BiomineralizationBiomineralization, also written biomineralisation, is the process by which living organisms produce minerals, often to harden or stiffen existing tissues. Such tissues are called mineralized tissues. It is an extremely widespread phenomenon; all six taxonomic kingdoms contain members that are able to form minerals, and over 60 different minerals have been identified in organisms. Examples include silicates in algae and diatoms, carbonates in invertebrates, and calcium phosphates and carbonates in vertebrates.
Silica cycleThe silica cycle is the biogeochemical cycle in which biogenic silica is transported between the Earth's systems. Silicon is considered a bioessential element and is one of the most abundant elements on Earth. The silica cycle has significant overlap with the carbon cycle (see carbonate–silicate cycle) and plays an important role in the sequestration of carbon through continental weathering, biogenic export and burial as oozes on geologic timescales.
Biogenic silicaBiogenic silica (bSi), also referred to as opal, biogenic opal, or amorphous opaline silica, forms one of the most widespread biogenic minerals. For example, microscopic particles of silica called phytoliths can be found in grasses and other plants. Silica is an amorphous metal oxide formed by complex inorganic polymerization processes. This is opposed to the other major biogenic minerals, comprising carbonate and phosphate, which occur in nature as crystalline iono-covalent solids (e.g.
Silicon dioxideSilicon dioxide, also known as silica, is an oxide of silicon with the chemical formula , most commonly found in nature as quartz. In many parts of the world, silica is the major constituent of sand. Silica is one of the most complex and most abundant families of materials, existing as a compound of several minerals and as a synthetic product. Notable examples include fused quartz, fumed silica, silica gel, opal and aerogels. It is used in structural materials, microelectronics (as an electrical insulator), and as components in the food and pharmaceutical industries.
Siliceous oozeSiliceous ooze is a type of biogenic pelagic sediment located on the deep ocean floor. Siliceous oozes are the least common of the deep sea sediments, and make up approximately 15% of the ocean floor. Oozes are defined as sediments which contain at least 30% skeletal remains of pelagic microorganisms. Siliceous oozes are largely composed of the silica based skeletons of microscopic marine organisms such as diatoms and radiolarians. Other components of siliceous oozes near continental margins may include terrestrially derived silica particles and sponge spicules.
Sponge spiculeSpicules are structural elements found in most sponges. The meshing of many spicules serves as the sponge's skeleton and thus it provides structural support and potentially defense against predators. Sponge spicules are made of calcium carbonate or silica. Large spicules visible to the naked eye are referred to as megascleres, while smaller, microscopic ones are termed microscleres. The composition, size, and shape of spicules are major characters in sponge systematics and taxonomy.
Small shelly faunaThe small shelly fauna, small shelly fossils (SSF), or early skeletal fossils (ESF) are mineralized fossils, many only a few millimetres long, with a nearly continuous record from the latest stages of the Ediacaran to the end of the Early Cambrian Period. They are very diverse, and there is no formal definition of "small shelly fauna" or "small shelly fossils". Almost all are from earlier rocks than more familiar fossils such as trilobites.
Silica gelSilica gel is an amorphous and porous form of silicon dioxide (silica), consisting of an irregular tridimensional framework of alternating silicon and oxygen atoms with nanometer-scale voids and pores. The voids may contain water or some other liquids, or may be filled by gas or vacuum. In the last case, the material is properly called silica xerogel. Silica xerogel with an average pore size of 2.4 nanometers has a strong affinity for water molecules and is widely used as a desiccant.
Fumed silicaFumed silica (CAS number 112945-52-5), also known as pyrogenic silica because it is produced in a flame, consists of microscopic droplets of amorphous silica fused into branched, chainlike, three-dimensional secondary particles which then agglomerate into tertiary particles. The resulting powder has an extremely low bulk density and high surface area. Its three-dimensional structure results in viscosity-increasing, thixotropic behavior when used as a thickener or reinforcing filler.
SilicateIn chemistry, a silicate is any member of a family of polyatomic anions consisting of silicon and oxygen, usually with the general formula [SiO4−x(4-2x)− ]n, where 0 ≤ x < 2. The family includes orthosilicate (x = 0), metasilicate (x = 1), and pyrosilicate (x = 0.5, n = 2). The name is also used for any salt of such anions, such as sodium metasilicate; or any ester containing the corresponding chemical group, such as tetramethyl orthosilicate.
MacromoleculeA macromolecule is a very large molecule important to biological processes, such as a protein or nucleic acid. It is composed of thousands of covalently bonded atoms. Many macromolecules are polymers of smaller molecules called monomers. The most common macromolecules in biochemistry are biopolymers (nucleic acids, proteins, and carbohydrates) and large non-polymeric molecules such as lipids, nanogels and macrocycles. Synthetic fibers and experimental materials such as carbon nanotubes are also examples of macromolecules.
Post-translational modificationPost-translational modification (PTM) is the covalent process of changing proteins following protein biosynthesis. PTMs may involve enzymes or occur spontaneously. Proteins are created by ribosomes translating mRNA into polypeptide chains, which may then change to form the mature protein product. PTMs are important components in cell signalling, as for example when prohormones are converted to hormones. Post-translational modifications can occur on the amino acid side chains or at the protein's C- or N- termini.
Cross-linkIn chemistry and biology a cross-link is a bond or a short sequence of bonds that links one polymer chain to another. These links may take the form of covalent bonds or ionic bonds and the polymers can be either synthetic polymers or natural polymers (such as proteins). In polymer chemistry "cross-linking" usually refers to the use of cross-links to promote a change in the polymers' physical properties. When "crosslinking" is used in the biological field, it refers to the use of a probe to link proteins together to check for protein–protein interactions, as well as other creative cross-linking methodologies.
TaphonomyTaphonomy is the study of how organisms decay and become fossilized or preserved in the paleontological record. The term taphonomy (from Greek táphos, τάφος 'burial' and nomos, νόμος 'law') was introduced to paleontology in 1940 by Soviet scientist Ivan Efremov to describe the study of the transition of remains, parts, or products of organisms from the biosphere to the lithosphere. The term taphomorph is used to describe fossil structures that represent poorly-preserved, deteriorated remains of a mixture of taxonomic groups, rather than of a single one.
Silicic acidIn chemistry, a silicic acid (sɪˈlɪsɪk) is any chemical compound containing the element silicon attached to oxide () and hydroxyl () groups, with the general formula or, equivalently, . Orthosilicic acid is a representative example. Silicic acids are rarely observed in isolation, but are thought to exist in aqueous solutions, including seawater, and play a role in biomineralization. They are typically colorless weak acids that are sparingly soluble in water.
PeptidePeptides are short chains of amino acids linked by peptide bonds. A polypeptide is a longer, continuous, unbranched peptide chain. Polypeptides which have a molecular mass of 10,000 Da or more are called proteins. Chains of fewer than twenty amino acids are called oligopeptides, and include dipeptides, tripeptides, and tetrapeptides. Peptides fall under the broad chemical classes of biological polymers and oligomers, alongside nucleic acids, oligosaccharides, polysaccharides, and others.
