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This article is about the class of chemicals. For the structures and properties of the standard proteinogenic amino acids, see List of standard amino acids.
Phenylalanine is one of the standard amino acids.
Phenylalanine is one of the standard amino acids. Phe redirects here For the BitTorrent feature see PHE. For the constellation see Phoenix (constellation.

In chemistry, an amino acid is a molecule containing both amine and carboxyl functional groups. Chemistry (from Egyptian kēme (chem meaning "earth") is the Science concerned with the composition structure and properties In Chemistry, a molecule is defined as a sufficiently stable electrically neutral group of at least two Atoms in a definite arrangement held together by Amines are Organic compounds and Functional groups that contain a basic Nitrogen Atom with a Lone pair. Carboxyl group or CO2H is a Functional group present in Amino acids and Carboxylic acids Its structure is composed of one carbon atom attached In Organic chemistry, functional groups are specific groups of Atoms within Molecules that are responsible for the characteristic Chemical reactions In biochemistry, this term refers to alpha-amino acids with the general formula H2NCHRCOOH, where R is an organic substituent. Biochemistry is the study of the chemical processes in living Organisms It deals with the Structure and function of cellular components such as [1] In the alpha amino acids, the amino and carboxylate groups are attached to the same carbon, which is called the α–carbon. Carbon (kɑɹbən is a Chemical element with the symbol C and its Atomic number is 6 The alpha carbon in Organic chemistry refers to the first carbon that attaches to a Functional group (the carbon is attached at the first or alpha position The various alpha amino acids differ in which side chain (R group) is attached to their alpha carbon. A side chain in Organic chemistry and Biochemistry is a part of a Molecule that is attached to a core structure They can vary in size from just a hydrogen atom in glycine through a methyl group in alanine to a large heterocyclic group in tryptophan. Glycine (abbreviated as Gly or G) is the Organic compound with the formula NH2CH2COOH In Chemistry, a methyl group is a Hydrophobic Alkyl Functional group named after Methane (4 Alanine (abbreviated as Ala or A) is an α- Amino acid with the Chemical formula HO2CCH(NH2CH3 Tryptophan (abbreviated as Trp or W) is one of the 20 standard amino acids, as well as an Essential amino acid in the Human diet

Beyond the amino acids that are found in all forms of life, many non-natural amino acids have vital roles in technology and industry. Life is a state that distinguishes Organisms from non-living objects such as non-life and dead organisms being manifested by growth through Metabolism For example, the chelating agents EDTA and nitrilotriacetic acid are alpha amino acids that are important in the chemical industry. Chelation is the binding or complexation of a bi- or multidentate Ligand. EDTA is a widely used abbreviation for the Chemical compound ethylenediaminetetraacetic acid (and many other names see table Nitrilotriacetic acid (NTA C6H9NO6 is a chemical compound used as a Chelating agent which forms Coordination compounds with metal The chemical industry comprises the companies that produce industrial chemicals

Contents

Overview

Alpha-amino acids are the building blocks of proteins. Proteins are large Organic compounds made of Amino acids arranged in a linear chain and joined together by Peptide bonds between the Carboxyl Amino acids combine in a condensation reaction that releases water and the new "amino acid residue" that is held together by a peptide bond. A condensation reaction is a Chemical reaction in which two Molecules or moieties ( Functional groups) combine to form one single molecule together with A peptide bond is a Chemical bond formed between two Molecules when the Carboxyl group of one molecule reacts with the Proteins are defined by their unique sequence of amino acid residues; this sequence is the primary structure of the protein. In Biochemistry, the primary structure of a biological molecule is the exact specification of its atomic composition and the chemical bonds connecting those atoms (including Just as the letters of the alphabet can be combined to form an almost endless variety of words, amino acids can be linked in varying sequences to form a vast variety of proteins.

Twenty standard amino acids are used by cells in protein biosynthesis, and these are specified by the general genetic code. The cell is the structural and functional unit of all known living Organisms It is the smallest unit of an organism that is classified as living and is often called Protein biosynthesis (synthesis is the process in which cells build Proteins The term is sometimes used to refer only to protein translation but more The genetic code is the set of rules by which information encoded in genetic material ( DNA or RNA sequences is translated into Proteins These 20 amino acids are biosynthesized from other molecules, but organisms differ in which ones they can synthesize and which ones must be provided in their diet. Biosynthesis is a phenomenon wherein Chemical compounds are produced from simpler Reagents Biosynthesis unlike Chemosynthesis, takes place within living The ones that cannot be synthesized by an organism are called essential amino acids. An essential amino acid or indispensable amino acid is an Amino acid that cannot be synthesized de novo by the organism (usually referring to

Functions in proteins

See also: Primary structure and Posttranslational modification
A polypeptide is a chain of amino acids.
A polypeptide is a chain of amino acids. In Biochemistry, the primary structure of a biological molecule is the exact specification of its atomic composition and the chemical bonds connecting those atoms (including Posttranslational modification (PTM is the chemical modification of a Protein after its translation. Peptides (from the Greek πεπτίδια, "small digestibles" are short Polymers formed from the linking in a defined order of α- Amino

