Polytene chromosome
Polytene chromosomes are large chromosomes which have thousands of DNA strands. They provide a high level of function in certain tissues such as salivary glands. Polytene chromosomes are first reported by E. G. Balbiani in 1881. Polytene chromosomes are found in dipteran flies: the best understood are those of Drosophila and Rhynchosciara, they are present in another group of arthropods of the class Collembola, a protozoan group Ciliophora, mammalian trophoblasts and antipodal, suspensor cells in plants. In insects, they are found in the salivary glands when the cells are not dividing, they are produced when repeated rounds of DNA replication without cell division forms a giant chromosome. Thus polytene chromosomes form when multiple rounds of replication produce many sister chromatids which stay fused together. Polytene chromosomes, at, are seen to have distinct thin banding patterns; these patterns were used to help map chromosomes, identify small chromosome mutations, in taxonomic identification.
Now they are used to study the function of genes in transcription. In addition to increasing the volume of the cells' nuclei and causing cell expansion, polytene cells may have a metabolic advantage as multiple copies of genes permits a high level of gene expression. In Drosophila melanogaster, for example, the chromosomes of the larval salivary glands undergo many rounds of endoreduplication, to produce large quantities of adhesive mucoprotein before pupation. Another example within the fly itself is the tandem duplication of various polytene bands located near the centromere of the X chromosome which results in the Bar phenotype of kidney-shaped eyes; the interbands are involved in the interaction with the active chromatin proteins, nucleosome remodeling, origin recognition complexes. Their primary functions are: to act as binding sites for RNA pol II, to initiate replication and, to start nucleosome remodeling of short fragments of DNA. In insects, polytene chromosomes are found in the salivary glands.
The large size of the chromosome is due to the presence of many longitudinal strands called chromonemata. They are 20 μm in diameter; the chromosomal strands are formed after repeated division of the chromosome in the absence of cytoplasmic division. This type of division is called endomitosis; the polytene chromosome contains two types of dark bands and interbands. The dark bands are darkly stained and the inter bands are stained with nuclear stains; the dark bands contain more DNA and less RNA. The interbands contain more RNA and less DNA; the amount of DNA in interbands ranges from 0.8 - 25%. The bands of polytene chromosomes become enlarged at certain times to form swellings called puffs; the formation of puffs is called puffing. In the regions of puffs, the chromonemata open out to form many loops; the puffing is caused by the uncoiling of individual chromomeres in a band. The puffs indicate the site of active genes; the chromonemata of puffs give out a series of many loops laterally. As these loops appear as rings, they are called Balbiani rings after the name of the researcher who discovered them.
They are formed of RNA and a few proteins. As they are the site of transcription, transcription mechanisms such as RNA polymerase and ribonucleoproteins are present. In protozoans, there is no transcription, since the puff consists only of DNA. Polytene chromosomes were observed in the larval salivary glands of Chironomus midges by Édouard-Gérard Balbiani in 1881. Balbiani described the chromosomal puffs among the tangled thread inside the nucleus, named it "permanent spireme". In 1890, he observed similar spireme in a ciliated protozoan Loxophyllum meleagris; the existence of such spireme in Drosophila melanogaster was reported by Bulgarian geneticist Dontcho Kostoff in 1930. Kostoff predicted that the discs which he observed were "the actual packets in which inherited characters are passed from generation to generation."The hereditary nature of these structures was not confirmed until they were studied in Drosophila melanogaster in the early 1930s by German biologists Emil Heitz and Hans Bauer.
In 1930, Heitz studied different species of Drosophila and found that all their interphase chromatins in certain cells were swollen and messy. In 1932, he collaborated with Karl Heinrich Bauer with whom he discovered that the tangled chromosomes having distinct bands are unique to the cells of the salivary glands, Malphigian tubules, brain of the flies Bibio hurtulunus and Drosophila funebris; the two papers were published in the early 1933. Unaware of these papers, an American geneticist Theophilus Shickel Painter reported in December 1933 the existence of giant chromosome in D. melanogaster. Learning of this, Heitz accused Painter of deliberately ignoring their original publication to claim priority of discovery. In 1935, Henry J. Muller and A. A. Prokofyeva established that the individual band or part of a band corresponds with a gene in Drosophila; the same year, P. C. Koller hesitantly introduced the name "polytene" to describe the giant chromosome, writing: It seems that we can regard these chromosomes as corresponding with paired pachytene chromosomes at meiosis in which the intercalary parts between chromomeres have been stretched and separated into smaller units, in which, instead of two threads lying side by side, we have 16 or more.
