Biology Dictionary
Alginate - Component of the cell walls of many rhodophytes and kelps. Alginates have an affinity for water, and so help to slow dessication when the algae are exposed to the air; they are commercially important in the production of paper, toothpaste, beer, and frozen foods.
Amino Acid - Refers to a class or type of molecules which constitute proteins. These molecules are polymerised together to form a string of amino acids known as a polypeptide.
The "Natural" Amino Acids Name Single Letter Code Multiple Letter Code Alanine A [ALA] Arginine R [ARG] Asparagine N [ASN] Aspartic Acid D [ASP] Cysteine C [CYS] Glutamic Acid E [GLU] Glutamine Q [GLN] Glycine G [GLY] Histidine H [HIS] Isoleucine I [ILE] Leucine L [LEU] Lysine K [LYS] Methionine M [MET] Phenylalanine F [PHE] Proline P [PRO] Serine S [SER] Threonine T [THR] Tryptophan W [TRP] Tyrosine Y [TYR] Valine V [VAL] ATP (Adenosine Triphosphate) - The primary molecule used by living organisms as fuel. ATP is relatively stable, high energy molecule used to fuel chemical reactions within cells.
Adventitious Roots - A root that grows from somewhere other than the primary root, for example, roots that arise from stems or leaves.
Alternation of Generations - Life cycle in which haploid and diploid generations alternate with each other.
Anemophily - Seed plants which are pollinated by wind are said to be anemophilous.
Angiosperm - A group of plants that produce seeds enclosed within an ovary, which may mature into a fruit; flowering plants.
Anther - The pollen producing tip of a stamen; part of a flower.
Antheridium - The organ on a gametophyte plant which produces the sperm cells.
Anthophyte - A flowering plant, or any of its closest relatives, such as the Bennettitales, Gnetales, or Pentoxylales.
Apical Meristem - Group of cells at the growing tip of a branch or root. It divides cells to create new tissues.
Archegonium - The organ on a gametophyte plant which produces the egg cell, and nurtures the young sporophyte.
Axil - The angle formed between a leaf stalk and the stem to which it is attached. In flowering plants, buds develop in the axils of leaves.
Amoeboid - Having no definite shape to the cell, able to change shape.
Amphiesma - The outer covering of a dinoflagellate, consisting of several membrane layers.
Aperture - Small opening, for example the opening in the test of a foram.
Absorbance - To take in, or ingest water and or dissolved minerals across a cell membrane. Different from ingestion.
Aerobic - Pertaining to the presence of free oxygen. Aerobic organisms require oxygen for their life processes.
Anaerobic - Pertaining to the absence of free oxygen. Anaerobic organisms do not require oxygen for their life processes, in fact oxygen is toxic to many of them. Most anaerobic organisms are bacteria or archaeans.
Autotroph - Any organism that is able to manufacture its own food. Most plants are autotrophs, as are many protists and bacteria. Contrast with consumer. Autotrophs may be Photoautotrophic, using light energy to manufacture food, or Chemoautotrophic, using chemical energy.
Activator - A protein that binds DNA and promotes the transcription of nearby DNA (often directionally, on one side of the binding site, but sometimes bidirectionally). An activator can do this by recruiting RNA polymerase (RNA-P), opening a cell's chromatin allowing access to the promoter region by RNA-P (in eukaryota). This blocks a repressor from binding.
Agar - Agar, not to be confused with agarose is a jelly like substance extracted from red algae known as agarophytes in the Rhodophyta phylum. Agar is a mixture composed of about 30% agaropectin and 70% agarose (used in electrophoretic gels). Agar is used as a solid medium for microbiology.
Agaropectin - One of the two main components of agar, composing about 30%, mainly composed of D-glucuronic acid and pyruvic acid.
Agarophytes - A seeweed typically a red algae. It can be used in biological experiments and for use in the creation of cell cultures.
Agarose - Agarose is a sugar or polysaccharide. It is a main component of agar, which is used a solid medium for microbial cultures. Agarose is used alone for the separation of DNA fragments in electrophoretic gels and chromatographic protein purification.
Molecular structure of the Agarose molecule.
The chemical composition of agarose is
, and its molecular weight is 306.2659 g/mol. AHL - They are a class of homoserine lactones with an acyl group. These are small molecules that can diffuse between cells. They typically act as a quorum sensing and signaling molecule as it can diffuse throughout a bacterial population such that the knowledge of the concentration of the AHL is shared between all bacteria. The bacteria can detect the AHL concentration by way of a transcription factor that can bind and be modulated by the AHL molecule. For example, the LuxI gene produces an AHL that can then bind LuxR, relieving its repressor on the corresponding promoter.
Allosteric Regulation - Allosteric regulation happens when a conformational change (the allosteric part) affects the function of a protein or enzyme. For example, a small molecule may bind a transcription factor and cause a conformational change that removes the TF's ability to bind DNA, rendering it inactive.
Alpha Helix - An alpha helix is an amino acid sequence pattern that results in a secondary structure in the form of a right handed helix. This helix is created by the donation of a hydrogen bond from the backbone N-H groups to the C=O groups. These interactions happen on average every three to four amino acids in a sequence, with about 13 atoms involved in one ring. See also β-sheet.
Human growth hormon cartoon rendition, depicting various alpha helices.
Alphavirus - Small, spherical, enveloped viruses with a genome of a single positive (sense) RNA strand. Ahphaviruses have been engineered into self replicating RNA and are commonly referred to as replicons.
Amphipathic - A compound or molecule that posses both a polar and non-polar component.
Amphoteric - A compound or molecule that can act as both an acid and a base.
Anhydrotetracycline (ATC) - A tetracycline analog that binds the TetR protein better than tetracycline.
Anneal - In the context of DNA assembly this means the coming together of complementary (or near-complementary, in some cases) sequences of DNA. This is often assisted by a change in temperature: two complementary sequences are often heated up (to say 95°C) and then allowed to cool down. The heating removes self-annealing, which causes secondary structures to form in the DNA, which might inhibit annealing to the other molecule. The cooling down allows the formation of hydrogen bonds between the two DNA strands. The opposite process to annealing is melting or denaturing of DNA, which happens at high temperatures.
Antibiotic Resistance Gene - These genes create a product that confers antibiotic resistance. For example, KanR confers resistance to the antibiotic kanamycin. This is often used for selection of microorganisms or others.
Antibiotics - Molecules or proteins which inhibit, and kill bacteria at given concentrations.
Antibody - Also known as an immunoglobulin (Ig), is a large, Y-shaped protein produced mainly by plasma cells that is used by the immune system to identify and neutralise pathogens such as bacteria and viruses. The average size of an antibody is about 10 nm in length (Reth 2013: Nature Immunology - Matching cellular dimensions with molecular sizes) and its molecular weight would be about 150 kDa (Padlan EA. Anatomy of the antibody molecule. Mol. Immunol. 1994;31:169-217).
Anticodon - A sequence of nucleotides that are complementary to codons. These are typically found in tRNA which allows for the matching of an amino acid to a codon.
Antigen - Any biological or synthetic molecule which causes an immune response when introduced into the body and is capable of reacting with the products of the immune system.
Antigenic Determinant - See Epitope.
Antigenicity - The capacity of a molecule to be recognised by the immune system. A substance can be antigenic without being immunogenic.
Antisense Sequence - A sequence of nucleotides complementary to a sense coding sequence, which may be either the strand of a DNA that undergoes transcription, or a messenger RNA molecule.
Apical - Referring to the tip or the apex of.
Apoptosis - The process of preprogrammed cell death which occurs in multicellular organisms. Do not confuse with necrosis, which is caused by trauma. Apoptosis is a normal part of an organisms physiology.
Aptamer - A sequence of RNA (or sometimes DNA) that folds into a particular 3D structure, enabling it to bind some ligand molecule, exempli gratia caffeine, with high specificity and strength. Binding of the ligand can sometimes induce a conformational change in the aptamer, which can be used as a signal for the binding event in the case of aptamer-based circuits.
Assay - A name for an investigative analytic lab technique used for gathering qualitative or quantitative data.
Assembly - Referring to adding genetic components together to form a new desired genetic sequence or genome in a laboratory; see DNA cloning.
Association Constant (Binding constant) - A special case of the equilibrium constant K. It is the inverse of the dissociation constant. It describes the binding and unbinding of a receptor (R) and a ligand (L).
See also dissociation constant.
ATT Site - Regions of DNA required for site-specific recombination.
Attenuation - To lessen or weaken the effect of something. For example, noise in a system can be attenuated with certain techniques, such as feedback, which can reduce the amount of noise or lessen its effect on the system.
Autoregulation - Self-regulation. exempli gratia, an electric heater may employ negative autoregulation in order to keep a steady temperature in the room. If it heats the room too much, the room gets hot; a temperature sensor detects this and turns the heater off. Once the room cools down, the sensor detects this event as well and turns the heater on. The heater regulates itself in this way. Gene expression is also autoregulatory; products regulate the expression of the gene (itself).
Adaptation - Change in a organism resulting from natural selection; a structure which is the result of such selection.
Anagensis - Evolutionary change along an unbranching lineage; change without speciation.
Ancestor - Any organism, population, or species from which some other organism, population, or species is descended by reproduction.
Abdomen - Region of the body furthest from the mouth. In insects, the third body region behind the head and thorax.
Ambulacra - The rows of feet found in echinoderms.
Amniote - Any of a group of land-dwelling vertebrates that have an amnion during embryonic development, including reptiles, birds, and mammals. Most extant mammals give live birth, the "egg" is retained inside the body during gestation; in humans the equivalent is known as amniotic sac.
Amniotic Egg - An egg that can be laid on land due to the presence of a fluid-filled amniotic sac (amnion) that cushions and protects the developing embryo.
Anapsid - A vertebrate distinguished by a skull with no openings in the side behind the eyes, e.g. turtles.
Anus - End of the digestive tract, or gut, through which waste products of digestion are excreted, as distinct from the mouth.
biochemistryistry - the study of those molecules used and manufactured by living things.
Bioluminescence - the production of light by a chemical reaction within an organism. The process occurs in many bacteria and protists, as well as certain animals and fungi.
Brevitoxin - neurotoxin produced by the dinoflagellate Ptychodiscus brevis.
Bipinnate - Describing a pinnate leaf in which the leaflets themselves are further subdivided in a pinnate fashion.
Bisporangiate - When a flower or cone produces both megaspores and microspores, it is said to be bisporangiate. Most flowers are bisporangiate.
Blade - Any broad and flattened region of a plant or alga, which allows for increased photosynthetic surface area.
Bract - Any reduced leaf-like structure associated with a cone or flower.
Bryophyte - Plants in which the gametophyte generation is the larger, persistent phase; they generally lack conducting tissues. Bryophytes include the Hepaticophyta (liverworts), Anthocerotophyta (hornworts), and Bryophyta (mosses).
Bacteriophage - Virus which infects and destroys a bacterial host. Some phages, however, will incorporate their DNA into that of their host, and remain dormant for an extended period. For this reason, they have become essential tools of genetic engineers.
Benthic - Organisms that live on the bottom of the ocean are called benthic organisms. They are not free-floating like pelagic organisms are.
Biomes - The world's major communities, classified according to the predominant vegetation and characterized by adaptations of organisms to that particular environment.
Biotic Factors - Living factors such as decomposers, scavengers and predators.
Boreal - Describes the northern biotic area that is dominated by tundra, taiga, and coniferous forests.
Backbone - Term used in DNA cloning to refer to a DNA construct that serves as destination for other DNA parts.
Bacteria - Bacteria are a microorganisms, classified as prokaryotes. They most often present themselves in a unicellular form and always lack a nucleus. Their genetic material floats freely inside the cell and can be organised into two different sets, a central circular chromosome and plasmids.
Bacterial Colony - A colony is a point of bacteria growing on a Petri dish. If the dishes are prepared correctly then this single point of bacteria should all be issue from the same stock, i.e. one single cell was deposited onto the medium and he is the one who divided in order to produce the others in the colony. All cells in a colony should be genetically identical.
Basal - Baseline level. For example, there might be basal gene expression in the absence of activators or in the presence of repressors. This is the minimum amount of gene expression. The basal expression level can drastically affect the performance of systems, exempli gratia in positive autoregulation.
Base Pair (bp) - A unit consiting of two complemtary nucleotides found in a DNA or RNA sequence; these are bound by weak hydrogen bonds.
Base - For a biological context see nitrogenous base, for a chemical context see pH.
Basepair - In the case of genetic material, a pair formed between two nitrogenous bases.
Binding Constant - Constant associated with the binding and unbinding reaction of receptor and ligand molecules.
BioBrick - DNA sequences which conform to a assembly standard that uses a specific restriction enzyme based protocol.
BioCAD - Information system that incorporates computer aided design tools for use in synthetic biology.
BioCompiler - The concept of a computer software compiler applied to the creation of GMOs (genetically modified organisms); see synthetic biology.
Biomarker - A measurable indicator related to a particular state of a biological system.
Bistability - A system with two stable states. The system will also have a third, metastable state by which the system may pass, per the definition of stability.
Blue Fluorescent Protein (BFP, eBFP) - A blue fluorescent protein. "E" denotes a newer enhanced version.
BsaI - Important restriction enzyme in DNA cloning protocols such as Golden Gate and MoClo.
Basal Group - The earliest diverging group within a clade; for instance, to hypothesize that sponges are basal animals is to suggest that the lineage(s) leading to sponges diverged from the lineage that gave rise to all other animals.
Bipedal - Describes an animal that walks on two legs.
Biramous - Arthropod appendages that are biramous have two branches, an outer branch and an inner branch. These branches may have separate functions; in crustaceans, for instance, the inner branch of a leg is used for walking, while the outer branch may be paddle-shaped or feathery and often functions as a gill. Contrast with uniramous.
Blood - Fluid which circulates throughout the body of an animal, distributing nutrients, and often oxygen as well.
Book Lung - A set of soft overlapping flaps, covered up by a plate on the abdomen, through which oxygen is taken up and carbon dioxide given off. Characteristic of many terrestrial arachnids such as scorpions and spiders.
Brain - Collection of nerve cells usually located at the anterior end of an animal, when present at all. The nerves coordinate information gathered by sense organs, locomotion, and most internal body activities.
Calcite - A common crystalline form of natural calcium carbonate, CaCO3, that is the basic constituent of limestone, marble, and chalk. Also called calcspar.
Calcium Carbonate - A white compound, CaCO3, that occurs naturally as marble, chalk, limestone, and calcite. It is used by many marine invertebrates, such as corals and echinoderms, and by protists, such as coccolithophorids, to construct their exoskeletons. Calcium carbonate, in the form of calcite, is also incorporated into the eggshells of amniotes, except for turtles whose eggs are composed of aragonite (CaCO3 + magnesium).
Carbohydrates - class of biochemistryical compounds which includes sugars, starch, chitin, and steroids.
Cathodoluminescence - An analytical technique used in geology and paleontology to analyze the different minerals in a sample, or diagenetic history of a sample — how crystals grew, were deformed, and were replaced. A beam of electrons is fired at a sample to produce visible light, which can then be used to interpret the mineralogical and diagenetic history of the sample.
Cellulose - carbohydrate polymer of the simple sugar glucose. It is found in the cell walls of plants and green algae, as well as dinoflagellates. Cellulose is the most abundant compound on earth that is manufactured by living things.
