Wednesday, 18 December 2013

Systematic

File:Biological classification L Pengo.svg

Branches of biology

  • Aerobiology – the study of airborne organic particles
  • Agriculture – the study of producing crops from the land, with an emphasis on practical applications
  • Anatomy – the study of form and function, in plants, animals, and other organisms, or specifically in humans
  • Arachnology – the study of arachnids
  • Astrobiology – the study of evolution, distribution, and future of life in the universe—also known as exobiologyexopaleontology, and bioastronomy
  • Biochemistry – the study of the chemical reactions required for life to exist and function, usually a focus on the cellular level
  • Bioengineering – the study of biology through the means of engineering with an emphasis on applied knowledge and especially related to biotechnology
  • Biogeography – the study of the distribution of species spatially and temporally

Gene

gene is the molecular unit of heredity of a living organism. It is widely accepted by the scientific community as a name given to some stretches of deoxyribonucleic acids (DNA) and ribonucleic acids (RNA) that code for a polypeptide or for an RNA chain that has a function in the organism, though there still are controversies about what plays the role of the genetic material.[1] Living beings depend on genes, as they specify all proteins and functional RNA chains. Genes hold the information to build and maintain an organism's cells and pass genetic traits to offspring. All organisms have many genes corresponding to various biological traits, some of which are immediately visible, such as eye coloror number of limbs, and some of which are not, such as blood type, increased risk for specific diseases, or the thousands of basicbiochemical processes that

Genetic code

The genetic code is the set of rules by which information encoded within genetic material (DNA or mRNA sequences) is translated into proteins by living cells. Biological decoding is accomplished by the ribosome, which links amino acids in an order specified by mRNA, using transfer RNA (tRNA) molecules to carry amino acids and to read the mRNA three nucleotides at a time. The genetic code is highly similar among all organisms and can be expressed in a simple table with 64 entries.

Heredity

Heredity is the passing of traits to offspring from its parents or ancestor. This is the process by which an offspring cell or organism acquires or becomes predisposed to the characteristics of its parent cell or organism. Through heredity, variations exhibited by individuals can accumulate and cause somespecies to evolve. The study of heredity in biology is called genetics, which includes the field of epigenetics.

Biology

Biology is a natural science concerned with the study of life and living organisms, including their structure, function, growth, evolution, distribution, and taxonomy.[1] Modern biology is a vast and eclectic field, composed of many branches and subdisciplines. However, despite the broad scope of biology, there are certain general and unifying concepts within it which govern all study and research, consolidating it into single, coherent field. Biology generally recognizes the cell as the basic unit of life, genes as the basic unit ofheredity, and evolution as the engine that propels the synthesis and creation of new species. It is also understood today that all organisms survive by consuming and transforming energy and by regulating their internal environment to maintain a stable and vital condition.
Subdisciplines of biology are defined by the scale at which organisms are studied, the kinds of organisms studied, and the methods used to study them: biochemistry examines the rudimentary chemistry of life; molecular biology studies the complex interactions among biological moleculesbotany studies the biology of plants; cellular biology examines the basic building block of all life, the cellphysiologyexamines the physical and chemical functions of tissuesorgans, and organ systems of an organism; evolutionary biology examines theprocesses that produced the diversity of life; and ecology examines how organisms interact in their environment.

