HydrolysisHydrolysis (haɪˈdrɒlɪsɪs; ) is any chemical reaction in which a molecule of water breaks one or more chemical bonds. The term is used broadly for substitution, elimination, and solvation reactions in which water is the nucleophile. Biological hydrolysis is the cleavage of biomolecules where a water molecule is consumed to effect the separation of a larger molecule into component parts. When a carbohydrate is broken into its component sugar molecules by hydrolysis (e.g.
Reducing sugarA reducing sugar is any sugar that is capable of acting as a reducing agent. In an alkaline solution, a reducing sugar forms some aldehyde or ketone, which allows it to act as a reducing agent, for example in Benedict's reagent. In such a reaction, the sugar becomes a carboxylic acid. All monosaccharides are reducing sugars, along with some disaccharides, some oligosaccharides, and some polysaccharides. The monosaccharides can be divided into two groups: the aldoses, which have an aldehyde group, and the ketoses, which have a ketone group.
Carbohydrate conformationCarbohydrate conformation refers to the overall three-dimensional structure adopted by a carbohydrate (saccharide) molecule as a result of the through-bond and through-space physical forces it experiences arising from its molecular structure. The physical forces that dictate the three-dimensional shapes of all molecules—here, of all monosaccharide, oligosaccharide, and polysaccharide molecules—are sometimes summarily captured by such terms as "steric interactions" and "stereoelectronic effects" (see below).
AnomerIn carbohydrate chemistry, a pair of anomers () is a pair of near-identical stereoisomers or diastereomers that differ at only the anomeric carbon, the carbon that bears the aldehyde or ketone functional group in the sugar's open-chain form. However, in order for anomers to exist, the sugar must be in its cyclic form, since in open-chain form, the anomeric carbon is planar and thus achiral. More formally stated, then, an anomer is an epimer at the hemiacetal/hemiketal carbon in a cyclic saccharide.
Anomeric effectIn organic chemistry, the anomeric effect or Edward-Lemieux effect is a stereoelectronic effect that describes the tendency of heteroatomic substituents adjacent to a heteroatom within a cyclohexane ring to prefer the axial orientation instead of the less hindered equatorial orientation that would be expected from steric considerations. This effect was originally observed in pyranose rings by J. T. Edward in 1955 when studying carbohydrate chemistry. The term anomeric effect was introduced in 1958.
Glycoside hydrolaseGlycoside hydrolases (also called glycosidases or glycosyl hydrolases) catalyze the hydrolysis of glycosidic bonds in complex sugars. They are extremely common enzymes with roles in nature including degradation of biomass such as cellulose (cellulase), hemicellulose, and starch (amylase), in anti-bacterial defense strategies (e.g., lysozyme), in pathogenesis mechanisms (e.g., viral neuraminidases) and in normal cellular function (e.g., trimming mannosidases involved in N-linked glycoprotein biosynthesis).
GlycosyltransferaseGlycosyltransferases (GTFs, Gtfs) are enzymes (EC 2.4) that establish natural glycosidic linkages. They catalyze the transfer of saccharide moieties from an activated nucleotide sugar (also known as the "glycosyl donor") to a nucleophilic glycosyl acceptor molecule, the nucleophile of which can be oxygen- carbon-, nitrogen-, or sulfur-based. The result of glycosyl transfer can be a carbohydrate, glycoside, oligosaccharide, or a polysaccharide. Some glycosyltransferases catalyse transfer to inorganic phosphate or water.
FuranoseA furanose is a collective term for carbohydrates that have a chemical structure that includes a five-membered ring system consisting of four carbon atoms and one oxygen atom. The name derives from its similarity to the oxygen heterocycle furan, but the furanose ring does not have double bonds. The furanose ring is a cyclic hemiacetal of an aldopentose or a cyclic hemiketal of a ketohexose. A furanose ring structure consists of four carbon and one oxygen atom with the anomeric carbon to the right of the oxygen.
PolysaccharidePolysaccharides (ˌpɒliˈsækəraɪd), or polycarbohydrates, are the most abundant carbohydrates found in food. They are long-chain polymeric carbohydrates composed of monosaccharide units bound together by glycosidic linkages. This carbohydrate can react with water (hydrolysis) using amylase enzymes as catalyst, which produces constituent sugars (monosaccharides, or oligosaccharides). They range in structure from linear to highly branched. Examples include storage polysaccharides such as starch, glycogen and galactogen and structural polysaccharides such as cellulose and chitin.
