NUCLEOTIDES

Nucleotides are molecules that, when joined together, make up the structural units of RNA and DNA. In addition, nucleotides play central roles in metabolism. In that capacity, they serve as sources of chemical energy (adenosine triphosphate and guanosine triphosphate), participate in cellular signaling (cyclic guanosine monophosphate and cyclic adenosine monophosphate), and are incorporated into important cofactors of enzymatic reactions (coenzyme A, flavin adenine dinucleotide, flavin mononucleotide, and nicotinamide adenine dinucleotide phosphate).

Nucleotide structure

A nucleotide is composed of a nucleobase (nitrogenous base), a five-carbon sugar (either ribose or 2'-deoxyribose), and one to three phosphate groups. Together, the nucleobase and sugar comprise a nucleoside. The phosphate groups form bonds with either the 2, 3, or 5-carbon of the sugar, with the 5-carbon site most common. Cyclic nucleotides form when the phosphate group is bound to two of the sugar's hydroxyl groups. Ribonucleotides are nucleotides where the sugar is ribose, and deoxyribonucleotides contain the sugar deoxyribose. Nucleotides can contain either a purine or a pyrimidine base.

Nucleic acids are polymeric macromolecules made from nucleotide monomers. In DNA, the purine bases are adenine and guanine, while the pyrimidines are thymine and cytosine. RNA uses uracil in place of thymine. also nucleotide plays an important role in thinking.

Adenine (A, Ade) is a nucleobase (a purine derivative) with a variety of roles in biochemistry including cellular respiration, in the form of both the energy-rich adenosine triphosphate (ATP) and the cofactors nicotinamide adenine dinucleotide (NAD) and flavin adenine dinucleotide (FAD), and protein synthesis, as a chemical component of DNA and RNA. The shape of adenine is complementary to either thymine in DNA or uracil in RNA.

Guanine (G) is one of the four main nucleobases found in the nucleic acids DNA and RNA, the others being adenine, cytosine, and thymine. In DNA, guanine is paired with cytosine. With the formula C5H5N5O, guanine is a derivative of purine, consisting of a fused pyrimidine-imidazole ring system with conjugated double bonds. Being unsaturated, the bicyclic molecule is planar. The guanine nucleoside is called guanosine.

Thymine (T, Thy) is one of the four nucleobases in the nucleic acid of DNA that are represented by the letters G–C–A–T. The others are adenine, guanine, and cytosine. Thymine is also known as 5-methyluracil, a pyrimidine nucleobase. As the name suggests, thymine may be derived by methylation of uracil at the 5th carbon. In RNA, thymine is replaced with uracil in most cases. In DNA, thymine(T) binds to adenine (A) via two hydrogen bonds, thus stabilizing the nucleic acid structures.

Thymine combined with deoxyribose creates the nucleoside deoxythymidine, which is synonymous with the term thymidine. Thymidine can be phosphorylated with one, two, or three phosphoric acid groups, creating, respectively, TMP, TDP, or TTP (thymidine mono-, di-, or triphosphate).

One of the common mutations of DNA involves two adjacent thymines or cytosine, which, in presence of ultraviolet light, may form thymine dimers, causing "kinks" in the DNA molecule that inhibit normal function.

Thymine could also be a target for actions of 5-fluorouracil (5-FU) in cancer treatment. 5-FU can be a metabolic analog of thymine (in DNA synthesis) or uracil (in RNA synthesis). Substitution of this analog inhibits DNA synthesis in actively-dividing cells.

Thymine bases are frequently oxidized to hydantoins over time after the death of an organism.

Cytosine (C) is one of the four main bases found in DNA and RNA, along with adenine, thymine and guanine. It is a pyrimidine derivative, with a heterocyclic aromatic ring and two substituents attached (an amine group at position 4 and a keto group at position 2). The nucleoside of cytosine is cytidine. In Watson-Crick base pairing, it forms three hydrogen bonds with guanine.

GENES

A gene is a unit of heredity in a living organism. It normally resides on a stretch of DNA that codes for a type of protein or for an RNA chain that has a function in the organism. All living things depend on genes, as they specify all proteins and functional RNA chains. Genes hold the information to build and maintain an organism's cells and pass genetic traits to offspring, although some organelles (e.g. mitochondria) are self-replicating and are not coded for by the organism's DNA.