Genetics

Genetics (from Ancient Greek γενετικός genetikos, "genitive" and that from γένεσις genesis, "origin"),[1][2][3] a discipline of biology, is the science of genes,heredity, and variation in living organisms.[4][5]
Genetics is the process of trait inheritance from parents to offspring, including the molecular structure and function of genes, gene behavior in the context of acell or organism (e.g. dominance and epigenetics), gene distribution, and variation and change in populations (such as through Genome-Wide Association Studies). Given that genes are universal to living organisms, genetics can be applied to the study of all living systems; including bacteriaplantsanimals, andhumans. The observation that living things inherit traits from their parents has been used since prehistoric times to improve crop plants and animals throughselective breeding.[6] The modern science of genetics, seeking to understand this process, began with the work of Gregor Mendel in the mid-19th century.[7]
Mendel observed that organisms inherit traits by way of discrete 'units of inheritance.' This term, still used today, is a somewhat ambiguous definition of agene. A more modern working definition of a gene is a portion (or sequence) of DNA that codes for a known cellular function. This portion of DNA is variable, it may be small or large, have a few subregions or many subregions. The word 'Gene' refers to portions of DNA that are required for a single cellular process or single function, more than the word refers to a single tangible item. A quick idiom that is often used (but not always true) is 'one gene, one protein' meaning a singular gene codes for a singular protein type in a cell. Another analogy is that a 'gene' is like a 'sentence' and 'nucleotides' are like 'letters'. A series of nucleotides can be put together without forming a gene (non-coding regions of DNA), like a string of letters can be put together without forming a sentence (babble). Nonetheless, all sentences must have letters, like all genes must have a nucleotides.
The sequence of nucleotides in a gene is read and translated by a cell to produce a chain of amino acids which in turn spontaneously fold into proteins. The order of amino acids in a protein corresponds to the order of nucleotides in the gene. This relationship between nucleotide sequence and amino acid sequence is known as the genetic code. The amino acids in a protein determine how it folds into its unique three-dimensional shape; a structure that is ultimately responsible for the proteins function. Proteins carry out many of the functions needed for cells to live. A change to the DNA in a gene can change a protein's amino acid sequence, thereby changing its shape and function, rendering the protein ineffective or even malignant (see: sickle cell anemia). When a gene change occurs, it is referred to as a mutation.
Although genetics plays a large role in the appearance and behavior of organisms, it is a combination of genetics with the organisms' experiences (aka. environment) that determines the ultimate outcome. Genes may be activated or inactivated, which is determined by a cell's or organism's environment, intracellularly and/or extracellularly. For example, while genes play a role in determining an organism's size, the nutrition and health it experiences after inception also have a large effect.

Fatty acid

In chemistry, and especially in biochemistry, a fatty acid is a carboxylic acid with a long aliphatic tail (chain), which is either saturated or unsaturated. Most naturally occurring fatty acids have a chain of an even number of carbon atoms, from 4 to 28.[1] Fatty acids are usually derived from triglycerides or phospholipids. When they are not attached to other molecules, they are known as "free" fatty acids. Fatty acids are important sources of fuel because, when metabolized, they yield large quantities of ATP. Many cell types can use either glucose or fatty acids for this purpose. In particular, heart and skeletal muscle prefer fatty acids. Despite long-standing assertions to the contrary, the brain can use fatty acids as a source of fuel[2][3] in addition to glucose and ketone bodies.

Glycerol

Glycerol (or glycerineglycerin) is a simple polyol (sugar alcohol) compound. It is a colorless, odorless, viscous liquid that is widely used inpharmaceutical formulations. Glycerol has three hydroxyl groups that are responsible for its solubility in water and its hygroscopic nature. The glycerol backbone is central to all lipids known as triglycerides. Glycerol is sweet-tasting and of low toxicity.

Lipids

Lipids are a group of naturally occurring molecules that include fatswaxessterols, fat-soluble vitamins (such as vitamins A, D, E, and K), monoglyceridesdiglyceridestriglyceridesphospholipids, and others. The main biological functions of lipids include storing energy, signaling, and acting as structural components of cell membranes.[4][5] Lipids have applications in the cosmetic and food industries as well as in nanotechnology.[6]
Lipids may be broadly defined as hydrophobic or amphiphilic small molecules; the amphiphilic nature of some lipids allows them to form structures such as vesiclesliposomes, or membranes in an aqueous environment. Biological lipids originate entirely or in part from two distinct types of biochemical subunits or "building-blocks":ketoacyl and isoprene groups.[4] Using this approach, lipids may be divided into eight categories: fatty acids,glycerolipidsglycerophospholipidssphingolipidssaccharolipids, and polyketides (derived from condensation of ketoacyl subunits); and sterol lipids and prenol lipids (derived from condensation of isoprene subunits).[4]
Although the term lipid is sometimes used as a synonym for fats, fats are a subgroup of lipids calledtriglycerides. Lipids also encompass molecules such as fatty acids and their derivatives (including tri-di-,monoglycerides, and phospholipids), as well as other sterol-containing metabolites such as cholesterol.[7]Although humans and other mammals use various biosynthetic pathways to both break down and synthesize lipids, some essential lipids cannot be made this way and must be obtained from the diet.