Chitin - A carbohydrate polymer found in the cell walls of fungi and in the exoskeletons of arthropods, which provides strength for support and protection.
Chlorophyll - The green-coloured pigment that absorbs light during photosynthesis, often found in plants, algae, and some bacteria; it includes a porphyrin ring, and often has a long hydrophobic tail.
Collagen - long proteins whose structure is wound into a triple helix. The resulting fibers have a high tensile strength. Collagen is a primary component of mammalian hair.
Carpel - A unit of the pistil; it is evolutionarily a modified leaf.
Cataphyll - In cycads, a scale-like modified leaf which protects the developing true leaves.
Columella - A small column of tissue which runs up through the center of a spore capsule. It is present in hornworts, mosses, and some rhyniophytes.
Compound Leaves - Leaves with two or more leaflets attached to a single leaf stem.
Cotyledon - The "seed leaves" produced by the embryo of a seed plant that serve to absorb nutrients packaged in the seed, until the seedling is able to produce its first true leaves and begin photosynthesis; the number of cotyledons is a key feature for the identification of the two major groups of flowering plants.
Capsid - The protein "shell" of a free virus particle.
Cell Cycle - Complete sequence of steps which must be performed by a cell in order to replicate itself, as seen from mitotic event to mitotic event. Most of the cycle consists of a growth period in which the cell takes on mass and replicates its DNA. Arrest of the cell cycle is an important feature in the reproduction of many organisms, including humans.
Cell Membrane - The outer membrane of a cell, which separates it from the environment. Also called a plasma membrane.
Cell Wall - Rigid structure deposited outside the cell membrane. Plants are known for their cell walls of cellulose, as are the green algae and certain protists, while fungi have cell walls of chitin.
Cell - The fundamental structural unit of all life. The cell consists primarily of an outer plasma membrane, which separates it from the environment; the genetic material (DNA), which encodes heritable information for the maintainance of life; and the cytoplasm, a heterogeneous assemblage of ions, molecules, and fluid.
Chloroplast - A chlorophyll-containing plastid found in algal and green plant cells.
Chromosome - Linear piece of eukaryotic DNA, often bound by specialised proteins known as histones.
Coenocytic - Condition in which an organism consists of filamentous cells with large central vacuoles, and whose nuclei are not partitioned into separate compartments. The result is a long tube containing many nuclei, with all the cytoplasm at the periphery.
Colonial - Condition in which many unicellular organisms live together in a somewhat coordinated group. Unlike true multicellular organisms, the individual cells retain their separate identities, and usually, their own membranes and cell walls.
Contractile Vacuole - In many protists, a specialised vacuole with associated channels designed to collect excess water in the cell. Microtubules periodically contract to force this excess water out of the cell, regulating the cell's osmotic balance.
Cytoplasm - All the contents of a cell, including the plasma membrane,but not including the nucleus.
Cytoskeleton - Integrated system of molecules within eukaryotic cells which provides them with shape, internal spatial organization, motility, and may assist in communication with other cells and the environment. Red blood cells, for instance, would be spherical instead of flat if it were not for their cytoskeleton.
Canopy - Layer of vegetation elevated above the ground, usually of tree braches and epiphytes. In tropical forests, the canopy may be more than 100 feet above the ground.
Carnivore - Literally, an organism that eats meat. Most carnivores are animals, but a few fungi, plants, and protists are as well.
Consumer - Any organism which must consume other organisms (living or dead) to satisfy its energy needs. Contrast with autotroph.
Cyst - A small, capsule-like sac that encloses an organism in its resting or larval stage, e.g., a resting spore of an alga.
C Terminus (C-ter) - Also called the carboxyl-terminus or the COOH-terminus, this refers to the end of an amino acid chain which holds the chemical group of COOH. Note this is the end of the chain which is generated last; the N terminus is the first to come out of the ribosome during translation.
CAG Promoter (pCAG) - The CAG promoter is a strong promoter for expressing proteins in mammalian cells. It is composed of Cytolomegalovirus' (CMV) promoter enhancer region, chicken β-Actin promoter its first intron and exon, finally the rabbit β-Globin splice acceptor. Hence: Cytomegalovirus Actin Globin = CAG.
Cascade - Referring to having two or more sequential functional elements.
cDNA - Refers to complementary DNA, often used in the context of rtPCR (reverse transcription); where the complement of a given sequence is generated.
Cell Culture - A cell culture is the act of growing cells. Many different methods for doing so exist. Including Petri dish with LA medium, (lysogeny broth plus agar), or even pure lysogeny broth medium.
Chaperone - Proteins that assist the covalent folding or unfolding and the assembly or disassembly of other macromolecular structures.
Characterisation - Referring to a system or element that can be measured and analysed to understand its workings and functions.
Chassis - Cells or strain which can be used for engineering and the creation of synthetic organisms. It is important for these organisms to be as minimal as possible or to not have any interfering metabolic pathways which those which we may want to insert.
Chromatin - Is a method of organising and highly compacting DNA. It is formed from a complex of various molecules including proteins, RNA, and of course DNA. Chromatin can be organised into two different forms; one which composes the other. Euchromatin and heterochromatin respectively.
Chromophore - The part of a molecule responsible for its colour.
Circular Prokaryote Chromosome - Strictly speaking prokaryotes do not have chromosomes. However the central continous mass of genetic material is referred to as its chromosome.
Cleavage - To cut or separate.
Cloning (Molecular Cloning) - The assembly and replication of new DNA constructs from existing pieces of DNA.
Codon - A triplet (three) of ribonucleotides in mRNA that encodes for an amino acid.
Note that whether or not a codon matches this table depends on the organism. Some organisms, especially microorganisms and bacteria often present modified readings of these codons (known as alternative codons). This is dependant on the presence or not of a tRNA capable of matching the DNA sequence (codon).
Common Start/Stop Codons RNA DNA Function Amino Acid Organisms AUG ATG Start Methionine General CUG CTG Start Leucine Mammals Rare AUA ATA Start Methionine Mitochondria AUU ATT Start Methionine GUG GTG Start Methionine Prokaryotes UUG TTG Start Methionine UAA TAA Stop Ochre Universal UAG TAG Stop Amber UGA TGA Stop Opal Commensal - Bacteria that live on an organism's body and cause no effect on health.
Competitive Inhibition - An inhibitor may compete with another molecule or molecules in the inhibition process.
Complementary - Complementary is refering the physical matching of two corresponding parts, this may be seen simply as two puzzle pieces fitting together. This term is often used when refering to genetic material and more specifically a pair of strands composed of either DNA/DNA or DNA/RNA or RNA/RNA, and even proteins with DNA or RNA.
Concentration - Concentration is the means by which an amount or mass of a disolved chemical compound is measured within a certain volume of free flowing fluid; liquid or gas.
Conformation - Is the physical structure and specific three dimensional form a protein takes. These 3D strucutres are key to the function of proteins.
Constitutive - Produced or active in relatively constant amounts. A constitutive promoter is constantly active. See also basal.
Context - The setting in which something occurs. Context is important in chemical or biochemistryical reactions, as some proteins or chemicals will not act or demonstrate normal activity relative to their chemical environments. This is often the case with proteins which will denature in the wrong pH.
Cooperativity - The ability for binding events to promote additional binding events. Exempli gratia the binding of the first oxygen molecule to hemoglobin makes the binding of the second oxygen molecule much more likely, which in turn makes the binding of the third molecule much more likely, et cetera. We often want to use repressors that exhibit cooperativity, as they exhibit a non-linear (exponential) response useful for creating devices that can be analysed with the digital abstraction.
Coupling - Connecting or pairing.
Crick Strand - A less-often-used nomenclature for the anti-sense DNA strand. This is the strand which is transcribed into pre-mRNA.
CRISPR Cas9 - A new tool based on the bacterial CRISPR-Cas system to target and cut DNA, thus allowing for targeted genome editing. CRISPR stands for clustered regularly interspaced short palindromic repeats.
Cross Talk - Interaction between two or more elements generally not meant to interact, this may or may not cause interferences in a system.
Cyan Fluorescent Protein (CFP) - A cyan (blue) fluorescent protein.
Cytomegalovirus (CMV) - A genus of viruses in the family of Herepesviridae. Its promotor CMV is a strong viral promoter commonly used in mammalian experiments and synthetic biology.
Character - Heritable trait possessed by an organism; characters are usually described in terms of their states, for example: "hair present" vs. "hair absent," where "hair" is the character, and "present" and "absent" are its states.
Clade - A monophyletic taxon; a group of organisms which includes the most recent common ancestor of all of its members and all of the descendants of that most recent common ancestor. From the Greek word "klados", meaning branch or twig.
Cladogenesis - The development of a new clade; the splitting of a single lineage into two distinct lineages; speciation.
Cladogram - A diagram, resulting from a cladistic analysis, which depicts a hypothetical branching sequence of lineages leading to the taxa under consideration. The points of branching within a cladogram are called nodes. All taxa occur at the endpoints of the cladogram.
Convergence - Similarities which have arisen independently in two or more organisms that are not closely related. Contrast with homology.
Crown Group - All the taxa descended from a major cladogenesis event, recognized by possessing the clade's synapomorphy. See: stem group.
Cephalon - In trilobites, the head shield bearing the eyes, antennae, and mouth.
Chaetae - Stiff bristles characteristic of annelids.
Chela - The claw of an arthropod.
Chelicera - The first pair of appendages of a chelicerate arthropod. Originally a short clawed appendage, the chelicerae of many arachnids are highly modified for feeding; in spiders, for instance, they are modified into poisonous fangs.
Chordate - An animal with a notochord (a cartilaginous rod that extends the length of the body), dorsal hollow nerve cord (a fluid-filled tube that runs the length of the body), gill slits or pouches, and a tail at some stage in its life cycle.
Clitellum - In annelids, a swelling of the body towards the head of the animal, where the gonads are located. Both oligochaetes and leeches have a clitellum.
Cnidocyst - The "stinging cell" of a cnidarian.
Coelom - Fluid-filled cavity within the body of an animal; usually refers to a cavity lined with specialised tissue peritoneum in which the gut is suspended. The structure and development of the coelom is an important character for recognizing major groups of animals.
Compound Eye - Found in many but not all arthropods, a compound eye is composed of a large number of small, closely packed simple eyes (ommatidia), each with its own lens and nerve receptors.
Cuticle - In animals, a multilayered, extracellular, external body covering, usually composed of fibrous molecules such as chitin or collagen, and sometimes strengthened by the deposition of minerals such as calcium carbonate. A waxy layer which seals the outer surface of land plants, helping to retain moisture.
Dinosteranes (Dinosteroids) - Chemicals found in dinoflagellates, which have been useful in documenting their existence early in the fossil record.
Double inverse/Lineweaver-Burk plot/double reciprocal plot - A graphical reprsentation of the Lineweaver-Burk equation used in enzyme cinetics. The plot allows us to derive useful information as to the nature of a Michaelis-Menten type reaction. The reciprocal of the formula is the following:
![An example of the double inverse plot. Multiple points must be calculated from the resulting formula. The condition that varies is concetration of the substrate experimentally: 1/[s].](/dictionaries/biology/double_inverse-1.svg)
An example of the double inverse plot. Multiple points must be calculated from the resulting formula. The condition that varies is concetration of the substrate experimentally: 1/[s].
Note that this equation's simplified form comes out to the form
. This can be described as a linear curve on a graph as shown. This method can be used to determine enzyme cinetics: Km, Vmax. The y-intercept of the graph is equivalent to the inverse of Vmax, and the x-intercept represents -1/KVm.
Enzyme inhibition shown using the double inverse. The different motifs formed by the curves allows us to deduce the type of inhibiton.
These representations also allow us to visualise the different forms of enzyme inhibition.
See also: Michaelis-Menten Kinetics, and Enzyme inhibition.
Dikaryotic - Having two different and distinct nuclei per cell; found in the fungi. A dikaryotic individual is called a dikaryon.
Diploid - Having two different sets of chromosomes in the same nucleus of each cell. Most metazoans and plants are diploid. Compare with haploid.
Double Membrane - In mitochondria and plastids, there is a two-layered membrane which surrounds the organelle. This is believed to be the result of endosymbiosis, with the outer membrane coming from the eukaryotic cell, and the inner membrane belonging to the original prokaryote which was "swallowed".
Decomposer - An organism that breaks down the tissue and/or structures of dead organisms.
Decomposition - The breakdown of dead organic material by detrivores or saprophytes.
Desiccation - The process of drying out. In biology, moisture loss in organisms.
Detritus - Accumulated organic debris from dead organisms, often an important source of nutrients in a food web.
Detrivore - Any organism which obtains most of its nutrients from the detritus in an ecosystem.
Disease - Organisms suffer from disease when their normal function is impaired by some genetic disorder, or more often from the activity of a parasite or other organism living within them. Many diseases are caused by viruses, bacteria, or fungi.
De Novo - From scratch. exempli gratia: de novo DNA synthesis is the synthesis of DNA from basic building blocks such as nucleotides or oligonucleotides, instead of creating a new DNA molecule that is a copy of an existing DNA molecule; that would be templated synthesis.
Degenerated Primer Library - A degenerate primer library is a mix of primers used in SELEX. These primers are obtained by chemical synthesis; note that in chemistry DNA sequences are generated in the reverse sense, 3' → 5'. These primers should contain common regions and "degenerated regions". These degenerated regions are denoted as N; N meaning any of the 4 nucleotides may occupy that spot. Note that if a sequence is ordered with 40N then that would mean that there are 440 = 1.2 · 1024 different sequences possible. Note the tube received will contain a mixture of all the different possible sequences and not just specific ones.
Reminder for mol, M, definition see Concentration, Matter, & Volumes
Degradation - The condition or process of destruction or being consumed torn apart. Biological material decays because the composing biological molecules are torn apart over time after seperation from, or death of said organism.
Derivative - 1. Represents the rate of change of a function. 2. Taken from or inspired from, one may derive an idea or information from an original source.
Desoxyribose - Desoxyribose is a form of sugar, this kind is special in that it is included in genetic material of the DNA kind. RNA includes another kind known as ribose.
Dextrose - Dextrose is a form of sugar otherwise known as glucose. This kind is special in that it is used as fuel for life. The name dextrose denotes specifically the D isomer. Do not confuse dextrose with desoxyribose, included in genetic material of DNA. In humans dextrose does not need to be metabolised and can be integrated and used directly in its current form by human cells.
Differentiation - The action or process of changing or morphing into another biological state. This term is often used in cellular biology for the "evolution" of cells through their developmental stages.
Diffusion - Diffusion is the act of disolving or mixing a chemical compound through another chemical fluid, either liquid or gas, through natural convection.
Dissociation Constant - The inverse or opposite of the association constant.
DNA Assembly - The process of putting together pieces of DNA into larger DNA constructs, exempli gratia plasmids.
DNA (Desoxyribonucleic Acid) - A molecule (nucleic acid) which carries most of the genetic instructions used in the development, function and reproduction of all known living organisms and many viruses. DNA is the primary compenent of chromosomes.
DNA a double helix molecule, the current known basis for life.
DNA is composed of two directional strands. The directionality of these strands is dictated by the orientation of the nucleotides that compose it; there is a 5' end and a 3' end.
Four different nucleotides compose DNA, these are differentiated by the nucleic bases they hold: adenine (A), thymine (T), guanine (G), and cytosine (C). These can grouped together chemically into the purine group A, T, and the pyrimidine group G, C. The two strands come together and bind through weak hydrogen bonds; A - T (2 bonds), and C - G (3 bonds).
