Complementarity (molecular biology)
In molecular biology, complementarity describes a relationship between two structures each following the lock-and-key principle. In nature complementarity is the base principle of DNA replication and transcription as it is a property shared between two DNA or RNA sequences, such that when they are aligned antiparallel to each other, the nucleotide bases at each position in the sequences will be complementary, much like looking in the mirror and seeing the reverse of things; this complementary base pairing allows cells to copy information from one generation to another and find and repair damage to the information stored in the sequences. The degree of complementarity between two nucleic acid strands may vary, from complete complementarity to no complementarity and determines the stability of the sequences to be together. Furthermore, various DNA repair functions as well as regulatory functions are based on base pair complementarity. In biotechnology, the principle of base pair complementarity allows the generation of DNA hybrids between RNA and DNA, opens the door to modern tools such as cDNA libraries.
While most complementarity is seen between two separate strings of DNA or RNA, it is possible for a sequence to have internal complementarity resulting in the sequence binding to itself in a folded configuration. Complementarity is achieved by distinct interactions between nucleobases: adenine, thymine and cytosine. Adenine and guanine are purines, while thymine and uracil are pyrimidines. Purines are larger than pyrimidines. Both types of molecules complement each other and can only base pair with the opposing type of nucleobase. In nucleic acid, nucleobases are held together by hydrogen bonding, which only works efficiently between adenine and thymine and between guanine and cytosine; the base complement A = T shares two hydrogen bonds. All other configurations between nucleobases would hinder double helix formation. DNA strands are oriented in opposite directions, they are said to be antiparallel. A complementary strand of DNA or RNA may be constructed based on nucleobase complementarity; each base pair, A=T vs. G≡C, takes up the same space, thereby enabling a twisted DNA double helix formation without any spatial distortions.
Hydrogen bonding between the nucleobases stabilizes the DNA double helix. Complementarity of DNA strands in a double helix make it possible to use one strand as a template to construct the other; this principle plays an important role in DNA replication, setting the foundation of heredity by explaining how genetic information can be passed down to the next generation. Complementarity is utilized in DNA transcription, which generates an RNA strand from a DNA template. DNA repair mechanisms such as proof reading are complementarity based and allow for error correction during DNA replication by removing mismatched nucleobases. Nucleic acids strands may form hybrids in which single stranded DNA may anneal with complementary DNA or RNA; this principle is the basis of performed laboratory techniques such as the polymerase chain reaction, PCR. Two strands of complementary sequence are referred to as anti-sense; the sense strand is the transcribed sequence of DNA or the RNA, generated in transcription.
While the anti-sense strand is the strand, complementary to the sense sequence. Self-complementarity refers to the fact that a sequence of DNA or RNA may fold back on itself, creating a double-strand like structure. Depending on how close together the parts of the sequence are that are self-complementary, the strand may form hairpin loops, bulges or internal loops. RNA is more to form these kinds of structures due to base pair binding not seen in DNA, such as guanine binding with uracil. Complementarity can be found between short nucleic acid stretches and a coding region or an transcribed gene, results in base pairing; these short nucleic acid sequences are found in nature and have regulatory functions such as gene silencing. Antisense transcripts are stretches of non coding mRNA that are complementary to the coding sequence. Genome wide studies have shown that RNA antisense transcripts occur within nature, they are believed to increase the coding potential of the genetic code and add an overall layer of complexity to gene regulation.
So far, it is known that 40% of the human genome is transcribed in both directions, underlining the potential significance of reverse transcription. It has been suggested that complementary regions between sense and antisense transcripts would allow generation of double stranded RNA hybrids, which may play an important role in gene regulation. For example, hypoxia-induced factor 1α mRNA and β-secretase mRNA are transcribed bidirectionally, it has been shown that the antisense transcript acts as a stabilizer to the sense script. MiRNAs, microRNA, are short RNA sequences that are complementary to regions of a transcribed gene and have regulatory functions. Current research indicates that circulating miRNA may be utilized as novel biomarkers, hence show promising evidence to be utilized in disease diagnostics. MiRNAs are formed from longer sequences of RNA that are cut free by a Dicer enzyme from an RNA sequence, from a regulator gene; these short strands bind to a RISC complex. They match up with sequences in the upstream region of a transcribed gene due to their complementarity to act as a silencer for the gene in three ways.
