Enzyme in the context of Biotin

Archaea (/ɑːrˈkiːə/ ar-KEE-ə) is a domain of organisms. Traditionally, Archaea included only its prokaryotic members, but has since been found to be paraphyletic, as eukaryotes are known to have evolved from archaea. Even though the domain Archaea cladistically includes eukaryotes, the term archaea (sing. archaeon /ɑːrˈkiːɒn/ ar-KEE-on; from Ancient Greek ἀρχαῖον arkhaîon 'ancient') in English still generally refers specifically to prokaryotic members of Archaea. Archaea were initially classified as bacteria, receiving the name archaebacteria (/ˌɑːrkibækˈtɪəriə/, in the Archaebacteria kingdom), but this term has fallen out of use. Archaeal cells have unique properties separating them from Bacteria and Eukaryota, including: cell membranes made of ether-linked lipids; metabolisms such as methanogenesis; and a unique motility structure known as an archaellum. Archaea are further divided into multiple recognized phyla. Classification is difficult because most have not been isolated in a laboratory and have been detected only by their gene sequences in environmental samples. It is unknown if they can produce endospores.

Archaea are often similar to bacteria in size and shape, although a few have very different shapes, such as the flat, square cells of Haloquadratum walsbyi. Despite this, archaea possess genes and several metabolic pathways that are more closely related to those of eukaryotes, notably for the enzymes involved in transcription and translation. Other aspects of archaeal biochemistry are unique, such as their reliance on ether lipids in their cell membranes, including archaeols. Archaea use more diverse energy sources than eukaryotes, ranging from organic compounds such as sugars, to ammonia, metal ions or even hydrogen gas. The salt-tolerant Halobacteria use sunlight as an energy source, and other species of archaea fix carbon (autotrophy), but unlike cyanobacteria, no known species of archaea does both. Archaea reproduce asexually by binary fission, fragmentation, or budding; unlike bacteria, no known species of Archaea form endospores. The first observed archaea were extremophiles, living in extreme environments such as hot springs and salt lakes with no other organisms. Improved molecular detection tools led to the discovery of archaea in almost every habitat, including soil, oceans, and marshlands. Archaea are particularly numerous in the oceans, and the archaea in plankton may be one of the most abundant groups of organisms on the planet.

Metabolism (/məˈtæbəlɪzəm/, from Greek: μεταβολή metabolē, "change") refers to the set of life-sustaining chemical reactions that occur within living organisms. The three main functions of metabolism are the conversion of energy in food into a usable form for cellular processes; the conversion of food to building blocks of macromolecules (biopolymers) such as proteins, lipids, nucleic acids, and some carbohydrates; and the excretion of metabolic wastes. These enzyme-catalyzed reactions allow organisms to grow, reproduce, maintain their structures, and respond to their environments. The word metabolism can also refer to all chemical reactions that occur in living organisms, including digestion and the transportation of substances into and between different cells. In a broader sense, the set of reactions occurring within the cells is called intermediary (or intermediate) metabolism.

Metabolic reactions may be categorized as catabolic—the breaking down of compounds (for example, of glucose to pyruvate by cellular respiration); or anabolic—the building up (biosynthesis) of compounds (such as proteins, carbohydrates, lipids, and nucleic acids). Usually, catabolism releases energy, and anabolism consumes energy.

The cell membrane (also known as the plasma membrane or cytoplasmic membrane, and historically referred to as the plasmalemma) is a semipermeable biological membrane that separates and protects the interior of a cell from the outside environment (the extracellular space). The cell membrane is a lipid bilayer, usually consisting of phospholipids and glycolipids; eukaryotes and some archaea typically have sterols (such as cholesterol in animals) interspersed between them as well, maintaining appropriate membrane fluidity at various temperatures. The membrane also contains membrane proteins, including integral proteins that span the membrane and serve as transporters, and peripheral proteins that attach to the surface of the cell membrane, acting as enzymes to facilitate interaction with the cell's environment. Glycolipids embedded in the outer lipid layer serve a similar purpose.

