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Nucleotides and Nucleosides
1360
N uc le o s o m e
The size of the nucleolus varies from virtually absent to occupying a quarter of the nuclear volume. No doubt this reflects the activity of a given cell in protein synthesis, and is controlled by regulatory mechanisms.
Further Reading
Carmo-Fonseca M, Mendes-Soares L and Campos I (2000) To be or not to be in the nucleosus. Nature Cell Biology 2: E107±E112. Scheer U and Hock R (1999) Structure and function of nucleosus. Current Opinion in Cell Biology 11: 385±390. Venema J and Tollervey D (1999) Ribosome synthesis in Saccharomyces cerivisiae. Annual Review of Genetics 33: 261±311. Weinstein LB and Steitz JA (1999) Guided tours: from precursor snoRNA to functional snoRNP. Current Opinion in Cell Biology 11: 378±384.
See also: Cell Cycle; Nucleus; Ribosomes
Nucleosome Copyright ß 2001 Academic Press doi: 10.1006/rwgn.2001.1939
The nucleosome is composed of repeating units of organization of chromatin fibers in chromosomes, comprising approx. 200 bp and two molecules each of the histones H2A, H2B, H3, and H4. Much of the DNA (around 140 bp) may be wound around a core made up of histones; the remainder attaches to adjacent nucleosomes, forming a structure resembling a string of beads. See also: Chromatin; Histones
Nucleotide Sequence See: DNA Sequencing
Nucleotides and Nucleosides B S Guttman Copyright ß 2001 Academic Press doi: 10.1006/rwgn.2001.0913
A `nucleotide' is a molecule consisting of a nitrogenous base, a sugar (ribose or deoxyribose), and a phosphate, usually considered as the subunit of a nucleic acid (but see below). A `nucleoside' consists of the base and sugar alone; it is converted into a nucleotide by phosphorylation ± addition of a phosphate (or phosphoryl) group.
Ribose and deoxyribose are pentose sugars, containing five carbon atoms, which are numbered 10 to 50 , the prime marks distinguishing these positions from the positions of the nitrogenous bases. They assume a furan ring form including carbons 10 to 40 and the oxygen bonded to the 40 carbon; the 50 carbon is a -CH2 group to the side of the ring, and it is here that the phosphate is attached. The base is always bonded to the 10 position. In ribose, positions 20 and 30 carry hydroxyl groups, but in 20 -deoxyribose, the 20 carbon carries only two hydrogen atoms. Nucleotides and nucleosides are named for their bases, so the nucleosides of adenine, cytosine, guanine, thymine, and uracil are, respectively, adenosine, cytidine, guanosine, thymidine, and uridine. The nucleotides are then designated adenosine 50 -phosphate, and so on; alternatively, they have been named adenylic acid, cytidylic acid, guanylic acid, thymidylic acid, and uridylic acid. The deoxy- forms of nucleosides should then be designated 20 -deoxyadenosine, and so on, and the nucleotides 20 -deoxyadenosine 50 phosphate, and so on. From the viewpoint of genetics, nucleotides are primarily important as the subunits (monomers) of nucleic acids, but they have much broader roles in metabolism. The cytoplasm of a cell is rich in nucleosides diphosphates and triphosphates ± that is, molecules with chains of two or three phosphates on the 50 position. These compounds are the principal energy-carriers in cells. (Other nucleotides with bases such as nicotinamide and flavin are also essential in energy metabolism.) Adenosine triphosphate (ATP) is employed as an energy source to drive many endergonic metabolic reactions (reactions that entail an increase in free energy, which is thermodynamically forbidden); other nucleoside triphosphates have similar but lesser roles in specific biosynthetic processes. In most reactions, the process is made exergonic (with a thermodynamically favorable decrease in free energy) by transferring the terminal phosphate (or phosphoryl) from the nucleoside triphosphate to some other molecule, leaving a nucleoside diphosphate. In some cases, the nucleoside triphosphate transfers its two terminal phosphates, leaving a nucleoside monophosphate. It is important to understand this metabolic role of nucleotides to make sense of polynucleotide (nucleic acid) synthesis. In polynucleotides, the nucleotides are connected by phosphodiester linkages between the 30 carbon of one and the 50 carbon of the next. A polynucleotide thus has a 50 end (with a free 50 -phosphate or triphosphate) and a 30 end, with a free 30 -hydroxyl group. Both DNA replication (see DNA Replication) and RNA transcription are catalyzed by polymerases that add nucleotides to the 30 end of a nascent (growing)
