Deoxyribonucleic acid is a molecule composed of two chains that coil around each other to form a double helix carrying the genetic instructions used in the growth, development and reproduction of all known organisms and many viruses. DNA and ribonucleic acid are nucleic acids; the two DNA strands are known as polynucleotides as they are composed of simpler monomeric units called nucleotides. Each nucleotide is composed of one of four nitrogen-containing nucleobases, a sugar called deoxyribose, a phosphate group; the nucleotides are joined to one another in a chain by covalent bonds between the sugar of one nucleotide and the phosphate of the next, resulting in an alternating sugar-phosphate backbone. The nitrogenous bases of the two separate polynucleotide strands are bound together, according to base pairing rules, with hydrogen bonds to make double-stranded DNA; the complementary nitrogenous bases are divided into two groups and purines. In DNA, the pyrimidines are cytosine. Both strands of double-stranded DNA store the same biological information.
This information is replicated as and when the two strands separate. A large part of DNA is non-coding, meaning that these sections do not serve as patterns for protein sequences; the two strands of DNA are thus antiparallel. Attached to each sugar is one of four types of nucleobases, it is the sequence of these four nucleobases along the backbone. RNA strands are created using DNA strands as a template in a process called transcription. Under the genetic code, these RNA strands specify the sequence of amino acids within proteins in a process called translation. Within eukaryotic cells, DNA is organized into long structures called chromosomes. Before typical cell division, these chromosomes are duplicated in the process of DNA replication, providing a complete set of chromosomes for each daughter cell. Eukaryotic organisms store most of their DNA inside the cell nucleus as nuclear DNA, some in the mitochondria as mitochondrial DNA, or in chloroplasts as chloroplast DNA. In contrast, prokaryotes store their DNA only in circular chromosomes.
Within eukaryotic chromosomes, chromatin proteins, such as histones and organize DNA. These compacting structures guide the interactions between DNA and other proteins, helping control which parts of the DNA are transcribed. DNA was first isolated by Friedrich Miescher in 1869, its molecular structure was first identified by Francis Crick and James Watson at the Cavendish Laboratory within the University of Cambridge in 1953, whose model-building efforts were guided by X-ray diffraction data acquired by Raymond Gosling, a post-graduate student of Rosalind Franklin. DNA is used by researchers as a molecular tool to explore physical laws and theories, such as the ergodic theorem and the theory of elasticity; the unique material properties of DNA have made it an attractive molecule for material scientists and engineers interested in micro- and nano-fabrication. Among notable advances in this field are DNA origami and DNA-based hybrid materials. DNA is a long polymer made from repeating units called nucleotides.
The structure of DNA is dynamic along its length, being capable of coiling into tight loops and other shapes. In all species it is composed of two helical chains, bound to each other by hydrogen bonds. Both chains are coiled around the same axis, have the same pitch of 34 angstroms; the pair of chains has a radius of 10 angstroms. According to another study, when measured in a different solution, the DNA chain measured 22 to 26 angstroms wide, one nucleotide unit measured 3.3 Å long. Although each individual nucleotide is small, a DNA polymer can be large and contain hundreds of millions, such as in chromosome 1. Chromosome 1 is the largest human chromosome with 220 million base pairs, would be 85 mm long if straightened. DNA does not exist as a single strand, but instead as a pair of strands that are held together; these two long strands coil in the shape of a double helix. The nucleotide contains both a segment of the backbone of a nucleobase. A nucleobase linked to a sugar is called a nucleoside, a base linked to a sugar and to one or more phosphate groups is called a nucleotide.