A modern working definition of a gene is "a locatable region of genomic sequence, corresponding to a unit of inheritance, which is associated with regulatory regions, transcribed regions, and or other functional sequence regions ". Colloquial usage of the term gene (e.g. "good genes, "hair color gene") may actually refer to an allele: a gene is the basic instruction, a sequence of nucleic acid (DNA or, in the case of certain viruses RNA), while an allele is one variant of that gene. Thus, when the mainstream press refers to "having" a "gene" for a specific trait, this is generally inaccurate. In most cases, all people would have a gene for the trait in question, but certain people will have a specific allele of that gene, which results in the trait variant. In the simplest case, the phenotypic variation observed may be caused by a single letter of the genetic code - a single nucleotide polymorphism.

The notion of a gene is evolving with the science of genetics, which began when Gregor Mendel noticed that biological variations are inherited from parent organisms as specific, discrete traits. The biological entity responsible for defining traits was later termed a gene, but the biological basis for inheritance remained unknown until DNA was identified as the genetic material in the 1940s. All organisms have many genes corresponding to many different biological traits, some of which are immediately visible, such as eye color or number of limbs, and some of which are not, such as blood type or increased risk for specific diseases, or the thousands of basic biochemical processes that comprise life.

The chemical structure of a four-base fragment of a DNA double helix.

The vast majority of living organisms encode their genes in long strands of DNA. DNA (deoxyribonucleic acid) consists of a chain made from four types of nucleotide subunits, each composed of: a five-carbon sugar (2'-deoxyribose), a phosphate group, and one of the four bases adenine, cytosine, guanine, and thymine. The most common form of DNA in a cell is in a double helix structure, in which two individual DNA strands twist around each other in a right-handed spiral. In this structure, the base pairing rules specify that guanine pairs with cytosine and adenine pairs with thymine. The base pairing between guanine and cytosine forms three hydrogen bonds, whereas the base pairing between adenine and thymine forms two hydrogen bonds. The two strands in a double helix must therefore be complementary, that is, their bases must align such that the adenines of one strand are paired with the thymines of the other strand, and so on.

Due to the chemical composition of the pentose residues of the bases, DNA strands have directionality. One end of a DNA polymer contains an exposed hydroxyl group on the deoxyribose; this is known as the 3' end of the molecule. The other end contains an exposed phosphate group; this is the 5' end. The directionality of DNA is vitally important to many cellular processes, since double helices are necessarily directional (a strand running 5'-3' pairs with a complementary strand running 3'-5'), and processes such as DNA replication occur in only one direction. All nucleic acid synthesis in a cell occurs in the 5'-3' direction, because new monomers are added via a dehydration reaction that uses the exposed 3' hydroxyl as a nucleophile.

The expression of genes encoded in DNA begins by transcribing the gene into RNA, a second type of nucleic acid that is very similar to DNA, but whose monomers contain the sugar ribose rather than deoxyribose. RNA also contains the base uracil in place of thymine. RNA molecules are less stable than DNA and are typically single-stranded. Genes that encode proteins are composed of a series of three-nucleotide sequences called codons, which serve as the words in the genetic language. The genetic code specifies the correspondence during protein translation between codons and amino acids. The genetic code is nearly the same for all known organisms.

Structure of a gene

Diagram of the "typical" eukaryotic protein-coding gene. Promoters and enhancers determine what portions of the DNA will be transcribed into the precursor mRNA (pre-mRNA). The pre-mRNA is then spliced into messenger RNA (mRNA) which is later translated into protein.

All genes have regulatory regions in addition to regions that explicitly code for a protein or RNA product. A regulatory region shared by almost all genes is known as the promoter, which provides a position that is recognized by the transcription machinery when a gene is about to be transcribed and expressed. A gene can have more than one promoter, resulting in RNAs that differ in how far they extend in the 5' end. Although promoter regions have a consensus sequence that is the most common sequence at this position, some genes have "strong" promoters that bind the transcription machinery well, and others have "weak" promoters that bind poorly. These weak promoters usually permit a lower rate of transcription than the strong promoters, because the transcription machinery binds to them and initiates transcription less frequently. Other possible regulatory regions include enhancers, which can compensate for a weak promoter. Most regulatory regions are "upstream"—that is, before or toward the 5' end of the transcription initiation site. Eukaryotic promoter regions are much more complex and difficult to identify than prokaryotic promoters.