N u l l H y p o t h e s i s 1361 chain. The incoming nucleotides being added to the chain are initially nucleoside triphosphates and thus carry enough energy to drive the endergonic process of forming phosphodiester linkages. Each linkage is made by connecting the terminal 30 -hydroxyl group of the chain to the 50 -phosphate of the incoming nucleotide, releasing a pyrophosphate (P2O7) molecule. Polynucleotide synthesis thus depends critically on the 30 -hydroxyl group on the end of the nascent chain. This fact forms the basis for the Sanger method of DNA sequencing (see DNA Sequencing), in which DNA replication is carried out in vitro in a mixture containing dideoxynucleotides, or, strictly speaking, dideoxynucleoside triphosphates ± molecules that lack oxygen atoms at both the 20 and 30 positions. The incorporation of one of these molecules into a nascent chain stops further synthesis, since the chain has no 30 -OH group. The use of this device in DNA sequencing is explained in the corresponding article. See also: DNA; DNA Replication; DNA Sequencing; Transcription
Nucleus M A Ferguson-Smith Copyright ß 2001 Academic Press doi: 10.1006/rwgn.2001.0916
The nucleus is the structure within the cell which contains the chromosomes and is bounded by a double-layered nuclear membrane. It is a large, often spherical structure whose shape depends on the nature of the cellular tissue from which it is derived. Thus, in hepatic cells and lymphocytes it is spherical, in squamous cells it is disk-shaped, and in smooth muscle cells it is torpedo-shaped. At interphase, the nucleus contains one or more prominent nucleoli within which the ribosomes are assembled. Transcription, RNA processing, and splicing occur within the nucleus as does DNA synthesis. See also: Cell Cycle; Nucleolus
Nude Mouse L Silver Copyright ß 2001 Academic Press doi: 10.1006/rwgn.2001.0917
A spontaneous mouse mutation occurred that caused homozygous mice to be born and live their lives without hair. For reasons unrelated to their nudeness, these
mice also had a nonfunctioning cellular immune system, a trait that was exploited by immunologists to understand how the immune system functions. See also: Pleiotropy
Null Hypothesis T P Speed Copyright ß 2001 Academic Press doi: 10.1006/rwgn.2001.0918
A null hypothesis is a statistical statement about a population, where this term is used in the statistical sense of a collection of units, associated with each of which is one or more quantitative or qualitative characteristics. A concrete example might be the population of the United States on a given day, with income as the characteristic of the units. A more abstract example is the collection of all possible offspring of a given mating pair of organisms, with genotype at a specified locus as the characteristic. Here the population is hypothetical. A third example might be the set of all base pairs in the genome of an organism, with the actual base at each position being the characteristic of interest. A null hypothesis might assert that the population average or population proportion associated with a characteristic has a given value. More generally, a null hypothesis is an arbitrary statistical statement about the distribution of one or more characteristics over a real or hypothetical population. Examples of null hypotheses abound in genetics, perhaps the most famous being those implicit in Mendel's first series of experiments, asserting that the proportion of offspring in the first generation from the hybrids exhibiting the recessive phenotype is exactly 25%. Here the population is the collection of all possible peas of that generation bred under the specified conditions, the characteristic is qualitative, namely the recessive or dominant phenotype, and the null hypothesis embodies the well-known Mendelian conclusion about the proportion of recessives in that generation. Another familiar null hypothesis in genetics arises in the context of experimental crosses or with pedigree data. With the population being the hypothetical one of all meiotic products of a specified class of mating pairs, and the characteristics being two-locus phase-known genotypes, the familiar null hypothesis of no linkage is equivalent to equal proportions of gametes of recombinant and parental types. Yet one more example might be the statement that the base composition in a given genome is 25% A, 25%C, 25% G, and 25% T.