Nuclear magnetic resonance spectroscopy of proteins(NMR)

Nuclear magnetic resonance spectroscopy of proteins (usually abbreviated protein NMR) is a field of structural biology in which NMR spectroscopy is used to obtain information about the structure and dynamics of proteins, and also nucleic acids, and their complexes. The field was pioneered by Richard R. Ernst and Kurt Wüthrich,[1] among others. Structure determination by NMR spectroscopy usually consists of several phases, each using a separate set of highly specialized techniques. The sample is prepared, measurements are made, interpretive approaches are applied, and a structure is calculated and validated.
NMR involves the quantum mechanical properties of the central core ("nucleus") of the atom. These properties depend on the local molecular environment, and their measurement provides a map of how the atoms are linked chemically, how close they are in space, and how rapidly they move with respect to each other. These properties are fundamentally the same as those used in the more familiar Magnetic Resonance Imaging (MRI), but the molecular applications use a somewhat different approach, appropriate to the change of scale from millimeters (of interest to radiologists) to nano-meters (bonded atoms are typically a fraction of a nano-meter apart), a factor of a million. This change of scale requires much higher sensitivity of detection and stability for long term measurement. In contrast to MRI, structural biology studies do not directly generate an image, but rely on complex computer calculations to generate three dimensional molecular models.
Currently most samples are examined in a solution in water, but methods are being developed to also work with solid samples. Data collection relies on placing the sample inside a powerful magnet, sending radio frequency signals through the sample, and measuring the absorption of those signals. Depending on the environment of atoms within the protein, the nuclei of individual atoms will absorb different frequencies of radio signals. Furthermore the absorption signals of different nuclei may be perturbed by adjacent nuclei. This information can be used to determine the distance between nuclei. These distances in turn can be used to determine the overall structure of the protein.
A typical study might involve how two proteins interact with each other, possibly with a view to developing small molecules which can be used to probe the normal biology of the interaction ("chemical biology") or to provide possible leads for pharmaceutical use ("drug development"). Frequently, the interacting pair of proteins may have been identified by studies of human genetics, indicating the interaction can be disrupted by unfavorable mutations, or they may play a key role in the normal biology of a "model" organism like the fruit fly, yeast, the worm C. elegans, or mice. To prepare a sample, methods of molecular biology are typically used to make quantities by bacterial fermentation. This also permits changing the isotopic composition of the molecule, which is desirable because the isotopes behave differently and provide methods for identifying overlapping NMR signals.

Chromatography

Chromatography [|krəʊmə|tɒgrəfi] (from Greek χρῶμα chroma "color" and γράφειν graphein "to write"[1]) is the collective term for a set of laboratory techniques for the separation of mixtures. The mixture is dissolved in a fluid called the mobile phase, which carries it through a structure holding another material called the stationary phase. The various constituents of the mixture travel at different speeds, causing them to separate. The separation is based on differential partitioning between the mobile and stationary phases. Subtle differences in a compound's partition coefficient result in differential retention on the stationary phase and thus changing the separation.
Chromatography may be preparative or analytical. The purpose of preparative chromatography is to separate the components of a mixture for more advanced use (and is thus a form of purification). Analytical chromatography is done normally with smaller amounts of material and is for measuring the relative proportions of analytes in a mixture. The two are not mutually exclusive.