One is by initiating translation. Two is by degrading the mRNA, and three is by providing a new double-stranded RNA seq
In geometry, parallel lines are lines in a plane which do not meet. By extension, a line and a plane, or two planes, in three-dimensional Euclidean space that do not share a point are said to be parallel. However, two lines in three-dimensional space which do not meet must be in a common plane to be considered parallel. Parallel planes are planes in the same three-dimensional space. Parallel lines are the subject of Euclid's parallel postulate. Parallelism is a property of affine geometries and Euclidean geometry is a special instance of this type of geometry. In some other geometries, such as hyperbolic geometry, lines can have analogous properties that are referred to as parallelism; the parallel symbol is ∥. For example, A B ∥ C D indicates that line AB is parallel to line CD. In the Unicode character set, the "parallel" and "not parallel" signs have codepoints U+2225 and U+2226, respectively. In addition, U+22D5 represents the relation "equal and parallel to". Given parallel straight lines l and m in Euclidean space, the following properties are equivalent: Every point on line m is located at the same distance from line l.
Line m is in the same plane as line l but does not intersect l. When lines m and l are both intersected by a third straight line in the same plane, the corresponding angles of intersection with the transversal are congruent. Since these are equivalent properties, any one of them could be taken as the definition of parallel lines in Euclidean space, but the first and third properties involve measurement, so, are "more complicated" than the second. Thus, the second property is the one chosen as the defining property of parallel lines in Euclidean geometry; the other properties are consequences of Euclid's Parallel Postulate. Another property that involves measurement is that lines parallel to each other have the same gradient; the definition of parallel lines as a pair of straight lines in a plane which do not meet appears as Definition 23 in Book I of Euclid's Elements. Alternative definitions were discussed by other Greeks as part of an attempt to prove the parallel postulate. Proclus attributes a definition of parallel lines as equidistant lines to Posidonius and quotes Geminus in a similar vein.
Simplicius mentions Posidonius' definition as well as its modification by the philosopher Aganis. At the end of the nineteenth century, in England, Euclid's Elements was still the standard textbook in secondary schools; the traditional treatment of geometry was being pressured to change by the new developments in projective geometry and non-Euclidean geometry, so several new textbooks for the teaching of geometry were written at this time. A major difference between these reform texts, both between themselves and between them and Euclid, is the treatment of parallel lines; these reform texts were not without their critics and one of them, Charles Dodgson, wrote a play and His Modern Rivals, in which these texts are lambasted. One of the early reform textbooks was James Maurice Wilson's Elementary Geometry of 1868. Wilson based his definition of parallel lines on the primitive notion of direction. According to Wilhelm Killing the idea may be traced back to Leibniz. Wilson, without defining direction since it is a primitive, uses the term in other definitions such as his sixth definition, "Two straight lines that meet one another have different directions, the difference of their directions is the angle between them."
Wilson In definition 15 he introduces parallel lines in this way. Wilson Augustus De Morgan reviewed this text and declared it a failure on the basis of this definition and the way Wilson used it to prove things about parallel lines. Dodgson devotes a large section of his play to denouncing Wilson's treatment of parallels. Wilson edited this concept out of the third and higher editions of his text. Other properties, proposed by other reformers, used as replacements for the definition of parallel lines, did not fare much better; the main difficulty, as pointed out by Dodgson, was that to use them in this way required additional axioms to be added to the system. The equidistant line definition of Posidonius, expounded by Francis Cuthbertson in his 1874 text Euclidean Geometry suffers from the problem that the points that are found at a fixed given distance on one side of a straight line must be shown to form a straight line; this must be assumed to be true. The corresponding angles formed by a transversal property, used by W. D. Cooley in his 1860 text, The Elements of Geometry and explained requires a proof of the fact that if one transversal meets a pair of lines in congruent corresponding angles all transversals must do so.
