molecular biology: dna

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For other uses, see DNA (disambiguation).

The structure of part of a DNA double helix

Deoxyribonucleic acid, or DNA is a nucleic acid molecule that contains the genetic instructions used in the development and functioning of all living organisms. The main role of DNA is the long-term storage of information and it is often compared to a set of blueprints, since DNA 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, which are held together by a backbone made of alternating sugars and phosphate groups. 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. Most of these RNA molecules are used to synthesize proteins, but others are used directly in structures such as ribosomes and spliceosomes.
Within cells, DNA is organized into structures called chromosomes and the set of chromosomes within a cell make up a genome. These chromosomes are duplicated before cells divide, in a process called DNA replication. Eukaryotic organisms such as animals, plants, and fungi store their DNA inside the cell nucleus, while in prokaryotes such as bacteria it is found in the cell's cytoplasm. Within the chromosomes, chromatin proteins such as histones compact and organize DNA, which helps control its interactions with other proteins and thereby control which genes are transcribed

protein /pro·tein/ (pro´ten) any of a group of complex organic compounds containing carbon, hydrogen, oxygen, nitrogen, and sulfur. Proteins, the principal constituents of the protoplasm of all cells, are of high molecular weight and consist of a-amino acids joined by peptide linkages. Twenty different amino acids are commonly found in proteins, each protein having a unique, genetically defined amino acid sequence that determines its specific shape and function. Their roles include enzymatic catalysis, transport and storage, coordinated motion, nerve impulse generation and transmission, control of growth and differentiation, immunity, and mechanical suppport.

AA protein see under amyloid.

acute phase protein any of the non-antibody proteins found in increased amounts in serum during the acute phase response, including C-reactive protein and fibrinogen.

AL protein see under amyloid.

amyloid A protein AA amyloid.

amyloid light chain protein AL amyloid.

amyloid precursor protein (APP) a large transmembrane glycoprotein expressed on the cell surface and of uncertain function; endocytosis and cleavage can produce abnormal 40 to 43 amino acid peptides which aggregate to form A, associated with Alzheimer's disease.

Bence Jones protein a low-molecular-weight, heat-sensitive urinary protein found in multiple myeloma, which coagulates when heated to 45°?55°C and redissolves partially or wholly on boiling.

binding protein

1. any protein able to specifically and reversibly bind other substances, such as ions, sugars, nucleic acids, or amino acids; they are believed to function in transport.

2. transport p.

protein C a vitamin K?dependent plasma protein that, when activated by thrombin, inhibits the clotting cascade by enzymatic cleavage of factors V and VIII and also enhances fibrinolysis. Deficiency results in recurrent venous thrombosis.

C4 binding protein a complement system regulatory protein that inhibits activation of the classical pathway.

complete protein one containing the essential amino acids in the proportion required in the human diet.

compound protein , conjugated protein any of those in which the protein is combined with nonprotein molecules or prosthetic groups other than as a salt; e.g., nucleoproteins, glycoproteins, lipoproteins, and metalloproteins.

C-reactive protein a globulin that forms a precipitate with the C-polysaccharide of the pneumonococcus; the most predominant of the acute phase proteins.

cystic fibrosis transmembrane regulator protein a transmembrane protein produced by the cystic fibrosis gene, primarily functioning as a chloride channel. Numerous mutated forms of the gene have been associated with clinical cystic fibrosis.

fibrillar protein any of the generally insoluble proteins that comprise the principal structural proteins of the body, e.g., collagens, elastins, keratin, actin, and myosin.

G protein any of a family of proteins of the intracellular portion of the plasma membrane that bind activated receptor complexes and, through conformational changes and cyclic binding and hydrolysis of GTP, effect alterations in channel gating and so couple cell surface receptors to intracellular responses.

glial fibrillary acidic protein (GFAP) the protein forming the glial filaments of the astrocytes and used as an immunohistochemical marker of these cells.

globular protein any of the water-soluble proteins yielding only a-amino acids on hydrolysis, including most of the proteins of the body, e.g., albumins and globulins.

guanyl-nucleotide-binding protein G p.

heat shock protein any of a group of proteins first identified as synthesized in response to hyperthermia, hypoxia, or other stresses and believed to enable cells to recover from these stresses. Many have been found to be molecular chaperones and are synthesized abundantly regardless of stress.

HIV proteins proteins specific to the human immunodeficiency virus; presence of certain specific HIV proteins together with certain HIV glycoproteins constitutes a serological diagnosis of HIV infection.

incomplete protein one having a ratio of essential amino acids different from that of the average body protein.

membrane cofactor protein (MCP) an inhibitor of complement activation found in most blood cells, endothelial and epithelial cells, and fibroblasts.

myeloma protein any of the abnormal immunoglobulins or fragments, such as Bence-Jones proteins, secreted by myeloma cells.

partial protein incomplete p.

plasma proteins all the proteins present in the blood plasma, including the immunoglobulins.

prion protein (PrP) a protein of uncertain function, in humans coded for by a gene on the short arm of chromosome 20. The protease-resistant core is the functional, and perhaps only, component of prions; several abnormal forms have been identified and are responsible for prion disease.

protein S a vitamin K?dependent plasma protein that inhibits blood clotting by serving as a cofactor for activated protein C.

S protein see vitronectin.