Double Stranded (DS) - Used as follows dsDNA or dsRNA, indicating that there are two complementary strands that are annealed together.
Downstream - Refers to an element, reactant, or location at a later stage in a series of elements or events.
Doxycycline (DOX) - An inducer molecule for TetR. Also see aTc.
Derived - Describes a character state that is present in one or more subclades, but not all, of a clade under consideration. A derived character state is inferred to be a modified version of the primitive condition of that character, and to have arisen later in the evolution of the clade. For example, "presence of hair" is a primitive character state for all mammals, whereas the "hairlessness" of whales is a derived state for one subclade within the Mammalia.
Diversity - Term used to describe numbers of taxa, or variation in morphology.
Diapsid - A vertebrate distinguished by a skull with two pairs of openings in the side behind the eyes, e.g., lizards, snakes, crocodiles, dinosaurs, and pterosaurs.
Elater - A cell or part of a cell which assists in dispersing spores. The elaters change shape as they lose or acquire water, and they will then push against surrounding spores.
Embryophyte - Synonym for the Plantae, as here defined. It includes all green photosynthetic organisms which begin the development of the sporophyte generation within the archegonium.
Enations - Flaps of tissue such as those found on psilophytes.
Endodermis - Literally "inner skin", this is a layer of cells which surrounds the central core of vascular tissue, and which helps to regulate the flow of water and dissolved substances.
Entomophily - Seed plants which are pollinated by insects are said to be entomophilous.
Epiphyte - A plant which grows upon another plant. The epiphyte does not "eat" the plant on which it grows, but merely uses the plant for structural support, or as a way to get off the ground and into the canopy environment.
Eustele - When a plant's vascular tissue develops in discrete bundles, it is said to have a eustele. See also protostele and siphonostele.
Endoplasmic Reticulum - (ER) network of membranes in eukaryotic cells which helps in control of protein synthesis and cellular organization.
Extracellular Matrix - (ECM) Region outside of metazoan cells which includes compounds attached to the plasma membrane, as well as dissolved substances attracted to the surface charge of the cells. The ECM functions both to keep animal cells adhered together, and well as buffering them from their environment.
Eyespot - Light-sensitive organelle found in many groups of protists, and in some metazoans.
Ecosystem - All the organisms in a particular region and the environment in which they live. The elements of an ecosystem interact with each other in some way, and so depend on each other either directly or indirectly.
Environment - The place in which an organism lives, and the circumstances under which it lives. Environment includes measures like moisture and temperature, as much as it refers to the actual physical place where an organism is found.
E. coli, Escherichia coli K12 Strain - The strains based on the K-12 strain cannot colonise the human gut and can thus be safely used as organisms in the lab; biosafety level 1 containment, the lowest level. It is for the simple build, fast replication, and banality of the K12 strain that E. coli and especially the K12 strain is favoured by laboratories across the world.
Electrophoresis - From electr(ic) and phoresis the action of carrying. The separation of ions (charged particules) by use of an electrical field. This allows for separation according to differences in mobility which is dependent on the charge/mass ratio. This technique is commonly used to separate pieces of DNA or proteins by size, shape, and charge. This technique can also be used for RNA.
- Variants of this technique are the following:
- Northern Blot
- Southern Blot
- Western Blot
- Two Dimensional Gel Electrophoresis (2D Gel)
- Capillary Electrophoresis
- Pulsed-Field Gel Electrophoresis
Elongation - A stage in translation where amino acids are added by the formation of peptide bonds.
Endogenous - Present in the cell naturally.
Endonuclease - A nuclease that cuts within a given genetic (either DNA or RNA) sequence as compared to an exonuclease which cuts at the extremity of the sequence.
Enhancer - Ameliorates transcription.
Entry Vector - Part of the Gateway DNA cloning system.
Enveloped Virus - A virus that has an outer wrapping known as an envelope. These viruses are wrapped in what was before the host's plasma membrane which is obtained in a process known as budding-off. Typically enveloped viruses are much weaker when exposed to the environment and need a host to survive. They do not survive on sterile surfaces.
Epitope (Antigenic Determinant) - Part of the structre of antigens, it is the smallest possible three dimensional structure to which an antibody can affix itself on said antigens.
Equilibrium - State at which opposing reactions in a biological system are balanced.
Escherichia coli (E. coli) - A family of bacteria. Certain strains of E. coli are favoured by scientist in labs, most often the K12 strain. Some strains of E. coli, can be pathogenic to humans. They have a small, ~4.6 megabasepair circular genome, are easily transformed, and replicate fast. Cell replication can be made to be limited by controlling DNA replication through predetermined growth conditions.
Euchromatin - Euchromatin is a form of chromatin which is most often most present in active and transcriptionally competent cells. DNA is wrapped around histone proteins to form what are known as nucleosomes. This DNA/protein structure resembles beads on a string.
Eukaryota - Organisms with membrane-bound organelles, and cytoskeletons. These organisms posses a nucleus which contains their genetic material, and is enclosed by the nuclear envelope. Protists, plants, animals, and fungi, all fall into this domain of life.
Expression Vector - A DNA vector that expresses a gene.
Expression - Expression refers the creation of something. In a biological context by convention it refers to the creation of a protein from a gene. Gene expression thus refers to the amount of a protein being produced from the gene in question.
Endosymbiosis - When one organism takes up permanent residence within another, such that the two become a single functional organism. Mitochondria and plastids are believed to have resulted from endosymbiosis.
Evolution - Darwin's definition: descent with modification. The term has been variously used and abused since Darwin to include everything from the origin of man to the origin of life.
Evolutionary Tree - A diagram which depicts the hypothetical phylogeny of the taxa under consideration. The points at which lineages split represent ancestor taxa to the descendant taxa appearing at the terminal points of the cladogram.
Extinction - When all the members of a clade or taxon die, the group is said to be extinct.
Ectoderm - The outer basic layer of tissue in those animals with true tissues. In vertebrates, for instance, the embryonic ectoderm differentiates into the skin and also the nervous system.
Endoderm - The innermost basic layer of tissue in those animals with true tissues. Forms the gut and its derivatives: in vertebrates, these include the liver, trachea, and lungs.
Epidermis - The outermost layer of cells or skin. This tissue often contains specialised cells for defense, gas exchange, or secretion.
Epithelium - Layer of cells which lines a body cavity; cells may be ciliated or unciliated, and may be squamous (flat, scale-shaped), cuboidal (cube-shaped), or columnar (column-shaped). Your stomach and cheeks are lined with epithelium.
Esophagus - That portion of the gut which connects the pharynx to the stomach.
Exoskeleton - An external, often hard, covering or integument that provides support and protection to the body.
Flagellin - protein which is the primary component of prokaryotic flagella.
Fucoxanthin - yellowish-brown pigment found in some members of the Chromista, including kelps and diatoms.
Fiber - Elongated and thickened cell found in xylem tissue. It strengthens and supports the surrounding cells.
Flower - Collection of reproductive structures found in flowering plants.
Fruit - In flowering plants, the structure which encloses the seeds. True fruits develop from the ovary wall, such as bananas and tomatoes, though not all fruits are edible, such as the dry pods of milkweed or the winged fruits of the maple.
Filament - Long chain of proteins, such as found in hair, muscle, or in flagella.
Fission - Division of single-celled organisms, especially prokaryotes, in which mitosis does not occur. Also used to refer to mitosis in certain unicellular fungi.
Flagellum - Hair-like structure attached to a cell, used for locomotion in many protists and prokaryotes. The prokaryotic flagellum differs from the eukaryotic flagellum in that the prokaryotic flagellum is a solid unit composed primarily of the protein flagellin, while the eukaryotic flagellum is composed of several protein strands bound by a membrane, and does not contain flagellin. The eukaryotic flagellum is sometimes referred to as an undulipodium.
Frustule - The mineral "skeleton" of a diatom or other unicellular organism.
Food Chain - All the interactions of predator and prey, included along with the exchange of nutrients into and out of the soil. These interactions connect the various members of an ecosystem, and describe how energy passes from one organism to another.
Frugivore - Animal which primarily eats fruit. Many bats and birds are frugivores.
FACS - A type offlow cytometry for sorting a mixture of cells into two or more containers, one cell at a time, based upon the fluorescent characteristics of each cell. Cells can be manipulated to express fluorescent properties in order to sort them by FACS.
Feedback - Occurs when outputs of a system are routed back as inputs as part of a chain. This idea is related to autoregulation.
Flow Cytometry - A laser based technology employed for counting cells, cell sorting, and biomarker detection. It works by suspending cells in a stream of fluid and passing them by an electronic detection apparatus.
Fluorescent Marker - Proteins which fluoresce can be used as biomarkers. A classic example is Green Fluorescent Protein (GFP).
Flux - The action or process of flowing in a biological system.
Fusion Protein - A single protein composed of two or more originally separate proteins.
Glucose - simple sugar, and the primary product of photosynthesis. It is polymerized to make cellulose and chitin.
Glycoprotein - A membrane-bound protein which has attached branching carbohydrates. These may function in cell-cell recognition, such as in human blood groups and immune system response, as well as in resisting compression of cells.
Guard Cells - Pair of cells which surround a stomate and regulate its size by altering their shape.
Gymnosperm - A plant that produces seeds, which are not enclosed; includes any seed plant that does not produce flowers.
Gynostemium - The central reproductive stalk of an orchid, which consists of a stamen and pistil fused together.
Golgi Apparatus - Eukaryotic organelle which package cell products, such as enzymes and hormones, and coordinate their transport to the outside of the cell.
Generalist - Organism which can survive under a wide variety of conditions, and does not specialize to live under any particular set of circumstances.
Grassland - Region in which the climate is dry for long periods of the summer, and freezes in the winter. Grasslands are characterized by grasses and other erect herbs, usually without trees or shrubs. Grasslands occur in the dry temperate interiors of continents, and first appeared in the Miocene.
Groundwater - Water found underground as a result of rainfall, ice and snow melt, submerged rivers, lakes, and springs. This water often carries minerals. These minerals can accumulate in the remains of buried organisms and eventually cause fossilization.
Galactosidase (GAL) - Part of an assay frequently used in genetics, molecular biology, and other life sciences. An active enzyme may be detected using X-Gal, which forms an intense blue product after cleavage by β-Galactosidase, and is easy to identify and quantify.
Gene of Interest (GOI) - Abbreviation for gene of interest.
Gibbs Free Energy - A state function discovered by Josiah Willard Gibbs called Gibbs Free Energy, Free Enthalpy, or G. This function is written at a given temperature as such:
. Exothermic reactions are instances where heat is liberated from the system; in this case enthalpy is negative (Δ<H). These systems are inherently unstable and thus spontaneous reactions.
Endothermic reactions are instances where heat is absorbed by the system; in this case enthalpy is positve (Δ>H).
Gibson Assembly - DNA cloning method which allows for the joining of multiple DNA fragments in a single, isothermal reaction.
Golden Gate - A DNA cloning method to simultaneously assemble multiple DNA fragments into a single piece using Type IIs restriction enzymes and T4 DNA ligase.
Green Fluorescent Protein (GFP, eGFP) - Green fluorescent protein. "E" denotes a newer enhanced version.
Gradualism - A model of evolution that assumes slow, steady rates of change. Charles Darwin's original concept of evolution by natural selection assumed gradualism. Contrast with punctuated equilibrium.
Gastrodermis - In cnidarians, the endodermis which lines the gut cavity. The term is often used instead of endodermis since cnidarians only have two tissue layers instead of three.
Genus - A category in the classification of plants and animals between species and family; genera- pl.
Gill Arches - Stiffenings which support the flesh between the gill slits of chordates. In most vertebrates, the first gill arches have been modified to form the jaw, and in tetrapods, the inner ear bones.
Gill Slit - A slitlike or porelike opening connecting the pharynx of a chordate with the outside of the body. Gill slits may contain the gills and be used for gas exchange, as in most fish, but may also be used for filter-feeding, or may be highly modified in land-dwelling vertebrates.
Gill - In aquatic animals, highly vascularized tissues with large surface area; these are extended out of the body and into the surrounding water for gas exchange.
Gnathobase - The expanded and hardened base of the appendage of many arthropods, notably trilobites, crustaceans, and marine cheliceramorphs. Used to macerate food items before ingestion.
Gut (enteron) - Body cavity formed between the mouth and anus in which food is digested and nutrients absorbed; it consists of the mouth, pharynx, esophagus, stomach, intestine, and anus, though some animals do not have all these regions.
Histone - Proteins attached to the DNA of eukaryotes which allows it to be packaged into chromosomes.
Hydrophilic - "Water loving". Hydrophilic compounds dissolve easily in water, and are usually polar.
Hydrophobic - "water fearing". Hydrophobic compounds do not dissolve easily in water, and are usually non-polar. Oils and other long hydrocarbons are hydrophobic.
Habit - The general growth pattern of a plant. A plant's habit may be described as creeping, trees, shrubs, vines, etc.
Herb - Generally any plant which does not produce wood, and is therefore not as large as a tree or shrub, is considered to be an herb.
Heterosporangiate - Producing two different kinds of sporangia, specifically microsporangia and megasporangia. Compare with heterosporous.
Heterosporous - Producing two different sizes or kinds of spores. These may come from the same or different sporangia, and may produce similar or different gametophytes. Contrast with homosporous, and compare with heterosporangiate.
Holdfast - Anchoring base of an alga.
Homosporous - Producing only one size or kind of spore. Contrast with heterosporous.
Hypha - Threadlike filaments that form the mycelium (body) of a fungus; hyphae- pl.
Haploid - Having a single set of chromosomes in the nucleus of each cell. Mosses, and many protists and fungi, are haploid, as are some insects, bryophytes, and the gametes of all organisms. Contrast with diploid.
Haptonema - Peg-like structure unique to the Prymnesiophyta; its function is not known.
Habitat - An organism's native environment.
Halophile - Organism which lives in areas of high salt concentration. These organisms must have special adaptations to permit them to survive under these conditions.
Herbivore - Literally, an organism that eats plants or other autotrophic organisms. The term is used primarily to describe animals.
Hairpin - A loop structure formed in both DNA or RNA. Common type of secondary structure in RNA molecules.
hBax - Human gene involved in the regulation of apoptosis.
HeLa - A commonly used cell line used in scientific research derived from the cervical cancer cells of Henrietta Lacks.
Hemoglobin - An iron containing metalloprotein complex which is essential for bonding, transporting, and distributing oxygen throughout the body. This protein complex circulates in the blood of most chordates and the roots of certain legumes; in chordates this is the means by which oxygen is delivered to the cells.
Heterochromatin - Euchromatin is wrapped into 30nm strcutures to form the megastructure known as heterochromatin. Heterochromatin is most often present in cells which are inactive, senescent, or otherwise dormant. This 30nm string composes the active chromosome during interphase.
Heterodimer - Formed by two different macromolecules.
Hierarchical Composition - Composition arranged in order or rank of hierarchy.
Holoenzyme - An active form of an enzyme that requires a cofactor to be active.
Homeostasis - The property of remaining stable in the face of changing external conditions. For example, maintaining a stable population of pancreatic β-Cells despite immune system malfunction resulting in Type I diabetes an artificial homeostasis system can be acheived by synthetic biology.
