A biomolecule or biological molecule is a loosely used term for molecules and ions that are present in organisms, essential to some typically biological process such as cell division, morphogenesis, or development. Biomolecules include large macromolecules (or polyanions) 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. Biomolecules are usually endogenous but may also be exogenous. For example, pharmaceutical drugs may be natural products or semisynthetic (biopharmaceuticals) or they may be totally synthetic.
Biology and its subsets of biochemistry and molecular biology study biomolecules and their reactions. Most biomolecules are organic compounds, and just four elements—oxygen, carbon, hydrogen, and nitrogen—make up 96% of the human body's mass. But many other elements, such as the various biometals, are present in small amounts.
The uniformity of specific types of molecules (the biomolecules) and of some metabolic pathways as invariant features between the diversity of life forms is called "biochemical universals" or "theory of material unity of the living beings", a unifying concept in biology, along with cell theory and evolution theory.
A diverse range of biomolecules exist, including:
|Biomonomers||Bio-oligo||Biopolymers||Polymerization process||Covalent bond name between monomers|
|Amino acids||Oligopeptides||Polypeptides, proteins (hemoglobin...)||Polycondensation||Peptide bond|
|Monosaccharides||Oligosaccharides||Polysaccharides (cellulose...)||Polycondensation||Glycosidic bond|
|Isoprene||Terpenes||Polyterpenes: cis-1,4-polyisoprene natural rubber and trans-1,4-polyisoprene gutta-percha||Polyaddition|
|Nucleotides||Oligonucleotides||Polynucleotides, nucleic acids (DNA, RNA)||Phosphodiester bond|
Nucleosides can be phosphorylated by specific kinases in the cell, producing nucleotides. Both DNA and RNA are polymers, consisting of long, linear molecules assembled by polymerase enzymes from repeating structural units, or monomers, of mononucleotides. DNA uses the deoxynucleotides C, G, A, and T, while RNA uses the ribonucleotides (which have an extra hydroxyl(OH) group on the pentose ring) C, G, A, and U. Modified bases are fairly common (such as with methyl groups on the base ring), as found in ribosomal RNA or transfer RNAs or for discriminating the new from old strands of DNA after replication.
Each nucleotide is made of an acyclic nitrogenous base, a pentose and one to three phosphate groups. They contain carbon, nitrogen, oxygen, hydrogen and phosphorus. They serve as sources of chemical energy (adenosine triphosphate and guanosine triphosphate), participate in cellular signaling (cyclic guanosine monophosphate and cyclic adenosine monophosphate), and are incorporated into important cofactors of enzymatic reactions (coenzyme A, flavin adenine dinucleotide, flavin mononucleotide, and nicotinamide adenine dinucleotide phosphate).
DNA structure is dominated by the well-known double helix formed by Watson-Crick base-pairing of C with G and A with T. This is known as B-form DNA, and is overwhelmingly the most favorable and common state of DNA; its highly specific and stable base-pairing is the basis of reliable genetic information storage. DNA can sometimes occur as single strands (often needing to be stabilized by single-strand binding proteins) or as A-form or Z-form helices, and occasionally in more complex 3D structures such as the crossover at Holliday junctions during DNA replication.
RNA, in contrast, forms large and complex 3D tertiary structures reminiscent of proteins, as well as the loose single strands with locally folded regions that constitute messenger RNA molecules. Those RNA structures contain many stretches of A-form double helix, connected into definite 3D arrangements by single-stranded loops, bulges, and junctions. Examples are tRNA, ribosomes, ribozymes, and riboswitches. These complex structures are facilitated by the fact that RNA backbone has less local flexibility than DNA but a large set of distinct conformations, apparently because of both positive and negative interactions of the extra OH on the ribose. Structured RNA molecules can do highly specific binding of other molecules and can themselves be recognized specifically; in addition, they can perform enzymatic catalysis (when they are known as "ribozymes", as initially discovered by Tom Cech and colleagues).
Monosaccharides are the simplest form of carbohydrates with only one simple sugar. They essentially contain an aldehyde or ketone group in their structure. The presence of an aldehyde group in a monosaccharide is indicated by the prefix aldo-. Similarly, a ketone group is denoted by the prefix keto-. Examples of monosaccharides are the hexoses, glucose, fructose, Trioses, Tetroses, Heptoses, galactose, pentoses, ribose, and deoxyribose. Consumed fructose and glucose have different rates of gastric emptying, are differentially absorbed and have different metabolic fates, providing multiple opportunities for 2 different saccharides to differentially affect food intake. Most saccharides eventually provide fuel for cellular respiration.