The cell membrane controls the movement of substances in and out of a cell, being selectively permeable to ions and organic molecules. In addition, cell membranes are involved in a variety of cellular processes such as cell adhesion, ion conductivity, and cell signaling and serve as the attachment surface for several extracellular structures, including the cell wall and the carbohydrate cell coat called the glycocalyx, as well as the intracellular network of protein fibers called the cytoskeleton. In the field of synthetic biology, cell membranes can be artificially reassembled.

Protein biosynthesis, or protein synthesis, is a core biological process, occurring inside cells, balancing the loss of cellular proteins (via degradation or export) through the production of fresh proteins. Proteins perform a number of critical functions as enzymes, structural proteins or hormones. Protein synthesis is a very similar process for both prokaryotes and eukaryotes but there are some distinct differences.

Protein synthesis can be divided broadly into two phases: transcription and translation. During transcription, a section of DNA encoding a protein, known as a gene, is converted into a molecule called messenger RNA (mRNA). This conversion is carried out by enzymes, known as RNA polymerases, in the nucleus of the cell. In eukaryotes, this mRNA is initially produced in a premature form (pre-mRNA) which undergoes post-transcriptional modifications to produce mature mRNA. The mature mRNA is exported from the cell nucleus via nuclear pores to the cytoplasm of the cell for translation to occur. During translation, the mRNA is read by ribosomes which use the nucleotide sequence of the mRNA to determine the sequence of amino acids. The ribosomes catalyze the formation of covalent peptide bonds between the encoded amino acids to form a polypeptide chain.

Mycelium (pl.: mycelia) is a root-like structure of a fungus consisting of a mass of branching, thread-like hyphae. Its normal form is that of branched, slender, entangled, anastomosing, hyaline threads. Fungal colonies composed of mycelium are found in and on soil and many other substrates. A typical single spore germinates into a monokaryotic mycelium, which cannot reproduce sexually; when two compatible monokaryotic mycelia join and form a dikaryotic mycelium, that mycelium may form fruiting bodies such as mushrooms. A mycelium may be minute, forming a colony that is too small to see, or may grow to span thousands of acres as in Armillaria.

Through the mycelium, a fungus absorbs nutrients from its environment. It does this in a two-stage process. First, the hyphae secrete enzymes onto or into the food source, which break down biological polymers into smaller units such as monomers. These monomers are then absorbed into the mycelium by facilitated diffusion and active transport.

The immune system is a network of biological systems that protects an organism from diseases. It detects and responds to a wide variety of pathogens, such as viruses, bacteria, and parasites, as well as cancer cells and objects, such as wood splinters—distinguishing them from the organism's own healthy tissue. Many species have two major subsystems of the immune system. The innate immune system provides a preconfigured response to broad groups of situations and stimuli. The adaptive immune system provides a tailored response to each stimulus by learning to recognize molecules it has previously encountered. Both use molecules and cells to perform their functions.

Nearly all organisms have some kind of immune system. Bacteria have a rudimentary immune system in the form of enzymes that protect against viral infections. Other basic immune mechanisms evolved in ancient plants and animals and remain in their modern descendants. These mechanisms include phagocytosis, antimicrobial peptides called defensins, and the complement system. Jawed vertebrates, including humans, have even more sophisticated defense mechanisms, including the ability to adapt to recognize pathogens more efficiently. Adaptive (or acquired) immunity creates an immunological memory leading to an enhanced response to subsequent encounters with that same pathogen. This process of acquired immunity is the basis of vaccination.

Honey is a sweet and viscous substance made by several species of bees, the best-known of which are honey bees. Honey is made and stored to nourish bee colonies. Bees produce honey by gathering and then refining the sugary secretions of plants (primarily floral nectar) or the secretions of other insects, like the honeydew of aphids. This refinement takes place both within individual bees, through regurgitation and enzymatic activity, and during storage in the hive, through water evaporation that concentrates the honey's sugars until it is thick and viscous.

Honey bees stockpile honey in the hive. Within the hive is a structure made from wax called honeycomb. The honeycomb is made up of hundreds or thousands of hexagonal cells, into which the bees regurgitate honey for storage. Other honey-producing species of bee store the substance in different structures, such as the pots made of wax and resin used by the stingless bee.