Homodimer - Formed by two macromolecules of the same kind.
Homogeneous - A substance or mixture of the same or similar kind or nature, contrary to heterogeneous which is a mixture of two or more unlike substances.
Homologous - Refers to the similarity in DNA sequences of different DNA fragments or regions.
Host - An organism that receives and houses another. Terminology often used when referring to parasites or symbiont. A host is used for nutrients and a place to live.
Hierarchy - A series in which each element is categorized into successive ranks or grades with each level subordinate to the one above.
Homology - Two structures are considered homologous when they are inherited from a common ancestor which possessed the structure. This may be difficult to determine when the structure has been modified through descent.
Hypothesis - A concept or idea that can be falsified by various scientific methods.
Head - That part of the body at the "front" end, where the brain, mouth, and most sensory organs are located.
Heart - Muscular pump which circulates the blood.
Histostructure - The organization and arrangement of tissue (“histo” is from the Greek word for tissue). Since eggshell is a tissue, eggshell histostructure describes the two- and three-dimensional organization of mineral crystals and shell components.
Integrin - adhesive protein of the extracellular matrix in animals.
Ion - An atom or small molecule which carries a positive or negative charge.
Isotopic Analysis - The study of the geochemistry of stable isotopes in naturally occurring sediments and biological structures. Stable isotopes are atomic variations of elements that are stable over long periods of time, meaning they do not radioactively decay. Several elements, like oxygen and carbon, have several stable forms. Oxygen, for example, occurs in nature as 16O and 18O — these two forms are isotopes. They have different numbers of neutrons (16O has two more neutrons than 18O), and and is therefore heavier. Because the two isotopes have different masses, chemical and physical reactions like bonding, evaporation, and precipitation occur at different frequencies. The ratio of stable isotopes is preserved in chemical compounds like water, ice, and calcium carbonate and provides information on the environmental conditions at the time the compound formed. For example, the ratio of 18O/16O in an ice sample is linked to the water temperature of ancient oceans, which in turn reflects ancient climates.
Inflorescence - A cluster of flowers.
Internode - The region of a stem between two nodes, when there is no branching of the vascular tissue.
Ingestion - The intake of water or food particles by "swallowing" them, taking them into the body cavity or into a vacuole. Contrast with absorption.
Inorganic - Not containing carbon. Not from living things, e.g., minerals, water, oxygen, etc.
Intertidal - The coastal zone measuring from the lowest to the highest tide mark. The intertidal zone is subject to alternating periods of flooding and drying.
Immunogenicity - Is the potential of a substance to induce an immune response. This depends on various factors:
- The species and state of the animal - its genome, immunological past, and physiological state.
- The degree of structural similarity of the antigen to the molecules of the target animal.
- The dose of the injected antigen.
- The physical and chemical characteristics of the antigen:
- Its size it must contain at least two epitopes in order to be fixed by an antibody.
- Its form if it is a particle or not.
- Its rigidity in order to be complementary to other paratopes.
In vitro - Used to refer to experiments conducted outside of a living animal. Exempli gratia cell cultures are often used in artificial containers to conduct experiments in controlled conditions on living cells.
In vivo - Used to refer to experiments conducted in a living animal. Exempli gratia mice are often used in labs to experiment on living organisms as they represent a well known and well defined mammalian analog.
Inhibition - A molecule that can cause the arrest or tamper the activity of a reaction is called an inhibitor. In the context of biology an inhibitor has a negative effect on a reaction catalysed by an enzyme. There are multiple cases into which an inhibition may be classed:
Types of inhibition, the concentration of of the inhibitor is the only thing that changes.
- Competitive inhibition: Km increased, Vmax unaffected. The inhibitor matches the active site and fixes itself there.
- Un-competitive inhibition: Km reduced, Vmax reduced. The inhibitor matches a zone close to the active site and thus impedes the substrate from fixing itself there.
- Non-competitive: Km unaffected, Vmax reduced. The inhibtor fixes itself somewhere else on the enzyme and changes the conformation of the active site.
Note
See also: Double inverse.
Initiation - The first step or the in protein translation ie, converting mRNA to an polypeptide chain.
Input Fluorescent Protein (IFP) - A fluorescent reporter for a system's input.
Integration - The event of a DNA fragment incorporating into another part of DNA.
Interface - A part where two systems or parts interact.
IPTG (Isopropyl β-D-1-thiogalactopyranoside) - An inducer molecule for LacI. Mimics allolactose, a product from the metabolism of lactose (id est a metabolite).
Ingroup - In a cladistic analysis, the set of taxa which are hypothesized to be more closely related to each other than any are to the outgroup.
Incubation - In birds and reptiles, the maintaining of a constant temperature during the development of the embryo. Birds incubate their eggs by sitting on them (also called brooding),while other animals, like crocodiles, bury their eggs in organic matter. If eggs are not incubated, the embryos within those eggs generally die. Some dinosaurs may have incubated their eggs by burial in sediment, in organic matter, or by brooding like birds.
Intestine - The portion of the digestive tract between the stomach and anus; it is the region where most of the nutrients and absorbed.
JAnus Kinase (JAK) - Janus from Latin and refrencing the two faced god; allusion to the presence of a kinase domain and a pseudokinase domain. The JAK enzyme is part of the cytosolic 4 tryosine kinase familly.
Jaw - Often loosely applied to any movable, toothed structures at or near the mouth of an animal, such as the scolecodonts of annelids. In vertebrates, the jaw is derived from the first gill arch.
Jointed - When stiff body parts are connected by a soft flexible region, the body is said to be jointed.
Kelp Forest - Marine ecosystem dominated by large kelps. These forests are restricted to cold and temperate waters, and are most common along the western coasts of continents. Kelp forests first appeared in the Miocene.
Kilobase (kb) - A set of one thousand DNA bases.
Kinase - An enzyme that adds a phosphate group to some chemical moiety. For enzymes, the resulting change in phosphorylation state can change the activity of the enzyme (reduce or increase it, change the substrate affinity, or change the reaction being catalysed). For DNA, a phosphate on the 5' end of a piece of DNA is required for it to be ligated to another piece of DNA.
Laminarin - a beta-glucan polysaccharide produced by many chromists through photosynthesis.
Lipids - a class of biochemistryical compounds which includes fats, oils, and waxes.
Luciferase - enzyme which activates luciferin to produce bioluminescence.
Luciferin - compound whose activated form emits light.
Lamina - Any broad and flattened region of a plant or alga, which allows for increased photosynthetic surface area.
Leaf Trace - The strand of vascular tissue which connects the leaf veins to the central vascular system of the stem.
Leaf - An organ found in most vascular plants; it consists of a flat lamina (blade) and a petiole (stalk). Many flowering plants have additionally a pair of small stipules near the base of the petiole.
Leaflet - In a compound leaf, the individual blades are called leaflets.
Lorica - A vase-shaped or cup-shaped outer covering. Found in many protists, including some flagellates, ciliates, chrysophytes, and choanoflagellates, as well as in some animal cells.
Lysosome - Eukaryotic organelle which carries digestive enzymes. The lyzosome fuses with a vacuolar membrane containing ingested particles, which are then acted upon by the enzymes.
Limnology - The study of river system ecology and life.
Litter - Leaf litter, or forest litter, is the detritus of fallen leaves and bark which accumulate in forests.
LacI - A gene encoding for the Lac repressor. In the absence of lactose, the Lac repressor halts production of the enzymes encoded by the lac operon.
Lactose - A sugar molecule, disacharide, composed of two different sugars: galactose and glucose. These two are linked by a β-1 → 4 glycosidic bond.
LasI - Part of the Las quorum sensing system. It binds to LasR to regulate several genes.
Ligand - A molecule (often small) that binds something (often much larger than the ligand) in a specific way. For example, an inducer molecule that binds a transcription factor is a ligand and caffeine is a ligand for a caffeine-specific RNA aptamer.
Ligase, Ligation - A ligase is an enzyme that catalyses the formation of a covalent bond between large molecules, exempli gratia DNA or RNA, for which it catalyses the formation of the phosphodiester bond in the backbone of the nucleic acid polymer Ligases can use single-stranded or double-stranded (more common) DNA (or even RNA) as the substrate but are often substrate to the type of substrate, while not being sequence-specific. All commonly used ligases require a 5' phosphate group on the substrate, which is absent from most synthetic oligonucleotides and thus have to be specifically ordered as such or enzymatically phosphorylated with a poly-nucleotide kinase (PNK).
Load Driver - A device used to engineer modularity in biological networks by mitigating retroactivity.
Load (Loading) - A load is a downstream element of a system exempli gratia binding sites for a regulatory protein that interacts with upstream elements and has an effect on the circuit function.
Logic Gate - An element implementing the notion of digital logic. Exempli gratia an AND gate. The behavior of a logic gate can be shown in a simple diagram known as a truth table; search for the name of your particular logic gate + truth table.
Lux System (LuxI/LuxR) - A family of cell density responsive transcriptional regulators that act as a quorum sensing system in bacteria.
Lineage - Any continuous line of descent; any series of organisms connected by reproduction by parent of offspring.
Librigenae - The "free cheeks"; separate, detachable portions of the trilobite cephalon.
Lophophore - Complex ring of hollow tentacles used as a feeding organ. The tentacles are covered by cilia, which generate a current to bring food particles into the mouth. The structure is only found in the brachiopods, phoronids, and bryozoans.
Magnoliid - Any member of the basal assemblage of flowering plants.
Mannoxylic - Wood in which there is a great deal of parenchyma tissue among the xylem is called mannoxylic. Cycads and pteridosperms have mannoxylic wood. Contrast with pycnoxylic.
Megaspore - In plants which are heterosporous, the larger kind of spore is called a megaspore; it usually germinates into a female (egg-producing) gametophyte. Contrast with microspore.
Meristem - Group of undifferentiated cells from which new tissues are produced. Most plants have apical meristems which give rise to the primary tissues of plants, and some have secondary meristems which add wood or bark.
Merophytes - Group of cells which have all been produced from the same initial cell. Leaves and stems in particular are often built from specific patterns of merophytes.
Microphyll - A kind of leaf, specifically one which has a single, unbranched vein in it. Microphylls are only found in the lycophytes.
Microspore - In plants which are heterosporous, the smaller kind of spore is called a microspore; it usually germinates into a male (sperm-producing) gametophyte. Contrast with megaspore.
Mycorrhizae - Symbiotic association between a fungus and the roots or rhizoids of a plant.
Mastigoneme - Small hair-like filaments found on the "hairy" flagellum of the Chromista.
Membrane - In biology, a boundary layer inside or around a living cell or tissue.
Mesokaryotic - Nuclear condition unique to the dinoflagellates in which the chromosomes remain permanently condensed.
Microtubules - Type of filament in eukaryotic cells composed of units of the protein tubulin. Among other functions, it is the primary structural component of the eukaryotic flagellum.
Microvilli - Thin fingerlike protrusions from the surface of a cell, often used to increase absorptive capacity or to trap food particles. The "collar" of choanoflagellates is actually composed of closely spaced microvilli.
Mitochondrion - Complex organelle found in most eukaryotes; believed to be descended from free-living bacteria that established a symbiotic relationship with a primitive eukaryote. Mitochondria are the site of most of the energy production in most eukaryotes; they require oxygen to function. See: double membrane.
Mitosis - The process of nuclear division in eukaryotes. It is one step in cytokinesis, or cellular division.
MTOC - (microtubule organizing center) MTOCs are bundles of protein tubes which may be found at the base of a eukaryotic flagellum. In animals, they also function in creating the arrays of microtubules that pull the chromosomes apart during mitosis.
Multicellular - Any organism which is composed of many cells is termed multicellular.
Macroscopic - Objects or organisms that are large enough to be seen with the naked eye.
Marine - Refers to the ocean.
Microscopic - Objects or organisms that are too small to be seen with the naked eye.
Monsoonal - Describes a climate pattern with a wind system that changes direction with the seasons; this pattern is dominant over the Arabian Sea and Southeast Asia.
Morphology - The form and structure of anything, usually applied to the shapes, parts, and arrangement of features in living and fossil organisms.
Machine - A set of parts that use energy to perform an action. A biological example is transcriptional machinery: a set of proteins harness the energy of nucleotide triphosphate bonds to polymerize RNA transcripts.
Macro - A prefix coming from Greek denoting a large scale.
Marker - In the context of DNA assembly, a gene that enables the screening or selection of bacteria containing our desired marker. This could be a gene that is toxic to the cell (negative selection; exempli gratia ccdB), a gene that confers antibiotic resistance (positive selection; exempli gratia KanR), or a gene that turns the bacterial colonies some colour (exempli gratia LacZ, or a fluorescent protein such as RFP).
Mass-Action Kinetics - A method of modelling chemical reaction rates. In this kinetic scheme, the rate of a reaction is proportional to the product of the concentrations of reacting species.
Master Equation - A form of chemical kinetic equation that describes the time evolution of all possible states of a chemical system. Master equations are commonly used in stochastic simulations in conjunction with the Gillespie algorithm simulations.
Melting Temperature - Melting temperature is referring the the dehybridisation temperature of DNA primers (most often). For calculating these temperatures, which are to be used when designating a PCR protocol, the following formulas are to be used:
For primers with a length inferiour to 14 nt the following is used:
For primers with a length superiour to 13 nt the following is used:
Both these formulas assume the following: 50 nM primer, 50 mM Na+, and pH 7.0. n(x) designates the number of whichever base.
Michaelis-Menten Kinetics - A chemical kinetic scheme for describing the rate of an enzyme-catalysed processes. It relates the rate of reaction rate V at which the product [P] is formed, to the depletion of the substrate [S] from which it is produced. These are linked by Km the Michaelis constant, which corresponds to the substrate [S] concentration at which the speed v is half the vmax.
There are a few terms to take into consideration before attacking the formula#miRna: vmax is the maximal speed at which the reaction will take place, (vmax/2) is half maximal speed, which brings us to km or the substrate concentration at which the rate of reaction will half speed.
A curve demonstrating a generique enzyme substrate reaction. The graph shows, a reaction rate/speed (concentration/s), in relation to a substrate concentration.
km can be isolated in the following way:
Its simplest formulation considers three processes:
- The binding of substrate to enzyme
- The unbinding of the substrate-enzyme complex
- The conversion of the enzyme-substrate complex to the product and the enzyme
Using mass-action kinetics and the assumption that enzyme concentrations are much smaller than substrate concentrations, we get an equation for the rate of product (P) production (initial velocity); where Vmax is the maximal velocity (saturating substrate conditions) and Km is the Michaelis constant (the substrate concentration at half-maximal velocity). More complex Michaelis-Menten formulations must be used if the release of the product from the enzyme-product complex is slow, ordered-binding is required, or inhibitors are present.
See also: Double inverse
miRNA - A micro RNA is a functional RNA that can inhibit the expression of a gene by either inhibiting translation through mostly unknown mechanisms, or destabilising the mRNA through the use of enzymes in the RNA interference (RNAi) pathway. Not all organisms have the RNAi pathway. Notable exclusions are all prokaryotes and baker's yeast, S. cerevisiae.
mKate - A far-red fluorescent protein.
MoClo - Modular cloning (MoClo) a hierarchical DNA assembly method built on Golden Gate technology. The use of a parts with standardised cloning sequences creates MoClo modularity. This modularity permits the automated construction of many MoClo constructs.
modRNA - Modified mRNA. Synthetic, chemically-modified mRNA that can be transfected into cells to induce expression of a protein of interest. Chemical modifications at the 5' end allow the transcript to evade harmful immune responses and prevent it from being degraded thus allowing prolonged protein expression.
