Chromosome 2
Chromosome 2 is one of the 23 pairs of chromosomes in humans. People have two copies of this chromosome. Chromosome 2 is the second-largest human chromosome, spanning more than 242 million base pairs and representing 8% of the total DNA in human cells. Chromosome 2 contains the HOXD homeobox gene cluster. All members of Hominidae except humans and Denisovans have 24 pairs of chromosomes. Humans have only 23 pairs of chromosomes. Human chromosome 2 is a result of an end-to-end fusion of two ancestral chromosomes; the evidence for this includes: The correspondence of chromosome 2 to two ape chromosomes. The closest human relative, the chimpanzee, has near-identical DNA sequences to human chromosome 2, but they are found in two separate chromosomes; the same is true of orangutan. The presence of a vestigial centromere. A chromosome has just one centromere, but in chromosome 2 there are remnants of a second centromere in the q21.3–q22.1 region. The presence of vestigial telomeres; these are found only at the ends of a chromosome, but in chromosome 2 there are additional telomere sequences in the q13 band, far from either end of the chromosome.
According to researcher Jacob W. Ijdo, "We conclude that the locus cloned in cosmids c8.1 and c29B is the relic of an ancient telomere-telomere fusion and marks the point at which two ancestral ape chromosomes fused to give rise to human chromosome 2." The following are some of the gene count estimates of human chromosome 2. Because researchers use different approaches to genome annotation their predictions of the number of genes on each chromosome vary. Among various projects, the collaborative consensus coding sequence project takes an conservative strategy. So CCDS's gene number prediction represents a lower bound on the total number of human protein-coding genes; the following is a partial list of genes on human chromosome 2. For complete list, see the link in the infobox on the right. Partial list of the genes located on p-arm of human chromosome 2: Partial list of the genes located on q-arm of human chromosome 2: The following diseases and traits are related to genes located on chromosome 2: National Institutes of Health.
"Chromosome 2". Genetics Home Reference. Retrieved 2017-05-06. "Chromosome 2". Human Genome Project Information Archive 1990–2003. Retrieved 2017-05-06
Chromosome 10
Chromosome 10 is one of the 23 pairs of chromosomes in humans. People have two copies of this chromosome. Chromosome 10 spans about 133 million base pairs and represents between 4 and 4.5 percent of the total DNA in cells. The following are some of the gene count estimates of human chromosome 10; because researchers use different approaches to genome annotation their predictions of the number of genes on each chromosome varies. Among various projects, the collaborative consensus coding sequence project takes an conservative strategy. So CCDS's gene number prediction represents a lower bound on the total number of human protein-coding genes; the following is a partial list of genes on human chromosome 10. For complete list, see the link in the infobox on the right; the following diseases are related to genes on chromosome 10: National Institutes of Health. "Chromosome 10". Genetics Home Reference. Retrieved 2017-05-06. "Chromosome 10". Human Genome Project Information Archive 1990–2003. Retrieved 2017-05-06
Enzyme
Enzymes are macromolecular biological catalysts. Enzymes accelerate chemical reactions; the molecules upon which enzymes may act are called substrates and the enzyme converts the substrates into different molecules known as products. All metabolic processes in the cell need enzyme catalysis in order to occur at rates fast enough to sustain life. Metabolic pathways depend upon enzymes to catalyze individual steps; the study of enzymes is called enzymology and a new field of pseudoenzyme analysis has grown up, recognising that during evolution, some enzymes have lost the ability to carry out biological catalysis, reflected in their amino acid sequences and unusual'pseudocatalytic' properties. Enzymes are known to catalyze more than 5,000 biochemical reaction types. Most enzymes are proteins; the latter are called ribozymes. Enzymes' specificity comes from their unique three-dimensional structures. Like all catalysts, enzymes increase the reaction rate by lowering its activation energy; some enzymes can make their conversion of substrate to product occur many millions of times faster.