N uc le o s o m e
The size of the nucleolus varies from virtually absent to occupying a quarter of the nuclear volume. No doubt this reflects the activity of a given cell in protein synthesis, and is controlled by regulatory mechanisms.
Further Reading
Carmo-Fonseca M, Mendes-Soares L and Campos I (2000) To be or not to be in the nucleosus. Nature Cell Biology 2: E107±E112. Scheer U and Hock R (1999) Structure and function of nucleosus. Current Opinion in Cell Biology 11: 385±390. Venema J and Tollervey D (1999) Ribosome synthesis in Saccharomyces cerivisiae. Annual Review of Genetics 33: 261±311. Weinstein LB and Steitz JA (1999) Guided tours: from precursor snoRNA to functional snoRNP. Current Opinion in Cell Biology 11: 378±384.
See also: Cell Cycle; Nucleus; Ribosomes
Nucleosome Copyright ß 2001 Academic Press doi: 10.1006/rwgn.2001.1939
The nucleosome is composed of repeating units of organization of chromatin fibers in chromosomes, comprising approx. 200 bp and two molecules each of the histones H2A, H2B, H3, and H4. Much of the DNA (around 140 bp) may be wound around a core made up of histones; the remainder attaches to adjacent nucleosomes, forming a structure resembling a string of beads. See also: Chromatin; Histones
Nucleotide Sequence See: DNA Sequencing
Nucleotides and Nucleosides B S Guttman Copyright ß 2001 Academic Press doi: 10.1006/rwgn.2001.0913
A `nucleotide' is a molecule consisting of a nitrogenous base, a sugar (ribose or deoxyribose), and a phosphate, usually considered as the subunit of a nucleic acid (but see below). A `nucleoside' consists of the base and sugar alone; it is converted into a nucleotide by phosphorylation ± addition of a phosphate (or phosphoryl) group.
Ribose and deoxyribose are pentose sugars, containing five carbon atoms, which are numbered 10 to 50 , the prime marks distinguishing these positions from the positions of the nitrogenous bases. They assume a furan ring form including carbons 10 to 40 and the oxygen bonded to the 40 carbon; the 50 carbon is a -CH2 group to the side of the ring, and it is here that the phosphate is attached. The base is always bonded to the 10 position. In ribose, positions 20 and 30 carry hydroxyl groups, but in 20 -deoxyribose, the 20 carbon carries only two hydrogen atoms. Nucleotides and nucleosides are named for their bases, so the nucleosides of adenine, cytosine, guanine, thymine, and uracil are, respectively, adenosine, cytidine, guanosine, thymidine, and uridine. The nucleotides are then designated adenosine 50 -phosphate, and so on; alternatively, they have been named adenylic acid, cytidylic acid, guanylic acid, thymidylic acid, and uridylic acid. The deoxy- forms of nucleosides should then be designated 20 -deoxyadenosine, and so on, and the nucleotides 20 -deoxyadenosine 50 phosphate, and so on. From the viewpoint of genetics, nucleotides are primarily important as the subunits (monomers) of nucleic acids, but they have much broader roles in metabolism. The cytoplasm of a cell is rich in nucleosides diphosphates and triphosphates ± that is, molecules with chains of two or three phosphates on the 50 position. These compounds are the principal energy-carriers in cells. (Other nucleotides with bases such as nicotinamide and flavin are also essential in energy metabolism.) Adenosine triphosphate (ATP) is employed as an energy source to drive many endergonic metabolic reactions (reactions that entail an increase in free energy, which is thermodynamically forbidden); other nucleoside triphosphates have similar but lesser roles in specific biosynthetic processes. In most reactions, the process is made exergonic (with a thermodynamically favorable decrease in free energy) by transferring the terminal phosphate (or phosphoryl) from the nucleoside triphosphate to some other molecule, leaving a nucleoside diphosphate. In some cases, the nucleoside triphosphate transfers its two terminal phosphates, leaving a nucleoside monophosphate. It is important to understand this metabolic role of nucleotides to make sense of polynucleotide (nucleic acid) synthesis. In polynucleotides, the nucleotides are connected by phosphodiester linkages between the 30 carbon of one and the 50 carbon of the next. A polynucleotide thus has a 50 end (with a free 50 -phosphate or triphosphate) and a 30 end, with a free 30 -hydroxyl group. Both DNA replication (see DNA Replication) and RNA transcription are catalyzed by polymerases that add nucleotides to the 30 end of a nascent (growing)