CarbohydrateA carbohydrate (ˌkɑːrboʊˈhaɪdreɪt) is a biomolecule consisting of carbon (C), hydrogen (H) and oxygen (O) atoms, usually with a hydrogen–oxygen atom ratio of 2:1 (as in water) and thus with the empirical formula (where m may or may not be different from n), which does not mean the H has covalent bonds with O (for example with , H has a covalent bond with C but not with O). However, not all carbohydrates conform to this precise stoichiometric definition (e.g.
Nucleic acid sequenceA nucleic acid sequence is a succession of bases within the nucleotides forming alleles within a DNA (using GACT) or RNA (GACU) molecule. This succession is denoted by a series of a set of five different letters that indicate the order of the nucleotides. By convention, sequences are usually presented from the 5' end to the 3' end. For DNA, with its double helix, there are two possible directions for the notated sequence; of these two, the sense strand is used.
Four-bar linkageIn the study of mechanisms, a four-bar linkage, also called a four-bar, is the simplest closed-chain movable linkage. It consists of four bodies, called bars or links, connected in a loop by four joints. Generally, the joints are configured so the links move in parallel planes, and the assembly is called a planar four-bar linkage. Spherical and spatial four-bar linkages also exist and are used in practice. Planar four-bar linkages are constructed from four links connected in a loop by four one-degree-of-freedom joints.
Amino acidAmino acids are organic compounds that contain both amino and carboxylic acid functional groups. Although over 500 amino acids exist in nature, by far the most important are the α-amino acids, from which proteins are composed. Only 22 α-amino acids appear in the genetic code of all life. Amino acids can be classified according to the locations of the core structural functional groups, as alpha- (α-), beta- (β-), gamma- (γ-) or delta- (δ-) amino acids; other categories relate to polarity, ionization, and side chain group type (aliphatic, acyclic, aromatic, containing hydroxyl or sulfur, etc.
Crystal structureIn crystallography, crystal structure is a description of the ordered arrangement of atoms, ions, or molecules in a crystalline material. Ordered structures occur from the intrinsic nature of the constituent particles to form symmetric patterns that repeat along the principal directions of three-dimensional space in matter. The smallest group of particles in the material that constitutes this repeating pattern is the unit cell of the structure.
Linkage (mechanical)A mechanical linkage is an assembly of systems connected to manage forces and movement. The movement of a body, or link, is studied using geometry so the link is considered to be rigid. The connections between links are modeled as providing ideal movement, pure rotation or sliding for example, and are called joints. A linkage modeled as a network of rigid links and ideal joints is called a kinematic chain. Linkages may be constructed from open chains, closed chains, or a combination of open and closed chains.
Watt's linkageIn kinematics, Watt's linkage (also known as the parallel linkage) is a type of mechanical linkage invented by James Watt in which the central moving point of the linkage is constrained to travel on a nearly straight line. It was described in Watt's patent specification of 1784 for the Watt steam engine. Today it is used in automobile suspensions, allowing the axle of a vehicle to travel vertically while preventing sideways motion. Watt's linkage consists of three bars bolted together in a chain.
BiomoleculeA biomolecule or biological molecule is a loosely used term for molecules present in organisms that are essential to one or more typically biological processes, such as cell division, morphogenesis, or development. Biomolecules include large macromolecules (or polyelectrolytes) such as proteins, carbohydrates, lipids, and nucleic acids, as well as small molecules such as primary metabolites, secondary metabolites and natural products. A more general name for this class of material is biological materials.
Sequence homologySequence homology is the biological homology between DNA, RNA, or protein sequences, defined in terms of shared ancestry in the evolutionary history of life. Two segments of DNA can have shared ancestry because of three phenomena: either a speciation event (orthologs), or a duplication event (paralogs), or else a horizontal (or lateral) gene transfer event (xenologs). Homology among DNA, RNA, or proteins is typically inferred from their nucleotide or amino acid sequence similarity.
Statistical classificationIn statistics, classification is the problem of identifying which of a set of categories (sub-populations) an observation (or observations) belongs to. Examples are assigning a given email to the "spam" or "non-spam" class, and assigning a diagnosis to a given patient based on observed characteristics of the patient (sex, blood pressure, presence or absence of certain symptoms, etc.). Often, the individual observations are analyzed into a set of quantifiable properties, known variously as explanatory variables or features.
Nucleic acid tertiary structureNucleic acid tertiary structure is the three-dimensional shape of a nucleic acid polymer. RNA and DNA molecules are capable of diverse functions ranging from molecular recognition to catalysis. Such functions require a precise three-dimensional structure. While such structures are diverse and seemingly complex, they are composed of recurring, easily recognizable tertiary structural motifs that serve as molecular building blocks. Some of the most common motifs for RNA and DNA tertiary structure are described below, but this information is based on a limited number of solved structures.
