Dictionary of useful biological terms and terminology used in genetic programming

A

• A DNA
  • The bonds are tilted with respect to the helix.
• A site
  • a site on a ribosome for a tRNA molecule carrying a single amino acid.
• Acentric
  • describes chromosome fragments which lack a centromere.
• Achiasmate division
  • meiosis where chiasmata formation does not occur.
• Acid
  • A compound which, when it dissociates in water gives out a hydrogen atom.
• Acidosis
  • An increase in acidity in a region.
    • Also increases the mutation rate.
    • May promote angiogenesis through VEGF.
• Acidura
  • A condition marked by abnormal amounts of acid in the urine.
• Acrocentric
  • Describes a chromosome where the centromere is postioned off centre.
• Acrosome
  • A thin cap surmounting the nucleus of a sperm
• Adaptive Radiation
  • From the original stocks of organisms many different froms will arise filling every available habitat.
• Adduct
  • A chemical compound which forms from the addition of two or more substances
• Adjacent 1 Segregation
  • When after a reciprical translocation a normal chromosome tries to pair with a transposed one leading to inviable products.
• Adjacent 2 Segregation
  • When homologous centromeres migrate to the same pole. (rare).
• Agonist
  • A substance (something which is naturally in the body) or drug which interacts with a receptor and causes a characteristic response from the receptor.
• Alleles
  • possible settings for a trait
  • in a Genetic Algorithm normally 0 or 1 (unless using larger alphabets)
• Allelic Series
  • The set of possible alleles for a gene.
• Allopatric
  • Geographically isolated populations.
• Allopolyploid
  • An organism which is composed of sets of chromosomes from different species.
• Allosteric enzymes
  • An enzyme which can exist in two different forms; active and inactive. When inactive the substrate will not fit the active site. These can be inhibited by an inhibitor attaching to another part of the enzyme whilst it is in an inactive form (ie. not the active site) then preventing the transformation into the active form.
• {alpha}-helix
  • result of hydrogen bonding between hydrogen and oxygen molecules.
• {alpha}-subunit
  • Part of a G-protein the alpha sununit is the part which binds to the GPCR.
  • Before it binds this subunit has GDP in it, but after binding this is replaced by GTP
  • At binding the Alpha subunit becomes dissociated from the beta and gamma subunits which reamin linked together
  • Binding also activates an effector molecule, which may stimulate or inhibit production of a protein, depending on the type of G-protein it is.
• Alternate Segregation
  • An alternative to adjacent 1 segregation whereby transposed chromosomes pair together, as do the normal ones. This leads to viable products.
• Alternation of Generations
  • Name of the cycle which organisms who spend part of their life as haploid and part as diploid go through.
• Amber codon
  • One of the stop codons, UAG.
• Amino acids
  • A specific group of molecules unified by a common structure.
  • They always have an amino group (NH2) and a carboxy1 group (COOH) and an R group, which is where they differ.
• Amorph
  • An orgnaism where there is a complete lack of a particular wild type function.
• Amphidiploid
  • an allopolyploid where it has 2 sets of chromosomes from each species.
• Amphipathic
  • where one side of a structure is hydrophilic and the other hydrophobic.
• Anaphase
  • A phase during mitosis where the chromatids part company and move, centromeres first, towards opposite poles of the spindle.
• Anaplerotic Reaction
  • A reaction which forms intermediaries of the TCA cycle
• Aneuploid
  • 'not euploid' ie. an individual which has a different number of chromosomes from any multiple of the expected number.
• Angiogensis
  • The growth and formation of blood vessels.
• Animal Pole
  • The end of the human egg which contains the nucleus.
• Anisogametes
  • Gametes which differ only slightly (in conjugate pairs).
• Anticodon
  • A site on a tRNA molecule which recognises an mRNA codon.
• Antimorph
  • An orgnaism where a particular function has the opposite effect to the wild type.
• Antiparrallel
  • Describes the fact that the two chains run in opposite directions.
• Antisense Strand
  • In transcription one strand of DNA is the sense strand whilst the other which is not used is the antisense strand.
• Apoptosis
  • A mechanism for cell death, which detects when things have gone wrong in the cell and causes it to die.
• AR
  • AutoRegressive Model
• ARMA
  • AutoRegressive Moving Average Model
• Ascospores
  • Products of meiosis between asexual spores and femuale nuclei.
• Asexual Spore
  • cells which can detactch and disperse to form new colonies or act as gametes.
• Atopic
  • A body part which develops in the wrong place.
• Autopolyploid
  • Organisms that have multiple sets of chromosomes from within one species.
• Autosomal Inheritance
  • Traits inherited in a Mendalian Manner
• Automsome
  • A non-sex chromosome.
• Autophagy
  • Digestion of a cell, or bits of a cell by enzymes from within that cell.
• auxotrophic
  • An organism which needs certain nutrients to grow.
• Axial Filament
  • runs down the centre of the middle piece and tail of a sperm.