Hence they are "polytene" rather than pachytene.
Genome
In the fields of molecular biology and genetics, a genome is the genetic material of an organism. It consists of DNA; the genome includes both the genes and the noncoding DNA, as well as mitochondrial DNA and chloroplast DNA. The study of the genome is called genomics; the term genome was created in 1920 by Hans Winkler, professor of botany at the University of Hamburg, Germany. The Oxford Dictionary suggests the name is a blend of the words chromosome. However, see omics for a more thorough discussion. A few related -ome words existed, such as biome and rhizome, forming a vocabulary into which genome fits systematically. A genome sequence is the complete list of the nucleotides that make up all the chromosomes of an individual or a species. Within a species, the vast majority of nucleotides are identical between individuals, but sequencing multiple individuals is necessary to understand the genetic diversity. In 1976, Walter Fiers at the University of Ghent was the first to establish the complete nucleotide sequence of a viral RNA-genome.
The next year, Fred Sanger completed the first DNA-genome sequence: Phage Φ-X174, of 5386 base pairs. The first complete genome sequences among all three domains of life were released within a short period during the mid-1990s: The first bacterial genome to be sequenced was that of Haemophilus influenzae, completed by a team at The Institute for Genomic Research in 1995. A few months the first eukaryotic genome was completed, with sequences of the 16 chromosomes of budding yeast Saccharomyces cerevisiae published as the result of a European-led effort begun in the mid-1980s; the first genome sequence for an archaeon, Methanococcus jannaschii, was completed in 1996, again by The Institute for Genomic Research. The development of new technologies has made genome sequencing cheaper and easier, the number of complete genome sequences is growing rapidly; the US National Institutes of Health maintains one of several comprehensive databases of genomic information. Among the thousands of completed genome sequencing projects include those for rice, a mouse, the plant Arabidopsis thaliana, the puffer fish, the bacteria E. coli.
In December 2013, scientists first sequenced the entire genome of a Neanderthal, an extinct species of humans. The genome was extracted from the toe bone of a 130,000-year-old Neanderthal found in a Siberian cave. New sequencing technologies, such as massive parallel sequencing have opened up the prospect of personal genome sequencing as a diagnostic tool, as pioneered by Manteia Predictive Medicine. A major step toward that goal was the completion in 2007 of the full genome of James D. Watson, one of the co-discoverers of the structure of DNA. Whereas a genome sequence lists the order of every DNA base in a genome, a genome map identifies the landmarks. A genome map is less detailed than aids in navigating around the genome; the Human Genome Project was organized to sequence the human genome. A fundamental step in the project was the release of a detailed genomic map by Jean Weissenbach and his team at the Genoscope in Paris. Reference genome sequences and maps continue to be updated, removing errors and clarifying regions of high allelic complexity.
The decreasing cost of genomic mapping has permitted genealogical sites to offer it as a service, to the extent that one may submit one's genome to crowdsourced scientific endeavours such as DNA. LAND at the New York Genome Center, an example both of the economies of scale and of citizen science. Viral genomes can be composed of either RNA or DNA; the genomes of RNA viruses can be either single-stranded or double-stranded RNA, may contain one or more separate RNA molecules. DNA viruses can have either double-stranded genomes. Most DNA virus genomes are composed of a single, linear molecule of DNA, but some are made up of a circular DNA molecule. Prokaryotes and eukaryotes have DNA genomes. Archaea have a single circular chromosome. Most bacteria have a single circular chromosome. If the DNA is replicated faster than the bacterial cells divide, multiple copies of the chromosome can be present in a single cell, if the cells divide faster than the DNA can be replicated, multiple replication of the chromosome is initiated before the division occurs, allowing daughter cells to inherit complete genomes and partially replicated chromosomes.
Most prokaryotes have little repetitive DNA in their genomes. However, some symbiotic bacteria have reduced genomes and a high fraction of pseudogenes: only ~40% of their DNA encodes proteins; some bacteria have auxiliary genetic material part of their genome, carried in plasmids. For this, the word genome should not be used as a synonym of chromosome. Eukaryotic genomes are composed of one or more linear DNA chromosomes; the number of chromosomes varies from Jack jumper ants and an asexual nemotode, which each have only one pair, to a fern species that has 720 pairs. A typical human cell has two copies of each of 22 autosomes, one inherited from each parent, plus two sex chromosomes, making it diploid. Gametes, such as ova, sperm and pollen, are haploid, meaning they carry only one copy of each chromosome. In addition to the chromosomes in the nucleus, organelles such as the chloroplasts and mitochondria have their own DNA. Mitochondria are sometimes said to have their own genome referred to as the "mitochondrial genome".
