approximately 3–4 billion years ago Further evolution was slow, and for about 3 billion years in the Precambrian eon, all organisms were microscopic. So, for most of the history of life on Earth the only form of life were microorganisms. Bacteria, algae and fungi have been identified in amber that is 220 million years old, which shows that the morphology of microorganisms has changed little since the triassic period.
Most microorganisms can reproduce rapidly and microbes such as bacteria can also freely exchange genes by conjugation, transformation and transduction between widely-divergent species.] This horizontal gene transfer, coupled with a high mutation rate and many other means of genetic variation, allows microorganisms to swiftly evolve (via natural selection) to survive in new environments and respond to environmental stresses. This rapid evolution is important in medicine, as it has led to the recent development of 'super-bugs' — pathogenic bacteria that are resistant to modern antibiotics
Microbes are also exploited by people in biotechnology, both in traditional food and beverage preparation, as well as modern technologies based on genetic engineering. However, pathogenic microbes are harmful, since they invade and grow within other organisms, causing diseases that kill millions of people, other animals, and plants every year.
Microorganisms are incredibly diverse and include bacteria, fungi, archaea, and protists, as well as some microscopic plants and animals. They do not include viruses and prions, which are generally classified as non-living. Most microorganisms are single-celled, or unicellular, but some multicellular organisms are microscopic, while some unicellular protists, and a bacteria called Thiomargarita namibiensis are visible to the naked eye.
Microorganisms live in all parts of the biosphere where there is liquid water, including hot springs, on the ocean floor, high in the atmosphere and deep inside rocks within the Earth's crust. Microorganisms are critical to nutrient recycling in ecosystems as they act as decomposers. As some microorganisms can fix nitrogen, they are a vital part of the nitrogen cycle, and recent studies indicate that airborne microbes may play a role in precipitation and weather.Single-celled microorganisms were the first forms of life to develop on earth, approximately 3–4 billion years ago Further evolution was slow, and for about 3 billion years in the Precambrian eon, all organisms were microscopic. So, for most of the history of life on Earth the only form of life were microorganisms. Bacteria, algae and fungi have been identified in amber that is 220 million years old, which shows that the morphology of microorganisms has changed little since the triassic period.
Most microorganisms can reproduce rapidly and microbes such as bacteria can also freely exchange genes by conjugation, transformation and transduction between widely-divergent species.] This horizontal gene transfer, coupled with a high mutation rate and many other means of genetic variation, allows microorganisms to swiftly evolve (via natural selection) to survive in new environments and respond to environmental stresses. This rapid evolution is important in medicine, as it has led to the recent development of 'super-bugs' — pathogenic bacteria that are resistant to modern antibiotics
Microbes are also exploited by people in biotechnology, both in traditional food and beverage preparation, as well as modern technologies based on genetic engineering. However, pathogenic microbes are harmful, since they invade and grow within other organisms, causing diseases that kill millions of people, other animals, and plants every year.
Genetically modified organism
A genetically modified organism (GMO) or genetically engineered organism (GEO) is an organism whose genetic material has been altered using genetic engineering techniques. These techniques are generally known as recombinant DNA technology. With recombinant DNA technology, DNA molecules from different sources are combined in vitro into one molecule to create a new gene. This DNA is then transferred into an organism and causes the expression of modified or novel traits.Examples of GMOs are highly diverse, and include transgenic (genetically modified by recombinant DNA methods) animals such as mice,fish, transgenic plants, or various microbes, such as fungi and bacteria. The generation and use of GMOs has many reasons, chief among them are their use in research that addresses fundamental or applied questions in biology or medicine, for the production of pharmaceuticals and industrial enzymes, and for direct, and often controversial, applications aimed at improving human health (e.g., gene therapy) or agriculture (e.g., golden rice). The term "genetically modified organism" does not always imply, but can include, targeted insertions of genes from one into another species. For example, a gene from a jellyfish, encoding a fluorescent protein called GFP, can be physically linked and thus co-expressed with mammalian genes to identify the location of the protein encoded by the GFP-tagged gene in the mammalian cell. These and other methods are useful and indispensable tools for biologists in many areas of research, including those that study the mechanisms of human and other diseases or fundamental biological processes in eukaryotic or prokaryotic cells.
Reverse genetics
Reverse genetics is an approach to discovering the function of a gene that proceeds in the opposite direction of so called forward genetic screens of classical genetics. Simply put, while forward genetics seeks to find the genetic basis of a phenotype or trait, reverse genetics seeks to find the possible phenotypes that may derive from a specific genetic sequence enumerated during DNA sequencing.