A biopolymer comprising multiple linked nucleotides is called a polynucleotide. The backbone of the DNA strand is made from alternating sugar residues; the sugar in DNA is 2-deoxyribose, a pentose sugar. The sugars are joined together by phosphate groups that form phosphodiester bonds between the third and fifth carbon atoms of adjacent sugar rings; these are known as the 3′-end, 5′-end carbons, the prime symbol being used to distinguish these carbon atoms from those of the base to which the deoxyribose forms a glycosidic bond. When imagining DNA, each phosphoryl is considered to "belong" to the nucleotide whose 5′ carbon forms a bond therewith. Any DNA strand therefore has one end at which there is a phosphoryl attached to the 5′ carbon of a ribose and another end a
The northern blot, or RNA blot, is a technique used in molecular biology research to study gene expression by detection of RNA in a sample. With northern blotting it is possible to observe cellular control over structure and function by determining the particular gene expression rates during differentiation and morphogenesis, as well as in abnormal or diseased conditions. Northern blotting involves the use of electrophoresis to separate RNA samples by size, detection with a hybridization probe complementary to part of or the entire target sequence; the term'northern blot' refers to the capillary transfer of RNA from the electrophoresis gel to the blotting membrane. However, the entire process is referred to as northern blotting; the northern blot technique was developed in 1977 by James Alwine, David Kemp, George Stark at Stanford University, with contributions from Gerhard Heinrich. Northern blotting takes its name from its similarity to the first blotting technique, the Southern blot, named for biologist Edwin Southern.
The major difference is. A general blotting procedure starts with extraction of total RNA from a homogenized tissue sample or from cells. Eukaryotic mRNA can be isolated through the use of oligo cellulose chromatography to isolate only those RNAs with a poly tail. RNA samples are separated by gel electrophoresis. Since the gels are fragile and the probes are unable to enter the matrix, the RNA samples, now separated by size, are transferred to a nylon membrane through a capillary or vacuum blotting system. A nylon membrane with a positive charge is the most effective for use in northern blotting since the negatively charged nucleic acids have a high affinity for them; the transfer buffer used for the blotting contains formamide because it lowers the annealing temperature of the probe-RNA interaction, thus eliminating the need for high temperatures, which could cause RNA degradation. Once the RNA has been transferred to the membrane, it is immobilized through covalent linkage to the membrane by UV light or heat.
After a probe has been labeled, it is hybridized to the RNA on the membrane. Experimental conditions that can affect the efficiency and specificity of hybridization include ionic strength, duplex length, mismatched base pairs, base composition; the membrane is washed to ensure that the probe has bound and to prevent background signals from arising. The hybrid signals are detected by X-ray film and can be quantified by densitometry. To create controls for comparison in a northern blot, samples not displaying the gene product of interest can be used after determination by microarrays or RT-PCR; the RNA samples are most separated on agarose gels containing formaldehyde as a denaturing agent for the RNA to limit secondary structure. The gels can be stained with ethidium bromide and viewed under UV light to observe the quality and quantity of RNA before blotting. Polyacrylamide gel electrophoresis with urea can be used in RNA separation but it is most used for fragmented RNA or microRNAs. An RNA ladder is run alongside the samples on an electrophoresis gel to observe the size of fragments obtained but in total RNA samples the ribosomal subunits can act as size markers.
Since the large ribosomal subunit is 28S and the small ribosomal subunit is 18S two prominent bands appear on the gel, the larger at close to twice the intensity of the smaller. Probes for northern blotting are composed of nucleic acids with a complementary sequence to all or part of the RNA of interest, they can be DNA, RNA, or oligonucleotides with a minimum of 25 complementary bases to the target sequence. RNA probes that are transcribed in vitro are able to withstand more rigorous washing steps preventing some of the background noise. CDNA is created with labelled primers for the RNA sequence of interest to act as the probe in the northern blot; the probes must be labelled either with radioactive isotopes or with chemiluminescence in which alkaline phosphatase or horseradish peroxidase break down chemiluminescent substrates producing a detectable emission of light. The chemiluminescent labelling can occur in two ways: either the probe is attached to the enzyme, or the probe is labelled with a ligand for which the ligand is attached to the enzyme.
X-ray film can detect both the radioactive and chemiluminescent signals and many researchers prefer the chemiluminescent signals because they are faster, more sensitive, reduce the health hazards that go along with radioactive labels. The same membrane can be probed up to five times without a significant loss of the target RNA. Northern blotting allows one to observe a particular gene's expression pattern between tissues, developmental stages, environmental stress levels, pathogen infection, over the course of treatment; the technique has been used to show overexpression of oncogenes and downregulation of tumor-suppressor genes in cancerous cells when compared to'normal' tissue, as well as the gene expression in the rejection of transplanted organs. If an upregulated gene is observed by an abundance of mRNA on the northern blot the sample can be sequenced to determine if the gene is known to researchers or if it is a novel finding; the expression patterns obtained under given conditions can provide insight into the function of that gene.