Disaccharides are formed when two monosaccharides, or two single simple sugars, form a bond with removal of water. They can be hydrolyzed to yield their saccharin building blocks by boiling with dilute acid or reacting them with appropriate enzymes. Examples of disaccharides include sucrose, maltose, and lactose.
Polysaccharides are polymerized monosaccharides, or complex carbohydrates. They have multiple simple sugars. Examples are starch, cellulose, and glycogen. They are generally large and often have a complex branched connectivity. Because of their size, polysaccharides are not water-soluble, but their many hydroxy groups become hydrated individually when exposed to water, and some polysaccharides form thick colloidal dispersions when heated in water. Shorter polysaccharides, with 3 - 10 monomers, are called oligosaccharides. A fluorescent indicator-displacement molecular imprinting sensor was developed for discriminating saccharides. It successfully discriminated three brands of orange juice beverage. The change in fluorescence intensity of the sensing films resulting is directly related to the saccharide concentration.
Lignin is a complex polyphenolic macromolecule composed mainly of beta-O4-aryl linkages. After cellulose, lignin is the second most abundant biopolymer and is one of the primary structural components of most plants. It contains subunits derived from p-coumaryl alcohol, coniferyl alcohol, and sinapyl alcohol and is unusual among biomolecules in that it is racemic. The lack of optical activity is due to the polymerization of lignin which occurs via free radical coupling reactions in which there is no preference for either configuration at a chiral center.
Lipids (oleaginous) are chiefly fatty acid esters, and are the basic building blocks of biological membranes. Another biological role is energy storage (e.g., triglycerides). Most lipids consist of a polar or hydrophilic head (typically glycerol) and one to three nonpolar or hydrophobic fatty acid tails, and therefore they are amphiphilic. Fatty acids consist of unbranched chains of carbon atoms that are connected by single bonds alone (saturated fatty acids) or by both single and double bonds (unsaturated fatty acids). The chains are usually 14-24 carbon groups long, but it is always an even number.
For lipids present in biological membranes, the hydrophilic head is from one of three classes:
Amino acids contain both amino and carboxylic acid functional groups. (In biochemistry, the term amino acid is used when referring to those amino acids in which the amino and carboxylate functionalities are attached to the same carbon, plus proline which is not actually an amino acid).
Modified amino acids are sometimes observed in proteins; this is usually the result of enzymatic modification after translation (protein synthesis). For example, phosphorylation of serine by kinases and dephosphorylation by phosphatases is an important control mechanism in the cell cycle. Only two amino acids other than the standard twenty are known to be incorporated into proteins during translation, in certain organisms:
The particular series of amino acids that form a protein is known as that protein's primary structure. This sequence is determined by the genetic makeup of the individual. It specifies the order of side-chain groups along the linear polypeptide "backbone".
Proteins have two types of well-classified, frequently occurring elements of local structure defined by a particular pattern of hydrogen bonds along the backbone: alpha helix and beta sheet. Their number and arrangement is called the secondary structure of the protein. Alpha helices are regular spirals stabilized by hydrogen bonds between the backbone CO group (carbonyl) of one amino acid residue and the backbone NH group (amide) of the i+4 residue. The spiral has about 3.6 amino acids per turn, and the amino acid side chains stick out from the cylinder of the helix. Beta pleated sheets are formed by backbone hydrogen bonds between individual beta strands each of which is in an "extended", or fully stretched-out, conformation. The strands may lie parallel or antiparallel to each other, and the side-chain direction alternates above and below the sheet. Hemoglobin contains only helices, natural silk is formed of beta pleated sheets, and many enzymes have a pattern of alternating helices and beta-strands. The secondary-structure elements are connected by "loop" or "coil" regions of non-repetitive conformation, which are sometimes quite mobile or disordered but usually adopt a well-defined, stable arrangement.
The overall, compact, 3D structure of a protein is termed its tertiary structure or its "fold". It is formed as result of various attractive forces like hydrogen bonding, disulfide bridges, hydrophobic interactions, hydrophilic interactions, van der Waals force etc.