Molecule - A molecule is a chemical compound composed of two or more atoms joined together by a covalent bond.
Monomer - The basic unit of a polymer; monomers compose up polymers. A nucleotide is the monomer of a strand of DNA, which is a polymer of desoxyribonucleic acids.
Motif - A commonly-reproduced pattern that has a similiar function across multiple systems. Examples of regulatory network motifs are negative autoregulation and feed-forward loops. Nucleotide sequence motifs are commonly-found sequences of nucleotides that may serve as transcription factor binding sites. Amino acid sequence motifs may reproduce common protein structures such as alpha helices.
mRNA - Messenger RNA is a functional RNA comprising codons to be translated by ribosomes to proteins. In eukaryotic systems, mRNA that has not been processed is referred to as precursor mRNA (pre-mRNA). This pre-mRNA is typically processed through the removal of introns, the addition of a polyA tail, and the addition of a 5' cap to create mature mRNA. Matured mRNA is what is translated by ribosomes.
- Mature Messenger RNA or mRNA has undergone the following steps.
- Introns have been removed.
- A PolyA tail has been added to the 3' end.
- A 5' cap has been added to the 5' end.
Multimer - A protein made up of multiple monomers. Notably, many transcription factor are active only in their multimeric form. Multimerisation allows the emergence of cooperativity.
Multiple Cloning Site (MCS) - A designed stretch of DNA with recognition sites for many common restriction enzymes. This region allows for the easy design, management, and cloning of DNA into larger environments, such as plasmids.
Monophyletic - Term applied to a group of organisms which includes the most recent common ancestor of all of its members and all of the descendants of that most recent common ancestor. A monophyletic group is called a clade.
Mammilla - In eggshell, the cone-like structure at the base of the shell unit where the shell unit attaches to the inner organic membrane.
Marsupial - A mammal that gives live birth to young that have gestated for only a short period of time. The young usually crawl into a pouch (the marsupium) or protected area and attach to their mother’s teat to finish developing. Examples of marsupials include kangaroos, opossums, and koalas.
Mesoderm - In animals with three tissue layers (i.e. all except sponges and cnidarians), the middle layer of tissue, between the ectoderm and the endoderm. In vertebrates, for instance, the mesoderm forms the skeleton, muscles, heart, spleen, and many other internal organs.
Mesogloea - Jellylike material between the outer ectoderm and the inner endoderm of cnidarians. May be very thin or may form a thick layer (as in many jellyfish).
Metabolism - The chemical processes within an organic body that supply the energy necessary for life. The rate of metabolic processes is sometimes used as a way to differentiate organisms. For example, mammals generally have a higher metabolism than reptiles and can thus sustain higher levels of activity for longer periods of time.
Microstructure - In eggshell, the shape, size, orientation, and distribution of components of the shell.
Monotreme - A mammal that lays eggs rather than giving live birth. Though laying eggs is a primitive reptilian trait, monotremes share many morphological, physiological, and reproductive characteristics with other mammals, making them true mammals. Extant monotremes include the duck-billed platypus and echidna.
Mouth - Front opening of the digestive tract, into which food is taken for digestion. In flatworms, the mouth is the only opening into the digestive cavity, and is located on the "belly" of the worm.
Mucus - Sticky secretion used variously for locomotion, lubication, or protection from foreign particles.
Muscle - Bundle of contractile cells which allow animals to move. Muscles must act against a skeleton to effect movement.
Myotome - Segment of the body formed by a region of muscle. The myotomes are an important feature for recognizing early chordates.
Neurotoxin - poison which interferes with nerve function, usually by affecting the flow of ions through the cell membrane.
Nucleic Acid - class of biochemistryical compounds which includes DNA and RNA. They are among the largest molecules known.
Nanometer - A unit of measure; one millionth (10-9) of a meter.
Nuclear Membrane - The double membrane which surrounds the eukaryotic nucleus. It has many pores in its surface which regulate the flow of large compounds into and out of the nucleus.
Nucleoid - Region in prokaryotes where the DNA is concentrated. Unlike a nucleus, it is not bound by a membrane.
Niche - The portion of the environment that a species occupies, defined in terms of the conditions under which an organism can survive, and the presence of other competing organisms.
Nitrogen Fixation - The conversion of gaseous nitrogen into a form usable by plants. Ususally by bacteria.
Nocturnal - Active only at night.
Nutrient Cycling - All the processes by which nutrients are transferred from one organism to another. For instance, the carbon cycle includes uptake of carbon dioxide by plants, ingestion by animals, and respiration and decay of the animal.
Nutrient - Any element or simple compound necessary for the health and survival of an organism. This includes air and water, as well as food.
Negative Autoregulation - A common regulatory network motif where the result of a process represses itself. An example would a repressor that represses its own transcription. Negative autorgulation can be harnessed to achieve faster convergence to steady state without the energetic waste of increased degradation i.e. positive autoregulation. It can also increase the stability of a species concentrations or induce oscillations depending on parameters.
Network - A group of two or more interacting sub-units. Each sub-units is called a node and the interactions between nodes are termed edges. Networks can be used to describe many different systems. Protein-protein interaction networks have proteins as nodes and the edges between them can be binding interactions. Microbiome studies may describe microbial species as nodes and define the edges as influences on growth rate.
Nitrogenous Base - A Nitrogen organic containing molecule, chemically is basic and is used in the structure of genetic material DNA and RNA; those used in heredity and biology are known as: A (Adenine), G (Guanine), T (Thymine), C (Cytosine), and U (Uracil); used in RNA instead of T.
Node - The region of a stem between two internodes; this is where branching of the vascular tissue into leaves or other appendages occurs.
Nuclease - An enzyme that creates a cut in the DNA backbone; RNA in some cases. Some nucleases are sequence specific, others are not. Some depend on the methylation state or other modifications of the substrate DNA. There are two main categories of nucleases, see endonuclease, and exonuclease.
Nucleic Base (Base) - In biology this refers to the basic building blocks of DNA and RNA. The primary nucleobases (nucleic bases) are Cytosine (C), Guanine (G), Adenine (A), Thymine (T) and Uracil (U).
Nucleoside - A glycosylamine that is can be thought of as a nucleotide without any phosphate groups. This term is commonly seen in the form of desoxynucleoside triphosphates (dNTPs), a necessary reagent for PCR reactions.
Nucleotide - The monomeric unit of DNA and RNA. A nucleotide comprises: A nitrogenous base, a five-carbon sugar (ribose or desoxyribose), at least one phosphate group and an organic base. See ribonucleotide for related.
A nucleotide is made of 3 parts:
- Nitrogenous base
- Five-carbon sugar; ribose or desoxyribose
- One minimum phosphate group
These single units, nucleotides, are the units by which large nucleic acids DNA/RNA are constructed by polymerisation.
Nucleus - A membrane-bound compartment found in most eukaryotic cells. It typically contains most of the cell's genetic information. This is the site of DNA replication and RNA synthesis. The entrance and exit of large molecules to and from the nucleus is mediated by nuclear pore complexes in the nuclear membrane.
Nematocyst - Older name for a cnidocyst.
Nerve Cord - Primary bundle of nerves in chordates, which connects the brain to the major muscles and organs of the body.
Nerve - A bundle of neurons, or nerve cells. More properly, it is a bundle of axons.
Neuron - A specialised cell that can react to stimuli and transmit impulses. A neuron consists of a body which contains the nucleus; dendrites, which are short branches off the body that receive incoming impulses; and a long axon which carries impulses away from the body and to the next neuron.
Notochord - Characteristic of chordates, the notochord is a stiff rod of tissue along the back of the body. In vertebrates, the backbone is deposited around the notochord and nerve cord.
Ossification - The process of bone formation. Special cells called osteoblasts secrete minerals that combine with a network of collagen fibers, forming the hard bone matrix.
Ovary - In flowering plants, the part of the flower which encloses the ovules. When the ovary matures, it becomes the fruit.
Ovule - In seed plants, the structure which gives rise to the seed.
Organelle - A membrane-bound structure in a eukaryotic cell that partitions the cell into regions which carry out different cellular functions, e.g., mitochondria, endoplasmic reticulum, lysosomes.
Omnivore - Literally, an organism that will eat anything. Refers to animals who do not restrict their diet to just plants or other animals.
Organic - Pertaining to compounds containing carbon. Also refers to living things or the materials made by living things. ant. - inorganic.
Oligo (Oligomer/Oligonucleotide) - Short polymers of nucleotides usually less than 200 nucleotides in length. They are typically chemically synthesized and have many uses in biotechnology. DNA oligos can be used as primers for PCR, targets in DNA microarrays, and as probes for Southern blots. Oligonucleotides can also refer to very short strands of DNA composed of some 10 nucleotides.
One Pot Reaction - A reaction occurring in a single test tube vs. having multi-step reactions that need to be combined appropriately. Preferred, as it reduces the manual work, material losses etc. compared to multi-pot reactions.
Open Reading Frame (ORF) - The translated part of an RNA moleucule.
Operator - The sequence of DNA to which a transcription factor binds. Operators sequences can be varied to alter the binding affinity of their respective transcription factor.
Origin of Replication (ORI) - The location in a genome (or within a replicating plasmid) at which DNA replication is initiated. Genes near origins of replication will typically have higher copy numbers on average.
Oscillator - A biomolecular system characterised by the periodic rise and fall of chemical species. Canonical synthetic biology include the metabolator and the repressilator.
Output Fluorescent Protein (OFP) - Output fluorescent protein. A fluorescent reporter GFP for a circuit's output.
Overhang - A short stretch of single-stranded DNA that "hangs off" a region of double-stranded double-stranded DNA. Two overhangs are compatible if they can anneal to form a double-stranded DNA with no gaps (there can be nicks in the backbone but no missing basepairs).
Outgroup - In a cladistic analysis, any taxon used to help resolve the polarity of characters, and which is hypothesized to be less closely related to each of the taxa under consideration than any are to each other.
Organ System - Collection of organs which have related roles in an organism's functioning. The nervous system, vascular system, and muscle system are all organ systems.
Organ - Collection of tissues which performs a particular function or set of functions in an animal or plant's body. The heart, brain, and skin are three organs found in most animals. The leaf, stem, and root are three organs found in most plants. Organs are composed of tissues, and may be organized into larger organ systems.
Osculum - The main opening through which filtered water is discharged. Found in sponges.
Ovulation - The process by which an egg (the female gamete) is released from the ovary. In animals other than mammals, with the exception of monotremes, this results in the laying of an egg outside of the body. When female mammals ovulate, the egg, if fertilized, is retained within the uterus.
Peptidoglycan - carbohydrate polymer cross-linked by proteins. It is found in the cell wall of Gram positive bacteria, where it stains with the dye crystal-violet.
Peridinin - carotenoid pigment found in dinoflagellates.
Phosphate - an ion consisting of a phosphorus atom and four oxygen atoms. Among other things, it is used in the constuction of nucleic acids.
Photosynthesis - biochemistryical process in which light energy is absorbed by chlorophyll, and is used to fuel the building of sugar molecules.
Phycocyanin - blue, water-soluble pigment found in the cyanobacteria and the red algae.
Phycoerythrin - red, water-soluble pigment found in the cyanobacteria and red algae.
Pigment - any colourful compound, used by living things to absorb or block sunlight, and in sexual displays.
Proteinaceous - describes any structure which is composed of protein.
Paleoherb - Any member of a group of basal flowering herbs which may be the closest relatives of the monocots. They include the water lilies, Piperales, and Aristolochiales.
Parenchyma - A generalized cell or tissue in a plant. These cells may manufacture or store food, and can often divide or differentiate into other kinds of cells.
Perennial - A plant which continues to grow after it has reproduced, usually meaning that it lives for several years.
Perianth - The sepals and petals of a flower are together called the perianth; literally "around the anthers".
Peristome - A set of cells or cell parts which surround the opening of a moss sporangium. In many mosses, they are sensitive to humidity, and will alter their shape to aid in spore dispersal.
Petal - One of the outer appendages of a flower, located between the outer sepals and the stamens. Petals often display bright colours that serve to attract pollinators.
Phloem - Nutrient-conducting tissue of vascular plants.
Phragmoplast - The cell plate formed during cell division.
Phytomelanin - a papery "sooty" black layer over the seed of plants in the Asparagales, which includes agaves, aloes, onions and hyacinths. It is an important character for defining the group.
Pinnately Compound - Leaves which are divided up like a feather are said to be pinnately compound.
Pistil - The central set of organs in a flower; it is composed of one or more carpels.
Pith - To severely damage the brain of a frog, also any central region of parenchyma tissue within a plant stem.
Pits - Thin regions of the cell wall in xylem conducting cells. Their structure is an important characteristic for recognizing different kinds of wood.
Plasmodesmata - Cytoplasmic connections between neighboring cells in plant tissues.
Platyspermic - Having seeds which are flattened and disc-like. Contrast with radiospermic.
Plicate - Folded like a paper fan, as in the leaves of palms, cyclanthoids, and some orchids.
Pollen Tube - In seed plants, the extension of the male gametophyte as it emerges from the pollen grain in search of the female gametophyte.
Pollen - The microspore of seed plants.
Pollination - Process of transferring the pollen from its place of production to the place where the egg cell is produced. This may be accomplished by the use of wind, water, insects, birds, bats, or other means. Pollination is usually followed by fertilization, in which sperm are released from the pollen grain to unite with the egg cell.
Pollinia - A mass of fused pollen produced by many orchids.
Protostele - When a plant's vascular tissue develops in a solid central bundle, it is said to have a protostele. See also siphonostele and eustele.
Pseudoelaters - Moisture-sensitive cells produced in the sporangium of hornworts.
Pteridophyte - Plant in which the sporophyte generation is the larger phase and in which the gametophyte lives an existence independent of its parent sporophyte. Pteridophytes are almost all vascular plants, and include the lycophytes, trimerophytes, sphenophytes, and ferns.
Pteridosperm - An extinct group of seed plants which bore fern-like leaves.
Pycnoxylic - Wood in which there is little or no parenchyma tissue among the xylem is called pycnoxylic. Conifers and flowering plants have pycnoxylic wood. Contrast with mannoxylic.
Plasma Membrane - Outer membrane of a cell, sometimes called the cell membrane. The term plasma membrane is used more frequently when discussing prokaryotes.
Plastid - Any of several pigmented cytoplasmic organelles found in plant cells and other organisms, having various physiological functions, such as the synthesis and storage of food.
Prokaryotic - Literally "before the nucleus", the term applies to all bacteria and archaea. Prokaryotic cells have no internal membranes or cytoskeleton. Their DNA is circular, not linear.
Protoplasm - All the contents of a cell, including the nucleus. (see: cytoplasm)
Pseudopodia - Fingerlike extensions from an amoeboid cell; literally "false feet".
Parasite - An organism that lives on or within a host (another organism); it obtains nutrients from the host without benefiting or killing (although it may damage) the host.
Pathogenic - Organism which causes a disease within another organism.
Pelagic - Pelagic organisms swim through the ocean, and may rise to the surface, or sink to the bottom. They are not confined to live on the bottom as benthic organisms do.
Periphyton - Dense strands of algal growth that cover the water surface between the emergant aquatic plants. Spirogyra is commonly responsible for this growth.