The DNA found within the chloroplast may be referred to as the "plastome". Like the bacteria they originated from and chloroplasts have a circular chromosome
Histone
In biology, histones are alkaline proteins found in eukaryotic cell nuclei that package and order the DNA into structural units called nucleosomes. They are the chief protein components of chromatin, acting as spools around which DNA winds, playing a role in gene regulation. Without histones, the unwound DNA in chromosomes would be long. For example, each human diploid cell has about 1.8 meters of DNA. When the diploid cells are duplicated and condensed during mitosis, the result is about 120 micrometers of chromosomes. Five major families of histones exist: H1/H5, H2A, H2B, H3, H4. Histones H2A, H2B, H3 and H4 are known as the core histones, while histones H1/H5 are known as the linker histones; the core histones all exist as dimers, which are similar in that they all possess the histone fold domain: three alpha helices linked by two loops. It is this helical structure that allows for interaction between distinct dimers in a head-tail fashion; the resulting four distinct dimers come together to form one octameric nucleosome core 63 Angstroms in diameter.
Around 146 base pairs of DNA wrap around this core particle 1.65 times in a left-handed super-helical turn to give a particle of around 100 Angstroms across. The linker histone H1 binds the nucleosome at the entry and exit sites of the DNA, thus locking the DNA into place and allowing the formation of higher order structure; the most basic such formation is the 10 nm fiber or beads on a string conformation. This involves the wrapping of DNA around nucleosomes with 50 base pairs of DNA separating each pair of nucleosomes. Higher-order structures include the 30 nm fiber and 100 nm fiber, these being the structures found in normal cells. During mitosis and meiosis, the condensed chromosomes are assembled through interactions between nucleosomes and other regulatory proteins. Histones are subdivided into canonical replication-dependent histones that are expressed during the S-phase of cell cycle and replication-independent histone variants, expressed during the whole cell cycle. In animals, genes encoding canonical histones are clustered along the chromosome, lack introns and use a stem loop structure at the 3’ end instead of a polyA tail.
Genes encoding histone variants are not clustered, have introns and their mRNAs are regulated with polyA tails. Complex multicellular organisms have a higher number of histone variants providing a variety of different functions. Recent data are accumulating about the roles of diverse histone variants highlighting the functional links between variants and the delicate regulation of organism development. Histone variants from different organisms, their classification and variant specific features can be found in "HistoneDB 2.0 - Variants" database. The following is a list of human histone proteins: The nucleosome core is formed of two H2A-H2B dimers and a H3-H4 tetramer, forming two nearly symmetrical halves by tertiary structure; the H2A-H2B dimers and H3-H4 tetramer show pseudodyad symmetry. The 4'core' histones are similar in structure and are conserved through evolution, all featuring a'helix turn helix turn helix' motif, they share the feature of long'tails' on one end of the amino acid structure - this being the location of post-translational modification.
Archaeal histone only contains a H3-H4 like dimeric structure made out of the same protein. Such dimeric structures can stack into a tall superhelix onto which DNA coils in a manner similar to nucleosome spools. Only some archaeal histones have tails, it has been proposed that histone proteins are evolutionarily related to the helical part of the extended AAA+ ATPase domain, the C-domain, to the N-terminal substrate recognition domain of Clp/Hsp100 proteins. Despite the differences in their topology, these three folds share a homologous helix-strand-helix motif. Using an electron paramagnetic resonance spin-labeling technique, British researchers measured the distances between the spools around which eukaryotic cells wind their DNA, they determined the spacings range from 59 to 70 Å. In all, histones make five types of interactions with DNA: Helix-dipoles form alpha-helixes in H2B, H3, H4 cause a net positive charge to accumulate at the point of interaction with negatively charged phosphate groups on DNA Hydrogen bonds between the DNA backbone and the amide group on the main chain of histone proteins Nonpolar interactions between the histone and deoxyribose sugars on DNA Salt bridges and hydrogen bonds between side chains of basic amino acids and phosphate oxygens on DNA Non-specific minor groove insertions of the H3 and H2B N-terminal tails into two minor grooves each on the DNA moleculeThe basic nature of histones, aside from facilitating DNA-histone interactions, contributes to their water solubility.
