biological functions of nucleic acids
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Nucleic acids are biological molecules essential for life, and include DNA (deoxyribonucleic acid) and RNA (ribonucleic acid). Together with proteins, nucleic acids make up the most important macromolecules; each is found in abundance in all living things. Nucleic acids were first discovered by Friedrich Miescher in 1871. Experimental studies of nucleic acids constitute a major part of modern biological and medical research, and form a foundation for genome and forensic science, as well as the biotechnology and pharmaceutical industries.
Occurrence and nomenclature
The term nucleic acid is the over all name for DNA and RNA, members of a family of biopolymers, and is synonymous with polynucleotide. Nucleic acids were named for their initial discovery within the cell nucleus, and for the presence of phosphate groups (related to phosphoric acid). Although first discovered within the nucleus of eukaryotic cells, nucleic acids are now known to be found in all life forms, including within bacteria, archaea, mitochondria, chloroplasts, viruses and viroids. All living cells and organelles contain both DNA and RNA, while viruses contain either DNA or RNA, but not usually both. The basic component of biological nucleic acids is the nucleotide, each of which contains a pentose sugar (ribose or deoxyribose), a phosphate group, and a nucleobase. Nucleic acids are also generated within the laboratory, through the use of enzymes (DNA and RNA polymerases) and by solid-phase chemical synthesis. The chemical methods also enable the generation of altered nucleic acids that are not found in nature, for example peptide nucleic acids.
Molecular composition and size
Nucleic acids can vary in size, but are generally very large molecules. Indeed, DNA molecules are probably the largest individual molecules known. Well-studied biological nucleic acid molecules range in size from 21 nucleotides (small interfering RNA) to large chromosomes (human chromosome 1 is a single molecule that contains 247 million base pairs).
In most cases, naturally occurring DNA molecules are double-stranded and RNA molecules are single-stranded. There are numerous exceptions, however--some viruses have genomes made of double-stranded RNA and other viruses have single-stranded DNA genomes, and, in some circumstances, nucleic acid structures with three or four strands can form.
Nucleic acids are linear polymers (chains) of nucleotides. Each nucleotide consists of three components: a purine or pyrimidinenucleobase (sometimes termed nitrogenous base or simply base), a pentosesugar; and a phosphate group. The substructure consisting of a nucleobase plus sugar is termed a nucleoside. Nucleic acid types differ in the structure of the sugar in their nucleotides - DNA contains 2'-deoxyribose while RNA contains ribose (where the only difference is the presence of a hydroxyl group). Also, the nucleobases found in the two nucleic acid types are different: adenine, cytosine, and guanine are found in both RNA and DNA, while thymine occurs in DNA and uracil occurs in RNA.
The sugars and phosphates in nucleic acids are connected to each other in an alternating chain (sugar-phosphate backbone) through phosphodiester linkages. In conventional nomenclature, the carbons to which the phosphate groups attach are the 3'-end and the 5'-end carbons of the sugar. This gives nucleic acids directionality, and the ends of nucleic acid molecules are referred to as 5'-end and 3'-end. The nucleobases are joined to the sugars via an N-glycosidic linkage involving a nucleobase ring nitrogen (N-1 for pyrimidines and N-9 for purines) and the 1' carbon of the pentose sugar ring.
Non-standard nucleosides are also found in both RNA and DNA and usually arise from modification of the standard nucleosides within the DNA molecule or the primary (initial) RNA transcript. Transfer RNA (tRNA) molecules contain a particularly large number of modified nucl
In molecular biology, the term double helix refers to the structure formed by double-stranded molecules of nucleic acids such as DNA and RNA. The double helical structure of a nucleic acid complex arises as a consequence of its secondary structure, and is a fundamental component in determining its tertiary structure. The term entered popular culture with the publication in 1968 of The Double Helix: A Personal Account of the Discovery of the Structure of DNA, by James Watson.
The DNA double helix is a spiral polymer of nucleic acids, held together by nucleotides which base pair together. In B-DNA, the most common double helical structure, the double helix is right-handed with about 10–10.5 nucleotides per turn. The double helix structure of DNA contains a major groove and minor groove, the major groove being wider than the minor groove. Given the difference in widths of the major groove and minor groove, many proteins which bind to DNA do so through the wider major groove.
The double-helix model of DNA structure was first published in the journal Nature by James D. Watson and Francis Crick in 1953, based upon the crucial X-ray diffraction image of DNA (labeled as "Photo 51") from Rosalind Franklin in 1952 , followed by her more clarified DNA image with Raymond Gosling, Maurice Wilkins, Alexander Stokes, and Herbert Wilson, as well as base-pairing chemical and biochemical information by Erwin Chargaff. The previous model was triple-stranded DNA.
Crick, Wilkins, and Watson each received one third of the 1962 Nobel Prize in Physiology or Medicine for their contributions to the discovery. (Franklin, whose breakthrough X-ray diffraction data was used to formulate the DNA structure, died in 1958, and thus was ineligible to be nominated for a Nobel Prize.)