An extreme example is orotidine 5'-phosphate decarboxylase, which allows a reaction that would otherwise take millions of years to occur in milliseconds. Chemically, enzymes are like any catalyst and are not consumed in chemical reactions, nor do they alter the equilibrium of a reaction. Enzymes differ from most other catalysts by being much more specific. Enzyme activity can be affected by other molecules: inhibitors are molecules that decrease enzyme activity, activators are molecules that increase activity. Many therapeutic drugs and poisons are enzyme inhibitors. An enzyme's activity decreases markedly outside its optimal temperature and pH, many enzymes are denatured when exposed to excessive heat, losing their structure and catalytic properties; some enzymes are used commercially, in the synthesis of antibiotics. Some household products use enzymes to speed up chemical reactions: enzymes in biological washing powders break down protein, starch or fat stains on clothes, enzymes in meat tenderizer break down proteins into smaller molecules, making the meat easier to chew.
By the late 17th and early 18th centuries, the digestion of meat by stomach secretions and the conversion of starch to sugars by plant extracts and saliva were known but the mechanisms by which these occurred had not been identified. French chemist Anselme Payen was the first to discover an enzyme, diastase, in 1833. A few decades when studying the fermentation of sugar to alcohol by yeast, Louis Pasteur concluded that this fermentation was caused by a vital force contained within the yeast cells called "ferments", which were thought to function only within living organisms, he wrote that "alcoholic fermentation is an act correlated with the life and organization of the yeast cells, not with the death or putrefaction of the cells."In 1877, German physiologist Wilhelm Kühne first used the term enzyme, which comes from Greek ἔνζυμον, "leavened" or "in yeast", to describe this process. The word enzyme was used to refer to nonliving substances such as pepsin, the word ferment was used to refer to chemical activity produced by living organisms.
Eduard Buchner submitted his first paper on the study of yeast extracts in 1897. In a series of experiments at the University of Berlin, he found that sugar was fermented by yeast extracts when there were no living yeast cells in the mixture, he named the enzyme that brought about the fermentation of sucrose "zymase". In 1907, he received the Nobel Prize in Chemistry for "his discovery of cell-free fermentation". Following Buchner's example, enzymes are named according to the reaction they carry out: the suffix -ase is combined with the name of the substrate or to the type of reaction; the biochemical identity of enzymes was still unknown in the early 1900s. Many scientists observed that enzymatic activity was associated with proteins, but others argued that proteins were carriers for the true enzymes and that proteins per se were incapable of catalysis. In 1926, James B. Sumner crystallized it; the conclusion that pure proteins can be enzymes was definitively demonstrated by John Howard Northrop and Wendell Meredith Stanley, who worked on the digestive enzymes pepsin and chymotrypsin.
These three scientists were awarded the 1946 Nobel Prize in Chemistry. The discovery that enzymes could be crystallized allowed their structures to be solved by x-ray crystallography; this was first done for lysozyme, an enzyme found in tears and egg whites that digests the coating of some bacteria. This high-resolution structure of lysozyme marked the beginning of the field of structural biology and the effort to understand how enzymes work at an atomic level of detail. An enzyme's name is derived from its substrate or the chemical reaction it catalyzes, with the word ending in -ase. Examples are alcohol dehydrogenase and DNA polymerase. Different enzymes that catalyze the same chemical reaction are called isozymes; the International Union of Biochemistry and Molecular Biology have developed a nomenclature for enzymes, the EC numbers. The first number broadly classifies the enzyme based on its mechanism; the top-level classification is: EC 1, Oxidoreductases: catalyze oxidation/reducti
Phosphorylation
In chemistry, phosphorylation of a molecule is the attachment of a phosphoryl group. Together with its counterpart, dephosphorylation, it is critical for many cellular processes in biology. Phosphorylation is important for protein function. Many proteins are phosphorylated temporarily, as are many sugars and other molecules. Protein phosphorylation is considered the most abundant post-translational modification in eukaryotes. Phosphorylation can occur on serine and tyrosine side chains through phosphoester bond formation, on histidine and arginine through phosphoramidate bonds, on aspartic acid and glutamic acid through mixed anhydride linkages. Recent evidence confirms widespread histidine phosphorylation at both the 1 and 3 N-atoms of the imidazole ring Recent work from 2017 suggests widespread human protein phosphorylation on multiple non-canonical amino acids, including motifs containing phosphorylated histidine, glutamate and lysine in HeLa cell extracts. Due to the chemical lability of these phosphorylated residues, in marked contrast to Ser and Tyr phosphorylation, the analysis of phosphorylated histidine using standard biochemical and mass spectrometric approaches is much more challenging and special procedures and separation techniques are required for their preservation alongside classical Ser and Tyr phosphorylation.