When two or more polypeptide chains (either of identical or of different sequence) cluster to form a protein, quaternary structure of protein is formed. Quaternary structure is an attribute of polymeric (same-sequence chains) or heteromeric (different-sequence chains) proteins like hemoglobin, which consists of two "alpha" and two "beta" polypeptide chains.
An apoenzyme (or, generally, an apoprotein) is the protein without any small-molecule cofactors, substrates, or inhibitors bound. It is often important as an inactive storage, transport, or secretory form of a protein. This is required, for instance, to protect the secretory cell from the activity of that protein. Apoenzymes become active enzymes on addition of a cofactor. Cofactors can be either inorganic (e.g., metal ions and iron-sulfur clusters) or organic compounds, (e.g., [Flavin group|flavin] and heme). Organic cofactors can be either prosthetic groups, which are tightly bound to an enzyme, or coenzymes, which are released from the enzyme's active site during the reaction.
Isoenzymes, or isozymes, are multiple forms of an enzyme, with slightly different protein sequence and closely similar but usually not identical functions. They are either products of different genes, or else different products of alternative splicing. They may either be produced in different organs or cell types to perform the same function, or several isoenzymes may be produced in the same cell type under differential regulation to suit the needs of changing development or environment. LDH (lactate dehydrogenase) has multiple isozymes, while fetal hemoglobin is an example of a developmentally regulated isoform of a non-enzymatic protein. The relative levels of isoenzymes in blood can be used to diagnose problems in the organ of secretion .
The Biomolecule Stretching Database contains information about the mechanostability of proteins based on their resistance to stretching.Conformation
Conformation generally means structural arrangement and may refer to:
Conformational isomerism, a form of stereoisomerism in chemistry
Conformation activity relationship between the biological activity and the conformation or conformational changes of a biomoleculeConformation–activity relationship
The conformation–activity relationship is the relationship between the biological activity and the chemical structure or conformational changes of a biomolecule. This terminology emphasizes the importance of dynamic conformational changes for the biological function, rather than the importance of static three-dimensional structure used in the analysis of structure activity relationships.The conformational changes usually take place during intermolecular association, such as protein–protein interaction or protein–ligand binding. A binding partner changes the conformation of a biomolecule (e.g. a protein) to enable or disable its biochemical activity.
Methods for analysis of conformation activity relationship vary from in silico or using experimental methods such as X-ray crystallography and NMR where the conformation before and after activity can be compared statically or using dynamic methods such as multi-parametric surface plasmon resonance, dual polarisation interferometry or circular dichroism where the kinetics as well as degree of conformational change can be quantified.Electro-switchable biosurface
An electro-switchable biosurface is a biosensor that can be used in conjunction with alternating or fixed electrical potentials in order to affect change in the structure and position (movement) of charged biomolecules such as DNA, RNA or oligopeptides bound to the biosurface. This is especially pronounced when the biomolecule has rigidity in its structure such as double stranded DNA.In turn, the changes caused by electrical potentials can be used to affect the biological function of the biomolecule by revealing or changing the access to molecular targets.Flavin mononucleotide
Flavin mononucleotide (FMN), or riboflavin-5′-phosphate, is a biomolecule produced from riboflavin (vitamin B2) by the enzyme riboflavin kinase and functions as prosthetic group of various oxidoreductases including NADH dehydrogenase as well as cofactor in biological blue-light photo receptors. During the catalytic cycle, a reversible interconversion of the oxidized (FMN), semiquinone (FMNH•) and reduced (FMNH2) forms occurs in the various oxidoreductases. FMN is a stronger oxidizing agent than NAD and is particularly useful because it can take part in both one- and two-electron transfers. In its role as blue-light photo receptor, (oxidized) FMN stands out from the 'conventional' photo receptors as the signaling state and not an E/Z isomerization.