Again, a new axiom is needed to justify this statement. The three properties above lead to three different methods of construction of parallel lines; because parallel lines in a Euclidean plane are equidistant there is a unique distance between the two parallel lines. Given the equations of two non-vertical, non-horizontal parallel lines, y = m x + b 1 y = m x + b 2
Biochemistry, sometimes called biological chemistry, is the study of chemical processes within and relating to living organisms. Biochemical processes give rise to the complexity of life. A sub-discipline of both biology and chemistry, biochemistry can be divided in three fields. Over the last decades of the 20th century, biochemistry has through these three disciplines become successful at explaining living processes. All areas of the life sciences are being uncovered and developed by biochemical methodology and research. Biochemistry focuses on understanding how biological molecules give rise to the processes that occur within living cells and between cells, which in turn relates to the study and understanding of tissues and organism structure and function. Biochemistry is related to molecular biology, the study of the molecular mechanisms by which genetic information encoded in DNA is able to result in the processes of life. Much of biochemistry deals with the structures and interactions of biological macromolecules, such as proteins, nucleic acids and lipids, which provide the structure of cells and perform many of the functions associated with life.
The chemistry of the cell depends on the reactions of smaller molecules and ions. These can be inorganic, for example water and metal ions, or organic, for example the amino acids, which are used to synthesize proteins; the mechanisms by which cells harness energy from their environment via chemical reactions are known as metabolism. The findings of biochemistry are applied in medicine and agriculture. In medicine, biochemists investigate the cures of diseases. In nutrition, they study how to maintain health wellness and study the effects of nutritional deficiencies. In agriculture, biochemists investigate soil and fertilizers, try to discover ways to improve crop cultivation, crop storage and pest control. At its broadest definition, biochemistry can be seen as a study of the components and composition of living things and how they come together to become life, in this sense the history of biochemistry may therefore go back as far as the ancient Greeks. However, biochemistry as a specific scientific discipline has its beginning sometime in the 19th century, or a little earlier, depending on which aspect of biochemistry is being focused on.
Some argued that the beginning of biochemistry may have been the discovery of the first enzyme, diastase, in 1833 by Anselme Payen, while others considered Eduard Buchner's first demonstration of a complex biochemical process alcoholic fermentation in cell-free extracts in 1897 to be the birth of biochemistry. Some might point as its beginning to the influential 1842 work by Justus von Liebig, Animal chemistry, or, Organic chemistry in its applications to physiology and pathology, which presented a chemical theory of metabolism, or earlier to the 18th century studies on fermentation and respiration by Antoine Lavoisier. Many other pioneers in the field who helped to uncover the layers of complexity of biochemistry have been proclaimed founders of modern biochemistry, for example Emil Fischer for his work on the chemistry of proteins, F. Gowland Hopkins on enzymes and the dynamic nature of biochemistry; the term "biochemistry" itself is derived from a combination of chemistry. In 1877, Felix Hoppe-Seyler used the term as a synonym for physiological chemistry in the foreword to the first issue of Zeitschrift für Physiologische Chemie where he argued for the setting up of institutes dedicated to this field of study.
The German chemist Carl Neuberg however is cited to have coined the word in 1903, while some credited it to Franz Hofmeister. It was once believed that life and its materials had some essential property or substance distinct from any found in non-living matter, it was thought that only living beings could produce the molecules of life. In 1828, Friedrich Wöhler published a paper on the synthesis of urea, proving that organic compounds can be created artificially. Since biochemistry has advanced since the mid-20th century, with the development of new techniques such as chromatography, X-ray diffraction, dual polarisation interferometry, NMR spectroscopy, radioisotopic labeling, electron microscopy, molecular dynamics simulations; these techniques allowed for the discovery and detailed analysis of many molecules and metabolic pathways of the cell, such as glycolysis and the Krebs cycle, led to an understanding of biochemistry on a molecular level. Philip Randle is well known for his discovery in diabetes research is the glucose-fatty acid cycle in 1963.