SAA protein serum amyloid A p.

serum proteins proteins in the blood serum, including immunoglobulins, albumin, complement, coagulation factors, and enzymes.

serum amyloid A protein SAA p.; a high-molecular-weight protein synthesized in the liver; it is an acute phase protein and circulates in association with HDL lipoprotein. It is the precursor to AA amyloid and accumulates in inflammation.

sphingolipid activator protein (SAP) any of a group of non-enzymatic lysosomal proteins that stimulate the actions of specific lysosomal hydrolases by binding and solubilizing their sphingolipid substrates.

transport protein a protein that binds to a substance and provides a transport system for it, either in the plasma or across a plasma membrane.

pro·tein (pr

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Types of Proteins

A protein molecule that consists of but a single polypeptide chain is said to be monomeric; proteins made up of more than one polypeptide chain, as many of the large ones are, are called oligomeric. Based upon chemical composition, proteins are divided into two major classes: simple proteins, which are composed of only amino acids, and conjugated proteins, which are composed of amino acids and additional organic and inorganic groupings, certain of which are called prosthetic groups prosthetic group, non-amino acid portions of certain protein molecules. The key part of the prosthetic group may be either organic (such as a vitamin ) or inorganic
..... Click the link for more information. . Conjugated proteins include glycoproteins glycoprotein
..... Click the link for more information. , which contain carbohydrates; lipoproteins lipoprotein
..... Click the link for more information. , which contain lipids; and nucleoproteins, which contain nucleic acids nucleic acid, any of a group of organic substances found in the chromosomes of living cells and viruses that play a central role in the storage and replication of
..... Click the link for more information. .
Classified by biological function, proteins include the enzymes enzyme, biological catalyst . The term enzyme comes from zymosis, the Greek word for fermentation , a process accomplished by yeast cells and long known to the
..... Click the link for more information. , which are responsible for catalyzing the thousands of chemical reactions of the living cell; keratin keratin (kĕr`ətĭn)
..... Click the link for more information. , elastin, and collagen collagen (kŏl`əjən)
..... Click the link for more information. , which are important types of structural, or support, proteins; hemoglobin hemoglobin
..... Click the link for more information. and other gas transport proteins; ovalbumin, casein casein (kā`sēn)
..... Click the link for more information. , and other nutrient molecules; antibodies antibody, protein produced by the immune system (see immunity ) in response to the presence in the body of antigens: foreign proteins or polysaccharides such as
..... Click the link for more information. , which are molecules of the immune system (see immunity immunity, ability of an organism to resist disease by identifying and destroying foreign substances or organisms.
..... Click the link for more information. ); protein hormones hormone, secretory substance carried from one gland or organ of the body via the bloodstream to more or less specific tissues, where it exerts some influence upon the
..... Click the link for more information. , which regulate metabolism metabolism, sum of all biochemical processes involved in life. Two subcategories of metabolism are anabolism, the building up of complex organic molecules from simpler
..... Click the link for more information. ; and proteins that perform mechanical work, such as actin actin, a protein abundantly present in many cells, especially muscle cells, that significantly contributes to the cell's structure and motility.
..... Click the link for more information. and myosin myosin (mī`əsĭn)
..... Click the link for more information. , the contractile muscle proteins.

Protein Structure

Every protein molecule has a characteristic three-dimensional shape, or conformation. Fibrous proteins, such as collagen and keratin, consist of polypeptide chains arranged in roughly parallel fashion along a single linear axis, thus forming tough, usually water-insoluble, fibers or sheets. Globular proteins, e.g., many of the known enzymes, show a tightly folded structural geometry approximating the shape of an ellipsoid or sphere.
Because the physiological activity of most proteins is closely linked to their three-dimensional architecture, specific terms are used to refer to different aspects of protein structure. The term primary structure denotes the precise linear sequence of amino acids that constitutes the polypeptide chain of the protein molecule. Automated techniques for amino-acid sequencing have made possible the determination of the primary structure of hundreds of proteins.
The physical interaction of sequential amino-acid subunits results in a so-called secondary structure, which often can either be a twisting of the polypeptide chain approximating a linear helix (α-configuration), or a zigzag pattern (β-configuration). Most globular proteins also undergo extensive folding of the chain into a complex three-dimensional geometry designated as tertiary structure. Many globular protein molecules are easily crystallized and have been examined by X-ray diffraction, a technique that allows the visualization of the precise three-dimensional positioning of atoms in relation to each other in a crystal.
The tertiary structure of several protein molecules has been determined from X-ray diffraction analysis. Two or more polypeptide chains that behave in many ways as a single structural and functional entity are said to exhibit quaternary structure. The separate chains are not linked through covalent chemical bonds but by weak forces of association.
The precise three-dimensional structure of a protein molecule is referred to as its native state and appears, in almost all cases, to be required for proper biological function (especially for the enzymes). If the tertiary or quaternary structure of a protein is altered, e.g., by such physical factors as extremes of temperature, changes in pH, or variations in salt concentration, the protein is said to be denatured; it usually exhibits reduction or loss of biological activity.

Protein Synthesis

The cell's ability to synthesize protein is, in essence, the expression of its genetic makeup. Protein synthesis is a sequence of chemical reactions that occur in four distinct stages, i.e., activation of the amino acids that ultimately will be joined together by peptide bonds; initiation of the polypeptide chain at a cell organelle known as the ribosome; elongation of the polypeptide by stepwise addition of single amino acids to the chain; and termination of amino-acid additions and release of the completed protein from the ribosome.
The information for the synthesis of specific amino-acid sequences is carried by a nucleic acid molecule called messenger RNA (see nucleic acid). Proteins are needed in the diet mainly for their amino acids, which the body uses to build new proteins (see nutrition nutrition, study of the materials that nourish an organism and of the manner in which the separate components are used for maintenance, repair, growth, and
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The mechanism of action of many widely used antibiotics, such as streptomycin streptomycin
..... Click the link for more information. , chloramphenicol chloramphenicol
..... Click the link for more information. , and tetracycline tetracycline
..... Click the link for more information. , can be understood in terms of their ability to interfere with some stage of protein synthesis in bacteria.