Many prokaryotic genes are organized into operons, or groups of genes whose products have related functions and which are transcribed as a unit. By contrast, eukaryotic genes are transcribed only one at a time, but may include long stretches of DNA called introns which are transcribed but never translated into protein (they are spliced out before translation). Splicing can also occur in prokaryotic genes, but is less common than in eukaryotes

Number of genes

Early estimates of the number of human genes that used expressed sequence tag data put it at 50 000–100 000. Following the sequencing of the human genome and other genomes, it has been found that rather few genes (~20 000 to 30 000 in human, mouse and fly, ~13 000 in roundworm, >46 000 in rice) encode all the proteins in an organism. These protein-coding sequences make up 1–2% of the human genome. A large part of the genome is transcribed however, to introns, retrotransposons and seemingly a large array of noncoding RNAs. Total number of proteins (the Earth's proteome) is estimated to be 5 million sequences.

DNA - The Secret of LIFE

We all know that elephants only give birth to little elephants, giraffes to giraffes, dogs to dogs and so on for every type of living creature. But why is this so?

The answer lies in a molecule called deoxyribonucleic acid (DNA), which contains the biological instructions that make each species unique. DNA, along with the instructions it contains, is passed from adult organisms to their offspring during reproduction.

Where is DNA found?

DNA is found inside a special area of the cell called the nucleus. Because the cell is very small, and because organisms have many DNA molecules per cell, each DNA molecule must be tightly packaged. This packaged form of the DNA is called a chromosome.

During DNA replication, DNA unwinds so it can be copied. At other times in the cell cycle, DNA also unwinds so that its instructions can be used to make proteins and for other biological processes. But during cell division, DNA is in its compact chromosome form to enable transfer to new cells.

Researchers refer to DNA found in the cell's nucleus as nuclear DNA. An organism's complete set of nuclear DNA is called its genome.

Besides the DNA located in the nucleus, humans and other complex organisms also have a small amount of DNA in cell structures known as mitochondria. Mitochondria generate the energy the cell needs to function properly.

In sexual reproduction, organisms inherit half of their nuclear DNA from the male parent and half from the female parent. However, organisms inherit all of their mitochondrial DNA from the female parent. This occurs because only egg cells, and not sperm cells, keep their mitochondria during fertilization.

What is DNA made of?

DNA is made of chemical building blocks called nucleotides. These building blocks are made of three parts: a phosphate group, a sugar group and one of four types of nitrogen bases. To form a strand of DNA, nucleotides are linked into chains, with the phosphate and sugar groups alternating.

The four types of nitrogen bases found in nucleotides are: adenine (A), , thymine (T), guanine (G) and cytosine (C). The order, or sequence, of these bases determines what biological instructions are contained in a strand of DNA. For example, the sequence ATCGTT might instruct for blue eyes, while ATCGCT might instruct for brown.

Each DNA sequence that contains instructions to make a protein is known as a gene. The size of a gene may vary greatly, ranging from about 1,000 bases to 1 million bases in humans.

The complete DNA instruction book, or genome, for a human contains about 3 billion bases and about 20,000 genes on 23 pairs of chromosomes.

What does DNA do?

DNA contains the instructions needed for an organism to develop, survive and reproduce. To carry out these functions, DNA sequences must be converted into messages that can be used to produce proteins, which are the complex molecules that do most of the work in our bodies.

How are DNA sequences used to make proteins?

DNA's instructions are used to make proteins in a two-step process. First, enzymes read the information in a DNA molecule and transcribe it into an intermediary molecule called messenger ribonucleic acid, or mRNA.

Next, the information contained in the mRNA molecule is translated into the "language" of amino acids, which are the building blocks of proteins. This language tells the cell's protein-making machinery the precise order in which to link the amino acids to produce a specific protein. This is a major task because there are 20 types of amino acids, which can be placed in many different orders to form a wide variety of proteins

                                               Who discovered DNA?

The German biochemist Frederich Miescher first observed DNA in the late 1800s. But nearly a century passed from that discovery until researchers unraveled the structure of the DNA molecule and realized its central importance to biology.

For many years, scientists debated which molecule carried life's biological instructions. Most thought that DNA was too simple a molecule to play such a critical role. Instead, they argued that proteins were more likely to carry out this vital function because of their greater complexity and wider variety of forms.