Amino acids are the basic structural building units of proteins. They form short polymer chains called peptides or longer chains called either polypeptides or proteins. A polymer is a large Molecule ( Macromolecule) composed of repeating Structural units typically connected by Covalent Chemical bonds Peptides (from the Greek πεπτίδια, "small digestibles" are short Polymers formed from the linking in a defined order of α- Amino Peptides (from the Greek πεπτίδια, "small digestibles" are short Polymers formed from the linking in a defined order of α- Amino Proteins are large Organic compounds made of Amino acids arranged in a linear chain and joined together by Peptide bonds between the Carboxyl The process of such formation from an mRNA template is known as translation, which is part of protein biosynthesis. Messenger ribonucleic acid ( mRNA) is a molecule of RNA encoding a chemical "blueprint" for a Protein product Translation is the first stage of Protein biosynthesis (part of the overall process of Gene expression) Twenty amino acids are encoded by the standard genetic code and are called proteinogenic or standard amino acids. The genetic code is the set of rules by which information encoded in genetic material ( DNA or RNA sequences is translated into Proteins Proteinogenic Amino acids also known as standard normal or primary amino acids are those 20 amino acids that are found in Proteins and that are coded for in the Other amino acids contained in proteins are usually formed by post-translational modification, which is modification after translation in protein synthesis. Posttranslational modification (PTM is the chemical modification of a Protein after its translation. These modifications are often essential for the function or regulation of a protein; for example, the carboxylation of glutamate allows for better binding of calcium cations, and the hydroxylation of proline is critical for maintaining connective tissues and responding to oxygen starvation. Carboxylation in Chemistry is a Chemical reaction in which a Carboxylic acid group is introduced in a Substrate. Glutamic acid (abbreviated as Glu or E) is one of the 20 Alpha Amino acids It is not among the human Essential amino acids Its Calcium (Ca2+ plays a vital role in the Anatomy, Physiology and Biochemistry of Organisms and of the cell, particularly Hydroxylation is any chemical process that introduces one or more hydroxyl groups (-OH into a compound (or radical thereby oxidizing it Proline (abbreviated as Pro or P) is an α- Amino acid, one of the twenty DNA -encoded amino acids Collagen is the main Protein of Connective tissue in Animals and the most abundant protein in Mammals making up about 50% of the whole-body protein Chronic Hypoxia is a pathological condition in which the body as a whole ( generalized hypoxia) or region of the body ( tissue hypoxia) is deprived of adequate Such modifications can also determine the localization of the protein, e. g. , the addition of long hydrophobic groups can cause a protein to bind to a phospholipid membrane. Phospholipids are a class of Lipids and are a major component of all Biological membranes All phospholipids contain a Diglyceride, a Phosphate

Non-protein functions

The 20 standard amino acids are either used to synthesize proteins and other biomolecules or oxidized to urea and carbon dioxide as a source of energy. Urea is an Organic compound with the Chemical formula ( N[[hydrogen H]]22 C[[oxygen O]] [2] The oxidation pathway starts with the removal of the amino group by a transaminase, the amino group is then fed into the urea cycle. In Biochemistry, a transaminase or an aminotransferase is an Enzyme that Catalyzes a type of reaction between an Amino acid and an The urea cycle (also known as the ornithine cycle) is a cycle of biochemical reactions occurring in many animals that produces Urea ( N[[hydrogen The other product of transamidation is a keto acid that enters the citric acid cycle. Keto acids are organic Acids containing a Ketone Functional group and a Carboxylic acid group [3] Glucogenic amino acids can also be converted into glucose, through gluconeogenesis. A glucogenic amino acid is an Amino acid that can be converted into Glucose through Gluconeogenesis. Gluconeogenesis (abreviated GNG) is a Metabolic pathway that results in the generation of Glucose from non- Carbohydrate carbon substrates such [4]

Hundreds of types of non-protein amino acids have been found in nature and they have multiple functions in living organisms. Microorganisms and plants can produce uncommon amino acids. A microorganism (also spelled micro organism or micro-organism and also called a microbe) is an Organism that is Microscopic (usually In microbes, examples include 2-aminoisobutyric acid and lanthionine, which is a sulfide-bridged alanine dimer. 2-Aminoisobutyric acid, or α-aminoisobutyric acid ( AIB) or α-methylalanine or 2-methylalanine, is an Amino acid with the Structural Lanthionine is a Nonproteinogenic Amino acid with the chemical formula (HOOC-CH(NH2-CH2-S-CH2-CH(NH2-COOH Both these amino acids are both found in peptidic lantibiotics such as alamethicin. Lantibiotics are a class of Peptide Antibiotics that contain polycyclic Thioether Amino acids as well as the unsaturated amino acids Alamethicin is a Peptide Antibiotic, produced by the fungus Trichoderma viride. [5] While in plants, 1-aminocyclopropane-1-carboxylic acid is a small disubstituted cyclic amino acid that is a key intermediate in the production of the plant hormone ethylene. Structure This Hydrocarbon has four Hydrogen Atoms bound to a pair of Carbon atoms that are connected by a Double bond. [6]

In humans, non-protein amino acids also have important roles, such as the neurotransmitter gamma-aminobutyric acid. See Chemical synapse for an introduction to concepts and terminology used in this article Gamma-aminobutyric acid (GABA is the chief inhibitory Neurotransmitter in the Mammalian Central nervous system. Many amino acids are used to synthesize other molecules, for example:

Hydroxyproline, hydroxylysine, and sarcosine are also non-protein amino acids. 4-Hydroxyproline, or hydroxyproline ( C 5 H 9 O 3 N) is an uncommon Amino acid, abbreviated as HYP 5-Hydroxylysine is an Amino acid with the molecular formula C6H14N2O3 Sarcosine is the N- Methyl derivative of Glycine. It is a natural Amino acid found in muscles and other body tissues The thyroid hormones are also alpha-amino acids. The thyroid hormones, Thyroxine ( T4) and Triiodothyronine ( T3) are Tyrosine -based Hormones produced

Some amino acids have even been detected in meteorites, especially in a type known as carbonaceous chondrites. A meteorite is a natural object originating in Outer space that survives an impact with the Earth 's surface A carbonaceous chondrite or a C-type chondrite is a type of chondritic Meteorite which contains high levels of Water and Organic compounds [7] This observation has prompted the suggestion that life may have arrived on earth from an extraterrestrial source. In the Natural sciences, Abiogenesis, or origin of life, is the study of how Life on Earth emerged from Inanimate Organic