Photic Zone - Region of the ocean through which light penetrates; and the place where photosynthetic marine organisms live.
Phytoplankton - Tiny, free-floating, photosynthetic organisms in aquatic systems. They include diatoms, desmids, and dinoflagellates.
Plankton - Very small, free-floating organisms of the ocean or other aquatic systems, including phytoplankton, which produce their own nutrients through photosynthesis, or zooplankton, which get their nutrients from organisms.
Pollinator - Animal which carries pollen from one seed plant to another, unwittingly aiding the plant in its reproduction. Common pollinators include insects, especially bees, butterflies, and moths, birds, and bats.
Predator - Organism which hunts and eats other organisms. This includes both carnivores, which eat animals, and herbivores, which eat plants.
Prey - Organism hunted and eaten by a predator.
Producer - Any organism which brings energy into an ecosystem from inorganic sources. Most plants and many protists are producers.
Paratope (Antigen Binding Site) - This is the part of an antibody which affixes itself to the antigen, it is composed of a small region of around 5 to 10 amino acids. For relevent information see epitope.
PEST Tag - A C-terminal tag that can be added to proteins to increase their endogenous degradation rate. Termed "PEST" because the peptide is rich in proline (P), glutamate (E), serine (S), and threonine (T).
Petri Dish - A petri dish is a small container used often for cell cultures. It is cylindrical and short, normally about 8.5 cm in diameter, and 1.5 cm in height. In microbiology Petri dishes are prepared with variants of lysogeny broth with agar which solidifies the medium into a gell. This is used for growing bacterial cells; other mediums are used for eukaryotic or other organisms.
Fo more information on Petri dish preparation follow the link: Petri Dish Preparation.Phylum - A category in taxonomy, this is used in the hierarchy of animal classification; below kindgom and above class.
Plasmid - A relatively small circular piece of DNA found in prokaryotes. These pieces of DNA are versatile and can be exchanged intra-species and inter-species; horizontal and vertical exchange respecitively.
These are usually on the order of tens of kilobases or less. Typical features of a plasmid include the origin of replication (ORI), a multiple cloning site, and a marker; such as an antibiotic resistance gene (in a lab setting).
Plate Reader - A device for measuring the absorbance, luminescence, or fluorescence of bulk cell culture, exempli gratia suspended bacteria. The name comes from reading the values of these properties in standard multi-well plate format, exempli gratia 96-well plates, where each well contains a sample.
Poly-Cistronic - Relating to the transcription of two or more adjacent cistrons (genes) into a single mRNA.
Polymerase Chain Reaction (PCR) - A thermocycled reaction involving repeated rounds of primer annealing, primer extension and dsDNA denaturing to amplify and/or modify DNA sequences.
Polymerase - An enzyme that catalyses polymerisation (fusion of fibers) from monomers; nucleotides to DNA or RNA.
Positive Autoregulation - A regulatory motif where a gene product activates its own production. This motif can exhibit bistability if a gene's basal production rate is below its switching threshold. Compared to negative autoregulation a system exhibiting positive autoregulation will take longer to converge to a given steady state.
Positive RNA (+RNA) - Positive RNA refers to the RNA sequences which can be translated into proteins. See sense sequence.
Potential Hydrogen Isoelectric Point (pHi) - This term is used when refering to protiens, and denotes the pH at which a protein is charged neutrally.
Primer - A short, single-stranded DNA used in DNA replication. A primer binds a region of single-stranded DNA to form a primer-template complex which allows DNA polymerase to synthesise the complementary strand (primer extension). Since most DNA polymerases are only able to catalyse the addition of a nucleotide to the 3' end of a DNA strand, primers are necessary for elongation. Primers are a necessary reagent for PCR.
Processitivity - An enzyme is processive if it acts on a polymeric substrate and catalyses a reaction on several of the monomeric subunits after binding the polymer. For example, DNA polymerase is a processive enzyme, as it binds the primer-template complex and then proceeds to create a new strand of DNA by moving along the template. Higher processivity means that the enzyme stays and acts on the polymer for longer. Exempli gratia a DNA polymerase can process thousands of nucleotides after a single binding event. Other processive enzymes include some exonucleases which constantly chew up the DNA, base by base and helicases which unwind double-stranded DNA.
Prokaryote - An organism without a nucleus, exempli gratia bacteria.
Promoter - A region of DNA that drives the expression of a gene following it on a piece of DNA. Most promoters are directional, meaning they drive the expression of a gene only on one side (3') of it. Some promoters are bidirectionally driven and will drive the expression on both the 5' and 3' side.
Propagation - In terms of plasmids, propagation is the ability of a plasmid to be replicated by its host organism. A properly-propagating plasmid will have an origin of replication that is able to recruit the DNA replication machinery of the organism. A plasmid that does not propagate will ultimately be diluted out of a replicating cell line due to cellular divisions.
Protein - A polymer of amino acids that typically folds into a particular shape; though proteins with less-defined shapes exist. Some proteins are multimeric, meaning they are a complex of many copies of the same amino acid sequences.
Protein strucutre, primary structure is the sequence of amino acids, secondary α helices and β sheets, tertiary structure the association of secondary strucutres and quaternary strucutres the association of tertiary structures.
Many proteins are enzymes, allowing them to catalyse specific reactions, others are structural. Proteins are created in the process of translation using information encoded by codons in a messenger RNA. Note that "natural" amino acids are L-amino acids (levogyre).
Paraphyletic - Term applied to a group of organisms which includes the most recent common ancestor of all of its members, but not all of the descendants of that most recent common ancestor.
Parsimony - Refers to a rule used to choose among possible cladograms, which states that the cladogram implying the least number of changes in character states is the best.
Phylogenetics - Field of biology that deals with the relationships between organisms. It includes the discovery of these relationships, and the study of the causes behind this pattern.
Phylogeny - The evolutionary relationships among organisms; the patterns of lineage branching produced by the true evolutionary history of the organisms being considered.
Plesiomorphy - A primitive character state for the taxa under consideration.
Polarity Of Characters - The states of characters used in a cladistic analysis, either original or derived.Original characters are those acquired by an ancestor deeper in the phylogeny than the most recent common ancestor of the taxa under consideration. Derived characters are those acquired by the most recent common ancestor of the taxa under consideration.
Polyphyletic - Term applied to a group of organisms which does not include the most recent common ancestor of those organisms; the ancestor does not possess the character shared by members of the group.
Primitive - Describes a character state that is present in the common ancestor of a clade. A primitive character state is inferred to be the original condition of that character within the clade under consideration. For example, "presence of hair" is a primitive character state for all mammals, whereas the "hairlessness" of whales is a derived state for one subclade within the Mammalia.
Pseudoextinction - The apparent disappearance of a taxon. In cases of pseudoextinction, this disappearance is not due to the death of all members, but the evolution of novel features in one or more lineages, so that the new clades are not recognized as belonging to the paraphyletic ancestral group, whose members have ceased to exist. The Dinosauria, if defined so as to exclude the birds, is an example of a group that has undergone pseudoextinction.
Punctuated Equilibrium - A model of evolution in which change occurs in relatively rapid bursts, followed by longer periods of stasis.
Papilla - Cellular outgrowths. These look like little bumps or fingers on the surface of cells.
Parapodia - A sort of "false foot" formed by extension of the body cavity. Polychaetes and some insect larvae have parapodia in addition to their legs, and these provide extra help in locomotion.
Pathology - 1. The study of disease and abnormalities. 2. The manifestation of a disease, injury, or abnormality, as in bone or eggshell for example.
Pedipalps - The second pair of appendages of cheliceromorphs. In many arachnids, such as spiders, the pedipalps are enlarged in the male and used for copulation.
Pharyngeal Slits - Characteristic of chordates, pharyngeal slits are openings through which water is taken into the pharynx, or throat. In primitive chordates the pharyngeal slits are used to strain water and filter out food particles; in fishes they are modified for respiration. Most terrestrial vertebrates have pharyngeal slits only in the embryonic stage.
Pharynx - Cavity in the digestive tract just past the mouth itself. May be muscularized for sucking or swallowing in various animals.
Placenta - In mammals, a tissue formed within the uterus through which nutrients are passed from the mother to the embryo (and later the fetus) and its wastes are removed. It is analogous to the protective membranes in the egg of other amniotes. placental. A mammal that gives live birth to well-developed young that have prolonged embryonic development within the mother’s uterus. Marsupial mammals also have a placenta, but the embryo spends less time developing in the uterus before birth. Placentals include animals as diverse as humans, elephants, dogs, and mice.
Pleurae - In trilobites and other arthropods, pleurae are elongated flat outgrowths from each body segment, that overlie and protect the appendages.
Pore - Any opening into or through a tissue or body structure.
Precocial - Describes young that are mobile and fairly self-sufficient at birth. Precocial young are generally well-developed (and large) at birth, born with their eyes open, and able to walk. Chickens and grebes are examples of precocial birds; sheep and guinea pigs are examples of precocial mammals.
Proboscis - Elongated organ, usually associated with the mouth. The proboscis is an important feeding appendage in echiurans.
Pygidium - In trilobites, the posterior division of the body, formed by fusion of the telson with one or more posterior pleurae.
Quantitative Polymerase Chain Reaction (qPCR) - Quantitative PCR. A method of determining the amount of a DNA sequence of interest that is present in a sample. By monitoring the amplification of a strand of DNA during PCR, the original quantity can be extrapolated. qPCR can be used to monitor gene expression by reverse transcribing mRNA into cDNA and then quantifying the cDNA through qPCR.
Quorum Sensing - The ability of an organism to detect population density of others and or a molecule. The canonical quorum sensing system is the AHL-Lux system first described in Aliivibrio fischeri (formerly classified as Vibrio fischeri). Quorum sensing systems have been co-opted by synthetic biologists to engineer cell-to-cell communication systems.
RbcL - a gene which is located in the chloroplast of photosynthetic organisms. It codes for the large subunit of the protein rubisco, and its sequence has been useful in plant phylogenies.
Rubisco - protein which fixes carbon in photosynthetic organisms. It binds molecules of carbon dioxide to a five-carbon molcule. Rubisco is the most common protein on earth.
Radicle - The end of a plant embryo which gives rise to the first root.
Radiospermic - Having seeds which are round or ovoid. Contrast with platyspermic.
Reticulate - Interconnecting, like a network.
Rhizoid - A cellular outgrowth of a plant that usually aids in anchoring to the surface and increasing surface area to acquire water or nutrients; found in mosses, liverworts, and hornworts.
Rhizome - A horizontal underground stem, such as found in many ferns, where only the leaves may stick up into the air; sphenophytes (horsetails and their relatives) spread via rhizomes, but also produce erect stems.
Root - Usually the below ground portion of a plant. Contrast with shoot.
Rosette - A series of whorls of leaves or leaf-like structure produced at the base of the stem, just above the ground.
Repeat Sequences - The length of a nucleotide sequence that is repeated in a tandem cluster.
Reticulopodia - Long thread-like pseudopodia that branch apart and rejoin, forming a fine network. They are characteristic of forams.
Rain Shadow - The dry region on the leeward side of a mountain range, where rainfall is noticeably less than on the windward side. For example, the White Mountains in east central California are in the rain shadow of the Sierra Nevada.
Riparian - Having to do with the edges of streams or rivers.
Rate of Change - How much a dependent variable changes for a given change in an independent variable. Graphically, it is the slope of a line where the independent variable is on the x-axis and the dependent variable is on the y. The rate of change at any point can be determined by taking the first derivative of a function with respect to the independent variable.
Recognition Site - The specific sequence recognised by a DNA-binding protein. Most commonly referred to when discussing the cut sites for restriction enzymes.
Recombination - The insertion or deletion of DNA sequence from a strand mediated by recombinases (enzymes which catalyse recombination). Cre Recombinase, from a bacteriophage, is a commonly-used recombinase that affects site-specific recombination between two LOX sites. Recombination is the basis of Gateway cloning technology.
Regulatory Element - Any element that regulates gene expression. Examples of cis-acting regulatory elements are operators, promotors, and leader peptides. Trans-acting regulatory elements are diffusible molecules such as transcription factors or trans-acting RNA in a toehold switch system.
Replication - The process of producing two identical copies of DNA from a single double helix. DNA replication begins at specific sequences termed origins of replication and requires polymerases, dNTPs, and other factors.
Replicon - A DNA or RNA molecule that replicates from a single origin of replication. Most prokaryotic chromosomes are a single replicon, while eukaryotic chromosomes typically have multiple replicons. "Replicon" is sometimes used to describe self-amplifying RNAs (RepRNA), which have the ability to replicate themselves within a transfected cell to provide continuous protein production.
Reporter - In the context of gene expression, a reporter allows the easy determination of transcription from a given promoter. Good reporters have an obvious phenotype such as the blue phenotype for LacZ in the presence of X-gal, or the fluorescence of a fluorescent protein. Quantification of protein production from a promoter as a function of reporter fluorescence is also possible.
Repressilator - One of the earliest oscillating synthetic circuits published by Elowitz and Leibler in 2000. It accomplishes oscillations through the use of a three-repressor ring oscillator circuit topology. The circuit was able to oscillate, but had issues with robustness.
Repressor - The suppression of gene expression from a promoter by a protein. Important repressors in synthetic biology are TetR, LacI, and cI (lambda repressor). Some repressors are inducible.
Response - How a system reacts to an input. Much information about a system's internal workings can be gleaned from observing its response to different types of input.
Restriction Enzyme - Enzymes that cut DNA in a site-specific manner. Typically, each restriction enzyme has a certain restriction site that it recognises. Standard restriction enzymes that cut within their recognition site are the basis of traditional cloning methods. Type IIS restriction enzymes, such BsaI, cut at a location outside of their recognition site and enable DNA assembly without the producing scar regions. Type IIS restriction enzymes are the basis of Golden Gate cloning methods.
Retroactivity - When the input/output behavior of an upstream model is affected by presence of downstream module(s). Retroactive effects can be reduced through the use of load driver circuits.
Reversed Tetracycline Trans-Activator (r-tTA) - Analogous to tTA, except that the function of DOX is reversed. DOX stabilises the DNA binding domain, facilitating promoter binding and activation of gene expression of promoters with tetracycline responsive elements (TREs). Referred to as the DOX-on system.
Ribonucleotides - Same as a nucleotide yet includes ribose instead of dextrose as the sugar component to the nucleic material; one is of course DNA and the other RNA.
Ribosome Binding Site (RBS) - A sequence upstream of the start codon that recruits ribosomes and allows translation. RBSs are well-defined in prokaryotic systems and are also known as Shine-Dalgarno sequences. Recruitment of ribosomes in eukaryotic systems is more complex and less-understood. RBS "strength" is a large factor in protein production rate and is determined by local RNA secondary and tertiary structure. RBS calculators allow the control of relative translation rates across different RBSs.
Ribosome - A protein-RNA complex that is responsible for translating mRNA into polypeptides i.e. proteins.
Riboswitch - A cis-acting regulatory element found in mRNA transcripts. Riboswitches form structures whose conformations are affected by small molecules. These conformational changes have the ability to turn expression of a transcript "ON" or "OFF". This switching is accomplished through a variety of mechanisms.
Ribozyme - An RNA molecule that is capable of catalysing chemical reactions. Many ribozymes of interest (hammerhead and hairpin) catalyse RNA cleavage and ligation reactions.