Glycolysis

Glycolysis (from glycose, an older term[1] for glucose + -lysis degradation) is themetabolic pathway that converts glucose C6H12O6, into pyruvate, CH3COCOO + H+. The free energy released in this process is used to form the high-energy compounds ATP (adenosine triphosphate) and NADH (reduced nicotinamide adenine dinucleotide).[2][3]
Glycolysis does not require or consume oxygen. The terms "aerobic glycolysis" and "anaerobic glycolysis" refer to glycolysis in the presence or absence of oxygen, respectively.
Glycolysis is a determined sequence of ten enzyme-catalyzed reactions. The intermediates provide entry points to glycolysis. For example, most monosaccharides, such as fructose and galactose, can be converted to one of these intermediates. The intermediates may also be directly useful. For example, the intermediate dihydroxyacetone phosphate (DHAP) is a source of the glycerol that combines with fatty acids to form fat.
Glycolysis occurs, with variations, in nearly all organisms, both aerobic andanaerobic. The wide occurrence of glycolysis indicates that it is one of the most ancient known metabolic pathways.[4] It occurs in the cytosol of the cell.
The most common type of glycolysis is the Embden–Meyerhof–Parnas (EMP pathway), which was first discovered by Gustav EmbdenOtto Meyerhof, and Jakub Karol Parnas. Glycolysis also refers to other pathways, such as the Entner–Doudoroff pathway and various heterofermentative and homofermentative pathways. However, the discussion here will be limited to the Embden–Meyerhof–Parnas pathway.[5]
The entire glycolysis pathway can be separated into two phases:[2]
  1. The Preparatory Phase – in which ATP is consumed and is hence also known as the investment phase
  2. The Pay Off Phase – in which ATP is produced.

Metabolic pathways

In biochemistrymetabolic pathways are series of chemical reactions occurring within a cell. In each pathway, a principal chemical is modified by a series of chemical reactionsEnzymescatalyze these reactions, and often require dietary minerals, vitamins, and other cofactors in order to function properly. Because of the many chemicals (a.k.a. "metabolites") that may be involved, metabolic pathways can be quite elaborate. In addition, numerous distinct pathways co-exist within a cell. This collection of pathways is called the metabolic network. Pathways are important to the maintenance of homeostasis within an organismCatabolic (break-down) and Anabolic (synthesis) pathways often work interdependently to create new biomolecules as the final end-products.
metabolic pathway involves the step-by-step modification of an initial molecule to form another product. The resulting product can be used in one of three ways:
  • To be used immediately,
  • To initiate another metabolic pathway, called a flux generating step
  • To be stored by the cell
A molecule called a substrate enters a metabolic pathway depending on the needs of the cell and the availability of the substrate. An increase in concentration of anabolic and catabolicintermediates and/or end-products may influence the metabolic rate for that particular pathway.

Amylase

Amylase /ˈæmɪlz/ is an enzyme that catalyses the hydrolysis of starch into sugars. Amylase is present in the saliva of humans and some other mammals, where it begins the chemical process of digestion. Foods that contain much starch but little sugar, such as rice and potato, taste slightly sweet as they are chewed because amylase turns some of their starch into sugar in the mouth. The pancreas and salivary gland makes amylase (alpha amylase) to hydrolyse dietary starch into disaccharides and trisaccharides which are converted by other enzymes to glucoseto supply the body with energy. Plants and some bacteria also produce amylase. As diastase, amylase was the first enzyme to be discovered and isolated (by Anselme Payen in 1833).[1]Specific amylase proteins are designated by different Greek letters. All amylases are glycoside hydrolases and act on α-1,4-glycosidic bonds.

Enzyme

Enzymes /ˈɛnzmz/ are large biological molecules responsible for the thousands of metabolic processes that sustain life.[1][2] They are highly selective catalysts, greatly accelerating both the rate and specificity of metabolic reactions, from the digestion of food to the synthesis of DNA. Most enzymes are proteins, although some catalytic RNA molecules have been identified. Enzymes adopt a specificthree-dimensional structure, and may employ organic (e.g. biotin) and inorganic (e.g. magnesium ioncofactors to assist in catalysis.
In enzymatic reactions, the molecules at the beginning of the process, called substrates, are converted into different molecules, calledproducts. Almost all chemical reactions in a biological cell need enzymes in order to occur at rates sufficient for life. Since enzymes are selective for their substrates and speed up only a few reactions from among many possibilities, the set of enzymes made in a cell determines which metabolic pathways occur in that cell.
Like all catalysts, enzymes work by lowering the activation energy (Ea) for a reaction, thus dramatically increasing the rate of the reaction. As a result, products are formed faster and reactions reach their equilibrium state more rapidly. Most enzyme reaction rates are millions of times faster than those of comparable un-catalyzed reactions. As with all catalysts, enzymes are not consumed by the reactions they catalyze, nor do they alter the equilibrium of these reactions. However, enzymes do differ from most other catalysts in that they are highly specific for their substrates. Enzymes are known to catalyze about 4,000 biochemical reactions.[3] A few RNA molecules called ribozymes also catalyze reactions, with an important example being some parts of the ribosome.[4][5] Synthetic molecules calledartificial enzymes also display enzyme-like catalysis.[6]
Enzyme activity can be affected by other molecules. Inhibitors are molecules that decrease enzyme activity; activators are molecules that increase activity. Many drugs and poisons are enzyme inhibitors. Activity is also affected by temperaturepressure, chemical environment (e.g., pH), and the concentration of substrate. Some enzymes are used commercially, for example, in the synthesis of antibiotics. In addition, some household products use enzymes to speed up biochemical reactions (e.g., enzymes in biological washing powders break down protein or fat stains on clothes; enzymes in meat tenderizers break down proteins into smaller molecules, making the meat easier to chew).