It is the principal form in which riboflavin is found in cells and tissues. It requires more energy to produce, but is more soluble than riboflavin.Fumagillin
Fumagillin is a complex biomolecule and used as an antimicrobial agent. It was isolated in 1949 from the microbial organism Aspergillus fumigatus.Heme A
Heme A (or haem A) is a heme, a coordination complex consisting of a macrocyclic ligand called a porphyrin, chelating an iron atom. Heme A is a biomolecule and is produced naturally by many organisms. Heme A, often appears a dichroic green/red when in solution, is a structural relative of heme B, a component of hemoglobin, the red pigment in blood.Holographic sensor
A holographic sensor is a device that comprises a hologram embedded in a smart material that detects certain molecules or metabolites. This detection is usually a chemical interaction that is transduced as a change in one of the properties of the holographic reflection (as in the Bragg reflector), either refractive index or spacing between the holographic fringes. The specificity of the sensor can be controlled by adding molecules in the polymer film that selectively interacts with the molecules of interest.
A holographic sensor aims to integrate the sensor component, the transducer and the display in one device for fast reading of molecular concentrations based in colorful reflections or wavelengths.Certain molecules that mimic biomolecule active sites or binding sites can be incorporated into the polymer that forms the holographic film in order to make the holographic sensors selective and/or sensitive to certain medical important molecules like glucose, etc.
The holographic sensors can be read from a fair distance because the transducer element is light that has been refracted and reflected by the holographic grating embedded in the sensor. Therefore, they can be used in industrial applications where non-contact with the sensor is required.
Other applications for holographic sensors are anti counterfeitingNanoparticle–biomolecule conjugate
A nanoparticle–biomolecule conjugate is a nanoparticle with biomolecules attached to its surface. Nanoparticles are minuscule particles, typically measured in nanometers (nm), that are used in nanobiotechnology to explore the functions of biomolecules. Properties of the ultrafine particles are characterized by the components on their surfaces more so than larger structures, such as cells, due to large surface area-to-volume ratios. Large surface area-to-volume-ratios of nanoparticles optimize the potential for interactions with biomolecules.Native state
In biochemistry, the native state of a protein or nucleic acid is its properly folded and/or assembled form, which is operative and functional. The native state of a biomolecule may possess all four levels of biomolecular structure, with the secondary through quaternary structure being formed from weak interactions along the covalently-bonded backbone. This is in contrast to the denatured state, in which these weak interactions are disrupted, leading to the loss of these forms of structure and retaining only the biomolecule's primary structure.
An alternate usage in metallurgy refers to metals which are found chemically uncombined in nature.Organocobalt chemistry
Organocobalt chemistry is the chemistry of organometallic compounds containing a carbon to cobalt chemical bond. Organocobalt compounds are involved in several organic reactions and the important biomolecule vitamin B12 has a cobalt-carbon bond. Many organocobalt compounds exhibit useful catalytic properties, the preeminent example being dicobalt octacarbonyl.Phosphagen
Phosphagens, also known as macroergic compounds, are high energy storage compounds, also known as high-energy phosphate compounds, chiefly found in muscular tissue in animals. They allow a high-energy phosphate pool to be maintained in a concentration range, which, if it all were adenosine triphosphate (ATP), would create problems due to the ATP-consuming reactions in these tissues. As muscle tissues can have sudden demands for lots of energy; these compounds can maintain a reserve of high-energy phosphates that can be used as needed, to provide the energy that could not be immediately supplied by glycolysis or oxidative phosphorylation. Phosphagens supply immediate but limited energy.
The actual biomolecule used as a phosphagen is dependent on the organism. The majority of animals use arginine as phosphagen; however, the phylum Chordata (i.e., animals with spinal cords) use creatine. Creatine phosphate, or phosphocreatine, is made from ATP by the enzyme creatine kinase in a reversible reaction:
Creatine + ATP ⇌ creatine phosphate + ADP (this reaction is Mg++-dependent)However, annelids (segmented worms) use a set of unique phosphagens; for example, earthworms use the compound lombricine.
Phosphagens were discovered by Philip Eggleton and his wife Grace Eggleton.Solvation shell
A solvation shell is the solvent interface of any chemical compound or biomolecule that constitutes the solute. When the solvent is water it is often referred to as a hydration shell or hydration sphere. The number of solvent molecules surrounding each unit of solute is called the hydration number of the solute.
A classic example is when water molecules arrange around a metal ion. For example, if the latter were a cation, the electronegative oxygen atom of the water molecule would be attracted electrostatically to the positive charge on the metal ion. The result is a solvation shell of water molecules that surround the ion. This shell can be several molecules thick, dependent upon the charge of the ion, its distribution and spatial dimensions.