Automated DNA sequencing generates large volumes of genomic sequence data relatively rapidly. Many genetic sequences are discovered in advance of other, less easily obtained, biological information. Reverse genetics attempts to connect a given genetic sequTo learn the influence a sequence has on phenotype, or to discover its biological function, researchers can engineer a change or disruption in the DNA. After this change has been made a researcher can look for the effect of such alterations in the whole organism. There are several different methods of reverse genetics that have proved useful:ence with specific effects on the organism.
Automated DNA sequencing generates large volumes of genomic sequence data relatively rapidly. Many genetic sequences are discovered in advance of other, less easily obtained, biological information. Reverse genetics attempts to connect a given genetic sequTo learn the influence a sequence has on phenotype, or to discover its biological function, researchers can engineer a change or disruption in the DNA. After this change has been made a researcher can look for the effect of such alterations in the whole organism. There are several different methods of reverse genetics that have proved useful:ence with specific effects on the organism.
Gene Therapy
Many mutations in a person's genes result in severe medical condition. These mutations cause the protein encoded by that gene to malfunction and cells that rely on this protein cannot function properly. This can cause problems for the tissues or organs. Conditions related to gene mutations are called genetic disorders. One way to fix the internal problems is gene therapy. By adding a corrected copy of the gene, the affected cells, tissues, and organs may work properly. As opposed to drug-based approaches, gene therapy repairs the underlying genetic defect.
Gene Therapy is the process to treat or alleviate diseases by genetically modifying the cells of the infected person, causing the gene to function properly. When a human disease gene has been recognized, molecular genetics tools can be used to explore the process of the gene in both
normal and pathogenic states. From there, the gene is transferred either in vivo or ex vivo and the body begins to identify the new gene. Gene therapy has to be repeated several times for the infected patient to continually be relieved.
Currently, gene therapy is still being experimented with and products are not approved by the U.S. Food and Drug Administration. There have been several set backs in the last 15 years that have restricted further measures on gene therapy. As there are unsuccessful attempts, there continues to be a growing number of successful gene therapy transfers which has furthered the research.
Major diseases that can be treated with gene therapy: infectious diseases (result of infection by a virus or bacterial pathogen), cancers, inherited disorders, immune system disorders
Gene Therapy is the process to treat or alleviate diseases by genetically modifying the cells of the infected person, causing the gene to function properly. When a human disease gene has been recognized, molecular genetics tools can be used to explore the process of the gene in both
normal and pathogenic states. From there, the gene is transferred either in vivo or ex vivo and the body begins to identify the new gene. Gene therapy has to be repeated several times for the infected patient to continually be relieved.
Currently, gene therapy is still being experimented with and products are not approved by the U.S. Food and Drug Administration. There have been several set backs in the last 15 years that have restricted further measures on gene therapy. As there are unsuccessful attempts, there continues to be a growing number of successful gene therapy transfers which has furthered the research.
Major diseases that can be treated with gene therapy: infectious diseases (result of infection by a virus or bacterial pathogen), cancers, inherited disorders, immune system disorders
Horizontal gene transfer
Horizontal gene transfer (HGT), also Lateral gene transfer (LGT), is any process in which an organism transfers genetic material to another cell that is not its offspring. By contrast, vertical transfer occurs when an organism receives genetic material from its ancestor, e.g. its parent or a species from which it evolved. Most thinking in genetics has focused on the more prevalent vertical transfer, but there is a recent awareness that horizontal gene transfer is a significant phenomenon
Techniques in Molecular Genetics
There are three general techniques used for molecular genetics: amplification, separation and detection, and expression. Specifically used for amplification is the Polymerase chain reaction, which is an “indispensable tool in a great variety of applications”. In the separation and detection technique DNA and mRNA are isolated from their cells. Gene expression in cells or organisms is done in a place or time that is not normal for that specific gene.
Wednesday, April 30, 2008
Polymerase Chain Reaction
The Polymerase Chain Reaction (or PCR) is a laboratory technique which greatly amplifies the amount of a short segment of DNA. It is based on the process by which DNA is copied in cells. Since replicated DNA is itself available for later replication, the PCR process can feed upon itself, leading to an accelerating increase to millions of copies over the original DNA sample.Polymerase Chain Reaction Polymerase Chain Reaction
PCR solves two of the major problems encountered in the analysis of DNA in an organism. The first problem is specificity - an area of interest may be as little as one unit of DNA among billions. Since PCR only amplifies a small segment (leaving the rest of the DNA largely unaltered), the required specificity of a later genetic assay might be reduced to just one part among hundreds. The second problem is sensitivity - a sample of DNA might contain just a few copies of an area of interest. By increasing that to millions (or billions) of copies, PCR greatly speeds or simplifies later genetic analysis.