Since the RNA is first separated by size, if only one probe type is used variance in the level of each band on the membrane can provide insight into the size of the product, suggesting alternative splice products of the same gene or r
A chemical compound is a chemical substance composed of many identical molecules composed of atoms from more than one element held together by chemical bonds. A chemical element bonded to an identical chemical element is not a chemical compound since only one element, not two different elements, is involved. There are four types of compounds, depending on how the constituent atoms are held together: molecules held together by covalent bonds ionic compounds held together by ionic bonds intermetallic compounds held together by metallic bonds certain complexes held together by coordinate covalent bonds. A chemical formula is a way of expressing information about the proportions of atoms that constitute a particular chemical compound, using the standard abbreviations for the chemical elements, subscripts to indicate the number of atoms involved. For example, water is composed of two hydrogen atoms bonded to one oxygen atom: the chemical formula is H2O. Many chemical compounds have a unique numerical identifier assigned by the Chemical Abstracts Service: its CAS number.
A compound can be converted to a different chemical composition by interaction with a second chemical compound via a chemical reaction. In this process, bonds between atoms are broken in both of the interacting compounds, bonds are reformed so that new associations are made between atoms. Any substance consisting of two or more different types of atoms in a fixed stoichiometric proportion can be termed a chemical compound, it follows from their being composed of fixed proportions of two or more types of atoms that chemical compounds can be converted, via chemical reaction, into compounds or substances each having fewer atoms. The ratio of each element in the compound is expressed in a ratio in its chemical formula. A chemical formula is a way of expressing information about the proportions of atoms that constitute a particular chemical compound, using the standard abbreviations for the chemical elements, subscripts to indicate the number of atoms involved. For example, water is composed of two hydrogen atoms bonded to one oxygen atom: the chemical formula is H2O.
In the case of non-stoichiometric compounds, the proportions may be reproducible with regard to their preparation, give fixed proportions of their component elements, but proportions that are not integral. Chemical compounds have a unique and defined chemical structure held together in a defined spatial arrangement by chemical bonds. Chemical compounds can be molecular compounds held together by covalent bonds, salts held together by ionic bonds, intermetallic compounds held together by metallic bonds, or the subset of chemical complexes that are held together by coordinate covalent bonds. Pure chemical elements are not considered chemical compounds, failing the two or more atom requirement, though they consist of molecules composed of multiple atoms. Many chemical compounds have a unique numerical identifier assigned by the Chemical Abstracts Service: its CAS number. There is varying and sometimes inconsistent nomenclature differentiating substances, which include non-stoichiometric examples, from chemical compounds, which require the fixed ratios.
Many solid chemical substances—for example many silicate minerals—are chemical substances, but do not have simple formulae reflecting chemically bonding of elements to one another in fixed ratios. It may be argued that they are related to, rather than being chemical compounds, insofar as the variability in their compositions is due to either the presence of foreign elements trapped within the crystal structure of an otherwise known true chemical compound, or due to perturbations in structure relative to the known compound that arise because of an excess of deficit of the constituent elements at places in its structure. Other compounds regarded as chemically identical may have varying amounts of heavy or light isotopes of the constituent elements, which changes the ratio of elements by mass slightly. Compounds are held together through a variety of different types of bonding and forces; the differences in the types of bonds in compounds differ based on the types of elements present in the compound.
London dispersion forces are the weakest force of all intermolecular forces. They are temporary attractive forces that form when the electrons in two adjacent atoms are positioned so that they create a temporary dipole. Additionally, London dispersion forces are responsible for condensing non polar substances to liquids, to further freeze to a solid state dependent on how low the temperature of the environment is. A covalent bond known as a molecular bond, involves the sharing of electrons between two atoms; this type of bond occurs between elements that fall close to each other on the periodic table of elements, yet it is observed between some metals and nonmetals. This is due to the mechanism of this type of bond. Elements that fall close to each other on the periodic table tend to have similar electronegativities, which means they have a similar affinity for electrons. Since neither element has a stronger affinity to donate or gain electrons, it causes the elements to share electrons so both elements have a more stable octet.