The importance of DNA became clear in 1953 thanks to the work of James Watson, Francis Crick, Maurice Wilkins and Rosalind Franklin. By studying X-ray diffraction patterns and building models, the scientists figured out the double helix structure of DNA - a structure that enables it to carry biological information from one generation to the next.

What is the DNA double helix?

Scientist use the term "double helix" to describe DNA's winding, two-stranded chemical structure. This shape - which looks much like a twisted ladder - gives DNA the power to pass along biological instructions with great precision.

To understand DNA's double helix from a chemical standpoint, picture the sides of the ladder as strands of alternating sugar and phosphate groups - strands that run in opposite directions. Each "rung" of the ladder is made up of two nitrogen bases, paired together by hydrogen bonds. Because of the highly specific nature of this type of chemical pairing, base A always pairs with base T, and likewise C with G. So, if you know the sequence of the bases on one strand of a DNA double helix, it is a simple matter to figure out the sequence of bases on the other strand.

DNA's unique structure enables the molecule to copy itself during cell division. When a cell prepares to divide, the DNA helix splits down the middle and becomes two single strands. These single strands serve as templates for building two new, double-stranded DNA molecules - each a replica of the original DNA molecule. In this process, an A base is added wherever there is a T, a C where there is a G, and so on until all of the bases once again have partners.

In addition, when proteins are being made, the double helix unwinds to allow a single strand of DNA to serve as a template. This template strand is then transcribed into mRNA, which is a molecule that conveys vital instructions to the cell's protein-making machinery.

ALL ABOUT CELL NUCLEUS

The nucleus was the first organelle to be discovered. The probably oldest preserved drawing dates back to the early microscopist Antonie van Leeuwenhoek (1632 – 1723). He observed a "Lumen", the nucleus, in the red blood cells of salmon. Unlike mammalian red blood cells, those of other vertebrates still possess nuclei. The nucleus was also described by Franz Bauer in 1804 and in more detail in 1831 by Scottish botanist Robert Brown in a talk at the Linnean Society of London. Brown was studying orchids microscopically when he observed an opaque area, which he called the areola or nucleus, in the cells of the flower's outer layer. He did not suggest a potential function. In 1838 Matthias Schleiden proposed that the nucleus plays a role in generating cells, thus he introduced the name "Cytoblast" (cell builder). He believed that he had observed new cells assembling around "cytoblasts". Franz Meyen was a strong opponent of this view having already described cells multiplying by division and believing that many cells would have no nuclei. The idea that cells can be generated de novo, by the "cytoblast" or otherwise, contradicted work by Robert Remak (1852) and Rudolf Virchow (1855) who decisively propagated the new paradigm that cells are generated solely by cells ("Omnis cellula e cellula"). The function of the nucleus remained unclear.

Between 1876 and 1878 Oscar Hertwig published several studies on the fertilization of sea urchin eggs, showing that the nucleus of the sperm enters the oocyte and fuses with its nucleus. This was the first time it was suggested that an individual develops from a (single) nucleated cell. This was in contradiction to Ernst Haeckel's theory that the complete phylogeny of a species would be repeated during embryonic development, including generation of the first nucleated cell from a "Monerula", a structureless mass of primordial mucus ("Urschleim"). Therefore, the necessity of the sperm nucleus for fertilization was discussed for quite some time. However, Hertwig confirmed his observation in other animal groups, e.g. amphibians and molluscs. Eduard Strasburger produced the same results for plants (1884). This paved the way to assign the nucleus an important role in heredity. In 1873 August Weismann postulated the equivalence of the maternal and paternal germ cells for heredity. The function of the nucleus as carrier of genetic information became clear only later, after mitosis was discovered and the Mendelian rules were rediscovered at the beginning of the 20th century; the chromosome theory of heredity was developed.

What is nucleus?