PCR has become a widely used tool for research in molecular genetics. It is also the basis for medical genetic testing, where individuals are screened for the presence of disease mutations. DNA Fingerprinting, the unique identification of individuals by patterns of variation in their DNA, is also based on PCR, and is used in criminal forensics and parental testing. The technique had such widespread impact that its inventor was awarded the Nobel Prize in 1993, just eight years after it was first reported
PCR solves two of the major problems encountered in the analysis of DNA in an organism. The first problem is specificity - an area of interest may be as little as one unit of DNA among billions. Since PCR only amplifies a small segment (leaving the rest of the DNA largely unaltered), the required specificity of a later genetic assay might be reduced to just one part among hundreds. The second problem is sensitivity - a sample of DNA might contain just a few copies of an area of interest. By increasing that to millions (or billions) of copies, PCR greatly speeds or simplifies later genetic analysis.
PCR has become a widely used tool for research in molecular genetics. It is also the basis for medical genetic testing, where individuals are screened for the presence of disease mutations. DNA Fingerprinting, the unique identification of individuals by patterns of variation in their DNA, is also based on PCR, and is used in criminal forensics and parental testing. The technique had such widespread impact that its inventor was awarded the Nobel Prize in 1993, just eight years after it was first reported
DNA
Deoxyribonucleic acid (DNA) is a nucleic acid that contains the genetic instructions used in the development and functioning of all known living organisms and some viruses. The main role of DNA molecules is the long-term storage of information. DNA is often compared to a set of blueprints or a recipe, since it contains the instructions needed to construct other components of cells, such as proteins and RNA molecules. The DNA segments that carry this genetic information are called genes, but other DNA sequences have structural purposes, or are involved in regulating the use of this genetic information.
Chemically, DNA is a long polymer of simple units called nucleotides, with a backbone made of sugars and phosphate groups joined by ester bonds. Attached to each sugar is one of four types of molecules called bases. It is the sequence of these four bases along the backbone that encodes information. This information is read using the genetic code, which specifies the sequence of the amino acids within proteins. The code is read by copying stretches of DNA into the related nucleic acid RNA, in a process called transcription.
Within cells, DNA is organized into structures called chromosomes. These chromosomes are duplicated before cells divide, in a process called DNA replication. Eukaryotic organisms (animals, plants, and fungi) store their DNA inside the cell nucleus, while in prokaryotes (bacteria and archae) it is found in the cell's cytoplasm. Within the chromosomes, chromatin proteins such as histones compact and organize DNA. These compact structures guide the interactions between DNA and other proteins, helping control which parts of the DNA are transcribed.
Chemically, DNA is a long polymer of simple units called nucleotides, with a backbone made of sugars and phosphate groups joined by ester bonds. Attached to each sugar is one of four types of molecules called bases. It is the sequence of these four bases along the backbone that encodes information. This information is read using the genetic code, which specifies the sequence of the amino acids within proteins. The code is read by copying stretches of DNA into the related nucleic acid RNA, in a process called transcription.
Within cells, DNA is organized into structures called chromosomes. These chromosomes are duplicated before cells divide, in a process called DNA replication. Eukaryotic organisms (animals, plants, and fungi) store their DNA inside the cell nucleus, while in prokaryotes (bacteria and archae) it is found in the cell's cytoplasm. Within the chromosomes, chromatin proteins such as histones compact and organize DNA. These compact structures guide the interactions between DNA and other proteins, helping control which parts of the DNA are transcribed.
