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    DNA Experiments

    DNA Background Information

    Definition

    DNA (Deoxyribonucleic acid) is a nucleic acid that contains the genetic instructions used in the development and functioning of all known living organisms and some viruses.

    Basics

    DNA, short for deoxyribonucleic acid (pronounced dee-OX-ee-RYE-bow-new-CLAY-ik AH-sid)), is the molecule that contains the genetic code of all organisms. This includes animals, plants, and bacteria. It is also used by some viruses, which are not living organisms but use DNA to infect organisms. DNA is found in each cell in the organism and tells that cells what proteins to make. A cell's proteins determine its function. DNA is inherited by children from their parents. This is why children share traits with their parents, such as skin, hair and eye color. The DNA in a person is a combination of some of the DNA from each of his or her parents.

    Structure of DNA: Chemical structure of DNA. The phosphate groups are yellow, the deoxyribonucleic sugars are orange, and the nitrogen bases are green, purple,pink, and blue. The atoms shown are: P=phosphorus O=oxygen N=nitrogen H=hydrogenDNA is shaped like a double helix, which is like a ladder twisted into a spiral. Each "leg" of the "ladder" is a line of nucleotides. A nucleotide is a molecule made up of deoxyribose (a kind of sugar with 5 carbon atoms), a phosphate group (made of phosphorus and oxygen), and a nitrogenous base. DNA is made of four types of nitrogenous base:

    • adenine (A)/(a)
    • thymine (T)/(t)
    • cytosine (C)/(c)
    • guanine (G)/(g)

    The "rungs" of the DNA ladder are each made of two bases, one base coming from each "leg". The bases connect in the middle: 'A' pairs with 'T', and 'C' pairs with 'G'. The bases are held together by hydrogen bonds.

    Adenine (A) and thymine (T) can pair up because they make two hydrogen bonds, and cytosine (C) and guanine (G) pair up to make three hydrogen bonds. Although the bases are always in fixed pairs, the pairs can come in any order. This way, DNA can write "codes" out of the "letters" that are the bases. These "codes" contain the message that tells the cell what to do.

    Copying DNA: When DNA is copied this is called DNA replication. Briefly, the hydrogen bonds holding together paired bases are broken and the molecule is split in half. (The "legs" of the "ladder" are separated.) This gives two single strands. New strands are formed by matching the bases (A with T and G with C) to make the 'missing' strands.

    First, an enzyme called DNA helicase splits the DNA down the middle by breaking the hydrogen bonds. Then after the DNA molecule is in two separate pieces, another molecule called DNA polymerase makes a new strand that matches each of the strands of the split DNA molecule. Each copy of a DNA molecule is made of half of the original (starting) molecule and half of new bases.

    Mutations: When DNA is copied mistakes are sometimes made - these are called mutations. There are three main types of mutations:

    • Deletions where one or more bases are left out.
    • Insertion where one or more extra base is put in.
    • Substitution where one or more bases are substituted for another base in the sequence

    Sometimes mutations are fatal for the cell or the organism - the protein made by the 'new' DNA does not work as it should. On the other hand, evolution is moved forward by mutations, when the new protein works better or is in some other way useful to the organism.

    Protein synthesis: DNA is what tells the cell how to make particular proteins. Proteins do most of the 'work' in cells and in the whole organism. Proteins are made out of smaller molecules called amino acids. To make a protein to do a particular job, the correct amino acids have to be joined up in the correct order. A piece of DNA that contains instructions to make a protein is called a gene.

    Proteins are made by 'machines' in the cell called ribosomes. Ribosomes read codons, "words" made of three base pairs that 'tell' the ribosome which amino acid to add. Ribosomes are found in the main body of the cell, but DNA is only found in the nucleus of the cell. The codon is part of the DNA, but DNA never leaves the nucleus. Because DNA cannot leave the nucleus, the cell makes a copy of the DNA, but in a new single strand form which is smaller and can get through the holes - pores - in the membrane of the nucleus and out into the cell.

    This one-stranded copy of DNA is called mRNA, for messenger RNA. The ribosome scans along an mRNA, reading the code while it makes protein. Another RNA called tRNA helps match the right amino acid to each codon.

    History: DNA was first isolated - extracted from cells - by Swiss physician Friedrich Miescher in 1869, when he was working on bacteria from the pus in surgical bandages. The molecule was found in the nucleus of the cells and so he called it "nuclein".