Zinc is a chemical element; it has symbol Zn and atomic number 30. It is a slightly brittle metal at room temperature and has a shiny blue whitish appearance when surface oxidation is removed. It is the first element in group 12 (IIB) of the periodic table. Zinc is the 24th most abundant element in Earth's crust, with an average concentration of 70 grams per ton. Zinc also has five stable isotopes; the most abundant of which, Zn-64, comprises nearly half of zinc's total abundance. In some respects, zinc is chemically similar to magnesium: both elements exhibit only one normal oxidation state (+2), and the Zn and Mg ions are of similar size. The most common zinc ore is sphalerite (zinc blende), a zinc sulfide mineral. The largest concentration of economically feasible lodes in descending order are located in China, Peru, and Australia, among others. Zinc is refined industrially by froth flotation of the ore, roasting, and final extraction using electricity (electrowinning).

Zinc is an essential trace element for humans, animals, plants and for microorganisms and is necessary for both prenatal and postnatal development. It is the second most abundant trace metal in humans after iron, an important cofactor for many enzymes, and the only metal which appears in all enzyme classes. Zinc is also an essential nutrient element for coral growth.

A herbivore is an animal anatomically and physiologically evolved to feed on plants, especially upon vascular tissues such as foliage, fruits or seeds, as the main component of its diet. These more broadly also encompass animals that eat non-vascular autotrophs such as mosses, algae and lichens, but do not include those feeding on decomposed plant matters (i.e. detritivores) or macrofungi (i.e. fungivores).

As a result of their plant-based diet, herbivorous animals typically have mouth structures (jaws or mouthparts) well adapted to mechanically break down plant materials, and their digestive systems have special enzymes (e.g. amylase and cellulase) to digest polysaccharides. Grazing herbivores such as horses and cattles have wide flat-crowned teeth that are better adapted for grinding grass, tree bark and other tougher lignin-containing materials, and many of them evolved rumination or cecotropic behaviors to better extract nutrients from plants. A large percentage of herbivores also have mutualistic gut flora made up of bacteria and protozoans that help to degrade the cellulose in plants, whose heavily cross-linking polymer structure makes it far more difficult to digest than the protein- and fat-rich animal tissues that carnivores eat.

Decomposers are organisms that break down dead organisms and release the nutrients from the dead matter into the environment around them. Decomposition relies on chemical processes similar to digestion in animals; in fact, many sources use the words digestion and decomposition interchangeably. In both processes, complex molecules are chemically broken down by enzymes into simpler, smaller ones. The term "digestion," however, is commonly used to refer to food breakdown that occurs within animal bodies, and results in the absorption of nutrients from the gut into the animal's bloodstream. This is contrasted with external digestion, meaning that, rather than swallowing food and then digesting it using enzymes located within a GI tract, an organism instead releases enzymes directly onto the food source, which is what decomposers do as compared to animals. After allowing the enzymes time to digest the material, the decomposer then absorbs the nutrients from the environment into its cells. Decomposition is often erroneously conflated with this process of external digestion, probably because of the strong association between fungi, which are external digesters, and decomposition.

The term "decomposer" refers to a role in an ecosystem, not to a particular class or type of organism, or even to a specific capacity of those organisms. The definition of "decomposer" therefore centers on the outcome of the decomposition process, rather than the types of organisms performing it. At the center of this definition are the organisms that benefit most directly from the increase in nutrient availability that results from decomposition; plants and other non-mobile (sessile) autotrophs cannot travel to seek out nutrients, and most cannot digest other organisms themselves. They must therefore rely on decomposers to free up nutrients from dead matter that they can then absorb.

The Golgi apparatus (/ˈɡɒldʒi/), also known as the Golgi complex, Golgi body, or simply the Golgi, is an organelle found in most eukaryotic cells. Part of the endomembrane system in the cytoplasm, it packages proteins into membrane-bound vesicles inside the cell before the vesicles are sent to their destination. It resides at the intersection of the secretory, lysosomal, and endocytic pathways. It is of particular importance in processing proteins for secretion, containing a set of glycosylation enzymes that attach various sugar monomers to proteins as the proteins move through the apparatus.

The Golgi apparatus was identified in 1898 by the Italian biologist and pathologist Camillo Golgi. The organelle was later named after him in the 1910s.