Histones are subject to post translational modification by enzymes on their N-terminal tails, but in their globular domains. Such modifications include methylation, acetylation, phosphorylation, SUMOylation, ADP-ribosylation; this affects their function of gene regulation. In general, genes that are active have less bound histone, while inactive genes are associated with histones during interphase, it a
Nucleosome
A nucleosome is a basic unit of DNA packaging in eukaryotes, consisting of a segment of DNA wound in sequence around eight histone protein cores. This structure is compared to thread wrapped around a spool. Nucleosomes form the fundamental repeating units of eukaryotic chromatin, used to pack the large eukaryotic genomes into the nucleus while still ensuring appropriate access to it. Nucleosomes are folded through a series of successively higher order structures to form a chromosome. Nucleosomes are thought to carry epigenetically inherited information in the form of covalent modifications of their core histones. Nucleosome positions in the genome are not random, it is important to know where each nucleosome is located because this determines the accessibility of the DNA to regulatory proteins. Nucleosomes were first observed as particles in the electron microscope by Don and Ada Olins in 1974, their existence and structure were proposed by Roger Kornberg; the role of the nucleosome as a general gene repressor was demonstrated by Lorch et al. in vitro, by Han and Grunstein in vivo in 1987 and 1988, respectively.
The nucleosome core particle consists of 146 base pairs of DNA wrapped in 1.67 left-handed superhelical turns around a histone octamer, consisting of 2 copies each of the core histones H2A, H2B, H3, H4. Core particles are connected by stretches of "linker DNA". Technically, a nucleosome is defined as the core particle plus one of these linker regions. Genome-wide nucleosome positioning maps are now available for many model organisms including mouse liver and brain. Linker histones such as H1 and its isoforms are involved in chromatin compaction and sit at the base of the nucleosome near the DNA entry and exit binding to the linker region of the DNA. Non-condensed nucleosomes without the linker histone resemble "beads on a string of DNA" under an electron microscope. In contrast to most eukaryotic cells, mature sperm cells use protamines to package their genomic DNA, most to achieve an higher packaging ratio. Histone equivalents and a simplified chromatin structure have been found in Archea, suggesting that eukaryotes are not the only organisms that use nucleosomes.
Pioneering structural studies in the 1980s by Aaron Klug's group provided the first evidence that an octamer of histone proteins wraps DNA around itself in about 1.7 turns of a left-handed superhelix. In 1997 the first near atomic resolution crystal structure of the nucleosome was solved by the Richmond group, showing the most important details of the particle; the human alpha-satellite palindromic DNA critical to achieving the 1997 nucleosome crystal structure was developed by the Bunick group at Oak Ridge National Laboratory in Tennessee. The structures of over 20 different nucleosome core particles have been solved to date, including those containing histone variants and histones from different species; the structure of the nucleosome core particle is remarkably conserved, a change of over 100 residues between frog and yeast histones results in electron density maps with an overall root mean square deviation of only 1.6Å. The nucleosome core particle consists of about 146 bp of DNA wrapped in 1.67 left-handed superhelical turns around the histone octamer, consisting of 2 copies each of the core histones H2A, H2B, H3, H4.
Adjacent nucleosomes are joined by a stretch of free DNA termed "linker DNA". Nucleosome core particles are observed when chromatin in interphase is treated to cause the chromatin to unfold partially; the resulting image, via an electron microscope, is "beads on a string". The string is the DNA; the nucleosome core particle is composed of histone proteins. Partial DNAse digestion of chromatin reveals its nucleosome structure; because DNA portions of nucleosome core particles are less accessible for DNAse than linking sections, DNA gets digested into fragments of lengths equal to multiplicity of distance between nucleosomes. Hence a characteristic pattern similar to a ladder is visible during gel electrophoresis of that DNA; such digestion can occur under natural conditions during apoptosis, because autodestruction of DNA is its role. The core histone proteins contains a characteristic structural motif termed the "histone fold", which consists of three alpha-helices separated by two loops. In solution, the histones form H2A-H2B heterodimers and H3-H4 heterotetramers.