General structure

Further information: List of standard amino acids
The general structure of an α-amino acid, with the amino group on the left and the carboxyl group on the right.
The general structure of an α-amino acid, with the amino group on the left and the carboxyl group on the right. Amines are Organic compounds and Functional groups that contain a basic Nitrogen Atom with a Lone pair. Carboxyl group or CO2H is a Functional group present in Amino acids and Carboxylic acids Its structure is composed of one carbon atom attached

In the structure shown at the right, R represents a side chain specific to each amino acid. A side chain in Organic chemistry and Biochemistry is a part of a Molecule that is attached to a core structure The central carbon atom, called Cα, is a chiral central carbon atom (with the exception of glycine) to which the two termini and the R-group are attached. Carbon (kɑɹbən is a Chemical element with the symbol C and its Atomic number is 6 The term chiral (pronounced /ˈkaɪɹ(əl̩/ is used to describe an object that is non- superimposable on its mirror image Amino acids are usually classified by the properties of the side chain into four groups. A chemical property is any of a material's properties that becomes evident during a Chemical reaction; that is any quality that can be established only by changing a substance's The side chain can make them behave like a weak acid, a weak base, a hydrophile if they are polar, and hydrophobe if they are nonpolar. A weak acid is an Acid that does not completely donate all of its hydrogens when dissolved in water In chemistry a weak base is a Chemical base that does not Ionize fully in an Aqueous solution. In Chemistry, a base is most commonly thought of as an aqueous substance that can accept Protons This refers to the Brønsted-Lowry theory of acids and Hydrophile, from the Greek (hydros "water" and φιλια (philia "friendship" refers to a physical property of a Molecule "Polar molecule" and "Non-polar" redirect here In Chemistry, hydrophobicity (from the combining form of water in Attic Greek hydro- and for fear phobos) refers to the physical property of "Polar molecule" and "Non-polar" redirect here The chemical structures of the 20 standard amino acids, along with their chemical properties, are catalogued in the list of standard amino acids.

The phrase "branched-chain amino acids" or BCAA is sometimes used to refer to the amino acids having aliphatic side chains that are non-linear; these are leucine, isoleucine, and valine. The phrase branched-chain amino acids or BCAA is sometimes used to refer to the Amino acids having Aliphatic side-chains that are non-linear In Organic chemistry, compounds composed of Carbon and Hydrogen are divided into two classes Aromatic compounds which contain Benzene rings Leucine (abbreviated as Leu or L) is an α- Amino acid with the Chemical formula HO2CCH(NH2CH2CH(CH32 Isoleucine (abbreviated as Ile or I) is an α- Amino acid with the Chemical formula HO2CCH(NH2CH(CH3CH2CH3 Valine (abbreviated as Val or V) is an α- Amino acid with the Chemical formula HO2CCH(NH2CH(CH32 Proline is the only proteinogenic amino acid whose side group links to the α-amino group and, thus, is also the only proteinogenic amino acid containing a secondary amine at this position. Proline (abbreviated as Pro or P) is an α- Amino acid, one of the twenty DNA -encoded amino acids Proteinogenic Amino acids also known as standard normal or primary amino acids are those 20 amino acids that are found in Proteins and that are coded for in the Proline has sometimes been termed an imino acid, but this is not correct in the current nomenclature. In Chemistry, an imino acid is any molecule that contains both imino (>C=NH and Carboxyl (-C(=O-OH Functional groups [8]

The two optical isomers of alanine.
The two optical isomers of alanine.

Isomerism

Most amino acids can exist in either of two optical isomers, called D and L. The term chiral (pronounced /ˈkaɪɹ(əl̩/ is used to describe an object that is non- superimposable on its mirror image The L-amino acids represent the vast majority of amino acids found in proteins. Proteins are large Organic compounds made of Amino acids arranged in a linear chain and joined together by Peptide bonds between the Carboxyl D-amino acids are found in some proteins produced by exotic sea-dwelling organisms, such as cone snails. The cone snails or cone shells, sometimes simply known as "cones" (family Conidae) are a Taxonomic family of medium-sized to large sophisticated [9] They are also abundant components of the peptidoglycan cell walls of bacteria. Not to be confused with Glycoprotein. Peptidoglycan, also known as murein, is a Polymer consisting of sugars and amino A cell wall is a tough flexible and sometimes fairly rigid layer surrounding a cell, located external to the Cell membrane, which provides the cell with structural The Bacteria ( singular: bacterium) are a large group of unicellular Microorganisms Typically a few Micrometres in length bacteria have [10]

The L and D conventions for amino acid configuration do not refer to the optical activity of the amino acid itself, but rather to the optical activity of the isomer of glyceraldehyde having the same stereochemistry as the amino acid. Glyceraldehyde is a Triose Monosaccharide with Chemical formula C 3 H 6 O 3 S-glyceraldehyde is levorotary, and R-glyceraldehyde is dexterorotary, and so S-amino acids are called L-amino acids even if they are not levorotary, and R-amino acids are likewise called D-amino acids even if they are not dexterorotary.

There are two exceptions to these general rules of amino acid isomerism. Firstly, glycine, where R = H, no isomerism is possible because the alpha-carbon bears two identical groups (hydrogen). Glycine (abbreviated as Gly or G) is the Organic compound with the formula NH2CH2COOH Secondly, in cysteine, the L = S and D = R assignment is reversed to L = R and D = S. Not to be confused with Cystine, its oxidized dimer Cysteine (abbreviated as Cys or C) is an α- Amino acid with Cysteine is structured in the same way as the other amino acids but the sulfur atom alters the interpretation of the Cahn-Ingold-Prelog priority rule. Sulfur or sulphur (ˈsʌlfɚ see spelling below) is the Chemical element that has the Atomic number 16

