Alanine in the context of Chirality

An essential amino acid, or indispensable amino acid, is an amino acid that cannot be synthesized from scratch by the organism fast enough to supply its demand, and must therefore come from the diet. Of the 21 amino acids common to all life forms, the nine amino acids humans cannot synthesize are valine, isoleucine, leucine, methionine, phenylalanine, tryptophan, threonine, histidine, and lysine.

Six other amino acids are considered conditionally essential in the human diet, meaning their synthesis can be limited under special pathophysiological conditions, such as prematurity in the infant or individuals in severe catabolic distress. These six are arginine, cysteine, glycine, glutamine, proline, and tyrosine. Six amino acids are non-essential (dispensable) in humans, meaning they can be synthesized in sufficient quantities in the body. These six are alanine, aspartic acid, asparagine, glutamic acid, serine, and selenocysteine (considered the 21st amino acid). Pyrrolysine (considered the 22nd amino acid), which is proteinogenic only in certain microorganisms, is not used by and therefore non-essential for most organisms, including humans.

Pyruvic acid (CH₃COCOOH) is the simplest of the alpha-keto acids, with a carboxylic acid and a ketone functional group. Pyruvate, the conjugate base, CH₃COCOO, is an intermediate in several metabolic pathways throughout the cell.

Pyruvic acid can be made from glucose through glycolysis, converted back to carbohydrates (such as glucose) via gluconeogenesis, or converted to fatty acids through a reaction with acetyl-CoA. It can also be used to construct the amino acid alanine and can be converted into ethanol or lactic acid via fermentation.

Phenylalanine (symbol Phe or F) is an essential α-amino acid with the formula C
₉H
₁₁NO
₂. It can be viewed as a benzyl group substituted for the methyl group of alanine, or a phenyl group in place of a terminal hydrogen of alanine. This essential amino acid is classified as neutral, and nonpolar because of the inert and hydrophobic nature of the benzyl side chain. The L-isomer is used to biochemically form proteins coded for by DNA. Phenylalanine is a precursor for tyrosine, the monoamine neurotransmitters dopamine, norepinephrine (noradrenaline), and epinephrine (adrenaline), and the biological pigment melanin. It is encoded by the messenger RNA codons UUU and UUC.

Phenylalanine is found naturally in the milk of mammals. It is used in the manufacture of food and drink products and sold as a nutritional supplement as it is a direct precursor to the neuromodulator phenethylamine. As an essential amino acid, phenylalanine is not synthesized de novo in humans and other animals, who must ingest phenylalanine or phenylalanine-containing proteins.

In chemistry, a molecule or ion is called chiral (/ˈkaɪrəl/) if it cannot be superposed on its mirror image by any combination of rotations, translations, and some conformational changes. This geometric property is called chirality (/kaɪˈrælɪti/). The terms are derived from Ancient Greek χείρ (cheir) 'hand'; which is the canonical example of an object with this property.

A chiral molecule or ion exists in two stereoisomers that are mirror images of each other, called enantiomers; they are often distinguished as either "right-handed" or "left-handed" by their absolute configuration or some other criterion. The two enantiomers have the same chemical properties, except when reacting with other chiral compounds. They also have the same physical properties, except that they often have opposite optical activities. A homogeneous mixture of the two enantiomers in equal parts, a racemic mixture, differs chemically and physically from the pure enantiomers.

Kynureninase or L-Kynurenine hydrolase (KYNU) (EC 3.7.1.3) is a PLP dependent enzyme that catalyses the cleavage of kynurenine (Kyn) into anthranilic acid (Ant). It can also act on 3-hydroxykynurenine (to produce 3-hydroxyanthranilate) and some other (3-arylcarbonyl)-alanines. Humans express one kynureninase enzyme that is encoded by the KYNU gene located on chromosome 2.

KYNU is part of the pathway for the catabolism of Trp and the biosynthesis of NAD cofactors from tryptophan (Trp).