Genetic disorder
A genetic disorder is a condition caused by abnormalities in genes or chromosomes. While some diseases, such as cancer, are due to genetic abnormalities acquired in a few cells during life, the term "genetic disease" most commonly refers to diseases present in all cells of the body and present since conception. Some genetic disorders are caused by chromosomal abnormalities due to errors in meiosis, the process which produces reproductive cells such as sperm and eggs. Examples include Down syndrome (extra chromosome 21), Turner Syndrome (45X0) and Klinefelter's syndrome (a male with 2 X chromosomes). Other genetic changes may occur during the production of germ cells by the parent. One example is the triplet expansion repeat mutations which can cause fragile X syndrome or Huntington's disease. Defective genes may also be inherited intact from the parents. In this case, the genetic disorder is known as a hereditary disease. This can often happen unexpectedly when two healthy carriers of a defective recessive gene reproduce, but can also happen when the defective gene is dominant. Currently about 4,000 genetic disorders are known, with more being discovered. Most disorders are quite rare and affect one person in every several thousands or millions. Cystic fibrosis is one of the most common genetic disorders; around 5% of the population of the United States carry at least one copy of the defective gene. Some types of recessive gene disorder confer an advantage in the heterozygous state in certain environments.
Genetic diseases are typically diagnosed and treated by geneticists. Genetic counselors assist the physicians and directly counsel patients. The study of genetic diseases is a scientific discipline whose theoretical underpinning is based on population genetics.
Genetic diseases are typically diagnosed and treated by geneticists. Genetic counselors assist the physicians and directly counsel patients. The study of genetic diseases is a scientific discipline whose theoretical underpinning is based on population genetics.
Cloning DNA in Bacteria
The word cloning for this type of amplification entails making multiple identical copies of a sequence of DNA. The target DNA sequence is then inserted into a [cloning vector]. Because this vector originates from a self-replicating virus, plasmid, or higher organism cell when the appropriate size DNA is inserted the “target and vector DNA fragments are then ligated and create a recombinant DNA molecule. The recombinant DNA molecules are then put into a bacteria strain (usually E. coli) which produces several identical copies by transformation. Transformation is the DNA uptake mechanism possessed by bacteria. However, only one recombinant DNA molecule can be cloned within a single bacteria cell, so each clone is of just one DNA insert.
Separation and Detection
In separation and detection DNA and mRNA are isolated from cells (the separation) and then detected simply by the isolation. Cell cultures are also grown to provide a constant supply of cells ready for isolation.
Cell (biology)
The cell is the structural and functional unit of all known living organisms. It is the smallest unit of an organism that is classified as living, and is sometimes called the building block of life.Some organisms, such as most bacteria, are unicellular (consist of a single cell). Other organisms, such as humans, are multicellular. (Humans have an estimated 100 trillion or 1014 cells; a typical cell size is 10 µm; a typical cell mass is 1 nanogram.) The largest known cell is an ostrich egg. In 1837 before the final cell theory was developed, a Czech Jan Evangelista Purkyně observed small "granules" while looking at the plant tissue through a microscope. The cell theory, first developed in 1839 by Matthias Jakob Schleiden and Theodor Schwann, states that all organisms are composed of one or more cells. All cells come from preexisting cells. Vital functions of an organism occur within cells, and all cells contain the hereditary information necessary for regulating cell functions and for transmitting information to the next generation of cells.
The word cell comes from the Latin cellula, meaning, a small room. The descriptive name for the smallest living biological structure was chosen by Robert Hooke in a book he published in 1665 when he compared the cork cells he saw through his microscope to the small rooms monks lived in.
The word cell comes from the Latin cellula, meaning, a small room. The descriptive name for the smallest living biological structure was chosen by Robert Hooke in a book he published in 1665 when he compared the cork cells he saw through his microscope to the small rooms monks lived in.
Tissue culture
Tissue culture is the growth of tissues and/or cells separate from the organism. This is typically facilitated via use of a liquid, semi-solid, or solid growth media, such as broth or agar. Tissue culture commonly refers to the culture of animal cells and tissues, while the more specific term plant tissue culture is used for plantIn modern usage, "tissue culture" generally refers to the growth of eukaryotic cells in vitro. It is often used interchangeably with cell culture to specifically describe the in vitro culturing of sperm donor cells.
However, "tissue culture" can also be used to refer to the culturing of tissue pieces, i.e. explant culture or whole organs, i.e. organ culture.s.
However, "tissue culture" can also be used to refer to the culturing of tissue pieces, i.e. explant culture or whole organs, i.e. organ culture.s.
DNA Isolation
DNA isolation extracts DNA from a cell in a pure form. First, the DNA is separated from cellular components such as proteins, RNA, and lipids. This is done by placing the chosen cells in a tube with a solution that mechanically, chemically, breaks the cells open. This solution contains enzymes, chemicals, and salts that breaks down the cells except for the DNA. It contains enzymes to dissolve proteins, chemicals to destroy all RNA present, and salts to help pull DNA out of the solution.