N u l l H y p o t h e s i s 1361 chain. The incoming nucleotides being added to the chain are initially nucleoside triphosphates and thus carry enough energy to drive the endergonic process of forming phosphodiester linkages. Each linkage is made by connecting the terminal 30 -hydroxyl group of the chain to the 50 -phosphate of the incoming nucleotide, releasing a pyrophosphate (P2O7) molecule. Polynucleotide synthesis thus depends critically on the 30 -hydroxyl group on the end of the nascent chain. This fact forms the basis for the Sanger method of DNA sequencing (see DNA Sequencing), in which DNA replication is carried out in vitro in a mixture containing dideoxynucleotides, or, strictly speaking, dideoxynucleoside triphosphates ± molecules that lack oxygen atoms at both the 20 and 30 positions. The incorporation of one of these molecules into a nascent chain stops further synthesis, since the chain has no 30 -OH group. The use of this device in DNA sequencing is explained in the corresponding article. See also: DNA; DNA Replication; DNA Sequencing; Transcription
Nucleus M A Ferguson-Smith Copyright ß 2001 Academic Press doi: 10.1006/rwgn.2001.0916
The nucleus is the structure within the cell which contains the chromosomes and is bounded by a double-layered nuclear membrane. It is a large, often spherical structure whose shape depends on the nature of the cellular tissue from which it is derived. Thus, in hepatic cells and lymphocytes it is spherical, in squamous cells it is disk-shaped, and in smooth muscle cells it is torpedo-shaped. At interphase, the nucleus contains one or more prominent nucleoli within which the ribosomes are assembled. Transcription, RNA processing, and splicing occur within the nucleus as does DNA synthesis. See also: Cell Cycle; Nucleolus
Nude Mouse L Silver Copyright ß 2001 Academic Press doi: 10.1006/rwgn.2001.0917
A spontaneous mouse mutation occurred that caused homozygous mice to be born and live their lives without hair. For reasons unrelated to their nudeness, these
mice also had a nonfunctioning cellular immune system, a trait that was exploited by immunologists to understand how the immune system functions. See also: Pleiotropy
Null Hypothesis T P Speed Copyright ß 2001 Academic Press doi: 10.1006/rwgn.2001.0918
A null hypothesis is a statistical statement about a population, where this term is used in the statistical sense of a collection of units, associated with each of which is one or more quantitative or qualitative characteristics. A concrete example might be the population of the United States on a given day, with income as the characteristic of the units. A more abstract example is the collection of all possible offspring of a given mating pair of organisms, with genotype at a specified locus as the characteristic. Here the population is hypothetical. A third example might be the set of all base pairs in the genome of an organism, with the actual base at each position being the characteristic of interest. A null hypothesis might assert that the population average or population proportion associated with a characteristic has a given value. More generally, a null hypothesis is an arbitrary statistical statement about the distribution of one or more characteristics over a real or hypothetical population. Examples of null hypotheses abound in genetics, perhaps the most famous being those implicit in Mendel's first series of experiments, asserting that the proportion of offspring in the first generation from the hybrids exhibiting the recessive phenotype is exactly 25%. Here the population is the collection of all possible peas of that generation bred under the specified conditions, the characteristic is qualitative, namely the recessive or dominant phenotype, and the null hypothesis embodies the well-known Mendelian conclusion about the proportion of recessives in that generation. Another familiar null hypothesis in genetics arises in the context of experimental crosses or with pedigree data. With the population being the hypothetical one of all meiotic products of a specified class of mating pairs, and the characteristics being two-locus phase-known genotypes, the familiar null hypothesis of no linkage is equivalent to equal proportions of gametes of recombinant and parental types. Yet one more example might be the statement that the base composition in a given genome is 25% A, 25%C, 25% G, and 25% T.