Urea

Urea or carbamide is an organic compound with the chemical formula CO(NH2)2. The molecule has two —NH2 groups joined by a carbonyl (C=O)functional group.
Urea serves an important role in the metabolism of nitrogen-containing compounds by animals and is the main nitrogen-containing substance in theurine of mammals. It is a colorless, odorless solid, highly soluble in water and practically non-toxic (LD50 is 15 g/kg for rat). Dissolved in water, it is neither acidic nor alkaline. The body uses it in many processes, the most notable one being nitrogen excretion. Urea is widely used in fertilizers as a convenient source of nitrogen. Urea is also an important raw material for the chemical industry.
The discovery by Friedrich Wöhler in 1828 that urea can be produced from inorganic starting materials was an important conceptual milestone in chemistry, as it showed for the first time that a substance previously known only as a byproduct of life could be synthesized in the laboratory without any biological starting materials, contradicting the widely held doctrine of vitalism.

Macromolecule

macromolecule is a very large molecule commonly created by polymerization of smaller subunits. In biochemistry, the term is applied to the four conventional biopolymers (nucleic acidsproteins, and carbohydrates),[2] as well as non-polymeric molecules with large molecular mass such as lipids and macrocycles. The individual constituent molecules of macromolecules are called monomers(mono=single, meros=part).

Nucleic acid

Nucleic acids are polymeric macromolecules, or large biological molecules, essential for all known forms of life. Nucleic acids, which include DNA (deoxyribonucleic acid) and RNA (ribonucleic acid), are made from monomers known as nucleotides. Each nucleotide has three components: a 5-carbon sugar, a phosphate group, and a nitrogenous base. If the sugar is deoxyribose, the polymer is DNA. If the sugar is ribose, the polymer is RNA.
Together with proteins, nucleic acids are the most important biological macromolecules; each is found in abundance in all living things, where they function in encoding, transmitting and expressing genetic information—in other words, information is conveyed through thenucleic acid sequence, or the order of nucleotides within a DNA or RNA molecule. Strings of nucleotides strung together in a specific sequence are the mechanism for storing and transmitting hereditary, or genetic, information via protein synthesis.
Nucleic acids were discovered by Friedrich Miescher in 1869.[3] Experimental studies of nucleic acids constitute a major part of modernbiological and medical research, and form a foundation for genome and forensic science, as well as the biotechnology and pharmaceutical industries.

Proteins

Proteins (/ˈprˌtnz/ or /ˈprti.ɨnz/) are large biological molecules, or macromolecules, consisting of one or more chains of amino acid residues. Proteins perform a vast array of functions within living organisms, including catalyzing metabolic reactionsreplicating DNAresponding to stimuli, and transporting molecules from one location to another. Proteins differ from one another primarily in their sequence of amino acids, which is dictated by thenucleotide sequence of their genes, and which usually results in folding of the protein into a specific three-dimensional structure that determines its activity.
A polypeptide is a single linear polymer chain derived from the condensation of amino acids. The individual amino acid residues are bonded together bypeptide bonds and adjacent amino acid residues. The sequence of amino acid residues in a protein is defined by the sequence of a gene, which is encoded in the genetic code. In general, the genetic code specifies 20 standard amino acids; however, in certain organisms the genetic code can include selenocysteine and—in certain archaeapyrrolysine. Shortly after or even during synthesis, the residues in a protein are often chemically modified by posttranslational modification, which alters the physical and chemical properties, folding, stability, activity, and ultimately, the function of the proteins. Sometimes proteins have non-peptide groups attached, which can be called prosthetic groups or cofactors. Proteins can also work together to achieve a particular function, and they often associate to form stable protein complexes.
Like other biological macromolecules such as polysaccharides and nucleic acids, proteins are essential parts of organisms and participate in virtually 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 signalingimmune responsescell 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 ofdigestion, animals break down ingested protein into free amino acids that are then used in metabolism.
Proteins may be purified from other cellular components using a variety of techniques such as ultracentrifugationprecipitationelectrophoresis, andchromatography; the advent of genetic engineering has made possible a number of methods to facilitate purification. Methods commonly used to study protein structure and function include immunohistochemistrysite-directed mutagenesisnuclear magnetic resonance and mass spectrometry.