Next, the DNA is separated from the solution by being spun in a centrifuge, which allows the DNA to collect in the bottom of the tube. After this cycle in the centrifuge the solution is poured off and the DNA is resuspended in a second solution that makes the DNA easy to work with in the future.
This results in a concentrated DNA sample that contains thousands of copies of each gene. For large scale projects such as sequencing the human genome, all this work is done by robots.
Next, the DNA is separated from the solution by being spun in a centrifuge, which allows the DNA to collect in the bottom of the tube. After this cycle in the centrifuge the solution is poured off and the DNA is resuspended in a second solution that makes the DNA easy to work with in the future.
This results in a concentrated DNA sample that contains thousands of copies of each gene. For large scale projects such as sequencing the human genome, all this work is done by robots.
Thymine
Thymine is one of the four bases in the nucleic acid of DNA that make up the letters ATGC. The others are adenine, guanine, and cytosine. Thymine (T) always pairs with adenine. Thymine is also known as 5-methyluracil, a pyrimidine nucleobase. As the name suggests, thymine may be derived by methylation of uracil at the 5th carbon. In RNA, thymine is replaced with uracil in most cases. In DNA, thymine(T) binds to adenine (A) via two hydrogen bonds to assist in stabilizing the nucleic acid structures.
Thymine combined with deoxyribose creates the nucleoside deoxythymidine, which is synonymous with the term thymidine. Thymidine can be phosphorylated with one, two, or three phosphoric acid groups, creating, respectively, TMP, TDP, or TTP .One of the common mutations of DNA involves two adjacent thymines or cytosine, which, in presence of ultraviolet light, may form thymine dimers, causing "kinks" in the DNA molecule that inhibit normal function.
Thymine could also be a target for actions of 5-fluorouracil (5-FU) in cancer treatment. 5-FU can be a metabolic analog of thymine (in DNA synthesis) or uracil (in RNA synthesis). Substitution of this analog inhibits DNA synthesis in actively-dividing cells.
Thymine bases are frequently oxidized to hydantoins over time after the death of an organism
Thymine combined with deoxyribose creates the nucleoside deoxythymidine, which is synonymous with the term thymidine. Thymidine can be phosphorylated with one, two, or three phosphoric acid groups, creating, respectively, TMP, TDP, or TTP .One of the common mutations of DNA involves two adjacent thymines or cytosine, which, in presence of ultraviolet light, may form thymine dimers, causing "kinks" in the DNA molecule that inhibit normal function.
Thymine could also be a target for actions of 5-fluorouracil (5-FU) in cancer treatment. 5-FU can be a metabolic analog of thymine (in DNA synthesis) or uracil (in RNA synthesis). Substitution of this analog inhibits DNA synthesis in actively-dividing cells.
Thymine bases are frequently oxidized to hydantoins over time after the death of an organism
Complementary DNA
In genetics, complementary DNA (cDNA) is DNA synthesized from a mature mRNA template in a reaction catalyzed by the enzyme reverse transcriptase. cDNA is often used to clone eukaryotic genes in prokaryotes. cDNA is also produced by retroviruses (such as HIV-1, HIV-2, Simian Immunodeficiency Virus, etc.) which is integrated into its host to create a provirus.The central dogma of molecular biology outlines that in synthesizing proteins, DNA is transcribed into mRNA, which is translated into protein. One difference between eukaryotic and prokaryotic genes is that eukaryotic genes can contain introns (intervening sequences), which are not coding sequences, and must be spliced out of the RNA primary transcript before it becomes mRNA and can be translated into protein. Prokaryotic genes have no introns, so their RNA is not subject to splicing.
Often it is desirable to express eukaryotic genes in prokaryotic cells. A simplified method of doing so would include the addition of eukaryotic DNA to a prokaryotic host, which would transcribe the DNA to mRNA and then translate it to protein. However, as eukaryotic DNA has introns, and since prokaryotes lack the machinery to splice them, the splicing of eukaryotic DNA must be done prior to adding the eukaryotic DNA into the host. This DNA which was made as a complementary to the RNA is called complementary DNA (cDNA). To obtain expression of the protein encoded by the eukaryotic cDNA, prokaryotic regulatory sequences would also be required .
Often it is desirable to express eukaryotic genes in prokaryotic cells. A simplified method of doing so would include the addition of eukaryotic DNA to a prokaryotic host, which would transcribe the DNA to mRNA and then translate it to protein. However, as eukaryotic DNA has introns, and since prokaryotes lack the machinery to splice them, the splicing of eukaryotic DNA must be done prior to adding the eukaryotic DNA into the host. This DNA which was made as a complementary to the RNA is called complementary DNA (cDNA). To obtain expression of the protein encoded by the eukaryotic cDNA, prokaryotic regulatory sequences would also be required .