Nucleic acid hybridization
Hybridization is the process of complementarybase pairs binding to form a double helix. Melting is the process by which the interactions between the strands of the double helix are broken, separating the two nucleic acid strands. These bonds are weak, easily separated by gentle heating, enzymes, or physical force. Melting occurs preferentially at certain points in the nucleic acid. T and A rich sequences are more easily melted than C and G rich regions. Particular base steps are also susceptible to DNA melting, particularly T A and T G base steps. These mechanical features are reflected by the use of sequences such as TATAAat the start of many genes to assist RNA polymerase in melting the DNA for transcription.
Strand separation by gentle heating, as used in PCR, is simple providing the molecules have fewer than about 10,000 base pairs (10 kilobase pairs, or 10 kbp). The intertwining of the DNA strands makes long segments difficult to separate. The cell avoids this problem by allowing its DNA-melting enzymes (helicases) to work concurrently with topoisomerases, which can chemically cleave the phosphate backbone of one of the strands so that it can swivel around the other. Helicases unwind the strands to facilitate the advance of sequence-reading enzymes such as DNA polymerase.
Base pair geometry
The geometry of a base, or base pair step can be characterized by 6 coordinates: Shift, slide, rise, tilt, roll, and twist. These values precisely define the location and orientation in space of every base or base pair in a nucleic acid molecule relative to its predecessor along the axis of the helix. Together, they characterize the helical structure of the molecule. In regions of DNA or RNA where the "normal" structure is disrupted, the change in these values can be used to describe such disruption.
For each base pair, considered relative to its predecessor, there are the following base pair geometries to consider:
- Propeller twist: rotation of one base with respect to the other in the same base pair.
- Shift: displacement along an axis in the base-pair plane perpendicular to the first, directed from the minor to the major groove.
- Slide: displacement along an axis in the plane of the base pair directed from one strand to the other.
- Rise: displacement along the helix axis.
- Tilt: rotation around this axis.
- vRoll: rotation around this axis.
- Twist: rotation around the helix axis.
- pitch: the number of base pairs per complete turn of the helix.
Rise and twist determine the handedness and pitch of the helix. The other coordinates, by contrast, can be zero. Slide and shift are typically small in B-DNA, but are substantial in A- and Z-DNA. Roll and tilt make successive base pairs less parallel, and are typically small. A [http://rutchem.rutgers.edu/~xiangjun/3DNA/images/bp_step_hel.gif diagram] of these coordinates can be found in [http://rutchem.rutgers.edu/~xiangjun/3DNA/examples.html 3DNA] website.
Note that "tilt" has often been used differently in the scientific literature, referring to the deviation of the first, inter-strand
A homologous trait is any characteristic of organisms that is derived from a common ancestor. This is contrasted to analogous traits: similarities between organisms that were not in the last common ancestor of the taxa being considered but rather evolved separately. As defined by Owen (1843), a homology is a "structural correspondence", whereas an analogy is a "non-correspondent similarity".
Whether or not a trait is homologous depends on both the taxonomic and anatomical level at which the trait is examined. For example, the bird and bat wing are homologous as forearms in tetrapods. However, they are not homologous as wings, because the organ served as a forearm (not a wing) in the last common ancestor of tetrapods. By definition, any homologous trait defines a clade—a monophyletictaxon in which all the members have the trait (or have lost it secondarily); and all non-members lack it.
A homologous trait may be homoplasious – that is, it has evolved independently, but from the same ancestral structure – plesiomorphic – that is, present in a common ancestor but secondarily lost in some of its descendants – or (syn)apomorphic – present in an ancestor and all of its descendants.
A homologous trait is often called a homolog (also spelled homologue). In genetics, the term "homolog" is used both to refer to a homologous protein, and to the gene (DNA sequence) encoding it.
Homology of structures
Shared ancestry can be evolutionary or developmental. Evolutionary ancestry means that structures evolved from some structure in a common ancestor; for example, the wings of bats and the arms of primates are homologous in this sense. Developmental ancestry means that structures arose from the same tissue in embryonal development; the ovaries of female humans and the testicles of male humans are homologous in this sense.
Homology is different from analogy, which describes the relation between characters that are apparently similar yet phylogenetically independent. The wings of a maple seed and the wings of an albatross are analogous but not homologous (they both allow the organism to travel on the wind, but they didn't both develop from the same structure). Analogy is commonly also referred to as homoplasy, which is further distinguished into parallelism, reversal, and convergence.
From the point of view of evolutionary developmental biology (evo-devo) where evolution is seen as the evolution of the development of organisms, Rolf Sattler emphasized that homology can also be partial. New structures can evolve through the combination of developmental pathways or parts of them. As a result hybrid or mosaic structures can evolve that exhibit partial homologies. For example, certain compound leaves of flowering plants are partially homologous both to leaves and shoots because they combine some traits of leaves and shoots.