The prominent role of protein phosphorylation in biochemistry is illustrated by the huge body of studies published on the subject. Phosphorylation of sugars is the first stage in their catabolism. Phosphorylation allows cells to accumulate sugars because the phosphate group prevents the molecules from diffusing back across their transporter. Phosphorylation of glucose is a key reaction in sugar metabolism because many sugars are first converted to glucose before they are metabolized further; the chemical equation for the conversion of D-glucose to D-glucose-6-phosphate in the first step of glycolysis is given by D-glucose + ATP → D-glucose-6-phosphate + ADPΔG° = −16.7 kJ/mol Researcher D. G. Walker of the University of Birmingham determined the presence of two specific enzymes in adult guinea pig liver, both of which catalyze the phosphorylation of glucose to glucose 6 phosphate; the two enzymes have been identified as a specific non-specific hexokinase. Hepatic cell is permeable to glucose, the initial rate of phosphorylation of glucose is the rate-limiting step in glucose metabolism by the liver and non-specific hexokinase.
The role of glucose 6-phosphate in glycogen synthase: High blood glucose concentration causes an increase in intracellular levels of glucose 6 phosphate in liver, skeletal muscle and fat tissue. And non-specific hexokinase. In liver, synthesis of glycogen is directly correlated by blood glucose concentration and in skeletal muscle and adipocytes, glucose has a minor effect on glycogen synthase. High blood glucose releases insulin, stimulating the trans location of specific glucose transporters to the cell membrane; the liver’s crucial role in controlling blood sugar concentrations by breaking down glucose into carbon dioxide and glycogen is characterized by the negative delta G value, which indicates that this is a point of regulation with. The hexokinase enzyme has a low Km, indicating a high affinity for glucose, so this initial phosphorylation can proceed when glucose levels at nanoscopic scale within the blood; the phosphorylation of glucose can be enhanced by the binding of Fructose-6-phosphate, lessened by the binding fructose-1-phosphate.
Fructose consumed in the diet is converted to F1P in the liver. This negates the action of F6P on glucokinase, which favors the forward reaction; the capacity of liver cells to phosphorylate fructose exceeds capacity to metabolize fructose-1-phosphate. Consuming excess fructose results in an imbalance in liver metabolism, which indirectly exhausts the liver cell’s supply of ATP. Allosteric activation by glucose 6 phosphate, which acts as an effector, stimulates glycogen synthase, glucose 6 phosphate may inhibit the phosphorylation of glycogen synthase by cyclic AMP-stimulated protein kinase. Phosphorylation of glucose is imperative in processes within the body. For example, phosphorylating glucose is necessary for insulin-dependent mechanistic target of rapamycin pathway activity within the heart; this further suggests a link between cardiac growth. Reversible phosphorylation of proteins is an important regulatory mechanism that occurs in both prokaryotic and eukaryotic organisms, it is estimated that 230,000, 156,000 and 40,000 phosphorylation sites exist in human and yeast, respectively.