He confirmed. High fat oxidation was responsible for the insulin resistance. Another significant historic event in biochemistry is the discovery of the gene, its role in the transfer of information in the cell; this part of biochemistry is called molecular biology. In the 1950s, James D. Watson, Francis Crick, Rosalind Franklin, Maurice Wilkins were instrumental in solving DNA structure and suggesting its relationship with genetic transfer of information. In 1958, George Beadle and Edward Tatum received the Nobel Prize for work in fungi showing that one gene produces one enzyme. In 1988, Colin Pitchfork was the first person convicted of murder with DNA evidence, which led to the growth of forensic science. More Andrew Z. Fire and Craig C. Mello received the 2006 Nobel Prize for discovering the role of RNA interference, in the silencing of gene expression. Around two dozen of the 92
In molecular biology, DNA replication is the biological process of producing two identical replicas of DNA from one original DNA molecule. DNA replication occurs in all living organisms acting as the basis for biological inheritance; the cell possesses the distinctive property of division. DNA is made up of a double helix of two complementary strands. During replication, these strands are separated; each strand of the original DNA molecule serves as a template for the production of its counterpart, a process referred to as semiconservative replication. As a result of semi-conservative replication, the new helix will be composed of an original DNA strand as well as a newly synthesized strand. Cellular proofreading and error-checking mechanisms ensure near perfect fidelity for DNA replication. In a cell, DNA replication begins at origins of replication, in the genome. Unwinding of DNA at the origin and synthesis of new strands, accommodated by an enzyme known as helicase, results in replication forks growing bi-directionally from the origin.
A number of proteins are associated with the replication fork to help in the initiation and continuation of DNA synthesis. Most prominently, DNA polymerase synthesizes the new strands by adding nucleotides that complement each strand. DNA replication occurs during the S-stage of interphase. DNA replication can be performed in vitro. DNA polymerases isolated from cells and artificial DNA primers can be used to start DNA synthesis at known sequences in a template DNA molecule. Polymerase chain reaction, ligase chain reaction, transcription-mediated amplification are examples. DNA exists as a double-stranded structure, with both strands coiled together to form the characteristic double-helix; each single strand of DNA is a chain of four types of nucleotides. Nucleotides in DNA contain a deoxyribose sugar, a phosphate, a nucleobase; the four types of nucleotide correspond to the four nucleobases adenine, cytosine and thymine abbreviated as A, C, G and T. Adenine and guanine are purine bases, while cytosine and thymine are pyrimidines.
These nucleotides form phosphodiester bonds, creating the phosphate-deoxyribose backbone of the DNA double helix with the nucleobases pointing inward. Nucleobases are matched between strands through hydrogen bonds to form base pairs. Adenine pairs with thymine, guanine pairs with cytosine. DNA strands have a directionality, the different ends of a single strand are called the "3′ end" and the "5′ end". By convention, if the base sequence of a single strand of DNA is given, the left end of the sequence is the 5′ end, while the right end of the sequence is the 3′ end; the strands of the double helix are anti-parallel with one being 5′ to 3′, the opposite strand 3′ to 5′. These terms refer to the carbon atom in deoxyribose to which the next phosphate in the chain attaches. Directionality has consequences in DNA synthesis, because DNA polymerase can synthesize DNA in only one direction by adding nucleotides to the 3′ end of a DNA strand; the pairing of complementary bases in DNA means that the information contained within each strand is redundant.
Phosphodiester bonds are stronger than hydrogen bonds. This allows the strands to be separated from one another; the nucleotides on a single strand can therefore be used to reconstruct nucleotides on a newly synthesized partner strand. DNA polymerases are a family of enzymes. DNA polymerases in general cannot initiate synthesis of new strands, but can only extend an existing DNA or RNA strand paired with a template strand. To begin synthesis, a short fragment of RNA, called a primer, must be created and paired with the template DNA strand. DNA polymerase adds a new strand of DNA by extending the 3′ end of an existing nucleotide chain, adding new nucleotides matched to the template strand one at a time via the creation of phosphodiester bonds; the energy for this process of DNA polymerization comes from hydrolysis of the high-energy phosphate bonds between the three phosphates attached to each unincorporated base. Free bases with their attached phosphate groups are called nucleotides; when a nucleotide is being added to a growing DNA strand, the formation of a phosphodiester bond between the proximal phosphate of the nucleotide to the growing chain is accompanied by hydrolysis of a high-energy phosphate bond with release of the two distal phosphates as a pyrophosphate.