    In 1919 this discovery was followed by the discovery by Phoebus Levene of the base, sugar and phosphate nucleotide unit. In the 1950's, Erwin Chargaff found that the amount of thymine (T) present in a molecule of DNA was roughly equal to the amount of adenine (A) present. He found that the same applies to guanine (G) and cytosine (C).

    A few years after Chargaff's discovery, a British scientist named Rosalind Franklin studied crystals of DNA and how they diffract beams of X-rays. She found that an "X" pattern was produced, showing that the crystal was probably helix shaped. Francis Crick and James Watson were also working on the structure of DNA and working from Franklin's results and using models of the bases worked out the shape of the molecule. How Watson and Crick got Franklin's results has been much debated. Crick, Watson and Maurice Wilkins were awarded the Nobel Prize in 1962 for their work on DNA - Rosalind Franklin had died in 1958.

    DNA replication is the process of copying a double-stranded DNA molecule. This process is important in all known life forms and the general mechanisms of DNA replication are not the same in prokaryotic and eukaryotic organisms. As each DNA strand holds the same genetic information, both strands can serve as templates for the reproduction of the opposite strand.

    DNA repair means a collection of processes by which a cell identifies and corrects damage to the DNA molecules that encode its genome.

    Genes are formed of DNA. DNA is a collection of chemical information that carries the instructions for making all the proteins a cell will ever need. Each gene contains a single set of instructions. These instructions usually code for a particular protein. Half of a person's genes come from the mother. The other half come from the father.

    Chromosomes are the parts of a cell which carry the genetic information. They are made up of DNA and protein. Each chromosome contains many genes. Chromosomes come in pairs: one from the mother; the other from the father. Cytologists label chromosomes with numbers.

    RNA is an acronym for ribonucleic acid, a nucleic acid. RNA is transcribed from DNA by an enzyme called RNA polymerase and further processed by other enzymes. RNA translates genes into proteins, transferring amino acids from the nucleus to the ribosome to form proteins, and also translating the transcript into proteins. This process is called translation.

    Topics of Interest

    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, or a code, 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 consists of two long polymers of simple units called nucleotides, with backbones made of sugars and phosphate groups joined by ester bonds. These two strands run in opposite directions to each other and are therefore anti-parallel. 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 long structures called chromosomes. These chromosomes are duplicated before cells divide, in a process called DNA replication. Eukaryotic organisms (animals, plants, fungi, and protists) store most of their DNA inside the cell nucleus and some of their DNA in organelles, such as mitochondria or chloroplasts. In contrast, prokaryotes (bacteria and archaea) store their DNA only in the 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.

    DNA is a long polymer made from repeating units called nucleotides. The DNA chain is 22 to 26 Ångströms wide (2.2 to 2.6 nanometres), and one nucleotide unit is 3.3 Å (0.33 nm) long. Although each individual repeating unit is very small, DNA polymers can be very large molecules containing millions of nucleotides. For instance, the largest human chromosome, chromosome number 1, is approximately 220 million base pairs long.

    In molecular biology, two nucleotides on opposite complementary DNA or RNA strands that are connected via hydrogen bonds are called a base pair (often abbreviated bp). In the canonical Watson-Crick base pairing, adenine (A) forms a base pair with thymine (T), as does guanine (G) with cytosine (C) in DNA. In RNA, thymine is replaced by uracil (U). Non-Watson-Crick base pairing with alternate hydrogen bonding patterns also occur, especially in RNA; common such patterns are Hoogsteen base pairs. Pairing is also the mechanism by which codons on messenger RNA molecules are recognized by anticodons on transfer RNA during protein translation. Some DNA- or RNA-binding enzymes can recognize specific base pairing patterns that identify particular regulatory regions of genes.

    , when applied in a molecular biology context, is a general concept used to compare the polarity of nucleic acid molecules, such as DNA or RNA, to other nucleic acid molecules. Depending on the context within molecular biology, sense may have slightly different meanings.

    In a "relaxed" double-helical segment of DNA, the two strands twist around the helical axis once every 10.4-10.5 base pairs of sequence. Adding or subtracting twists, as some enzymes can do, imposes strain. If a DNA segment under twist strain were to be closed into a circle by joining its two ends and then it is allowed to move freely, the circular DNA would contort into new shape, such as a simple figure-eight. Such a contortion is a supercoil.