RNA Binding Protein (RNA-BP) - A protein that binds to an RNA sequence as its substrate. Naturally, these proteins serve a variety of roles in post-transcriptional regulation. Recently, bacteriophage coat proteins such as PP7 and MS2 have been used to target RNA sequences that have had RBP binding sites integrated into them. Fusion of these RBPs to fluorescent proteins allows the real-time monitoring of mRNA transcription.
RNA Interference (RNAi) - A biological process by which double-stranded RNA (dsRNA) inhibits the expression of genes complementary to its sequence. RNAi is thought to have evolved as a defense against viruses (some of which have dsRNA genomes) and it has been shown to have an important role during development. This system can also be exploited to induce artificial gene knockdown through the introduction of synthetic dsRNAs or vectors that express siRNAs.
While most eukaryotes have RNAi machinery, S. cerevisiae notably lacks it. Prokaryotes also do not possess RNAi machinery.
RNA Polymerase (RNA-P) - RNA polymerase; the protein complex that transcribes RNA from DNA. In prokaryotes RNA-P, promoter specificity is determined by the presence of a sigma factor and the complex usually binds to the -35 and -10 elements (35bp and 10bp upstream of the start codon) of genes. Occlusion of these sites through transcription factor binding is a common mechanism of genetic repression. In eukaryotes, mRNA transcription is carried out by RNA polymerase II, but other RNA-P types are responsible for the production of transfer RNAs (tRNA), ribosomal RNAs (rRNA), and some regulatory RNAs.
RNA-Seq - RNA sequencing. A method of obtaining a snapshot of genetic transcripts present in an organism. mRNAs can be isolated from a cell by their polyA tail and then reverse transcribed into cDNA. Next-generation sequencing methods can then be used to sequence this cDNA, which allows the reconstruction of the cell's transcriptome.
RNA - Ribonucleic acid; polymeric molecules made up of nucleotide monomers. RNA has many biological functions from information carrying (mRNA) to catalytic activity (ribozymes); its primary function however, is to transmit information from longterm storage (DNA) to active machinery proteins. RNA is often found folded unto itself instead of in a double strand type; which is often the case with DNA. RNA is composed of 4 different kinds of nucleotides with the nitrogenous bases: A (Adenine), U (Uracil), C (Cytosine), and G (Guanine). RNA notably contains U instead of T (thymine) as DNA does. RNA also does not contain desoxyribose as DNA does but ribose instead. The 18S ribosomal RNA sequence has been used in many groups of organisms to reconstruct phylogeny.
rtPCR - Reverse transcription polymerase chain reaction (see PCR), this technique uses a special form of polymerase to reverse the transcription process. This allows for us to go from a sample of RNA to the associated DNA.
Radiation - Event of rapid cladogenesis, believed to occur under conditions where a new feature permits a lineage to move into a new niche or new habitat, and is then called an adaptive radiation.
Rank - In traditional taxonomy, taxa are ranked according to their level of inclusiveness. Thus a genus contains one or more species, a family includes one or more genera, and so on.
Reticulation - Joining of separate lineages on a phylogenetic tree, generally through hybridization or through lateral gene transfer. Fairly common in certain land plant clades; reticulation is thought to be rare among metazoans.
Saxitoxin - neurotoxin found in a variety of dinoflagellates. If ingested, it may cause respiratory failure and cardiac arrest.
Scanning Electron Microscope (SEM) - A special kind of microscope that scans samples with a high-energy beam of electrons to produce a high-resolution, detailed, three-dimensional image. An SEM can magnify a sample up to 250 times that of the best light microscopes.
Silica - amorphous silicon dioxide (glass). It is a structural component in many organisms, such as diatoms and horsetails.
Spongin - proteinacous compound of which the spicules in Demospongiae are composed.
Starch - a complex polymer of glucose, used by plants and green algae to store surplus sugar for later use.
Sugar - A generic name for soluble carbohydrate moelcules, often contained in food.
Secondary Growth - Growth in a plant which does not occur at the tips of the stems or roots. Secondary growth produces wood and bark in seed plants.
Sepal - The outermost structures of a flower.
Shoot - Usually, the above ground portion of a plant, bearing the leaves. Contrast with root.
Siphonostele - When a plant's vascular tissue develops as a central cylinder, it is said to have a siphonostele. See also protostele and eustele.
Spermatophyte - A seed plant.
Sporangiophore - A stalk to which sporangia are attached.
Sporangium - A chamber inside of which spores are produced through meiosis.
Sporophyll - Any leaf which bears sporangia is called a sporophyll.
Stamen - Part of a flower, the tip of which produces pollen and is called the anther.
Stigma - The sticky tip of a pistil. Or, the dense region of pigments found in many photosynthetic protists which is sensitive to light, and thus functions somewhat like a miniature eye.
Stipe - A scientific term for "stalk".
Stipules - Paired appendages found at the base of the leaves of many flowering plants.
Stomata - Openings in the epidermis of a stem or leaf of a plant which permit gas exchange with the air. In general, all plants except liverworts have stomata in their sporophyte stage.
Streptophytes - The clade consisting of the plants plus their closest relatives, the charophytes.
Strobilus - A tightly clustered group of sporophylls arranged on a central stalk; commonly termed a "cone" or "flower".
Style - The narrow stalk of the pistil, located above the ovary but below the stigma.
Synangium - A cluster of sporangia which have become fused in development.
Salinity - A measure of the salt concentration of water. Higher salinity means more dissolved salts.
Saprophyte - Organism which feeds on dead and decaying organisms, allowing the nutrients to be recycled into the ecosystem. Fungi and bacteria are two groups with many important saprophytes.
Scavenger - An organism that feeds upon dead and dying organisms.
Seaweed - Any large photosynthetic protist, including rhodophytes and kelps. Seaweeds are not true plants, but like plants they can make their own food.
Specialist - Organism which has adopted a lifestyle specific to a particular set of conditions. Contrast with generalist.
Substrate - "Supporting surface" on which an organism grows. The substrate may simply provide structural support, or may provide water and nutrients. A substrate may be inorganic, such as rock or soil, or it may be organic, such as wood.
Symbiosis - A relationship between two organisms that live in intimate contact with each other; includes mutualism (both organisms benefit, they rely on each other for survival), parasitism (one organism benefits at its host's expense) and commensalism (one partner benefits and the other is neither benefitted nor harmed).
Sachharomyces cerevisiae - A single-celled species of yeast which is commonly used in biology and syntetic biology. Notably this eukaryotic organism does not have RNAi machinery.
Scaffold - A structure on which elements can be brought together to be close in space. For example, the enzymes involved in the same pathway can be brought together in proximity on an RNA scaffold by fusing the enzymes with RNA-binding proteins and thus increase the efficiency of the pathway, as substrates do not need to diffuse far to reach the next enzyme in the pathway.
Scar Sequence - An unavoidable sequence arising from technicalities of a DNA assembly process. For example, Gateway assembly leaves a scar after the recombination occurs.
Screening - A method to obtain a set of organisms exempli gratia a bacterial colony, with a particular genotype or phenotype by considering many members of a large pool of variants. Each member is assessed for its suitability, causing more work than selection, where the undesired members are eliminated.
Secondary Structure - A secondary structure in a protein refers to the the three dimensional form which a polypetidic chain takes: either α helices, β sheets, β turns, and even ω loops. See protein for an illustration.
The primary strucutre refers to the sequence of amino acids composing the chain, and the tertiary strucutre the association of secondary structures.
Selection - A phenomena by which organisms reproduce differentially; some more than others. This process results in some genotypes/phenotypes dominating a population.
Selection can be positive (organisms with a trait survive to the next round) or negative (organisms that do not have a trait survive to the next round).
In a lab setting this can be used as a method for directed evolution typically with bacteria. This approach can be less work than screening, as only the "interesting" organisms survive, rather than all organisms.
Sense Sequence - Positive RNA is the RNA version of sense DNA (also called positive); this strand would be translateable into a protein. A sense sequence of nucleotides is complementary to an antisense coding sequence.
Sensitivity - How well a method can pick up true positives; calculated by dividing the number of true positives by the number of true positives added to the number of false negatives.
Sequence - A suite of specific or unique values. In biology a sequence refers to a suite of nucleotides in a certain order; which can define a gene.
Sequencing - The process of determining the nucleic acid sequence of a piece of DNA or of a whole organism.
Signal - A function conveying information. A signal can take and be encoded in many forms, exempli gratia the voltage of a wire or the concentration of a chemical species. Systems can act on signals to modify them or to produce new signals.
Southern Blot - A lab technique used for the detection of specific DNA sequences in a sample. Sothern blotting typically involves a first migration by classic electrophoresis then a "blotting" step by a membrane which uptakes the DNA from the gell, then the probe which is complementary to the strand of interest is introduced. This probe is typically marked by a radioactive strand or an antibody. This reveals if the sequence of interest was found in the sample or not.
Species - A slippery concept contested even today. Current consensus states that a species is a group of like individuals which are capable of reproduction typically by sexual reproduction.
Specificity - How well a method can distinguish between true positives and false positives; also called the true negative rate and calculated by dividing the number of true negatives by the number of true negatives added to the number of false positives.
Often at odds with sensitivity (increasing specificity typically decreases sensitivity; this can be observed with a receiver operating characteristic curve, which plots 1 minus specificity against sensitivity).
Stability Analysis - A mathematical technique for determining at which conditions systems are stable.
Stable Steady State - A steady state to which all systems return to after a small enough perturbation.
State Variable - A variable dedicated to describing a state of a system, exempli gratia the concentration of a species, the volume of a cell or any other measurable quantity.
Stateful - Having a state, having memory. For example, a toggle switch is stateful since it has two states. Combinational logic circuits are not stateful, they do not have any memory of previous inputs or states.
Steady State - A state of the system which does not evolve over time, given that there are no perturbations. Steady states can be stable or unstable, indicating their response to small perturbations (stable means the system returns to the steady state and unstable means it does not).
Stochastic - Random, non-deterministic. A stochastic model enables modeling of discrete systems containing a small number of species, where deterministic, continuous models may give inappropriate predictions. Stochastic simulations enable predicting properties other than the mean, bulk behaviour of a system. Stochastic simulations can show unexpected properties of systems which deterministic-continuous models might not.
Strand - A single DNA molecule or RNA. Such a strand has directionality, typically depicted as going from 5' (the end of the strand with the phosphate group) to 3' (the end of the strand with the -OH group).
Subunit - Subunit refers to a component part of a whole, this can be used when talking of parts of a multichain protein.
Synthetic Biology - An interdisciplinary domain of study, focused on engineering and creating novel forms of useful life.
Synthetic biology can be applied in industry, medicine, or even artificial intelligence research (wetware). It combines skills from life science, mathematics, engineering, chemistry, physical and computer science. Synthetic biology can be applied in industry, medicine, or even artificial intelligence research (wetware). It combines skills from life science, mathematics, engineering, chemistry, physical and computer science. Synthetic biology can be applied in industry, medicine, or even artificial intelligence research (wetware). It combines skills from life science, mathematics, engineering, chemistry, physical and computer science.
System - A collection of devices and other components operating together to carry out some set of functions.
Sister Group - The two clades resulting from the splitting of a single lineage.
Stasis - A period of little or no discernible change in a lineage.
Stem Group - All the taxa in a clade preceding a major cladogenesis event. They are often difficult to recognize because they may not possess synapomorpies found in the crown group.
Synapomorphy - A character which is derived, and because it is shared by the taxa under consideration, is used to infer common ancestry.
Systematics - Field of biology that deals with the diversity of life. Systematics is usually divided into the two areas of phylogenetics and taxonomy.
Segmentation - In many animals, the body is divided into repeated subunits called segments, such as those in centipedes, insects, and annelids. Segmentation is the state of having or developing a body plan in this way.
Septum - Partition which divides up a larger region into smaller ones, such as in the central body cavity of some anthozoa.
Siphon - Opening in molluscs or in urochordates which draws water into the body cavity. In many molluscs, the siphon may be used to expel water forcibly, providing a means of propulsion.
Skeleton - Support structure in animals, against which the force of muscles acts. Vertebrates have a skeleton of bone or cartilage; arthropods have one made of chitin; while many other invertebrates use a hydrostatic skeleton, which is merely an incompressible fluid-filled region of their body.
Spicule - Crystalline or mineral deposits found in sponges, sea cucumbers, or urochordates. They are structural components in many sponges, and may serve a protective function in other organisms.
Spiracle - In insects and some other terrestrial arthropods, a small opening through which air is taken into the tracheae. Insects have several spiracles, arranged along the sides of the abdomen.
Spongocoel - Central body cavity of sponges.
Synapsid - A vertebrate distinguished by a skull with one pair of openings in the sidebehind the eyes, e.g., mammals and their close relatives.
Tepal - When the sepals and petals of a flower are indistinguishable, they are referred to as tepals. Tepals are common in many groups of monocots.
Thalloid - Plants which have no roots, stems, or leaves are called thalloid, such as liverworts and hornworts.
Tracheophyte - Any member of the clade of plants possessing vascular tissue; a vascular plant.
Tree - Any tall plant, including many conifers and flowering plants, as well as extinct lycophytes and sphenophytes.
Tuber - An underground stem which has been modified for storage of nutrients, such as a potato.
Turgor Pressure - Force exerted outward on a cell wall by the water contained in the cell. This force gives the plant rigidity, and may help to keep it erect.
Test - A hard shelll produced by some unicellular protists; may be made of calcium carbonate, silica, or sand grains.
Theca - General term for any stiff outer covering of a unicellular protist, and usually made up of interlocking plates. dinoflagellates and diatoms are examples of protists with thecae.
Transduction - Viral transfer of DNA to new host.
Trichocyst - Organelle in ciliates and dinoflagellates which releases long filamentous proteins when the cell is disturbed. Used as a defense against would-be predators.
Temperate - Region in which the climate undergoes seasonal change in temperature and moisture. Temperate regions of the earth lie primarily between 30 and 60 degrees latitude in both hemispheres.
Terrestrial - Living on land, as opposed to marine or aquatic.
Tropical - Region in which the climate undergoes little seasonal change in either temperature or rainfall. Tropical regions of the earth lie primarily between 30 degrees north and south of the equator.
Tundra - A vast, mostly flat, treeless Arctic region of Europe, Asia, and North America in which the subsoil is permanently frozen. The dominant vegetation is low-growing lichens, mosses, and stunted shrubs.
Tag - A tag enables an experimenter to follow or extract a particular molecule, molecular species or even whole cells. Exempli gratia the His-tag enables experimenters to enrich for species containing said tag using columns (a nickel column for the His-tag). Fluorescent tags enable measurement with devices like plate readers or flow cytometers.
TALE, TALER, TALEN - Transcription activator-like effectors (TALEs) are DNA binding proteins that have a "code" relating just two specific amino acids in their DNA-binding regions to a nucleotide in the DNA that is recognised. This "code" has been used by researchers to create a variety of TALE proteins that bind specific DNA operator sites.
TALE operator sites can be placed near transcriptional start sites to block RNA polymerase binding and thus repress gene expression. TALEs used for this purpose are called TALE repressors, or TALERs. TALEs can also be modified to have nuclease activity, and cut DNA at specific locations in the genome. These are refered to TALE nucleases, or TALENs.