Oxidative phosphorylation or electron transport-linked phosphorylation or terminal oxidation, is the metabolic pathway in which cells use enzymes to oxidize nutrients, thereby releasing chemical energy in order to produce adenosine triphosphate (ATP). In eukaryotes, this takes place inside mitochondria. Almost all aerobic organisms carry out oxidative phosphorylation. This pathway is so pervasive because it releases more energy than fermentation.

In aerobic respiration, the energy stored in the chemical bonds of glucose is released by the cell in glycolysis and subsequently the citric acid cycle, producing carbon dioxide and the energetic electron donors NADH and FADH₂. Oxidative phosphorylation uses these molecules and O₂ to produce ATP, which is used throughout the cell whenever energy is needed. During oxidative phosphorylation, electrons are transferred from the electron donors to a series of electron acceptors in a series of redox reactions ending in oxygen, whose reaction releases half of the total energy.

In biochemistry, a metabolic pathway is a linked series of chemical reactions occurring within a cell. The reactants, products, and intermediates of an enzymatic reaction are known as metabolites, which are modified by a sequence of chemical reactions catalyzed by enzymes. In most cases of a metabolic pathway, the product of one enzyme acts as the substrate for the next. However, side products are considered waste and removed from the cell.

Different metabolic pathways function in the position within a eukaryotic cell and the significance of the pathway in the given compartment of the cell. For instance, the electron transport chain and oxidative phosphorylation all take place in the mitochondrial membrane. In contrast, glycolysis, pentose phosphate pathway, and fatty acid biosynthesis all occur in the cytosol of a cell.

Nitrogen fixation is a chemical process by which molecular dinitrogen (N
₂) is converted into ammonia (NH
₃). It occurs both biologically and abiologically in chemical industries. Biological nitrogen fixation or diazotrophy is catalyzed by enzymes called nitrogenases. These enzyme complexes are encoded by the Nif genes (or Nif homologs) and contain iron, often with a second metal (usually molybdenum, but sometimes vanadium).

Some nitrogen-fixing bacteria have symbiotic relationships with plants, especially legumes, mosses and aquatic ferns such as Azolla. Looser non-symbiotic relationships between diazotrophs and plants are often referred to as associative, as seen in nitrogen fixation on rice roots. Nitrogen fixation occurs between some termites and fungi. It occurs naturally in the air by means of NO_x production by lightning.

ATP synthase is an enzyme that catalyzes the formation of the energy storage molecule adenosine triphosphate (ATP) using adenosine diphosphate (ADP) and inorganic phosphate (P_i). ATP synthase is a molecular machine. The overall reaction catalyzed by ATP synthase is:

• ADP + P_i + 2H_out ⇌ ATP + H₂O + 2H_in

ATP synthase lies across a cellular membrane and forms an aperture that protons can cross from areas of high concentration to areas of low concentration, imparting energy for the synthesis of ATP. This electrochemical gradient is generated by the electron transport chain and allows cells to store energy in ATP for later use. In prokaryotic cells ATP synthase lies across the plasma membrane, while in eukaryotic cells it lies across the inner mitochondrial membrane. Organisms capable of photosynthesis also have ATP synthase across the thylakoid membrane, which in plants is located in the chloroplast and in cyanobacteria is located in the cytoplasm.

Lactose intolerance is caused by a lessened ability or a complete inability to digest lactose, a sugar found in dairy products. Humans vary in the amount of lactose they can tolerate before symptoms develop. Symptoms may include abdominal pain, bloating, diarrhea, flatulence, and nausea. These symptoms typically start thirty minutes to two hours after eating or drinking something containing lactose, with the severity typically depending on the amount consumed. Lactose intolerance does not cause damage to the gastrointestinal tract.

Lactose intolerance is due to the lack of the enzyme lactase in the small intestines to break lactose down into glucose and galactose. There are four types: primary, secondary, developmental, and congenital. Primary lactose intolerance occurs as the amount of lactase declines as people grow up. Secondary lactose intolerance is due to injury to the small intestine. Such injury could be the result of infection, celiac disease, inflammatory bowel disease, or other diseases. Developmental lactose intolerance may occur in premature babies and usually improves over a short period of time. Congenital lactose intolerance is an extremely rare genetic disorder in which little or no lactase is made from birth. The reduction of lactase production starts typically in late childhood or early adulthood, but prevalence increases with age.