Ionic bonding occurs when valence electrons are transferred between elements. Opposite to covalent bonding, this chemical bond creates two oppositely charged ions; the metals in ionic bonding
Lysis refers to the breaking down of the membrane of a cell by viral, enzymic, or osmotic mechanisms that compromise its integrity. A fluid containing the contents of lysed cells is called a lysate. In molecular biology and cell biology laboratories, cell cultures may be subjected to lysis in the process of purifying their components, as in protein purification, DNA extraction, RNA extraction, or in purifying organelles. Many species of bacteria are subject to lysis by the enzyme lysozyme, found in animal saliva, egg white, other secretions. Phage lytic enzymes produced during bacteriophage infection are responsible for the ability of these viruses to lyse bacterial cells. Penicillin and related β-lactam antibiotics cause the death of bacteria through enzyme-mediated lysis that occurs after the drug causes the bacterium to form a defective cell wall. If the cell wall is lost, the bacterium is referred as a protoplast, if penicillin was used on gram-positive bacteria, spheroplast, if penicillin was used on gram-negative bacteria.
Cytolysis occurs when a cell bursts due to an osmotic imbalance that has caused excess water to move into the cell. Cytolysis can be prevented by several different mechanisms, including the contractile vacuole that exists in some paramecia, which pump water out of the cell. Cytolysis does not occur under normal conditions in plant cells because plant cells have a strong cell wall that contains the osmotic pressure, or turgor pressure, that would otherwise cause cytolysis to occur. Oncolysis refers of a tumour, it is used to refer to the reduction of any swelling. Plasmolysis is the contraction of cells within plants due to the loss of water through osmosis. In a hypertonic environment, the cell membrane peels off of the cell wall and the vacuole collapses; these cells will wilt and die unless the flow of water caused by osmosis can stop the contraction of the cell membrane. Erythrocytes' hemoglobin release free radicals in response to pathogens; this can damage the pathogens. Cell lysis is used in laboratories to purify or further study their contents.
Lysis in the laboratory may be affected by other chaotropic agents. Mechanical disruption of cell membranes, as by repeated freezing and thawing, pressure, or filtration may be referred to as lysis. Many laboratory experiments are sensitive to the choice of lysis mechanism; the unprocessed solution after lysis but before any further extraction steps is referred to as a crude lysate. For example, lysis is used in western and Southern blotting to analyze the composition of specific proteins and nucleic acids individually or as complexes. Depending on the detergent used, either all or some membranes are lysed. For example, if only the cell membrane is lysed gradient centrifugation can be used to collect certain organelles. Lysis is used for protein purification, DNA extraction, RNA extraction. Cell disruption Cell unroofing Crenation Hemolysis Lysogenic Pitted keratolysis
Safety data sheet
A safety data sheet, material safety data sheet, or product safety data sheet is a document that lists information relating to occupational safety and health for the use of various substances and products. SDSs are a used system for cataloging information on chemicals, chemical compounds, chemical mixtures. SDS information may include instructions for the safe use and potential hazards associated with a particular material or product, along with spill-handling procedures. SDS formats can vary from source to source within a country depending on national requirements. A SDS for a substance is not intended for use by the general consumer, focusing instead on the hazards of working with the material in an occupational setting. There is a duty to properly label substances on the basis of physico-chemical, health or environmental risk. Labels can include hazard symbols such as the European Union standard symbols; the same product can have different formulations in different countries. The formulation and hazard of a product using a generic name may vary between manufacturers in the same country.