Kinases phosphorylate proteins and phosphatases dephosphorylate proteins. Many enzymes and receptors "off" by phosphorylation and dephosphorylation. Reversible phosphorylation results in a conformational change in the structure in many enzymes and receptors, causing them to become activated or deactivated. Phosphorylation occurs on serine, threonine and histidine residues in eukaryotic proteins. Histidine phosphorylation of eukaryotic proteins appears to be much more frequent than tyrosine phos
Chromosome 5
Chromosome 5 is one of the 23 pairs of chromosomes in humans. People have two copies of this chromosome. Chromosome 5 spans about 181 million base pairs and represents 6% of the total DNA in cells. Chromosome 5 has one of the lowest gene densities; this is explained by numerous gene-poor regions that display a remarkable degree of non-coding and syntenic conservation with non-mammalian vertebrates, suggesting they are functionally constrained. Because chromosome 5 is responsible for many forms of growth and development changes may cause cancers. One example would be acute myeloid leukemia; the following are some of the gene count estimates of human chromosome 5. Because researchers use different approaches to genome annotation their predictions of the number of genes on each chromosome varies. Among various projects, the collaborative consensus coding sequence project takes an conservative strategy. So CCDS's gene number prediction represents a lower bound on the total number of human protein-coding genes.
The following is a partial list of genes on human chromosome 5. For complete list, see the link in the infobox on the right; the following are some of the diseases related to genes located on chromosome 5: The following conditions are caused by changes in the structure or number of copies of chromosome 5: Cri-du-chat syndrome is caused by a deletion of the end of the short arm of chromosome 5. This chromosomal change is written as 5p-; the signs and symptoms of cri-du-chat syndrome are related to the loss of multiple genes in this region. Researchers have not identified all of these genes or determined how their loss leads to the features of the disorder, they have discovered, that a larger deletion tends to result in more severe mental retardation and developmental delays in people with cri-du-chat syndrome. Researchers have defined narrow regions of the short arm of chromosome 5 that are associated with particular features of cri-du-chat syndrome. A specific region designated 5p15.3 is associated with a cat-like cry, a nearby region called 5p15.2 is associated with mental retardation, small head, distinctive facial features.
Familial Adenomatous Polyposis is caused by a deletion of the APC tumor suppressor gene on the long arm of chromosome 5. This chromosomal change results in thousands of colonic polyps which gives the patient a 100% risk of colon cancer if total colectomy is not done. Chromosome 5q deletion syndrome is caused by the deletion of the q arm of chromosome 5; this deletion has been linked to several blood related disorders including Myelodysplastic syndrome and Erythroblastopenia. This is a different condition than Cri-du-chat, mentioned above. Other changes in the number or structure of chromosome 5 can have a variety of effects, including delayed growth and development, distinctive facial features, birth defects, other medical problems. Changes to chromosome 5 include an extra segment of the short or long arm of the chromosome in each cell, a missing segment of the long arm of the chromosome in each cell, a circular structure called ring chromosome 5. A ring chromosome occurs. National Institutes of Health.
"Chromosome 5". Genetics Home Reference. Retrieved 2017-05-06. "Chromosome 5". Human Genome Project Information Archive 1990–2003. Retrieved 2017-05-06
Sugar
Sugar is the generic name for sweet-tasting, soluble carbohydrates, many of which are used in food. The various types of sugar are derived from different sources. Simple sugars are called monosaccharides and include glucose and galactose. "Table sugar" or "granulated sugar" refers to a disaccharide of glucose and fructose. In the body, sucrose is hydrolysed into glucose. Sugars are found in the tissues of most plants, but sucrose is concentrated in sugarcane and sugar beet, making them ideal for efficient commercial extraction to make refined sugar. Sugarcane originated in tropical Indian subcontinent and Southeast Asia, is known of from before 6,000 BP, sugar beet was first described in writing by Olivier de Serres and originated in southwestern and Southeast Europe along the Atlantic coasts and the Mediterranean Sea, in North Africa, Macaronesia, to Western Asia. In 2016, the combined world production of those two crops was about two billion tonnes. Other disaccharides include lactose. Longer chains of sugar molecules are called polysaccharides.