Reactions

As amino acids have both a primary amine group and a primary carboxyl group, these chemicals can undergo most of the reactions associated with these functional groups. Amines are Organic compounds and Functional groups that contain a basic Nitrogen Atom with a Lone pair. Carboxyl group or CO2H is a Functional group present in Amino acids and Carboxylic acids Its structure is composed of one carbon atom attached These include nucleophilic addition, amide bond formation and imine formation for the amine group and esterification, amide bond formation and decarboxylation for the carboxylic acid group. In Organic chemistry, a nucleophilic addition reaction is an Addition reaction where in a Chemical compound a π bond is removed by the creation In Chemistry, an amide is one of three kinds of Compounds (sometimes called acid amide the organic Functional group characterized Alkylimino-de-oxo-bisubstitution in Organic chemistry is the Organic reaction of Carbonyl compounds with Amines to Imines. Esterification is the general name for a Chemical reaction in which two reactants (typically an alcohol and an acid form an Ester as the reaction product In Chemistry, an amide is one of three kinds of Compounds (sometimes called acid amide the organic Functional group characterized Decarboxylation is any Chemical reaction in which a Carboxyl group (-COOH is split off from a compound as Carbon dioxide (CO2 The multiple side chains of amino acids can also undergo chemical reactions. The types of these reactions are determined by the groups on these side chains and are discussed in the articles dealing with each specific type of amino acid.

Peptide bond formation

The condensation of two amino acids to form a peptide bond.
The condensation of two amino acids to form a peptide bond. A peptide bond is a Chemical bond formed between two Molecules when the Carboxyl group of one molecule reacts with the
For more details on this topic, see Peptide bond. A peptide bond is a Chemical bond formed between two Molecules when the Carboxyl group of one molecule reacts with the

As both the amine and carboxylic acid groups of amino acids can react to form amide bonds, one amino acid molecule can react with another and become joined through an amide linkage. This polymerization of amino acids is what creates proteins. In Polymer chemistry, polymerization is a process of reacting Monomer Molecules together in a Chemical reaction to form three-dimensional networks This condensation reaction yields the newly formed peptide bond and a molecule of water. A condensation reaction is a Chemical reaction in which two Molecules or moieties ( Functional groups) combine to form one single molecule together with A peptide bond is a Chemical bond formed between two Molecules when the Carboxyl group of one molecule reacts with the In cells, this reaction does not occur directly; instead the amino acid is first activated by attachment to a transfer RNA molecule through an ester bond. Transfer RNA (abbreviated tRNA) is a small RNA (usually about 74-95 nucleotides that transfers a specific Amino acid to a growing polypeptide chain at Esters are a class of Chemical compounds and Functional groups Esters consist of an inorganic or organic Acid in which at least This aminoacyl-tRNA is produced in an ATP-dependent reaction carried out by an aminoacyl tRNA synthetase. Adenosine-5'-triphosphate ( ATP) is a multifunctional Nucleotide that is most important as a " molecular currency" of intracellular Energy An aminoacyl tRNA synthetase ( aaRS) is an Enzyme that catalyzes the Esterification of a specific Amino acid or its precursor to one of all its compatible [11] This aminoacyl-tRNA is then a substrate for the ribosome, which catalyzes the attack of the amino group of the elongating protein chain on the ester bond. Ribosomes ( from ribo nucleic acid and "Greek soma ( meaning body") are complexes of RNA and Protein that [12] As a result of this mechanism, all proteins made by ribosomes are synthesized starting at their N-terminus and moving towards their C-terminus.

However, not all peptide bonds are formed in this way. In a few cases, peptides are synthesized by specific enzymes. For example, the tripeptide glutathione is an essential part of the defenses of cells against oxidative stress. Glutathione ( GSH) is a Tripeptide. It contains an unusual Peptide linkage between the amine group of Cysteine and the Carboxyl This peptide is synthesized in two steps from free amino acids. [13] In the first step gamma-glutamylcysteine synthetase condenses cysteine and glutamic acid through a peptide bond formed between the side-chain carboxyl of the glutamate (the gamma carbon of this side chain) and the amino group of the cysteine. Gamma-glutamylcysteine synthetase (EC 6322 (glutamate cysteine ligase GCL is the first enzyme in the Glutathione biosynthesis pathway Not to be confused with Cystine, its oxidized dimer Cysteine (abbreviated as Cys or C) is an α- Amino acid with Glutamic acid (abbreviated as Glu or E) is one of the 20 Alpha Amino acids It is not among the human Essential amino acids Its This dipeptide is then condensed with glycine by glutathione synthetase to form glutathione. Glycine (abbreviated as Gly or G) is the Organic compound with the formula NH2CH2COOH Glutathione synthetase (EC 6323 is the second enzyme in the Glutathione biosynthesis pathway [14]

In chemistry, peptides are synthesized by a variety of reactions. One of the most used in solid-phase peptide synthesis, which uses the aromatic oxime derivatives of amino acids as activated units. In Organic chemistry, peptide synthesis is the production of Peptides which are Organic compounds in which multiple Amino acids are linked via These are added in sequence onto the growing peptide chain, which is attached to a solid resin support. [15]

Zwitterions

An amino acid, in its (1) unionized and (2) zwitterionic forms.
An amino acid, in its (1) unionized and (2) zwitterionic forms.

As amino acids have both the active groups of an amine and a carboxylic acid they can be considered both acid and base. At a certain pH known as the isoelectric point, the amine group has a positive charge (is protonated) and the acid group a negative charge (is deprotonated). The isoelectric point (pI is the PH at which a particular Molecule or surface carries no net electrical charge. In chemistry protonation is the addition of a proton ( H[[Cation +]] to an Atom, Molecule, or Ion. Deprotonation is a Chemistry term that refers to the removal of a Proton ( Hydrogen Cation H+ from a Molecule, forming The exact value is specific to each different amino acid. This ion is known as a zwitterion, which comes from the German word Zwitter meaning "hybrid". A zwitterion (first part pronounced "tsvitter" from German " Zwitter " &mdash "hybrid" " Hermaphrodite " is a A zwitterion can be extracted from the solution as a white crystalline structure with a very high melting point, due to its dipolar nature. Near-neutral physiological pH allows most free amino acids to exist as zwitterions.