Terminator - The process of termination is the stopping of transcription. This occurs due to particular sequences, terminator sequences, within the DNA. Some terminators cause termination by causing the RNA to fold into structures that cause the RNA to release it. Others recruit proteins which pull the freshly synthesised (nascent) RNA out of the RNA polymerase or cause the release by other mechanisms.
Tetracycline Trans-activator (tTA) - Is a fusion of a tetracycline-destabilising DNA binding domain and the VP16 trans-activation domain. Thus, in the presence of DOX (an analog of tetracycline) tTA can no longer bind to its target promoter
Thermocycler - A machine that can rapidly change temperatures in a programmable fashion, exempli gratia in loops (cycles of steps). Used for running reactions such as PCR.
Thermolabile - Refers to a protein, enzyme, or molecule that is (generally) negatively impacted or destroyed/denatures by heat. An example would be a thermosensitive origin of replication or a thermolabile T5 exonuclease.
Thermostable - Resistant to high temperature. A thermostable enzyme is still active at elevated temperatures (exempli gratia near boiling) and have been found in organisms that live in extreme environments, exempli gratia deep sea thermal vents.
Tight junction - Intercellular structure which forms an almost perfect continuous seal between two adjacent epithelial cells close to their apical (side which faces the lumen) side. The tightness of the seal may vary depending on the kind of epithelium. It acts as a filter which lets water and some other ions come through and into the organism. These tight junctions are also important in halting the diffusion of proteins and cytoplasmique glycolipids from the apical side of the cell to the basolateral side.
Timescale Separation - A method for simplifying time-dependent systems. It is often the case that a system has processes which have timescales (how long it takes for the system to reach equilibrium) differing by one or more orders of magnitude. For example, the timescale of transcription factors binding to DNA is short, as the binding equilibrium is reached within milliseconds or less. However, the process of producing a mature protein can take minutes or more. Hence, when analysing a system where both processes occur, the binding can be considered to be at equilibrium when discussing how protein dynamics look.
Timing Diagram - A diagram showing how a system behaves and evolves over time. For digital systems, a timing diagram shows the state of the system (and possibly signals within the system) at each tick of a clock. Often a timing diagram is depicted as a table, where each row shows a signal and each column shows an instance of time. The value in the table is the value of the particular signal at the particular time. Another way to depict the timing diagram is to draw a value trace over time for each signal and stack them such that time flows left to right.
Topology - In the context of regulatory networks, the topology refers to the way the nodes (exempli gratia genes) are connected (which kinds of arrows go from which nodes to which nodes). An abstract gene-regulatory network has some topology that could be implemented by many ways by choosing the suitable components for each node.
Toxin - A substance (small molecule, peptide, protein) that kills cells or even whole organisms. Toxin-antitoxin pairs can be useful in biotechnology where the presence of the antitoxin confers resistance to the toxin, enabling selection. Producing a toxin as the output of a circuit can be used in medical applications, exempli gratia to kill cancerous cells or infectious bacteria.
Trans/Cis - Trans means two things on opposite sides from one another, and cis means to things which are on the same side.
Transactivation Domain, TAD - A domain of a transcription factor that interacts with the transcriptional machinery, cofactors, and/or chromatin modifying machinery (eukaryotes only) in order to facilitate formation of the transcriptional initiation complex (TIC).
Transcription Factor, TF - A protein that binds operator sequences in the promoter or enhancer regions distal from the promoter. Activates or represses transcription depending on the presence of a trans-activation or trans-repression domain, respectively. Also can contain a signal-sensing domain, which allows for external regulation of DNA-binding or cellular localisation, exempli gratia by small molecules or hormones.
Transcription - Transcription is the process of creating an RNA transcript based on information in DNA. A promoter drives transcription and decides when and how much transcript is made. The transcript or resulting mRNA is then transformed into a protein in a process called translation.
Transcriptional Fusion - A mechanism for generating several transcripts from the same input. For example, using the same promoter for different genes causes all of the genes to be transcribed if the appropriate input is present. Several transcripts can sometimes also be produced if processing of a single transcript creates several, exempli gratia if there is a self-cleaving RNA element in the transcript. These transcripts are produced in equal amounts, but can contain different information. See Translational Fusion.
Transcriptome - Refers to the set of all RNA molecules produced and contained by one cell or population of cells.
Transcriptomes can be studied and built by DNA microarray assays and next-gen sequencing such as RNA seq.
Transfection - The process of introducing new genetic material into cells, mostly used when talking about mammalian cells (similar to transformation in bacteria).
Transformation - The process of introducing new genetic material into cells, mostly used when talking about bacterial cells (similar to transfection in mammalian cells). Transformation can be performed by electrical and or chemical means, exempli gratia electroporation.
Translation - The process of creating a peptide i.e. protein (sequence of amino acids). Exempli gratia a protein or enzyme) based on the sequence of an mRNA. The ribosome is the key enzyme in this process, which also requires tRNAs charged with amino acids. Amino acids are linked together through peptide bonds.
Translational Fusion - A protein fusion where the two proteins are translated together. The coding sequences of translationally fused proteins are on the same mRNA and form a single polypeptide chain when translated.
tRNA - Transfer RNA. These special RNAs have a particular structure and many chemical modifications. They are charged with amino acids; the charged tRNAs are then used in protein synthesis i.e. translation. The tRNA has a three nucleotide anticodon loop, which complements a three nucleotide codon on an mRNA in the ribosome, enabling the ribosome to create a new peptide chain from the sequence of an mRNA.
Two Substrate Enzyme - An enzyme mechanism refers to the way a reaction occurs, that is the order of binding. Here we consider an enzyme that intakes two different substrates, the reaction can happen in five different ways:
Enzyme with two substrates can have various different mechanisms. Described by the diagrams, also shown the double inverses associated to the reactions and the substrates.
- Sequential random dependent mechanism.
- Sequential random independant mechanism.
- Sequential ordered mechanism.
- Ping-pong mechanism.
- Theorell-Chance mechanism.
Type II Restriction Enzymes - These restriction enzymes are used to cleave double-stranded DNA in a location that is outside the recognition sequence of the enzyme. They are particularly useful for DNA assembly, as they enable creating arbitrary overhang sequences. Commonly used Type IIs enzymes include BsaI and BbsI, which are both used in Golden Gate or MoClo assembly.
Taxon - Any named group of organisms, not necessarily a clade; a taxon may be designated by a Latin name or by a letter, number, or any other symbol; taxa- pl.
Taxonomy - The science of naming and classifying organisms.
Telson - The last segment of the abdomen in many arthropods. May be flat and paddlelike, buttonlike, or long and spiny, as in the horseshoe crabs.
Tentacles - Appendages which are flexible, because they have no rigid skeleton. Cnidarians and molluscs are two kinds of orgnaisms which may have tentacles.
Tetrapod - An animal with four limbs that evolved from a common fish ancestor during the Devonian Period (~365 million years ago). Tetrapods include amphibians, reptiles, birds, and mammals. Though "tetrapod" literally translates to "four-footed," many animals in this group have limbs adapted for different modes of transportation. Humans walk upright on two legs; the legs of whales, dolphins, and other marine mammals have evolved into fins and flippers; and snakes have lost their legs all together. Tetrapods are generally thought of as terrestrial animals, but some, like dolphins and whales, have returned to marine habitats.
Thorax - In insects, the second body region, between the head and thorax. It is the region where the legs and wings are attached.
Tissue - A group of cells with a specific function in the body of an organism. Lung tissue, vascular tissues, and muscle tissue are all kinds of tissues found in some animals. Tissues are usually composed of similar cells, and are often organized into larger units called organs.
Tracheae - Internal tubes through which air is taken for respiration. Vertebrates with lungs have a single trachea carrying air to the lungs, while insects and some other land-living arthropods have a complex network of tracheae carrying air from the spiracles to all parts of the body.
Tube Feet - Extensions of the water-vascular system of echinoderms, protruding from the body and often ending in suckers. May be used for locomotion and/or for maintaining a tight grip on prey or on the bottom.
Tubercle - Any small rounded protrusion. In pycnogonids and some cheliceramorph arthropods, the central eyes are carried on a tubercle.
Ultrastructure - The detailed structure of a specimen, such as a cell, tissue, or organ, that can be observed only by electron microscopy. Also called fine structure. In eggshell, ultrastructure refers to the three-dimensional arrangement of mineral crystals and organic matter. It is described in terms of calcite or aragonite mineralogy and the transition between different zones of organization within the shell. Distinct zones of organization are called ultrastructure zones.
Undulipodium - Another term for a eukaryotic flagellum.
Upwelling - The raising of benthic nutrients to the surface waters. This occurs in regions where the flow of water brings currents of differing temperatures together, and increases productivity of the ecosystem.
Unicellular - A type of organism which is wholly contained inside a single cell. Bacteria and yeast are prime examples of unicellular life.
Untranslated Region (UTR) - Sequences in the 5' and 3' ends of an mRNA that are transcribed, but not translated. UTRs often harbor regulatory elements, for example protein binding sites (including the ribosome binding site), miRNA binding sites, secondary structures exempli gratia riboswitches.
Uniramious - Among arthropods, uniramous refers to appendages that have only one branch. Insects, centipedes and millipedes, and their relatives are uniramous arthropods; land-living chelicerates such as scorpions, spiders,and mites are also uniramous but probably descended from ancestors with biramous appendages. Contrast with biramous.
Vegetative Growth - Growth of a plant by division of cells, without sexual reproduction.
Venation - The arrangement and pattern of veins in a leaf.
Vacuole - Membrane-bound fluid-filled space within a cell. In most plant cells, there is a single large vacuole filling most of the cell's volume. Some bacterial cells contain gas vacuoles.
Variance - A statistical measure describing the spread of a random variable around its mean. A tight distribution has small variance and thus most of the values are close to the mean. The variance is related to the standard deviation by
Mathematically, ; the variance is the expectation of the square of the difference of the random variable from its mean. The variance can also be calculated by taking the difference of the expectation of the square of the variable and the expectation of the variable, squared: Vesicle - Vesicles are lipid bilayer structures that contain liquid and materials of interest. DNA, RNA and proteins can all be delivered to cultured cells using vesicles created in a mixture of the desired payload. As the vesicles form, they encapsulate the nucleic acids and proteins in the mixture. The vesicles can merge with the cell outer layer or be endocytosed, both leading to the delivery of the payload (though through different biological mechanisms). Reagents are commercially available for this purpose, optimised for different payload types, amounts, and sizes.
Virus - A virus can be simply explained as a protein and genetic material complex. These are pseudoorganisms and there is much debate as to whether they should or not be classified as living. Viruses have no metabolism and are incapable or reproduction without parasitic use of a host cell's biological machinery. Some viruses may contain DNA or RNA in the case of RNA it may be either positive RNA or negative.
Viruses are complex "organisms" with a variety of forms, shapes, and sizes. Some present simple parasitic cycles while others integrate completely into the host's DNA as HIV does. See enveloped virus.
VP16 - Herpes simplex virus (HSV) viral protein 16 (VP16) trans-activation domain (TAD). Stongly activates gene expression in eukaryotic cells when fused to a DNA binding protein, commonly Gal4.
Vicariance - Speciation which occurs as a result of the separation and subsequent isolation of portions of an orginal population.
Vascular - Refers to a network of tubes which distribute nutrients and remove wates from the tissues of the body. Large multicellular animals must rely on a vascular system to keep their cells nourished and alive.
Vertebra - A component of the vertebral column, or backbone, found in vertebrates.
Whorl - An arrangement of appendages, such as branches or leaves, such that all are equally spaced around the stem at the same point, much like the spokes of a wheel or the ribs of an umbrella
Wood - A secondary tissue found in seed plants which consists largely of xylem tissue.
Watson Strand (5' → 3') - The sense strand complementary to the Crick strand (3' ← 5'). This strand matches the mRNA sequence after T-S are replaced with U-S.
Western Blot (immunoblot) - A lab technique used for detecting the expression of specific proteins in a tissue sample or extract.
The first step is generally to migrate the proteins by a classic electrophoretic gel, then to "blot" the gel with a membrane (normally nitrocellulose or polyvinyldene fluoride) which holds antibodies specific to the protein of interest. This will only reveal the bands which contained said protein.
Xylem - Water transporting tissues found in vascular plants.
X-Gal - A colourless galactose derivative. When cleaved by β-galactosidase (encoded by the LacZ gene), gives rise to two products: galactose and an indole. Indole spontaneously forms a dimer which has a blue colour. This allows to test for the presence of β-galactosidase activity and by extension the activity or presence of the LacZ gene.
Yeast - A class of mostly unicellular eukaryotic organisms. These easy-to-culture organisms are often used in biology and synthetic biology as test organisms or chassis. Commonly used yeast species include Saccharomyces cerevisiae (brewer's yeast or baker's yeast; unlike other eukaryotes it is missing the RNAi machinery). Some notable species are Kluyveromyces lactis which can convert lactose to lactic acid, and Schizosaccharomyces pombe fission yeast; this yeast has RNAi machinery.
Yellow Fluorescent Protein (YFP/eYFP) - Yellow fluorescent protein. "E" denotes newer enhanced version.
Zinc Finger (ZF) - A DNA binding protein motif, often seen in transcription factors. In the folded motif, a zinc ion is coordinated by amino acid helices and sheets. Many motifs bind sequence-specifically (3-4 base pairs) and can be combined together to bind longer sequences (9-12 basepairs). While a "code" exist (mapping of motifs to sequences), technologies like TALEs or CRISPR/Cas9 are often preferred for engineering DNA binding proteins, as the code is more clear and specific in these; increasing the rate of success.
2D Electrophoresis - A 2D electrophoresis, is a variant of the electrophoresis lab method. Usually the first electrophoresis is done to migrate proteins based on their mobility which is dependent on the charge/mass ratio. Then a second migration is done in the other dimension, or perpendicular to the first; now migrating the proteins based on their potential hydrogen isoelectric point (pHi). By doing this we can reveal different proteins that might have been hidden all in one band.
3 Prime End (3') - The 3' or 3 prime end of a DNA or RNA molecule is the end that holds the hydroxyl group (-OH). The other end of a nucleic strand is the 5' or 5 prime end , which has the phosphate group (-PO4). For an illustration see the figure for DNA.
5 Prime End (5') - The 5' or 5 prime end of a DNA or RNA molecule is the end that holds the terminal phosphate (-PO4). This allows for the formation of the phosphodiester bond between two nucleotides. The other end of a nucleic strand is the 3' or 3 prime end , which has the hydroxyl group (-OH). For an illustration see the figure for DNA.
β-Cells - β-cells are a type of cell found in the pancreas, the pancreatic islets more precisely. These cells are responsible for the synthesis and secretion of insulin and amylin.
They make up around 50 - 70% of all the cells in the islets. People with type-I diabetes have their β-cells iradicated and thus produce no insulin.
β-Galactosidase (lactase, β-gal, beta-gal) - Is a glycoside hydrolase enzyme which catalyses the breakdown of β-galactosides into monosaccharides. It is commonly used in molecular biology as a reporter gene to monitor gene expression. Microorganisms, or other, producing this enzyme can break down x-gal (5-bromo-4-chloro-3-indolyl-β-d-galactopyranoside), an artificial chromogenic substrate. Cleavage of this substrate produces a blue colour. It can be mixed in petri dishes; known as blue/white screening.
This enzyme can be split into two complimentary peptides LacZα and LacZΩ; neither active by itself but together can break down x-gal.