Some other chemical substances, such as glycerol and sugar alcohols, may have a sweet taste, but are not classified as sugar. Sucrose is used in prepared foods, is sometimes added to commercially available beverages, may be used by people as a sweetener for foods and beverages; the average person consumes about 24 kilograms of sugar each year, or 33.1 kilograms in developed countries, equivalent to over 260 food calories per day. As sugar consumption grew in the latter part of the 20th century, researchers began to examine whether a diet high in sugar refined sugar, was damaging to human health. Excessive consumption of sugar has been implicated in the onset of obesity, cardiovascular disease and tooth decay. Numerous studies have tried to clarify those implications, but with varying results because of the difficulty of finding populations for use as controls that consume little or no sugar. In 2015, the World Health Organization recommended that adults and children reduce their intake of free sugars to less than 10%, encouraged a reduction to below 5%, of their total energy intake.
The etymology reflects the spread of the commodity. From Sanskrit शर्करा, meaning "ground or candied sugar," "grit, gravel", came Persian shakar, whence Arabic سكر, whence Medieval Latin succarum, whence 12th-century French sucre, whence the English word sugar. Italian zucchero, Spanish azúcar, Portuguese açúcar came directly from Arabic, the Spanish and Portuguese words retaining the Arabic definite article; the earliest Greek word attested is σάκχαρις. The English word jaggery, a coarse brown sugar made from date palm sap or sugarcane juice, has a similar etymological origin: Portuguese jágara from the Malayalam ചക്കരാ, itself from the Sanskrit शर्करा. Sugar has been produced in the Indian subcontinent since ancient times and its cultivation spread from there into modern-day Afghanistan through the Khyber Pass, it was not plentiful or cheap in early times, in most parts of the world, honey was more used for sweetening. People chewed raw sugarcane to extract its sweetness. Sugarcane was a native of Southeast Asia.
Different species seem to have originated from different locations with Saccharum barberi originating in India and S. edule and S. officinarum coming from New Guinea. One of the earliest historical references to sugarcane is in Chinese manuscripts dating to 8th century BCE, which state that the use of sugarcane originated in India. In the tradition of Indian medicine, the sugarcane is known by the name Ikṣu and the sugarcane juice is known as Phāṇita, its varieties and characterics are defined in nighaṇṭus such as the Bhāvaprakāśa. Sugar remained unimportant until the Indians discovered methods of turning sugarcane juice into granulated crystals that were easier to store and to transport. Crystallized sugar was discovered by the time of the Imperial Guptas, around the 5th century CE. In the local Indian language, these crystals were called khanda, the source of the word candy. Indian sailors, who carried clarified butter and sugar as supplies, introduced knowledge of sugar along the various trade routes they travelled.
Traveling Buddhist monks took sugar crystallization methods to China. During the reign of Harsha in North India, Indian envoys in Tang China taught methods of cultivating sugarcane after Emperor Taizong of Tang made known his interest in sugar. China established its first sugarcane plantations in the seventh century. Chinese documents confirm at least two missions to India, initiated in 647 CE, to obtain technology for sugar refining. In the Indian subcontinent, the Middle East and China, sugar became a staple of cooking and desserts. Nearchus, admiral of Alexander of Macedonia, knew of sugar during the year 325 B. C. because of his participation in the campaign of India led by Alexander. The Greek physician Pedanius Dioscorides in the 1st century CE described sugar in his medical treatise De Materia Medica, Pliny the Elder, a 1st-century CE Roman, described sugar in his Natural History: "Sugar is made in Arabia as well, but Indian sugar is better, it is a kind of honey found in cane, white as gum, it crunches between the teeth.
It comes in lumps the size of a hazelnut. Sugar is used only for medical purposes." Crusaders brought sugar back to Europe after their campaigns in the Hol
Gene
In biology, a gene is a sequence of nucleotides in DNA or RNA that codes for a molecule that has a function. During gene expression, the DNA is first copied into RNA; the RNA can be directly functional or be the intermediate template for a protein that performs a function. The transmission of genes to an organism's offspring is the basis of the inheritance of phenotypic trait; these genes make up different DNA sequences called genotypes. Genotypes along with developmental factors determine what the phenotypes will be. Most biological traits are under the influence of polygenes as well as gene–environment interactions; some genetic traits are visible, such as eye color or number of limbs, some are not, such as blood type, risk for specific diseases, or the thousands of basic biochemical processes that constitute life. Genes can acquire mutations in their sequence, leading to different variants, known as alleles, in the population; these alleles encode different versions of a protein, which cause different phenotypical traits.