The C-terminus (also known as the carboxyl-terminus, carboxy-terminus, C-terminal tail, carboxy tail, C-terminal end, or COOH-terminus) is the end of an amino acid chain (protein or polypeptide), terminated by a free carboxyl group (-COOH). When the protein is translated from messenger RNA, it is created from N-terminus to C-terminus. The convention for writing peptide sequences is to put the C-terminal end on the right and write the sequence from N- to C-terminus.

The N-terminus (also known as the amino-terminus, NH₂-terminus, N-terminal end or amine-terminus) is the start of a protein or polypeptide, referring to the free amine group (-NH₂) located at the end of a polypeptide. Within a peptide, the amine group is bonded to the carboxylic group of another amino acid, making it a chain. That leaves a free carboxylic group at one end of the peptide, called the C-terminus, and a free amine group on the other end called the N-terminus. By convention, peptide sequences are written N-terminus to C-terminus, left to right (in LTR writing systems). This correlates the translation direction to the text direction, because when a protein is translated from messenger RNA, it is created from the N-terminus to the C-terminus, as amino acids are added to the carboxyl end of the protein.

An oligopeptide (oligo-, "a few"), is a peptide consisting of two to twenty amino acids, including dipeptides, tripeptides, tetrapeptides, and other polypeptides. Some of the major classes of naturally occurring oligopeptides include aeruginosins, cyanopeptolins, microcystins, microviridins, microginins, anabaenopeptins, and cyclamides. Microcystins are best studied because of their potential toxicity impact in drinking water. A review of some oligopeptides found that the largest class are the cyanopeptolins (40.1%), followed by microcystins (13.4%).

A tripeptide is a peptide derived from three amino acids joined by two or sometimes three peptide bonds. As for proteins, the function of peptides is determined by the constituent amino acids and their sequence. In terms of scientific investigations, the dominant tripeptide is glutathione (γ-L-Glutamyl-L-cysteinylglycine), which serves many roles in many forms of life.

A tetrapeptide is a peptide, classified as an oligopeptide, since it only consists of four amino acids joined by peptide bonds. Many tetrapeptides are pharmacologically active, often showing affinity and specificity for a variety of receptors in protein-protein signaling. Present in nature are both linear and cyclic tetrapeptides (CTPs), the latter of which mimics protein reverse turns which are often present on the surface of proteins and druggable targets. Tetrapeptides may be cyclized by a fourth peptide bond or other covalent bonds.

Aquaporins, also called water channels, are channel proteins from a larger family of major intrinsic proteins that form pores in the membrane of biological cells, mainly facilitating transport of water between cells. The cell membranes of a variety of different bacteria, fungi, animal and plant cells contain aquaporins through which water can flow more rapidly into and out of the cell than by diffusing through the phospholipid bilayer. Aquaporins have six membrane-spanning α-helical domains with both carboxylic and amino terminals on the cytoplasmic side. Two hydrophobic loops contain conserved asparagine–proline–alanine ("NPA motif") which form a barrel surrounding a central pore-like region that contains additional protein density. Because aquaporins are usually always open and are prevalent in just about every cell type, this leads to a misconception that water readily passes through the cell membrane down its concentration gradient. Water can pass through the cell membrane through simple diffusion because it is a small molecule, and through osmosis, in cases where the concentration of water outside of the cell is greater than that of the inside. However, because water is a polar molecule this process of simple diffusion is relatively slow, and in tissues with high water permeability the majority of water passes through aquaporin.

The 2003 Nobel Prize in Chemistry was awarded jointly to Peter Agre for the discovery of aquaporins and Roderick MacKinnon for his work on the structure and mechanism of potassium channels.

D-Amino acids are amino acids where the stereogenic carbon alpha to the amino group has the D-configuration. For most naturally occurring amino acids, this carbon has the L-configuration. D-Amino acids are occasionally found in nature as residues in proteins. They are formed from ribosomally derived D-amino acid residues.

Amino acids, as components of peptides, peptide hormones, structural and immune proteins, are the most important bioregulators involved in all life processes along with nucleic acids, carbohydrates and lipids. "Environmental ᴅ-amino acids are thought to be derived from organic diagenesis such as racemization and release from bacterial cell walls and even from microbial production."