Histones dimerise about their long α2 helices in an anti-parallel orientation, and, in the case of H3 and H4, two such dimers form a 4-helix bundle stabilised by extensive H3-H3’ interaction. The H2A/H2B dimer binds onto the H3/H4 tetramer due to interactions between H4 and H2B, which include the formation of a hydrophobic cluster; the histone octamer is formed by a central H3/H4 tetramer sandwiched between two H2A/H2B dimers. Due to the basic charge of all four core histones, the histone octamer is stable only in the presence of DNA or high salt concentrations; the nucleosome contains over 120 direct protein-DNA interactions and several hundred water-mediated ones. Direct protein - DNA interactions are not spread evenly about the octamer surface but rather located at discrete site
Isochromosome
An isochromosome is an unbalanced structural abnormality in which the arms of the chromosome are mirror images of each other. The chromosome consists of two copies of either the long arm or the short arm because isochromosome formation is equivalent to a simultaneous duplication and deletion of genetic material. There is partial trisomy of the genes present in the isochromosome and partial monosomy of the genes in the lost arm. An isochromosome can be abbreviated as i. For example, an isochromosome of chromosome 17 containing two q arms can be identified as i. Isochromosomes can be created during mitosis and meiosis through a misdivision of the centromere or U-type strand exchange. Under normal separation of sister chromatids in metaphase, the centromere will divide longitudinally, or parallel to the long axis of the chromosome. An isochromosome is created when the centromere is divided transversely, or perpendicular to the long axis of the chromosome; the division is not occurring in the centromere itself, but in an area surrounding the centromere known as a pericentric region.
It is proposed. Although the resulting chromosome may appear monocentric with only one centromere, it is isodicentric with two centromeres close to each other. Misdivision of the centromere can produce monocentric isochromosomes, but they are not as common as dicentric isochromosomes. A more common mechanism in the formation of isochromosomes is through the breakage and fusion of sister chromatids, most occurring in early anaphase of mitosis or meiosis. A double-stranded break in the pericentric region of the chromosome is repaired when the sister chromatids, each containing a centromere, are fused together; this U-type exchange of genetic material creates an isodicentric chromosome. Misdivision of the centromere and U-type exchange can occur in sister chromatids, thus creating an isochromosome with genetically identical arms. However, U-type exchange can occur for homologous chromosomes which creates an isochromosome with homologous arms; this exchange between homologues is most due to homologous sequences containing low copy repeats.
Regardless of the chromosome involved in U-type exchange, the acentric fragment of the chromosome is lost, thus creating a partial monosomy of genes located in that portion of the acentric chromosome. The most common isochromosome is the X sex chromosome. Acrocentric autosomal chromosomes 13, 14, 15, 21, 22 are common candidates for isochromosome formation. Chromosomes containing smaller arms are more to become isochromosomes because the loss of genetic material in those arms can be tolerated. Turner syndrome is a condition in females in which there is partial or complete loss of one X chromosome; this causes symptoms such as growth and sexual development problems. In 15% of Turner syndrome patients, the structural abnormality is isochromosome X, composed of two copies of the q arm. A majority of i are created by U-type strand exchange. A breakage and reunion in the pericentric region of the p arm results in a dicentric isochromosome; some of the p arm can be found in this formation of i, but a majority of the genetic material on the p arm is lost so it is considered absent.
Since the p-arm of the X chromosome contains genes that are necessary for normal sexual development, Turner's syndrome patients experience phenotypic effects. Alternatively, the increase in dosage of genes on the q arm may be involved in a 10-fold increase in risk of i Turner's patients developing autoimmune thyroiditis, a disease in which the body creates antibodies to target and destroy thyroid cells. Neoplasia is uncontrolled cell growth. In many different forms of neoplasia, isochromosome 17q is the most frequent neoplasia associated isochromosome and corresponds with poor patient survival. Unique DNA sequences, known as low copy repeats, occur in the pericentric region of the p arm, so a crossover event in that area can create a dicentric isochromosome through U-type strand exchange; the neoplasia created from i is caused by a decrease and increase in gene dosage from the monosomy of the p arm and trisomy of the q arm, respectively. Many candidate tumour suppressor genes are found on the lost p arm, allowing the tumour cell population to be maintained.