B

• B DNA
  • The bonds are perpendicular to the direction of the helix.
• Bacteriophage
  • A virus specific to bacteria
• Balbiani Rings
  • Regions of a polytene chromosome which appear to be greatly distended.
• Barr Body
  • A highly condensed X-chromosome which appears as a densely staining spot in a cell, and occurs early on in the female development of all mammals and persists throughout all subsequent meiotic divisions. This makes the X-c hromosome inactive.
• Base
  • A compound which can take up the hydrogen atom from an acid dissociating in water.
• Bead Theory
  • An erroneous theory, which holds that a chromosome is a linear array of genes.
• {Beta}-sheets
  • hydrogen bonded sets of {beta}-strands.
• {Beta}-stacks
  • collections of {beta}-sheets.
• {Beta}-strands
  • sections of polypeptide which don't coil.
• Biclustering
  • Performing simultaneous row and column clustering on a matrix of data (ie. clustering samples and genes in transcriptomic data)
• Bioactivity
  • any affect on, interaction with or response from living tissue
  • the affect of a given agent on living tissue
• Biochemical Homology
  • The science of confirming phylogenetic relationships through cell structure or composition.
• Biochemical Mutation
  • Loss or change of the biochemical properties of a cell through mutation.
• Biological Marker
  • A test or set of tests which correlates with alterations in a given physiological or biochemical pathway.
• Biosynthetic Pathway
  • The steps in which molecules are synthesised in series, each synthesis cataylsed by an enzyme.
• Bivalent
  • a pair of homologous chromosomes
• Blastocyst
  • An early stage embryo in which some differentiation has occured.
• Breakdown
  • A breakdown reaction is one where AB -> A + B, they are catabolic and exergonic.
• Bridging cross
  • creating a new species to allow you to cross two otherwise non-interfertile speices.
• Brush Border (or Striated Border)
  • The fuzzy line formed by microvilli when viewed through a microscope.
• Budding
  • A method of asexual reproduction whereby an outgrowth is developped which is later detached from the parent.
• Buffer
  • A compound which resists changes in pH when diluted in water, or having more acid or alkali added.