In cell biology, the nucleus (pl. nuclei; from Latin nucleus or nuculeus, meaning kernel) is a membrane enclosed organelle found in eukaryotic cells. It contains most of the cell's genetic material, organized as multiple long linear DNAmolecules in complex with a large variety of proteins, such as histones, to form chromosomes. The genes within these chromosomes are the cell's nuclear genome. The function of the nucleus is to maintain the integrity of these genes and to control the activities of the cell by regulating gene expression — the nucleus is therefore the control center of the cell. The main structures making up the nucleus are the nuclear envelope, a double membrane that encloses the entire organelle and separates its contents from the cellular cytoplasm, and the nuclear lamina, a meshwork within the nucleus that adds mechanical support, much like the cytoskeleton supports the cell as a whole. Because the nuclear membrane is impermeable to most molecules, nuclear pores are required to allow movement of molecules across the envelope. These pores cross both of the membranes, providing a channel that allows free movement of small molecules and ions. The movement of larger molecules such as proteins is carefully controlled, and requires active transport regulated by carrier proteins. Nuclear transport is crucial to cell function, as movement through the pores is required for both gene expression and chromosomal maintenance.

Although the interior of the nucleus does not contain any membrane-bound subcompartments, its contents are not uniform, and a number of subnuclear bodies exist, made up of unique proteins, RNA molecules, and particular parts of the chromosomes. The best known of these is the nucleolus, which is mainly involved in the assembly of ribosomes. After being produced in the nucleolus, ribosomes are exported to the cytoplasm where they translate mRNA.

The nucleoskeleton

The nucleoskeletal framework that remains insoluble after treatment of nuclei with non-ionic detergents, followed by nuclease treatment and high salt extraction to remove chromatin and soluble proteins, is generally termed the nuclear matrix. This nucleoskeleton consists of two parts namely, the nuclear lamina and a network of intricately structured fibres connected to the lamina and distributed throughout the nuclear volume. These highly structured fibre assemblies have been shown to be attached to an underlying network of 10 nm core filaments (Nickerson, 2001). The nuclear lamins A, B and C are the major structural components of the peripheral lamina. Additional proteins that connect the lamina to the nuclear envelope and the heterochromatin are clustered at the nuclear periphery. Other nuclear matrix-associated components like hnRNP complexes, newly transcribed full-length mRNA, RNA polymerase I and II, various transcription factors and spliceosomal complexes are positioned on the underlying network of branched 10 nm filaments that is connected to the nuclear lamina (Jackson and Cook, 1988; He et al., 1990; Nickerson et al., 1997). These associations might be dynamic and allow for considerable plasticity in nuclear architecture and function. Furthermore, numerous studies have suggested the presence of an organizing structure such as the nuclear matrix to coordinate the spatial regulation of DNA synthesis (Dijkwel et al., 1979; Berezney and Buchholtz, 1981; Collins and Chu, 1987; Vaughn et al., 1990; Hozak et al., 1993; 1994). The major candidate proteins that are likely to comprise the nucleoskeleton are lamins and nuclear actin. Nuclear pore complexesIn eukaryotic cells, the genetic information is stored in the nucleus and protein synthesis occurs in the cytoplasm. This compartmentalization offers additional regulation of gene expression, at the expense of a large amount of energy, to ensure the bidirectional movement of macromolecules between the two compartments through the nuclear pore complexes (NPCs). For example, different classes of RNA synthesized in the nucleus, including messenger RNA (mRNA), ribosomal RNA (rRNA), small nuclear RNA (snRNA) and transfer RNA (tRNA) have to be exported from the nucleus to the cytoplasm. Similarly, a large number of nuclear proteins and matured small nuclear ribonucleoproteins (snRNPs) are actively imported into the nucleus. The NPC has been shown to have a remarkable structure with a total mass of 124 x 106 daltons (Reichelt et al., 1990). It has a wheel-like array of a spoke ring complex, a central transporter, a cytoplasmic ring and a nuclear octagonal ring that serve as attachment sites for the cytoplasmic filaments and the nuclear basket complex respectively. The components of the spoke ring complex are interconnected to form a lumenal ring that is attached to the nuclear lamina (Yang et al., 1998). Small metabolites and molecules can freely diffuse through the NPC, which provides an aqueous channel of approximately 9 nm in diameter. However, larger macromolecules such as proteins require the presence of a signal sequence rich in basic amino acids called the nuclear localization signal (NLS) for active transport into the nucleus through the NPC. Several receptors for nucleocytoplasmic transport pathways have been identified. These receptors recognize the NLSs of their cargoes and mediate their transport. These receptors fall under a related family of shuttling transport factors called importins and exportins. These factors interact with distinct classes of transport cargoes by recognizing their NLSs, and share the ability to bind to a subset of nuclear pore proteins, also called nucleoporins. The molecular interaction of importins and exportins with their cargoes and the nucleoporins is an energy-dependent process.