A number of molecules of solvent are involved in the solvation shell around anions and cations from a dissolved salt in a solvent. Metal ions in aqueous solutions form metal aquo complexes. This number can be determined by various methods like compressibility and NMR measurements among others.Targeted alpha-particle therapy
Targeted alpha-particle therapy (or TAT) is an in-development method of targeted radionuclide therapy of various cancers. It employs radioactive substances which undergo alpha decay to treat diseased tissue at close proximity. It has the potential to provide highly targeted treatment, especially to microscopic tumour cells. Targets include leukemias, lymphomas, gliomas, melanoma, and peritoneal carcinomatosis. As in diagnostic nuclear medicine, appropriate radionuclides can be chemically bound to a targeting biomolecule which carries the combined radiopharmaceutical to a specific treatment point.It has been said that "α-emitters are indispensable with regard to optimisation of strategies for tumour therapy".Tetramer
A tetramer () (tetra-, "four" + -mer, "parts") is an oligomer formed from four monomers or subunits. The associated propriety is called tetramery. An example from inorganic chemistry is titanium methoxide with the empirical formula Ti(OCH3)4, which is tetrameric in the solid state and has the molecular formula Ti4(OCH3)16. An example from organic chemistry is kobophenol A, a substance that is formed by combining four molecules of resveratrol.In biochemistry, it similarly refers to a biomolecule formed of four units, that are the same (homotetramer), i.e. as in Concanavalin A or different (heterotetramer), i.e. as in hemoglobin. Hemoglobin has 4 similar sub-units while immunoglobulins have 2 very different sub-units. The different sub-units may have each their own activity, such as binding biotin in avidin tetramers, or have a common biological property, such as the allosteric binding of oxygen in hemoglobin.Thiamine triphosphate
Thiamine triphosphate (ThTP) is a biomolecule found in most organisms including bacteria, fungi, plants and animals. Chemically, it is the triphosphate derivative of the vitamin thiamine.Toponome
The toponome is the spatial network code of proteins and other biomolecules in morphologically intact cells and tissues. It is mapped and decoded by imaging cycler microscopy (ICM) in situ able to co-map many thousand supermolecules in one sample (tissue section or cell sample at high subcellular resolution). The term "toponome" is derived from the ancient Greek nouns "topos" (τόπος; place, position) and "nomos" (νόμος; law), and the term "toponomics" refers to the study of the toponome. It was introduced by Walter Schubert in 2003. It addresses the fact that the network of biomolecules in cells and tissues follows topological rules enabling coordinated actions. For example, the cell surface toponome provides the spatial protein interaction code for the execution of a cell movement, a "code of conduct". This is intrinsically dependent on the specific spatial arrangement of similar and dissimilar compositions of supermolecules (compositional periodicity) with a specific spatial order along a cell surface membrane. This spatial order is periodically repeated when the cell tries to enter the exploratory state from the spherical state (spatial periodicity). This spatial toponome code is hierarchically organized with lead biomolecule(s), anti-colocated (absent) biomolecule(s) and wildcard molecules which are variably associated with the lead biomolecule(s). It has been shown that inhibition of lead molecule(s) in a surface membrane leads to disassembly of the corresponding biomolecular network and loss of function.VNI (molecule)
VNI is an experimental drug for treating Chagas disease currently being studied at Vanderbilt University. The molecule acts by inhibiting Trypanosoma cruzi sterol 14α-desmethylase activity in vitro. It exhibits no toxicity in mouse cells and unlike the related compounds posaconazole and fluconazole, increasing the dose is not required to maintain anti-parasitic activity.According to the researchers, "VNI cures the acute and chronic forms of Chagas disease in mice, with 100% survival and no observable side effects. Low cost (<$0.10/mg ), oral bioavailability, favorable pharmacokinetics, and low toxicity make this compound an exceptional candidate for clinical trials. The efficacy of VNI provides additional compelling support for efficacious antiparasitic treatment of chronic Chagas disease, further validating CYP51 as a viable drug targeting T. cruzi, and it opens a new opportunity for therapeutic cure of patients. Although widespread searches for other new drugs that target T. cruzi are surely being pursued, there are millions of patients with this debilitating illness who need immediate therapy, and VNI or a derivative might fulfill this need."
|Nucleic acid structure|