C

• Calluses
  • Cell colonies grown from single cells of plants.
• Canonical Genetic Algorithm
  • The algorithm as specified by Holland.
• Carbohydrate
  • Compounds made up of carbon, hydrogen and oxygen eg. sugar and starch.
• Carcinogen
  • A compound capable of causing cancer.
• Cell Plate
  • The new wall which grows across the middle of the cell during telophase in plants.
• Cellular Genetic Algorithm
  • use many processors each running a Genetic Algorithm, but each processor can only exchange strings with those physically near it.
• Centrioles
  • Important organelles for mitosis. They consist of a pair of short rods outside the nuclear membrane, but are not found in higher plants.
  • During prophase they lie at the end of the spindle.
• Centromere
  • Region where chromatids are joined during prophase.
• Centromere Mapping
  • The locating of the centromeres in relation to the genes on the chromosome.
• CHC Algorithm
  • monotonically collects the best strings found so far, and prevents incest within the population by specifying a minimum hamming distance between the strings before they can reproduce.
• Chiasmata
  • Points where non-sister chromatids remain in contact as they separate in meiosis and crossover occurs here.
• Chromatids
  • Pairs of chromosomes which lie close to each other during prophase.
• Chromatid Interference
  • Crossover between two non-sister chromatids affecting the probability of crossover between the same chromatids again.
• Chromatin
  • a mixture of DNA and protein of which chromosomes are composed.
• Chromatin Threads
  • The form chromosomes are in during interphase, whereby they are strung out.
• Chromatophores
  • Cells which allow skin colour to change (eg. chameleon)
• Chromocentre
  • the point where chromosomes are joined together.
• Chromomere
  • Definition to be added !!!!
• Chromosomes
  • strings of DNA that serve as 'blueprints' for the organism.
  • Or in GA candidate solution to the problem
• Chromosone interference
  • Interference acting along the chromosome.
• Chromosome Puffs
  • Areas of RNA synthesis found in DNA strands, they appear at different places during different stages of development.
• Chromosome Theory
  • The theory that genes are part of the chromosomes.
• Chrondroblasts
  • Cells which make cartilage
• Cilia
  • Short micro tubule found on the surface of some cells.
• Cistron
  • a unit of genetic function
  • a region of genetic material which code for one polypeptide chain.
• Clique
  • A collection of points in a network which are fully connected.
• Clones
  • A population of identical cells all derived assexually from a single cell.
• Closed promoter complex
  • A holoenzyme and a promoter bound together.
• CLOUDS
  • A modeling technique developped by Tim Ebbels at Imperial, based on the idea that classes are represented by a probability density function which is contructed by summing Gaussians densities which are centred at each data point.
• Codominance
  • Two alleles have equal dominance with respect to each other. eg. blood groups A and B in humans.
  • when heterozygotes show phenotypes of BOTH homozygotes.
• Codon
  • A triplet of bases specifying an amino acid.
• Coefficent of coincidence
  • Ratio of observed to expected double recombinants.
• Coenzyme
  • a complex non-protein organic cofactor molecule.
• Cofactor
  • A substance which must be present before an enzyme will work.
• Colchicine
  • A chemical applied to monoploid plants to make them double their chromosomes so that they can produce seed.
• Colloidal Suspensions
  • Sections of proteins split up in water so they have a greater surface area and can absorb water and other things and hold molecules in position in the cell.
• Colony
  • A clump of cells produced as a result of plating.
• Compact Representation
  • one in which the desired schematas are unlikely to be disrupted by crossover.
• Competant
  • tissue which will respond to induction.
  • Cells which are able to be transformed (in the second sense)
• Competitive Inhibition
  • The inhibitor attaches to the active site of the enzyme so that the substrate can't. This process is reversible and slows the reaction.
• Complementary Gene Action (or complementation)
  • An organism must have at least one dominant allele of both genes to show the dominant phenotype.
• Complementation
  • see complementary gene action.
• Conditional Mutation
  • A mutation which is only expressed in particular environmental conditions.
• Conidia
  • Long chains of assexual spores found in some fungi.
• Conjugated proteinProtein
  • A protein combined with another compound
• Conjugation
  • DNA segments transfered via direct cell-cell contact in prokaryotic organisms.
• Conservative Replication
  • Produces one completely new duplex and the parental duplex remains intact.
• Constitutive heterochromatin
  • The dark regions of the heterochromatin pattern which are a permanent feature of that chromosome, as opposed to faculative heterochromatin .
• Copy-Choice Model
  • A theory that crossover doesn't occur by physical breakage, but by linkings crossing over during the copying stage.
• Core enzyme
  • a single RNA polymerase without a sigma factor, as opposed to a holoenzyme
• Cortical
  • relating to the cortex
• Cortical Granules
  • Form a layer just beneath the surface in a human egg.
• Coupling Conformation
  • When the dominant alleles naturally pair together as they were together in the parental combination.
• Covalent Bonding
  • sharing of electrons between atoms.
• Cross
  • often used to mean cross-polinate
• Crossover Products (or recombinants)
  • The two new combinations generated by crossover.
• Cryoscopy
  • a technique for determining molecular weight by dissolving it and measuring the freezing point.
• CV
  • Cross Validation - a method for checking for overfitting of a model by rebuilding it n times each time with a section of the data left out for testing
• CVA
  • Canonical Variates Analysis
• Cytogenetics
  • Study of normal and abnormal chromomsome sets and their genetic properties
• Cytokine
  • A small short-lived protein which is released by a cell to regulate the activity of another cell. Similar in many ways to hormones, but their levels tend to vary much more widely than hormones. Historically they are associated with the immune system.
• Cytoplasmic Inheritance
  • In some organisms some characteristics are determined by genes that are not in the nucleus, but are in the cytoplasm.