    The structure of DNA shows a variety of forms, both double-stranded and single-stranded. The mechanical properties of DNA, which are directly related to its structure, are a significant problem for cells. Every process which binds or reads DNA is able to use or modify the mechanical properties of DNA for purposes of recognition, packaging and modification. The extreme length (a chromosome may contain a 10 cm long DNA strand), relative rigidity and helical structure of DNA has led to the evolution of histones and of enzymes such as topoisomerases and helicases to manage a cell's DNA. The properties of DNA are closely related to its molecular structure and sequence, particularly the weakness of the hydrogen bonds and electronic interactions that hold strands of DNA together compared to the strength of the bonds within each strand.

    A branched DNA assay is a test for specific nucleic acid chains, and is typically used to detect retroviruses such as HIV. However, the assay can be used to detect and quantitate other types of RNA or DNA target. In the assay, branched DNA is mixed with a sample to be tested. The detection is done using a non-radioactive method and does not require preamplification of the nucleic acid to be detected. The assay entirely relies on hybridization. Enzymes are used to indicate the extent of hybridization but are not used to manipulate the nucleic acids. Thus, small amounts of a nucleic acid can be detected and quantified without a reverse transcription step (in the case of RNA) and/or PCR. The assay can be run as a "high throughput assay", unlike quantitative Northern-blotting or the RNAse-protection assay, which are labor-intensive and thus difficult to perform on a large number of samples. The other major high throughput technique employed in the quantitation of specific RNA molecules is quantitative PCR, after reverse transcription of the RNA to cDNA.

    DNA nanotechnology is a subfield of nanotechnology which seeks to use the unique molecular recognition properties of DNA and other nucleic acids to create novel, controllable structures out of DNA. The DNA is thus used as a structural material rather than as a carrier of genetic information, making it an example of bionanotechnology. This has possible applications in molecular self-assembly and in DNA computing.

    Mutations are changes in the DNA sequence of a cell's genome and are caused by radiation, viruses, transposons and mutagenic chemicals, as well as errors that occur during meiosis or DNA replication. They can also be induced by the organism itself, by cellular processes such as hypermutation.

    Chromatin is the complex combination of DNA and protein that makes up chromosomes. It is found inside the nuclei of eukaryotic cells. It is divided between heterochromatin (condensed) and euchromatin (extended) forms. The major components of chromatin are DNA (Genetic Formula) and histone proteins, although many other chromosomal proteins have prominent roles too. The functions of chromatin are to package DNA into a smaller volume to fit in the cell, to strengthen the DNA to allow mitosis and meiosis, and to serve as a mechanism to control expression and DNA replication. Chromatin contains genetic material-instructions to direct cell functions. Changes in chromatin structure are affected by chemical modifications of histone proteins such as methylation (DNA and proteins) and acetylation (proteins), and by non-histone, DNA-binding proteins.

    Non-coding DNA describes DNA which does not contain instructions for making proteins. In eukaryotes, a large percentage of many organisms' total genome sizes is noncoding DNA. Some noncoding DNA is involved in regulating the activity of coding regions. However, much of this DNA has no known function and is sometimes referred to as "junk DNA".

    The genetic code is the set of rules by which information encoded in genetic material (DNA or RNA sequences) is translated into proteins (amino acid sequences) by living cells. The code defines a mapping between tri-nucleotide sequences, called codons, and amino acids. A triplet codon in a nucleic acid sequence usually specifies a single amino acid (though in some cases the same codon triplet in different locations can code unambiguously for two different amino acids, the correct choice at each location being determined by context). Because the vast majority of genes are encoded with exactly the same code, this particular code is often referred to as the canonical or standard genetic code, or simply the genetic code, though in fact there are many variant codes. Thus the canonical genetic code is not universal. For example, in humans, protein synthesis in mitochondria relies on a genetic code that varies from the canonical code.

    Transcription, or RNA synthesis, is the process of creating an equivalent RNA copy of a sequence of DNA. Both RNA and DNA are nucleic acids, which use base pairs of nucleotides as a complementary language that can be converted back and forth from DNA to RNA in the presence of the correct enzymes. During transcription, a DNA sequence is read by RNA polymerase, which produces a complementary, antiparallel RNA strand. As opposed to DNA replication, transcription results in an RNA complement that includes uracil (U) in all instances where thymine (T) would have occurred in a DNA complement.