The Globally Harmonized System of Classification and Labelling of Chemicals contains a standard specification for safety data sheets. The SDS follows a 16 section format, internationally agreed and for substances the SDS should be followed with an Annex which contains the exposure scenarios of this particular substance; the 16 sections are: SECTION 1: Identification of the substance/mixture and of the company/undertaking 1.1. Product identifier 1.2. Relevant identified uses of the substance or mixture and uses advised against 1.3. Details of the supplier of the safety data sheet 1.4. Emergency telephone number SECTION 2: Hazards identification 2.1. Classification of the substance or mixture 2.2. Label elements 2.3. Other hazards SECTION 3: Composition/information on ingredients 3.1. Substances 3.2. Mixtures SECTION 4: First aid measures 4.1. Description of first aid measures 4.2. Most important symptoms and effects, both acute and delayed 4.3. Indication of any immediate medical attention and special treatment needed SECTION 5: Firefighting measures 5.1.
Extinguishing media 5.2. Special hazards arising from the substance or mixture 5.3. Advice for firefighters SECTION 6: Accidental release measure 6.1. Personal precautions, protective equipment and emergency procedures 6.2. Environmental precautions 6.3. Methods and material for containment and cleaning up 6.4. Reference to other sections SECTION 7: Handling and storage 7.1. Precautions for safe handling 7.2. Conditions for safe storage, including any incompatibilities 7.3. Specific end use SECTION 8: Exposure controls/personal protection 8.1. Control parameters 8.2. Exposure controls SECTION 9: Physical and chemical properties 9.1. Information on basic physical and chemical properties 9.2. Other information SECTION 10: Stability and reactivity 10.1. Reactivity 10.2. Chemical stability 10.3. Possibility of hazardous reactions 10.4. Conditions to avoid 10.5. Incompatible materials 10.6. Hazardous decomposition products SECTION 11: Toxicological information 11.1. Information on toxicological effects SECTION 12: Ecological information 12.1.
Toxicity 12.2. Persistence and degradability 12.3. Bioaccumulative potential 12.4. Mobility in soil 12.5. Results of PBT and vPvB assessment 12.6. Other adverse effects SECTION 13: Disposal considerations 13.1. Waste treatment methods SECTION 14: Transport information 14.1. UN number 14.2. UN proper shipping name 14.3. Transport hazard class 14.4. Packing group 14.5. Environmental hazards 14.6. Special precautions for user 14.7. Transport in bulk according to Annex II of MARPOL73/78 and the IBC Code SECTION 15: Regulatory information 15.1. Safety and environmental regulations/legislation specific for the substance or mixture 15.2. Chemical safety assessment SECTION 16: Other information 16.2. Date of the latest revision of the SDS In Canada, the program known as the Workplace Hazardous Materials Information System establishes the requirements for SDSs in workplaces and is administered federally by Health Canada under the Hazardous Products Act, Part II, the Controlled Products Regulations. Safety data sheets have been made an integral part of the system of Regulation No 1907/2006.
The original requirements of REACH for SDSs have been further adapted to take into account the rules for safety data sheets of the Global Harmonised System and the implementation of other elements of the GHS into EU legislation that were introduced by Regulation No 1272/2008 via an update to Annex II of REACH. The SDS must be supplied in an official language of the Member State where the substance or mixture is placed on the market, unless the Member State concerned provide otherwise; the European Chemicals Agency has published a guidance document on the compilation of safety data sheets. The German Federal Water Management Act requires that substances be evaluated for negative influence on the physical, chemical or biological characteristics of water; these are classified into numeric water hazard classes. WGK nwg: Non-water polluting substance WGK 1: Slightly water polluting substance WGK 2: Water polluting substance WGK 3: Highly water polluting substance This section contributes to a better understanding of the regulations governing SDS within the South African framework.
As regulations may change, it is the responsibility of the reader to verify the validity of the regulations mentioned in text. As globalisation increased and countries engaged in cross-border trade, the quantity of hazardous material crossing international borders a
Ribonucleic acid is a polymeric molecule essential in various biological roles in coding, decoding and expression of genes. RNA and DNA are nucleic acids, along with lipids and carbohydrates, constitute the four major macromolecules essential for all known forms of life. Like DNA, RNA is assembled as a chain of nucleotides, but unlike DNA it is more found in nature as a single-strand folded onto itself, rather than a paired double-strand. Cellular organisms use messenger RNA to convey genetic information that directs synthesis of specific proteins. Many viruses encode their genetic information using an RNA genome; some RNA molecules play an active role within cells by catalyzing biological reactions, controlling gene expression, or sensing and communicating responses to cellular signals. One of these active processes is protein synthesis, a universal function in which RNA molecules direct the assembly of proteins on ribosomes; this process uses transfer RNA molecules to deliver amino acids to the ribosome, where ribosomal RNA links amino acids together to form proteins.