Hydrophilic and hydrophobic amino acids

Depending on the polarity of the side chain, amino acids vary in their hydrophilic or hydrophobic character. "Polar molecule" and "Non-polar" redirect here Hydrophile, from the Greek (hydros "water" and φιλια (philia "friendship" refers to a physical property of a Molecule In Chemistry, hydrophobicity (from the combining form of water in Attic Greek hydro- and for fear phobos) refers to the physical property of These properties are important in protein structure and protein-protein interactions. Proteins are an important class of biological Macromolecules present in all biological organisms made up of such elements as Carbon, Hydrogen Protein-protein interactions refer to the association of Protein molecules and the study of these associations from the perspective of Biochemistry, Signal transduction The importance of the physical properties of the side chains comes from the influence this has on the amino acid residues' interactions with other structures, both within a single protein and between proteins. The distribution of hydrophilic and hydrophobic amino acids determines the tertiary structure of the protein, and their physical location on the outside structure of the proteins influences their quaternary structure. In Biochemistry and Chemistry, the tertiary structure of a Protein or any other Macromolecule is its three-dimensional structure as defined In Biochemistry, quaternary structure is the arrangement of multiple folded Protein molecules in a multi-subunit complex For example, soluble proteins have surfaces rich with polar amino acids like serine and threonine, while integral membrane proteins tend to have outer ring of hydrophobic amino acids that anchors them into the lipid bilayer, and proteins anchored to the membrane have a hydrophobic end that locks into the membrane. Serine (abbreviated as Ser or S) is an Organic compound with the formula H[[oxygen O]]2 CCH NH sub>2CH2OH Threonine (abbreviated as Thr or T) is an α- Amino acid with the Chemical formula HO2CCH(NH2CH(OHCH3 An Integral Membrane Protein ( IMP) is a Protein Molecule (or assembly of proteins that is permanently attached to the Biological membrane. In Chemistry, hydrophobicity (from the combining form of water in Attic Greek hydro- and for fear phobos) refers to the physical property of A lipid bilayer or bilayer lipid membrane ( BLM) is a membrane composed of Lipid molecules (usually Phospholipids. Similarly, proteins that have to bind to positively-charged molecules have surfaces rich with negatively charged amino acids like glutamate and aspartate, while proteins binding to negatively-charged molecules have surfaces rich with positively charged chains like lysine and arginine. Recently a new scale of hydrophobicity based on the free energy of hydrophobic association has been proposed. [16]

Hydrophilic and hydrophobic interactions of the proteins do not have to rely only on the sidechains of amino acids themselves. By various posttranslational modifications other chains can be attached to the proteins, forming hydrophobic lipoproteins or hydrophilic glycoproteins. Posttranslational modification (PTM is the chemical modification of a Protein after its translation. A lipoprotein is a biochemical assembly that contains both Proteins and Lipids The lipids or their derivatives may be covalently or non-covalently bound Not to be confused with Peptidoglycan. Glycoproteins are proteins that contain Oligosaccharide chains ( Glycans) covalently attached

Table of standard amino acid abbreviations and side chain properties

Main article: List of standard amino acids
Amino Acid 3-Letter 1-Letter Side chain polarity Side chain acidity or basicity of neutral species Hydropathy index[17]
Alanine Ala A nonpolar neutral 1. The hydropathy index of an Amino acid is a number representing the Hydrophobic or Hydrophilic properties of its side-chain Alanine (abbreviated as Ala or A) is an α- Amino acid with the Chemical formula HO2CCH(NH2CH3 8
Arginine Arg R polar basic (strongly) -4. Arginine (abbreviated as Arg or R) is an α- Amino acid. The L-form is one of the 20 most common natural amino acids 5
Asparagine Asn N polar neutral -3. Asparagine (abbreviated as Asn or N; Asx or B represent either asparagine or Aspartic acid) is one of the 20 most common natural 5
Aspartic acid Asp D polar acidic -3. Aspartic acid (abbreviated as Asp or D; Asx or B represent either aspartic acid or Asparagine) is an α- Amino acid 5
Cysteine Cys C polar neutral 2. Not to be confused with Cystine, its oxidized dimer Cysteine (abbreviated as Cys or C) is an α- Amino acid with 5
Glutamic acid Glu E polar acidic -3. Glutamic acid (abbreviated as Glu or E) is one of the 20 Alpha Amino acids It is not among the human Essential amino acids Its 5
Glutamine Gln Q polar neutral -3. Glutamine (abbreviated as Gln or Q; the abbreviation Glx or Z represents either glutamate or Glutamic acid) is one of the 20 5
Glycine Gly G nonpolar neutral -0. Glycine (abbreviated as Gly or G) is the Organic compound with the formula NH2CH2COOH 4
Histidine His H polar basic (weakly) -3. Histidine (abbreviated as His or H) is one of the 20 standard Amino acids present in Proteins In the Nutritional sense in 2
Isoleucine Ile I nonpolar neutral 4. Isoleucine (abbreviated as Ile or I) is an α- Amino acid with the Chemical formula HO2CCH(NH2CH(CH3CH2CH3 5
Leucine Leu L nonpolar neutral 3. Leucine (abbreviated as Leu or L) is an α- Amino acid with the Chemical formula HO2CCH(NH2CH2CH(CH32 8
Lysine Lys K polar basic -3. Lysine (abbreviated as Lys or K) is an α- Amino acid with the Chemical formula HO2CCH(NH2(CH24NH2 9
Methionine Met M nonpolar neutral 1. Methionine ( abbreviated as Met or M) is an α- Amino acid with the Chemical formula HO2CCH(NH2CH2CH2SCH3 9
Phenylalanine Phe F nonpolar neutral 2. Phe redirects here For the BitTorrent feature see PHE. For the constellation see Phoenix (constellation. 8
Proline Pro P nonpolar neutral -1. Proline (abbreviated as Pro or P) is an α- Amino acid, one of the twenty DNA -encoded amino acids 6
Serine Ser S polar neutral -0. Serine (abbreviated as Ser or S) is an Organic compound with the formula H[[oxygen O]]2 CCH NH sub>2CH2OH 8
Threonine Thr T polar neutral -0. Threonine (abbreviated as Thr or T) is an α- Amino acid with the Chemical formula HO2CCH(NH2CH(OHCH3 7
Tryptophan Trp W nonpolar neutral -0. Tryptophan (abbreviated as Trp or W) is one of the 20 standard amino acids, as well as an Essential amino acid in the Human diet 9
Tyrosine Tyr Y polar neutral -1. Tyrosine (abbreviated as Tyr or Y) or 4-hydroxyphenylalanine, is one of the 20 Amino acids that are used by cells to synthesize 3
Valine Val V nonpolar neutral 4. Valine (abbreviated as Val or V) is an α- Amino acid with the Chemical formula HO2CCH(NH2CH(CH32 2