It is debated whether the loss of tumour suppressor gene p53, located on 17p, is involved in the central pathogenesis of some neoplasia. The presence of one p53 gene can be functionally active, but its relation to other oncogenes can alter its expression levels when present only in one copy. Since the genetic sequences involved in i neoplasia are large, it is difficult to determine which genes, or combination of genes, are involved in tumour growth
Homologous chromosome
A couple of homologous chromosomes, or homologs, are a set of one maternal and one paternal chromosome that pair up with each other inside a cell during meiosis. Homologs have the same genes in the same loci where they provide points along each chromosome which enable a pair of chromosomes to align with each other before separating during meiosis; this is the basis for Mendelian inheritance which characterizes inheritance patterns of genetic material from an organism to its offspring parent developmental cell at the given time and area. Chromosomes are linear arrangements of condensed deoxyribonucleic acid and histone proteins, which form a complex called chromatin. Homologous chromosomes are made up of chromosome pairs of the same length, centromere position, staining pattern, for genes with the same corresponding loci. One homologous chromosome is inherited from the organism's mother. After mitosis occurs within the daughter cells, they have the correct number of genes which are a mix of the two parents' genes.
In diploid organisms, the genome is composed of one set of each homologous chromosome pair, as compared to tetraploid organisms which may have two sets of each homologous chromosome pair. The alleles on the homologous chromosomes may be different, resulting in different phenotypes of the same genes; this mixing of maternal and paternal traits is enhanced by crossing over during meiosis, wherein lengths of chromosomal arms and the DNA they contain within a homologous chromosome pair are exchanged with one another. Early in the 1900s William Bateson and Reginald Punnett were studying genetic inheritance and they noted that some combinations of alleles appeared more than others; that data and information was further explored by Thomas Morgan. Using test cross experiments, he revealed that, for a single parent, the alleles of genes near to one another along the length of the chromosome move together. Using this logic he concluded that the two genes he was studying were located on homologous chromosomes.
On during the 1930s Harriet Creighton and Barbara McClintock were studying meiosis in corn cells and examining gene loci on corn chromosomes. Creighton and McClintock discovered that the new allele combinations present in the offspring and the event of crossing over were directly related; this proved interchromosomal genetic recombination. Homologous chromosomes are chromosomes which contain the same genes in the same order along their chromosomal arms. There are two main properties of homologous chromosomes: the length of chromosomal arms and the placement of the centromere; the actual length of the arm, in accordance with the gene locations, is critically important for proper alignment. Centromere placement can be characterized by four main arrangements, consisting of being either metacentric, acrocentric, or telocentric. Both of these properties are the main factors for creating structural homology between chromosomes. Therefore, when two chromosomes of the exact structure exist, they are able to pair together to form homologous chromosomes.
Since homologous chromosomes are not identical and do not originate from the same organism, they are different from sister chromatids. Sister chromatids result after DNA replication has occurred, thus are identical, side-by-side duplicates of each other. Humans have a total of 46 chromosomes, but there are only 22 pairs of homologous autosomal chromosomes; the additional 23rd pair is the sex chromosomes, X and Y. If this pair is made up of an X and Y chromosome the pair of chromosomes is not homologous because their size and gene content differ greatly; the 22 pairs of homologous chromosomes contain the same genes but code for different traits in their allelic forms since one was inherited from the mother and one from the father. So humans have two homologous chromosome sets in each cell, meaning humans are diploid organisms. Homologous chromosomes are important in the processes of mitosis, they allow for the recombination and random segregation of genetic material from the mother and father into new cells.
Meiosis is a round of two cell divisions that results in four haploid daughter cells that each contain half the number of chromosomes as the parent cell. It reduces the chromosome number in a germ cell by half by first separating the homologous chromosomes in meiosis I and the sister chromatids in meiosis II; the process of meiosis I is longer than meiosis II because it takes more time for the chromatin to replicate and for the homologous chromosomes to be properly oriented and segregated by the processes of pairing and synapsis in meiosis I. During meiosis, genetic recombination and crossing over produces daughter cells that each contain different combinations of maternally and paternally coded genes; this recombination of genes allows for the introduction of new allele pairings and genetic variation. Genetic variation among organisms helps make a population more stable by providing a wider range of genetic traits for natural selection to act on. In prophase I of meiosis I, each chromosome is aligned with its homologous partner and pairs completely.