Amino acid

Amino acids (/əˈmn//əˈmn/, or /ˈæmɪn/) are biologically important organic compounds composed of amine (-NH2) and carboxylic acid (-COOH)functional groups, along with a side-chain specific to each amino acid. The key elements of an amino acid are carbonhydrogenoxygen, and nitrogen, though other elements are found in the side-chains of certain amino acids. About 500 amino acids are known[1] and can be classified in many ways. Structurally they can be classified according to the functional groups' locations as alpha- (α-), beta- (β-), gamma- (γ-) or delta- (δ-) amino acids; other categories relate to polaritypH level, and side chain group type (aliphaticacyclicaromatic, containing hydroxyl or sulfur, etc.) In the form of proteins, amino acids comprise the second largest component (after water) of human musclescells and other tissues.[2] Outside proteins, amino acids perform critical roles in processes such as neurotransmitter transport and biosynthesis.
Amino acids having both the amine and carboxylic acid groups attached to the first (alpha-) carbon atom have particular importance in biochemistry. They are known as 2-, alpha-, or α-amino acids (generic formula H2NCHRCOOH in most cases[3] where R is an organic substituent known as a "side-chain");[4] often the term "amino acid" is used to refer specifically to these. They include the 22 proteinogenic ("protein-building") amino acids[5][6][7] which combine into peptide chains ("polypeptides") to form the building blocks of a vast array of proteins.[8] These are all L-stereoisomers ("left-handedisomers) although a few D-amino acids ("right-handed") occur in bacterial envelopes and some antibiotics.[9] Twenty of the proteinogenic amino acids are encoded directly by triplet codonsin the genetic code and are known as "standard" amino acids. The other two ("non-standard" or "non-canonical") are pyrrolysine (found in methanogenic organisms and other eukaryotes) and selenocysteine (present in many noneukaryotes as well as most eukaryotes). For example, 25 human proteins include selenocysteine (Sec) in their primary structure,[10] and the structurally characterized enzymes (selenoenzymes) employ Sec as the catalytic moiety in their active sites.[11] Pyrrolysine and selenocysteine are encoded via variant codons; for example, selenocysteine is encoded by stop codon and SECIS element.[12][13][14] Codon–tRNA combinations not found in nature can also be used to "expand" the genetic code and create novel proteins known as alloproteinsincorporating non-proteinogenic amino acids.[15][16][17]
Many important proteinogenic and non-proteinogenic amino acids also play critical non-protein roles within the body. For example: in the human brain, glutamate (standard glutamic acid) and gamma-amino-butyric acid("GABA", non-standard gamma-amino acid) are respectively the main excitatory and inhibitory neurotransmitters;[18] hydroxyproline (a major component of the connective tissue collagen) is synthesised fromproline; the standard amino acid glycine is used to synthesise porphyrins used in red blood cells; and the non-standard carnitine is used in lipid transport.
9 of the 20 standard amino acids are called "essential" for humans because they cannot be created from othercompounds by the human body, and so must be taken in as food. Others may be conditionally essential for certain ages or medical conditions. Essential amino acids may also differ between species.[19]
Because of their biological significance, amino acids are important in nutrition and are commonly used innutritional supplementsfertilizers, and food technology. Industrial uses include the production of drugs,biodegradable plastics and chiral catalysts.Table of Amino Acids.