In addition to the normal amino acid codes, placeholders were used historically in cases where chemical or crystallographic analysis of a peptide or protein could not completely establish the identity of a certain residue in a structure. Proteins are found in every cell and are essential to every biological process Protein structure is very complex determining a protein's structure involves first X-ray crystallography is a method of determining the arrangement of Atoms within a Crystal, in which a beam of X-rays strikes a crystal and scatters The ones they could not resolve between are these pairs of amino-acids:

Ambiguous Amino Acids 3-Letter 1-Letter
Asparagine or aspartic acid Asx B
Glutamine or glutamic acid Glx Z
Leucine or Isoleucine Xle J
Unspecified or unknown amino acid Xaa X

Unk is sometimes used instead of Xaa, but is less standard.

Nonstandard amino acids

The amino acid selenocysteine.
The amino acid selenocysteine. Selenocysteine is an Amino acid that is present in several Enzymes (for example Glutathione peroxidases tetraiodothyronine 5' deiodinases

Aside from the twenty standard amino acids, there are a vast number of "non-standard" amino acids. Two of these can be specified by the genetic code, but are rather rare in proteins. Selenocysteine is incorporated into some proteins at a UGA codon, which is normally a stop codon. Selenocysteine is an Amino acid that is present in several Enzymes (for example Glutathione peroxidases tetraiodothyronine 5' deiodinases The genetic code is the set of rules by which information encoded in genetic material ( DNA or RNA sequences is translated into Proteins [18] Pyrrolysine is used by some methanogenic archaea in enzymes that they use to produce methane. Pyrrolysine is a naturally occurring genetically coded Amino acid used by some Methanogenic Archaea in Enzymes that are part of their Methane Methanogens are Archaea that produce Methane as a Metabolic byproduct in Anoxic conditions Enzymes are Biomolecules that catalyze ( ie increase the rates of Chemical reactions Almost all enzymes are Proteins Methane is a Chemical compound with the molecular formula. It is the simplest Alkane, and the principal component of Natural gas. It is coded for with the codon UAG. [19]

Examples of nonstandard amino acids that are not found in proteins include lanthionine, 2-aminoisobutyric acid, dehydroalanine and the neurotransmitter gamma-aminobutyric acid. Lanthionine is a Nonproteinogenic Amino acid with the chemical formula (HOOC-CH(NH2-CH2-S-CH2-CH(NH2-COOH 2-Aminoisobutyric acid, or α-aminoisobutyric acid ( AIB) or α-methylalanine or 2-methylalanine, is an Amino acid with the Structural Dehydroalanine (or (alpha-(beta-di-dehydroalanine) is an uncommon Amino acid found in Peptides of microbial origin (an unsaturated Gamma-aminobutyric acid (GABA is the chief inhibitory Neurotransmitter in the Mammalian Central nervous system. Nonstandard amino acids often occur as intermediates in the metabolic pathways for standard amino acids — for example ornithine and citrulline occur in the urea cycle, part of amino acid catabolism. In Biochemistry, a metabolic pathway is a series of chemical reactions occurring within a cell. Ornithine is an Amino acid which plays a role in the Urea cycle. The Organic compound citrulline is an α- Amino acid. Its name is derived from citrullus, the Latin word for Watermelon, from which The urea cycle (also known as the ornithine cycle) is a cycle of biochemical reactions occurring in many animals that produces Urea ( N[[hydrogen For the related metabolic process see Anabolism. Catabolism is the set of Metabolic pathways which break down molecules into [20]

Nonstandard amino acids are usually formed through modifications to standard amino acids. For example, homocysteine is formed through the transsulfuration pathway or by the demethylation of methionine via the intermediate metabolite S-adenosyl methionine,[21] while dopamine is synthesized from l-DOPA, and hydroxyproline is made by a posttranslational modification of proline. Homocysteine is a Chemical compound with the formula HSCH2CH2CH(NH2CO2H The transsulfuration pathway is a Metabolic pathway that converts Cysteine to Homocysteine, through the intermediate Cystathionine. S -Adenosyl methionine (SAM is a Coenzyme involved in Methyl group transfers 4-Hydroxyproline, or hydroxyproline ( C 5 H 9 O 3 N) is an uncommon Amino acid, abbreviated as HYP Posttranslational modification (PTM is the chemical modification of a Protein after its translation. Proline (abbreviated as Pro or P) is an α- Amino acid, one of the twenty DNA -encoded amino acids [22]