Enzymatic hydrolysis of the resulting pyrophosphate into inorganic phosphate consumes a second high-energy phosphate bond and renders the reaction irreversible. In general, DNA polymerases are accurate, with an intrinsic error rate of less than one mistake for every 107 nucleotides added. In addition, some DNA polymerases have proofreading ability. Post-replication mismatch repair mechanisms monitor the DNA for errors, being capable of distinguishing mismatches in the newly synthesized DNA strand from the original strand sequence. Together, these three discrimination steps enable replication fidelity of less than one mistake for every 109 nucleotides added; the rate of DNA replication in a living cell was first measured as the rate of phage T4 DNA elongation in phage-infected E. coli. During the period of exponential DNA increase at 37 °C, the rate was 749 nucleotides per second
Peptides are short chains of amino acid monomers linked by peptide bonds. The covalent chemical bonds are formed when the carboxyl group of one amino acid reacts with the amino group of another; the shortest peptides are dipeptides, consisting of 2 amino acids joined by a single peptide bond, followed by tripeptides, etc. A polypeptide is a long and unbranched peptide chain. Hence, peptides fall under the broad chemical classes of biological oligomers and polymers, alongside nucleic acids and polysaccharides, etc. Peptides are distinguished from proteins on the basis of size, as an arbitrary benchmark can be understood to contain 50 or fewer amino acids. Proteins consist of one or more polypeptides arranged in a biologically functional way bound to ligands such as coenzymes and cofactors, or to another protein or other macromolecule, or to complex macromolecular assemblies. While aspects of the lab techniques applied to peptides versus polypeptides and proteins differ, the size boundaries that distinguish peptides from polypeptides and proteins are not absolute: long peptides such as amyloid beta have been referred to as proteins, smaller proteins like insulin have been considered peptides.
Amino acids that have been incorporated into peptides are termed "residues" due to the release of either a hydrogen ion from the amine end or a hydroxyl ion from the carboxyl end, or both, as a water molecule is released during formation of each amide bond. All peptides except cyclic peptides have an N-terminal and C-terminal residue at the end of the peptide. Many kinds of peptides are known, they have been categorized according to their sources and function. According to the Handbook of Biologically Active Peptides, some groups of peptides include plant peptides, bacterial/antibiotic peptides, fungal peptides, invertebrate peptides, amphibian/skin peptides, venom peptides, cancer/anticancer peptides, vaccine peptides, immune/inflammatory peptides, brain peptides, endocrine peptides, ingestive peptides, gastrointestinal peptides, cardiovascular peptides, renal peptides, respiratory peptides, opiate peptides, neurotrophic peptides, blood–brain peptides; some ribosomal peptides are subject to proteolysis.
These function in higher organisms, as hormones and signaling molecules. Some organisms produce peptides as antibiotics, such as microcins. Peptides have posttranslational modifications such as phosphorylation, sulfonation, palmitoylation and disulfide formation. In general, peptides are linear. More exotic manipulations do occur, such as racemization of L-amino acids to D-amino acids in platypus venom. Nonribosomal peptides are assembled by enzymes, not the ribosome. A common non-ribosomal peptide is glutathione, a component of the antioxidant defenses of most aerobic organisms. Other nonribosomal peptides are most common in unicellular organisms and fungi and are synthesized by modular enzyme complexes called nonribosomal peptide synthetases; these complexes are laid out in a similar fashion, they can contain many different modules to perform a diverse set of chemical manipulations on the developing product. These peptides are cyclic and can have complex cyclic structures, although linear nonribosomal peptides are common.
Since the system is related to the machinery for building fatty acids and polyketides, hybrid compounds are found. The presence of oxazoles or thiazoles indicates that the compound was synthesized in this fashion. Peptide fragments refer to fragments of proteins that are used to identify or quantify the source protein; these are the products of enzymatic degradation performed in the laboratory on a controlled sample, but can be forensic or paleontological samples that have been degraded by natural effects. Use of peptides received prominence in molecular biology for several reasons; the first is that peptides allow the creation of peptide antibodies in animals without the need of purifying the protein of interest. This involves synthesizing antigenic peptides of sections of the protein of interest; these will be used to make antibodies in a rabbit or mouse against the protein. Another reason is that techniques such as mass spectrometry enable the identification of proteins based on the peptide masses and sequence that result from their fragmentation.
Peptides have been used in the study of protein structure and function. For example, synthetic peptides can be used as probes to see where protein-peptide interactions occur- see the page on Protein tags. Inhibitory peptides are used in clinical research to examine the effects of peptides on the inhibition of cancer proteins and other diseases. For example, one of the most promising application is through peptides that target LHRH; these particular peptides act as an agonist, meaning that they bind to a cell in a way that regulates LHRH receptors. The process of inhibiting the cell receptors suggests that peptides could be beneficial in treating prostate cancer, but additional investigations and experiments are required before their cancer-fighting attributes can be considered definitive; the peptide families in this section are ribosomal peptides with hormonal activity. All of these peptides are synthesized by cells as longer "propeptides" or "proproteins" and truncated prior to exiting the cell.