Homology of sequences in genetics
Homology among proteins and DNA is often concluded on the basis of sequence similarity, especially in bioinformatics. For example, in general, if two or more genes have highly similar DNA sequences, it is likely that they are homologous. But sequence similarity may also arise without common ancestry: short sequences may be similar by chance, and sequences may be similar because both were selected to bind to a particular protein, such as a transcription factor. Such sequences are similar but not homologous. Sequence regions that are homologous are also called conserved. This is not to be confused with conservation in amino acid sequences in which the amino acid at a specific position has been substituted with a different one with functionally equivalent physicochemical properties.
The phrase "percent homology" is sometimes used but is incorrect. "Percent identity" or "percent similarity" should be used to quantify the similarity between the biomolecule sequences. For two naturally occurring sequences, percent identity is a factual measurement, whereas homology is a hypothesis supported by evidence. One can, however, refer to partial homology where a fraction of the sequences compared (are presumed to) share descent, while the rest does not. For example, partial homology may result from a gene fusion event.
Many algorithms exist to cluster protein sequences into sequence families, which are sets of mutually homologous sequences. (See sequence clustering and sequence alignment.) Some specialized biological databases collect homologous sequences in animal genomes: HOVERGEN, HOMOLENS, HOGENOM.
Homologous sequences are of two types: orthologous and paralogous.
Homologous sequences are orthologous if they were separated by a speciation event: when a species diverges into two separate species, the divergent copies of a single gene in the resulting species are said to be orthologous. Orthologs, or orthologous genes, are genes in different species that are similar to each other because they originated from a common ancestor. The term "ortholog" was coined in 1970 by Walter Fitch.
The strongest evidence that two similar genes are orthologous is the result of a phylogenetic analysis of the gene lineage. Genes that are found within one clade are orthologs, descended from a common ancestor. Orthologs often, but not always, have the same function.
Orthologous sequences provide useful in
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Answers:controls the synthesis of RNA development of new cells and transportation and synthesis of more nucleic acids
Answers:Definition:any of a group of long, linear macromolecules, either DNA or various types of RNA, that carry genetic information directing all cellular functions: composed of linked nucleotides. Function: genetic material that makes up protein.
Answers:The five "types" of nucleic acids are Constituents DNA, RNA, Nucleic acid analogues, and Cloning vectors. See fig. Types of Nucleic acids: http://en.wikipedia.org/wiki/Nucleic_acid Here you find a list of nucleic acids: http://www.bvl.bund.de/nn_1115098/EN/06__Genetic__Engineering/ZKBS/01__Allg__Stellungnahmen/10__cell__biology/onkogene.html
Answers:nucleic acid is a complex, high-molecular-weight biochemical macromolecule composed of nucleotide chains that convey genetic information. The most common nucleic acids are deoxyribonucleic acid (DNA) and ribonucleic acid (RNA). Nucleic acids are found in all living cells and viruses. Artificial nucleic acids include peptide nucleic acid (PNA), Morpholino and locked nucleic acid (LNA), as well as glycol nucleic acid (GNA) and threose nucleic acid (TNA). Each of these is distinguished from naturally occurring DNA or RNA by changes to the backbone of the molecule Chemical structure The term "nucleic acid" is the generic name of a family of biopolymers, named for their prevalence in cellular nuclei. The monomers from which nucleic acids are constructed are called nucleotides. Each nucleotide consists of three components: a nitrogenous heterocyclic base, either a purine or a pyrimidine; a pentose sugar; and a phosphate group. Different nucleic acid types differ in the structure of the sugar in their nucleotides; DNA contains 2-deoxyriboses while RNA contains ribose. Likewise, the nitrogenous bases found in the two nucleic acids are different: adenine, cytosine, and guanine are in both RNA and DNA, while thymine only occurs in DNA and uracil only occurs in RNA. Other rare nucleic acid bases can occur, for example inosine in strands of mature transfer RNA. Nucleic acids are usually either single-stranded or double-stranded, though structures with three or more strands can form. A double-stranded nucleic acid consists of two single-stranded nucleic acids hydrogen-bonded together. RNA is usually single-stranded, but any given strand may fold back upon itself to form double-helical regions. DNA is usually double-stranded, though some viruses have single-stranded DNA as their genome. The sugars and phosphates in nucleic acids are connected to each other in an alternating chain, linked by shared oxygens, forming a phosphodiester functional group. In conventional nomenclature, the carbons to which the phosphate groups are attached are the 3' and the 5' carbons of the sugar. The bases extend from a glycosidic linkage to the 1' carbon of the pentose sugar ring. Hydrophobic interaction of nucleic acids is poorly understood. For example, nucleic acids are insoluble in ethanol, TCA, and diluted hydrochloric acid; but they are soluble in diluted NaOH and HCl. Hope this helps