Uses in technology

Amino acid derivative Use in industry
Aspartame (aspartyl-phenylalanine-1-methyl ester) Low-calorie artificial sweetener
5-HTP (5-hydroxytryptophan) Treatment for depression and the neurological problems of phenylketonuria. Aspartame (or APM) (ˈæspɚteɪm or /əˈspɑrteɪm/ is the name for an artificial non- Saccharide Sweetener, aspartyl-phenylalanine-1-methyl 5-Hydroxytryptophan or 5-HTP is a naturally-occurring Amino acid, a precursor to the Neurotransmitter Serotonin and an intermediate Phenylketonuria ( PKU) is an Autosomal recessive Genetic disorder characterized by a deficiency in the enzyme Phenylalanine hydroxylase
L-DOPA (L-dihydroxyphenylalanine) Treatment for Parkinsonism. Parkinsonism (also known as Parkinson's syndrome, atypical Parkinson's, or secondary Parkinson's) is a neurological Syndrome characterized
Monosodium glutamate Food additive that enhances flavor. Monosodium glutamate, also known as sodium glutamate and MSG, is a Sodium salt of the non-essential Amino acid Glutamic acid Food additives are substances added to food to preserve flavour or improve its taste and appearance Confers the taste umami. is one of the five Basic tastes sensed by specialized receptor cells present on the human Tongue.

Nutritional importance

Further information: Protein in nutrition

Of the 20 standard proteinogenic amino acids, 8 are called essential amino acids because the human body cannot synthesize them from other compounds at the level needed for normal growth, so they must be obtained from food. Proteins are broken down in the Stomach during Digestion by Enzymes known as Proteases into smaller Polypeptides to provide An essential amino acid or indispensable amino acid is an Amino acid that cannot be synthesized de novo by the organism (usually referring to The human body is the entire physical and mental structure of a Human Organism. A chemical compound is a substance consisting of two or more different elements chemically bonded together in a fixed proportion by Mass. [23] However, the situation is a little more complicated since cysteine, tyrosine, histidine and arginine are semiessential amino acids in children, because the metabolic pathways that synthesize these amino acids are not fully developed. Not to be confused with Cystine, its oxidized dimer Cysteine (abbreviated as Cys or C) is an α- Amino acid with Tyrosine (abbreviated as Tyr or Y) or 4-hydroxyphenylalanine, is one of the 20 Amino acids that are used by cells to synthesize Histidine (abbreviated as His or H) is one of the 20 standard Amino acids present in Proteins In the Nutritional sense in Arginine (abbreviated as Arg or R) is an α- Amino acid. The L-form is one of the 20 most common natural amino acids [24] The amounts required also depend on the age and health of the individual, so it is hard to make general statements about the dietary requirement for some amino acids.

Essential Nonessential
Isoleucine Alanine
Leucine Asparagine
Lysine Aspartate
Methionine Cysteine*
Phenylalanine Glutamate
Threonine Glutamine*
Tryptophan Glycine*
Valine Proline*
Arginine* Serine*
Histidine* Tyrosine*

(*) Essential only in certain cases. Isoleucine (abbreviated as Ile or I) is an α- Amino acid with the Chemical formula HO2CCH(NH2CH(CH3CH2CH3 Alanine (abbreviated as Ala or A) is an α- Amino acid with the Chemical formula HO2CCH(NH2CH3 Leucine (abbreviated as Leu or L) is an α- Amino acid with the Chemical formula HO2CCH(NH2CH2CH(CH32 Asparagine (abbreviated as Asn or N; Asx or B represent either asparagine or Aspartic acid) is one of the 20 most common natural Lysine (abbreviated as Lys or K) is an α- Amino acid with the Chemical formula HO2CCH(NH2(CH24NH2 Aspartic acid (abbreviated as Asp or D; Asx or B represent either aspartic acid or Asparagine) is an α- Amino acid Methionine ( abbreviated as Met or M) is an α- Amino acid with the Chemical formula HO2CCH(NH2CH2CH2SCH3 Not to be confused with Cystine, its oxidized dimer Cysteine (abbreviated as Cys or C) is an α- Amino acid with Phe redirects here For the BitTorrent feature see PHE. For the constellation see Phoenix (constellation. Glutamic acid (abbreviated as Glu or E) is one of the 20 Alpha Amino acids It is not among the human Essential amino acids Its Threonine (abbreviated as Thr or T) is an α- Amino acid with the Chemical formula HO2CCH(NH2CH(OHCH3 Glutamine (abbreviated as Gln or Q; the abbreviation Glx or Z represents either glutamate or Glutamic acid) is one of the 20 Tryptophan (abbreviated as Trp or W) is one of the 20 standard amino acids, as well as an Essential amino acid in the Human diet Glycine (abbreviated as Gly or G) is the Organic compound with the formula NH2CH2COOH Valine (abbreviated as Val or V) is an α- Amino acid with the Chemical formula HO2CCH(NH2CH(CH32 Proline (abbreviated as Pro or P) is an α- Amino acid, one of the twenty DNA -encoded amino acids Arginine (abbreviated as Arg or R) is an α- Amino acid. The L-form is one of the 20 most common natural amino acids Serine (abbreviated as Ser or S) is an Organic compound with the formula H[[oxygen O]]2 CCH NH sub>2CH2OH Histidine (abbreviated as His or H) is one of the 20 standard Amino acids present in Proteins In the Nutritional sense in Tyrosine (abbreviated as Tyr or Y) or 4-hydroxyphenylalanine, is one of the 20 Amino acids that are used by cells to synthesize [25][26]

Several common mnemonics have evolved for remembering the ten amino acids often described as essential. A mnemonic device (nəˈmɒnɪk is a Memory aid Commonly met mnemonics are often verbal something such as a very short poem or a special word used to help a person remember PVT TIM HALL ("Private Tim Hall") uses the first letter of each of these amino acids. A Private is a Soldier of the lowest Military rank (equivalent to NATO Rank Grades OR-1 to OR-3 depending on the force served in [27] Another mnemonic that frequently occurs in student practice materials beneath "AH TV TILL Past Midnight", is "These ten valuable amino acids have long preserved life in man". [28]