In prophase I, the DNA has undergone replication so each chromosome consists of two identical chromatids connected by a common centromere. During the zygotene stage of prophase I, the homologous chromosomes pair up with each other; this pairing occurs by a synapsis process where the synaptonemal complex - a protein scaffold - is assembled and joins the homologous chromosomes along their lengths. Cohesin crosslinking occurs between the homologous chromosomes and helps them resist being pulled apart until anaphase. Genetic crossing-over, a type of recombination, occurs during the pachytene stage of prophase I
Base pair
A base pair is a unit consisting of two nucleobases bound to each other by hydrogen bonds. They form the building blocks of the DNA double helix and contribute to the folded structure of both DNA and RNA. Dictated by specific hydrogen bonding patterns, Watson–Crick base pairs allow the DNA helix to maintain a regular helical structure, subtly dependent on its nucleotide sequence; the complementary nature of this based-paired structure provides a redundant copy of the genetic information encoded within each strand of DNA. The regular structure and data redundancy provided by the DNA double helix make DNA well suited to the storage of genetic information, while base-pairing between DNA and incoming nucleotides provides the mechanism through which DNA polymerase replicates DNA and RNA polymerase transcribes DNA into RNA. Many DNA-binding proteins can recognize specific base-pairing patterns that identify particular regulatory regions of genes. Intramolecular base pairs can occur within single-stranded nucleic acids.
This is important in RNA molecules, where Watson–Crick base pairs permit the formation of short double-stranded helices, a wide variety of non-Watson–Crick interactions allow RNAs to fold into a vast range of specific three-dimensional structures. In addition, base-pairing between transfer RNA and messenger RNA forms the basis for the molecular recognition events that result in the nucleotide sequence of mRNA becoming translated into the amino acid sequence of proteins via the genetic code; the size of an individual gene or an organism's entire genome is measured in base pairs because DNA is double-stranded. Hence, the number of total base pairs is equal to the number of nucleotides in one of the strands; the haploid human genome is estimated to be about 3.2 billion bases long and to contain 20,000–25,000 distinct protein-coding genes. A kilobase is a unit of measurement in molecular biology equal to 1000 base pairs of DNA or RNA; the total amount of related DNA base pairs on Earth is estimated at 5.0×1037 and weighs 50 billion tonnes.
In comparison, the total mass of the biosphere has been estimated to be as much as 4 TtC. Hydrogen bonding is the chemical interaction. Appropriate geometrical correspondence of hydrogen bond donors and acceptors allows only the "right" pairs to form stably. DNA with high GC-content is more stable than DNA with low GC-content. But, contrary to popular belief, the hydrogen bonds do not stabilize the DNA significantly; the larger nucleobases and guanine, are members of a class of double-ringed chemical structures called purines. Purines are complementary only with pyrimidines: pyrimidine-pyrimidine pairings are energetically unfavorable because the molecules are too far apart for hydrogen bonding to be established. Purine-pyrimidine base-pairing of AT or GC or UA results in proper duplex structure; the only other purine-pyrimidine pairings would be AC and GT and UG. The GU pairing, with two hydrogen bonds, does occur often in RNA. Paired DNA and RNA molecules are comparatively stable at room temperature, but the two nucleotide strands will separate above a melting point, determined by the length of the molecules, the extent of mispairing, the GC content.
Higher GC content results in higher melting temperatures. On the converse, regions of a genome that need to separate — for example, the promoter regions for often-transcribed genes — are comparatively GC-poor. GC content and melting temperature must be taken into account when designing primers for PCR reactions; the following DNA sequences illustrate pair double-stranded patterns. By convention, the top strand is written from the 5' end to the 3' end. A base-paired DNA sequence: ATCGATTGAGCTCTAGCG TAGCTAACTCGAGATCGCThe corresponding RNA sequence, in which uracil is substituted for thymine in the RNA strand: AUCGAUUGAGCUCUAGCG UAGCUAACUCGAGAUCGC Chemical analogs of nucleotides can take the place of proper nucleotides and establish non-canonical base-pairing, leading to errors in DNA replication and DNA transcription; this is due to their isosteric chemistry. One common mutagenic base analog is 5-bromouracil, which resembles thymine but can base-pair to guanine in its enol form. Other chemicals, known as DNA intercalators, fit into the gap between adjacent bases on a single strand and induce frameshift mutations by "masquerading" as a base, causing the DNA replication machinery to skip or insert additional nucleotides at the intercalated site.
Most intercalators are known or suspected carcinogens. Examples include ethidium acridine. An unnatural base pair is a designed subunit of DNA, created in a laboratory and does not occur in nature. DNA sequences have been described which use newly created nucleobases to form a third base pair, in addition to the two ba