DNA polymerase
A DNA polymerase is an enzyme that assists in DNA replication. Such enzymes catalyze the polymerization of deoxyribonucleotides alongside a DNA strand, which they "read" and use as a template. The newly-polymerized molecule is complementary to the template strand and identical to the template's partner strand.
DNA polymerase is considered to be a holoenzyme since it requires a magnesium ion as a co-factor to function properly. In the absence of the magnesium ion, it is referred to as an apoenzyme.
DNA-Polymerase initiates DNA replication by binding to a piece of single-stranded DNA.
DNA polymerase is considered to be a holoenzyme since it requires a magnesium ion as a co-factor to function properly. In the absence of the magnesium ion, it is referred to as an apoenzyme.
DNA-Polymerase initiates DNA replication by binding to a piece of single-stranded DNA.
mRNA Isolation
Expressed DNA that codes for the synthesis of a protein is the final goal for scientists and this expressed DNA is obtained by isolation mRNA (Messenger RNA). First, laboratories use a normal cellular modification of mRNA that adds up to 200 adenine nucleotides to the end of the molecule (poly(A) tail). Once this has been added, the cell is ruptured and its cell contents are exposed to synthetic beads that are coated with thymine string nucleotides. Because Adenine and Thymine pair together in DNA, the poly(A) tail and synthetic beads are attracted to one another, and once they bind in this process the cell components can be washed away without removing the mRNA. Once the mRNA has been isolated, reverse transcriptase is employed to convert it to single-stranded DNA, from which a stable double-stranded DNA is produced using DNA polymerase. Complementary DNA (cDNA) is much more stable than mRNA and so, once the double-stranded DNA has been produced it represents the expressed DNA sequence scientists look for.
Human Genome Project
The Human Genome Project (HGP) was an international scientific research project with a primary goal to determine the sequence of chemical base pairs which make up DNA and to identify the approximately 25,000 genes of the human genome from both a physical and functional standpoint.
The project began in 1990 initially headed by James D. Watson at the U.S. National Institutes of Health. A working draft of the genome was released in 2000 and a complete one in 2003, with further analysis still being published. A parallel project was conducted by the private company Celera Genomics. Most of the sequencing was performed in universities and research centers from the United States, Canada and Great Britain. The mapping of human genes is an important step in the development of medicines and other aspects of health care.
While the objective of the Human Genome Project is to understand the genetic makeup of the human species, the project also has focused on several other nonhuman organisms such as E. coli, the fruit fly, and the laboratory mouse. It remains one of the largest single investigational projects in modern science.
The HGP originally aimed to map the nucleotides contained in a haploid reference human genome (more than three billion). Several groups have announced efforts to extend this to diploid human genomes including the International HapMap Project, Applied Biosystems, Perlegen, Illumina, JCVI, Personal Genome Project, and Roche-454.
The "genome" of any given individual (except for identical twins and cloned animals) is unique; mapping "the human genome" involves sequencing multiple variations of each gene. The project did not study the entire DNA found in human cells; some heterochromatic areas (about 8% of the total) remain un-sequenced.
The project began in 1990 initially headed by James D. Watson at the U.S. National Institutes of Health. A working draft of the genome was released in 2000 and a complete one in 2003, with further analysis still being published. A parallel project was conducted by the private company Celera Genomics. Most of the sequencing was performed in universities and research centers from the United States, Canada and Great Britain. The mapping of human genes is an important step in the development of medicines and other aspects of health care.
While the objective of the Human Genome Project is to understand the genetic makeup of the human species, the project also has focused on several other nonhuman organisms such as E. coli, the fruit fly, and the laboratory mouse. It remains one of the largest single investigational projects in modern science.
The HGP originally aimed to map the nucleotides contained in a haploid reference human genome (more than three billion). Several groups have announced efforts to extend this to diploid human genomes including the International HapMap Project, Applied Biosystems, Perlegen, Illumina, JCVI, Personal Genome Project, and Roche-454.
The "genome" of any given individual (except for identical twins and cloned animals) is unique; mapping "the human genome" involves sequencing multiple variations of each gene. The project did not study the entire DNA found in human cells; some heterochromatic areas (about 8% of the total) remain un-sequenced.
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