They are released into the bloodstream. Magainin family Cecropin famil
Nucleic acids are the biopolymers, or small biomolecules, essential to all known forms of life. The term nucleic acid is the overall name for DNA and RNA, they are composed of nucleotides, which are the monomers made of three components: a 5-carbon sugar, a phosphate group and a nitrogenous base. If the sugar is a compound ribose, the polymer is RNA. Nucleic acids are the most important of all biomolecules, they are found in abundance in all living things, where they function to create and encode and store information in the nucleus of every living cell of every life-form organism on Earth. In turn, they function to transmit and express that information inside and outside the cell nucleus—to the interior operations of the cell and to the next generation of each living organism; the encoded information is contained and conveyed via the nucleic acid sequence, which provides the'ladder-step' ordering of nucleotides within the molecules of RNA and DNA. Strings of nucleotides are bonded to form helical backbones—typically, one for RNA, two for DNA—and assembled into chains of base-pairs selected from the five primary, or canonical, which are: adenine, guanine and uracil.
Using amino acids and the process known as protein synthesis, the specific sequencing in DNA of these nucleobase-pairs enables storing and transmitting coded instructions as genes. In RNA, base-pair sequencing provides for manufacturing new proteins that determine the frames and parts and most chemical processes of all life forms. Nuclein were discovered by Friedrich Miescher in 1869. In the early 1880s Albrecht Kossel further purifies the substance and discovers its acidic properties, he also identifies the nucleobases. In 1889 Richard Altmann creates the term nucleic acid In 1938 Astbury and Bell published the first X-ray diffraction pattern of DNA. In 1953 Watson and Crick determined the structure of DNA. Experimental studies of nucleic acids constitute a major part of modern biological and medical research, form a foundation for genome and forensic science, the biotechnology and pharmaceutical industries; the term nucleic acid is the overall name for DNA and RNA, members of a family of biopolymers, is synonymous with polynucleotide.
Nucleic acids were named for their initial discovery within the nucleus, for the presence of phosphate groups. Although first discovered within the nucleus of eukaryotic cells, nucleic acids are now known to be found in all life forms including within bacteria, mitochondria, chloroplasts and viroids.. All living cells contain both DNA and RNA, while viruses contain either DNA or RNA, but not both; the basic component of biological nucleic acids is the nucleotide, each of which contains a pentose sugar, a phosphate group, a nucleobase. Nucleic acids are generated within the laboratory, through the use of enzymes and by solid-phase chemical synthesis; the chemical methods enable the generation of altered nucleic acids that are not found in nature, for example peptide nucleic acids. Nucleic acids are very large molecules. Indeed, DNA molecules are the largest individual molecules known. Well-studied biological nucleic acid molecules range in size from 21 nucleotides to large chromosomes. In most cases occurring DNA molecules are double-stranded and RNA molecules are single-stranded.
There are numerous exceptions, however—some viruses have genomes made of double-stranded RNA and other viruses have single-stranded DNA genomes, and, in some circumstances, nucleic acid structures with three or four strands can form. Nucleic acids are linear polymers of nucleotides; each nucleotide consists of three components: a purine or pyrimidine nucleobase, a pentose sugar, a phosphate group. The substructure consisting of a nucleobase plus sugar is termed a nucleoside. Nucleic acid types differ in the structure of the sugar in their nucleotides–DNA contains 2'-deoxyribose while RNA contains ribose; the nucleobases found in the two nucleic acid types are different: adenine and guanine are found in both RNA and DNA, while thymine occurs in DNA and uracil occurs in RNA. The sugars and phosphates in nucleic acids are connected to each other in an alternating chain through phosphodiester linkages. In conventional nomenclature, the carbons to which the phosphate groups attach are the 3'-end and the 5'-end carbons of the sugar.