    Protein synthesis is the process in which cells build proteins. The term is sometimes used to refer only to protein translation but more often it refers to a multi-step process, beginning with amino acid synthesis and transcription of nuclear DNA into messenger RNA which is then used as input to translation.

    DNA replication, the basis for biological inheritance, is a fundamental process occurring in all living organisms to copy their DNA. This process is "semiconservative" in that each strand of the original double-stranded DNA molecule serves as template for the reproduction of the complementary strand. Hence, following DNA replication, two identical DNA molecules have been produced from a single double-stranded DNA molecule. Cellular proofreading and error-checking mechanisms ensure near perfect fidelity for DNA replication.

    DNA-binding proteins are proteins that are composed of DNA-binding domains and thus have a specific or general affinity for either single or double stranded DNA. Sequence-specific DNA-binding proteins generally interact with the major groove of B-DNA, because it exposes more functional groups that identify a base pair. However there are some known narrow-groove DNA-binding ligands such as Netropsin, Distamycin, Hoechst 33258, Pentamidine and others

    Genetic recombination is a process by which a molecule of nucleic acid (usually DNA; but can also be RNA) is broken and then joined to a different DNA molecule. Recombination can occur between similar molecules of DNA, as in homologous recombination, or dissimilar molecules of DNA as in non-homologous end joining. Recombination is a common method of DNA repair in both bacteria and eukaryotes. In eukaryotes, recombination occurs in meiosis as a way of facilitating chromosomal crossover. The crossover process leads to offspring having different combinations of genes from their parents, and can occasionally produce new chimeric alleles. In organisms with an adaptive immune system, a type of genetic recombination called V(D)J recombination helps immune cells rapidly diversify and adapt to recognize new pathogens. The shuffling of genes brought about by genetic recombination is thought to have many advantages, as it is a major engine of genetic variation and also allows asexually reproducing organisms to avoid Muller's ratchet.

    The RNA world hypothesis proposes that a world filled with life based on ribonucleic acid (RNA) predates the current world of life based on deoxyribonucleic acid (DNA). RNA, which can both store information like DNA and act as an enzyme, may have supported cellular or pre-cellular life. Some hypotheses as to the origin of life present RNA-based catalysis and information storage as the first step in the evolution of cellular life.

    Genetic engineering, recombinant DNA technology, genetic modification/manipulation (GM) and gene splicing are terms that apply to the direct manipulation of an organism's genes. Genetic engineering is different from traditional breeding, where the organism's genes are manipulated indirectly. Genetic engineering uses the techniques of molecular cloning and transformation to alter the structure and characteristics of genes directly. Genetic engineering techniques have found some successes in numerous applications. Some examples are in improving crop technology, the manufacture of synthetic human insulin through the use of modified bacteria, the manufacture of erythropoietin in hamster ovary cells, and the production of new types of experimental mice such as the oncomouse (cancer mouse) for research.

    DNA profiling (also called DNA testing, DNA typing, or genetic fingerprinting) is a technique employed by forensic scientists to assist in the identification of individuals on the basis of their respective DNA profiles. DNA profiles are encrypted sets of numbers that reflect a person's DNA makeup, which can also be used as the person's identifier. DNA profiling should not be confused with full genome sequencing. It is used in, for example, parental testing and rape investigation.

    Bioinformatics is the application of information technology and computer science to the field of molecular biology. The term bioinformatics was coined by Paulien Hogeweg in 1979 for the study of informatic processes in biotic systems. Its primary use since at least the late 1980s has been in genomics and genetics, particularly in those areas of genomics involving large-scale DNA sequencing. Bioinformatics now entails the creation and advancement of databases, algorithms, computational and statistical techniques, and theory to solve formal and practical problems arising from the management and analysis of biological data. Over the past few decades rapid developments in genomic and other molecular research technologies and developments in information technologies have combined to produce a tremendous amount of information related to molecular biology. It is the name given to these mathematical and computing approaches used to glean understanding of biological processes. Common activities in bioinformatics include mapping and analyzing DNA and protein sequences, aligning different DNA and protein sequences to compare them and creating and viewing 3-D models of protein structures.

    Source: Wikipedia (All text is available under the terms of the GNU Free Documentation License and Creative Commons Attribution-ShareAlike License.)

    Genetic genealogy is the application of genetics to traditional genealogy. Genetic genealogy involves the use of genealogical DNA testing to determine the level of genetic relationship between individuals.

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