See also

References and notes

  1. ^ Proline is an exception to this general formula. The genetic code is the set of rules by which information encoded in genetic material ( DNA or RNA sequences is translated into Proteins Amino acid dating is a technique used to estimate age in a wide variety ofsituations It lacks the NH2 group because of the cyclization of the side chain.
  2. ^ Sakami W, Harrington H. "Amino acid metabolism". Annu Rev Biochem 32: 355-98. PMID 14144484.  
  3. ^ Brosnan J (2000). "Glutamate, at the interface between amino acid and carbohydrate metabolism". J Nutr 130 (4S Suppl): 988S-90S. PMID 10736367.  
  4. ^ Young V, Ajami A (2001). "Glutamine: the emperor or his clothes?". J Nutr 131 (9 Suppl): 2449S-59S; discussion 2486S-7S. PMID 11533293.  
  5. ^ Whitmore L, Wallace B (2004). "Analysis of peptaibol sequence composition: implications for in vivo synthesis and channel formation. ". Eur Biophys J 33 (3): 233-7. PMID 14534753.  
  6. ^ Alexander L, Grierson D (2002). "Ethylene biosynthesis and action in tomato: a model for climacteric fruit ripening". J Exp Bot 53 (377): 2039-55. PMID 12324528.  
  7. ^ Llorca J (2004). "Organic matter in meteorites.". Int Microbiol 7 (4): 239-48. PMID 15666244.  
  8. ^ Claude Liebecq (Ed) Biochemical Nomenclature and Related Documents, 2nd edition, Portland Press, 1992, pages 39-69 ISBN 978-1855780057
  9. ^ Pisarewicz K, Mora D, Pflueger F, Fields G, Marí F (2005). "Polypeptide chains containing D-gamma-hydroxyvaline. ". J Am Chem Soc 127 (17): 6207-15. PMID 15853325.  
  10. ^ van Heijenoort J (2001). "Formation of the glycan chains in the synthesis of bacterial peptidoglycan.". Glycobiology 11 (3): 25R-36R. PMID 11320055.  
  11. ^ Ibba M, Söll D (2001). "The renaissance of aminoacyl-tRNA synthesis". EMBO Rep 2 (5): 382-7. PMID 11375928.  
  12. ^ Lengyel P, Söll D (1969). "Mechanism of protein biosynthesis". Bacteriol Rev 33 (2): 264-301. PMID 4896351.  
  13. ^ Wu G, Fang Y, Yang S, Lupton J, Turner N (2004). "Glutathione metabolism and its implications for health". J Nutr 134 (3): 489-92. PMID 14988435.  
  14. ^ Meister A (1988). "Glutathione metabolism and its selective modification". J Biol Chem 263 (33): 17205–8. PMID 3053703.  
  15. ^ Carpino, L. A. (1992) 1-Hydroxy-7-azabenzotriazole. An efficient Peptide Coupling Additive. J. Am. Chem. Soc. 115, 4397-4398.
  16. ^ Urry, D. W. (2004). "The change in Gibbs free energy for hydrophobic association - Derivation and evaluation by means of inverse temperature transitions". Chemical Physics Letters 399 (1-3): 177-183.  
  17. ^ Kyte J & RF Doolittle (1982). "A simple method for displaying the hydropathic character of a protein". J. Mol. Biol. (157): 105-132. PMID 7108955.  
  18. ^ Driscoll D, Copeland P. "Mechanism and regulation of selenoprotein synthesis. ". Annu Rev Nutr 23: 17-40. PMID 12524431.  
  19. ^ Krzycki J (2005). "The direct genetic encoding of pyrrolysine. ". Curr Opin Microbiol 8 (6): 706-12. PMID 16256420.  
  20. ^ Curis E, Nicolis I, Moinard C, Osowska S, Zerrouk N, Bénazeth S, Cynober L (2005). "Almost all about citrulline in mammals". Amino Acids 29 (3): 177-205. PMID 16082501.  
  21. ^ Brosnan J, Brosnan M (2006). "The sulfur-containing amino acids: an overview". J Nutr 136 (6 Suppl): 1636S-1640S. PMID 16702333.  
  22. ^ Kivirikko K, Pihlajaniemi T. "Collagen hydroxylases and the protein disulfide isomerase subunit of prolyl 4-hydroxylases". Adv Enzymol Relat Areas Mol Biol 72: 325-98. PMID 9559057.  
  23. ^ Young VR (1994). "Adult amino acid requirements: the case for a major revision in current recommendations". J. Nutr. 124 (8 Suppl): 1517S–1523S. PMID 8064412.  
  24. ^ Imura K, Okada A (1998). "Amino acid metabolism in pediatric patients". Nutrition 14 (1): 143-8. PMID 9437700.  
  25. ^ Fürst P, Stehle P (2004). "What are the essential elements needed for the determination of amino acid requirements in humans?". J. Nutr. 134 (6 Suppl): 1558S–1565S. PMID 15173430.  
  26. ^ Reeds PJ (2000). "Dispensable and indispensable amino acids for humans". J. Nutr. 130 (7): 1835S–40S. PMID 10867060.  
  27. ^ Chapter 39 PVT TIM HALL. Retrieved on 2007-09-29. Year 2007 ( MMVII) was a Common year starting on Monday of the Gregorian calendar in the 21st century. Events 522 BC - Darius I of Persia kills the Magian usurper Gaumâta securing his hold as king of the Persian Empire.
  28. ^ Memory aids for medical biochemistry. http://mednote.co.kr/Yellownote/BIOCHMNEMON.htm Access date 25 February 2006

Further reading

External links

Dictionary

amino acid

-noun

  1. (organic chemistry) Any organic compound containing both an amino and a carboxylic acid functional group.
  2. (biochemistry) Any of the twenty naturally occurring α-amino acids (having the amino, and carboxylic acid groups on the same carbon atom), and a variety of side chains, that combine, via peptide bonds, to form proteins.
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