Like DNA, most biologically active RNAs, including mRNA, tRNA, rRNA, snRNAs, other non-coding RNAs, contain self-complementary sequences that allow parts of the RNA to fold and pair with itself to form double helices. Analysis of these RNAs has revealed that they are structured. Unlike DNA, their structures do not consist of long double helices, but rather collections of short helices packed together into structures akin to proteins. In this fashion, RNAs can achieve chemical catalysis. For instance, determination of the structure of the ribosome—an RNA-protein complex that catalyzes peptide bond formation—revealed that its active site is composed of RNA; each nucleotide in RNA contains a ribose sugar, with carbons numbered 1' through 5'. A base is attached to the 1' position, in general, cytosine, guanine, or uracil. Adenine and guanine are purines and uracil are pyrimidines. A phosphate group is attached to the 5' position of the next; the phosphate groups have a negative charge each. The bases form hydrogen bonds between cytosine and guanine, between adenine and uracil and between guanine and uracil.
However, other interactions are possible, such as a group of adenine bases binding to each other in a bulge, or the GNRA tetraloop that has a guanine–adenine base-pair. An important structural component of RNA that distinguishes it from DNA is the presence of a hydroxyl group at the 2' position of the ribose sugar; the presence of this functional group causes the helix to take the A-form geometry, although in single strand dinucleotide contexts, RNA can also adopt the B-form most observed in DNA. The A-form geometry results in a deep and narrow major groove and a shallow and wide minor groove. A second consequence of the presence of the 2'-hydroxyl group is that in conformationally flexible regions of an RNA molecule, it can chemically attack the adjacent phosphodiester bond to cleave the backbone. RNA is transcribed with only four bases, but these bases and attached sugars can be modified in numerous ways as the RNAs mature. Pseudouridine, in which the linkage between uracil and ribose is changed from a C–N bond to a C–C bond, ribothymidine are found in various places.
Another notable modified base is hypoxanthine, a deaminated adenine base whose nucleoside is called inosine. Inosine plays a key role in the wobble hypothesis of the genetic code. There are more than 100 other occurring modified nucleosides; the greatest structural diversity of modifications can be found in tRNA, while pseudouridine and nucleosides with 2'-O-methylribose present in rRNA are the most common. The specific roles of many of these modifications in RNA are not understood. However, it is notable that, in ribosomal RNA, many of the post-transcriptional modifications occur in functional regions, such as the peptidyl transferase center and the subunit interface, implying that they are important for normal function; the functional form of single-stranded RNA molecules, just like proteins requires a specific tertiary structure. The scaffold for this structure is provided by secondary structural elements that are hydrogen bonds within the molecule; this leads to several recognizable "domains" of secondary structure like hairpin loops and internal loops.
Since RNA is charged, metal ions such as Mg2+ are needed to stabilise many secondary and tertiary structures. The occurring enantiomer of RNA is D-RNA composed of D-ribonucleotides. All chirality centers are located in the D-ribose. By the use of L-ribose or rather L-ribonucleotides, L-RNA can be synthesized. L-RNA is much more stable against degradation by RNase. Like other structured biopolymers such as proteins, one can define topology of a folded RNA molecule; this is done based on arrangement of intra-chain contacts within a folded RNA, termed as circuit topology. Synthesis of RNA is catalyzed by an enzyme—RNA polymerase—using DNA as a template, a process known as transcription. Initiation of transcription begins with the binding of the enzyme to a promoter sequence in the DNA; the DNA double helix is unwound by the helicase activity of the enzyme. The enzyme progresses along the template strand in the 3’ to 5’ direction, synthesizing a complementary RNA molecule with elongation occ