Usage of the term "having a gene" refers to containing a different allele of the same, shared gene. Genes evolve due to natural selection / survival of the fittest and genetic drift of the alleles; the concept of a gene continues to be refined. For example, regulatory regions of a gene can be far removed from its coding regions, coding regions can be split into several exons; some viruses store their genome in RNA instead of DNA and some gene products are functional non-coding RNAs. Therefore, a broad, modern working definition of a gene is any discrete locus of heritable, genomic sequence which affect an organism's traits by being expressed as a functional product or by regulation of gene expression; the term gene was introduced by Danish botanist, plant physiologist and geneticist Wilhelm Johannsen in 1909. It is inspired by the ancient Greek: γόνος, that means offspring and procreation; the existence of discrete inheritable units was first suggested by Gregor Mendel. From 1857 to 1864, in Brno, he studied inheritance patterns in 8000 common edible pea plants, tracking distinct traits from parent to offspring.
He described these mathematically as 2n combinations where n is the number of differing characteristics in the original peas. Although he did not use the term gene, he explained his results in terms of discrete inherited units that give rise to observable physical characteristics; this description prefigured Wilhelm Johannsen's distinction between phenotype. Mendel was the first to demonstrate independent assortment, the distinction between dominant and recessive traits, the distinction between a heterozygote and homozygote, the phenomenon of discontinuous inheritance. Prior to Mendel's work, the dominant theory of heredity was one of blending inheritance, which suggested that each parent contributed fluids to the fertilisation process and that the traits of the parents blended and mixed to produce the offspring. Charles Darwin developed a theory of inheritance he termed pangenesis, from Greek pan and genesis / genos. Darwin used the term gemmule to describe hypothetical particles. Mendel's work went unnoticed after its first publication in 1866, but was rediscovered in the late 19th century by Hugo de Vries, Carl Correns, Erich von Tschermak, who reached similar conclusions in their own research.
In 1889, Hugo de Vries published his book Intracellular Pangenesis, in which he postulated that different characters have individual hereditary carriers and that inheritance of specific traits in organisms comes in particles. De Vries called these units "pangenes", after Darwin's 1868 pangenesis theory. Sixteen years in 1905, Wilhelm Johannsen introduced the term'gene' and William Bateson that of'genetics' while Eduard Strasburger, amongst others, still used the term'pangene' for the fundamental physical and functional unit of heredity. Advances in understanding genes and inheritance continued throughout the 20th century. Deoxyribonucleic acid was shown to be the molecular repository of genetic information by experiments in the 1940s to 1950s; the structure of DNA was studied by Rosalind Franklin and Maurice Wilkins using X-ray crystallography, which led James D. Watson and Francis Crick to publish a model of the double-stranded DNA molecule whose paired nucleotide bases indicated a compelling hypothesis for the mechanism of genetic replication.
In the early 1950s the prevailing view was that the genes in a chromosome acted like discrete entities, indivisible by recombination and arranged like beads on a string. The experiments of Benzer using mutants defective in the rII region of bacteriophage T4 showed that individual genes have a simple linear structure and are to be equivalent to a linear section of DNA. Collectively, this body of research established the central dogma of molecular biology, which states that proteins are translated from RNA, transcribed from DNA; this dogma has since been shown to have exceptions, such as reverse transcription in retroviruses. The modern study of genetics at the level of DNA is known as molecular genetics. In 1972, Walter Fiers and his team were the first to determine the sequence of a gene: that of Bacteriophage MS2 coat protein; the subsequent development of chain-termination DNA sequencing in 1977 by Frederick Sanger improved the efficiency of sequencing and turned it into a routine laboratory tool.
An automated version of the Sanger method was used in early phases of the