This gives nucleic acids directionality, the ends of nucleic acid molecules are referred to as 5'-end and 3'-end. The nucleobases are joined to the sugars via an N-glycosidic linkage involving a nucleobase ring nitrogen and the 1' carbon of the pentose sugar ring. Non-standard nucleosides are found in both RNA and DNA and arise from modification of the standard nucleosides within the DNA molecule or the primary RNA transcript. Transfer RNA molecules contain a large number of modified nucleosides. Double-stranded nucleic acids are made up of complementary sequences, in which extensive Watson-Crick base pairing results in a repeated and quite uniform double-helical three-dimensional structure. In contrast, single-stranded
Amino acids are organic compounds containing amine and carboxyl functional groups, along with a side chain specific to each amino acid. The key elements of an amino acid are carbon, hydrogen and nitrogen, although other elements are found in the side chains of certain amino acids. About 500 occurring amino acids are known and can be classified in many ways, they can be classified according to the core structural functional groups' locations as alpha-, beta-, gamma- or delta- amino acids. In the form of proteins, amino acid residues form the second-largest component of human muscles and other tissues. Beyond their role as residues in proteins, amino acids participate in a number of processes such as neurotransmitter transport and biosynthesis. In biochemistry, amino acids having both the amine and the carboxylic acid groups attached to the first carbon atom have particular importance, they are known as α-amino acids. They include the 22 proteinogenic amino acids, which combine into peptide chains to form the building-blocks of a vast array of proteins.
These are all L-stereoisomers, although a few D-amino acids occur in bacterial envelopes, as a neuromodulator, in some antibiotics. Twenty of the proteinogenic amino acids are encoded directly by triplet codons in the genetic code and are known as "standard" amino acids; the other two are selenocysteine, pyrrolysine. Pyrrolysine and selenocysteine are encoded via variant codons. N-formylmethionine is considered as a form of methionine rather than as a separate proteinogenic amino acid. Codon–tRNA combinations not found in nature can be used to "expand" the genetic code and form novel proteins known as alloproteins incorporating non-proteinogenic amino acids. Many important proteinogenic and non-proteinogenic amino acids have biological functions. For example, in the human brain and gamma-amino-butyric acid are the main excitatory and inhibitory neurotransmitters. Hydroxyproline, a major component of the connective tissue collagen, is synthesised from proline. Glycine is a biosynthetic precursor to porphyrins used in red blood cells.
Carnitine is used in lipid transport. Nine proteinogenic amino acids are called "essential" for humans because they cannot be produced from other compounds by the human body and so must be taken in as food. Others may be conditionally essential for medical conditions. Essential amino acids may differ between species; because of their biological significance, amino acids are important in nutrition and are used in nutritional supplements, fertilizers and food technology. Industrial uses include the production of drugs, biodegradable plastics, chiral catalysts; the first few amino acids were discovered in the early 19th century. In 1806, French chemists Louis-Nicolas Vauquelin and Pierre Jean Robiquet isolated a compound in asparagus, subsequently named asparagine, the first amino acid to be discovered. Cystine was discovered in 1810, although its monomer, remained undiscovered until 1884. Glycine and leucine were discovered in 1820; the last of the 20 common amino acids to be discovered was threonine in 1935 by William Cumming Rose, who determined the essential amino acids and established the minimum daily requirements of all amino acids for optimal growth.
The unity of the chemical category was recognized by Wurtz in 1865, but he gave no particular name to it. Usage of the term "amino acid" in the English language is from 1898, while the German term, Aminosäure, was used earlier. Proteins were found to yield amino acids after enzymatic acid hydrolysis. In 1902, Emil Fischer and Franz Hofmeister independently proposed that proteins are formed from many amino acids, whereby bonds are formed between the amino group of one amino acid with the carboxyl group of another, resulting in a linear structure that Fischer termed "peptide". In the structure shown at the top of the page, R represents a side chain specific to each amino acid; the carbon atom next to the carboxyl group is called the α–carbon. Amino acids containing an amino group bonded directly to the alpha carbon are referred to as alpha amino acids; these include amino acids such as proline which contain secondary amines, which used to be referred to as "imino acids". The alpha amino acids are the most common form found in nature, but only when occurring in the L-isomer.
The alpha carbon is a chiral carbon atom, with the exception of glycine which has two indistinguishable hydrogen atoms on the alpha carbon. Therefore, all alpha amino acids but glycine can exist in either of two enantiomers, called L or D amino acids, which are mirror images of each other. While L-amino acids represent all of the amino acids found in proteins during translation in the ribosome, D-amin