D

• Decarboxylase
  • Enzymes which remove COOH groups from molecules.
• Defining Length (of a schema)
  • distance between its outermost defined bits
• Degree of Degenerency
  • For a given amino acid this is determined by the number of codons for tha acid which have no wobble and the number which do have a wobble.
• Dehydrase
  • Enzymes which remove water.
• Dehydrogenase
  • Enzymes which remove hydrogen atoms.
• Deletion
  • A chromosome mutation whereby the chromosome breaks in 2 places and the section in between drops out before it joins up again. Generally all but the shortest deletions are lethal.
  • A gene mutation whereby one or more nucleotides are deleted from the DNA sequence.
• Deletion Loop
  • Loop formed when a homolg which has undergone a deletion and a normal homolog try to pair up and find they can't pair properly.
• Deme
  • place the individuals from your genetic algorithm population in a grid, then a deme is an area round a point on the grid within which individuals can breed. The demes overlap throughout the grid.
  • a genetically isolated unit of the population
• Denature
  • to inactivate enzymes by excessive heat.
• Deoxyribonucleic Acid
  • DNA
• Developmental Noise
  • the variation in phenotype caused by random events in development.
• Detoxication
  • The metabolic process by which toxins are changed into less toxic things, or things more readily excretable.
• Diagnostic (biomarker)
  • A test or set of test which determine the presence or absense of a specific disease. It must be disease-specific, determinative and binary.
• Diakinesis
  • A stage of prophase 1 in meiosis whereby there is further chromosome shortening and otherwise basically the same as diplotene.
• Dicentric Bridge
  • The connection of the homologous centromeres durring paracentric inversion.
• Differential Centrifugation
  • The process which is used to isolate different types of organelles by spinning the cells at different speeds to separate the bits of different weights (often done using a kitchen blender!!)
• Differential Region
  • The bits of the X and Y chromosomes which don't pair.
• Dioecious
  • A term used to describe species which have 2 sexes.
• Diploid
  • organisms whose chromosomes are organised in pairs
• Diplotene
  • A stage of prohase 1 in meiosis whereby each member of a homologous pair produces two sister chromatids and the synapsed structure now contains bundles of 4 homologous chromatids. The pairing between homologs becomes less tight and chiasmata appear.
• Disomic
  • When a haploid speices has n+1 chromosomes.
• Dispersive Replication
  • Daughter duplexes contain segments of parental DNA and segments of new DNA.
• Distal
  • further away
• DmodX
  • Distance to model in X-Space, generally equivalent to the some function of the residuals of the model
• DNA
  • Definition to be added !!!!
• DNA Ligase
  • An enzyme which joins together broken bits of DNA.
• DNA Polymerase
  • The enzyme which catalyses the replication reaction of DNA.
• Dominant Mutation
  • A change to a non-wild type dominant allele.
• Donor
  • Term used for one of the two participants in bacterial conjugation. To be a donor you must have the sex factor which is not present in the recipient.
• Double Infection
  • See mixed infection
• Double trisomic
  • When the number of chromosomes is 2n+1+1.
• Duplicate Genes
  • An organism must have at least one dominant allele of either gene to express it.
• Duplication
  • A chromosome mutation whereby a section replicates.

E

• Ectopic
  • Describes when DNA is inserted into a site other than its normal site.
• Electronegativity
  • the power of an atom in a molecule to attract electrons.
• Elongation
  • The middle stage of transcription, in which the sigma factor dissociates from the RNA polymerase and the 'transcription bubble' moves along the template.
• Elute
  • to remove an absorbed material from an abosrobant by dissolving
• EM
  • Expectation Maximisation
• Endergonic
  • Describes a reaction which needs energy to take place.
• Endogenote
  • When there is a complete genome in the recipient cell.
• Endoplasmic Reticulum
  • The matrix of cavities which the cytoplasm within a cell is organised into.
• Enzyme
  • protein which catalyses one of the chemical reactions in the cell.
  • Literally means 'in yeast'.
• Epidermal Cells
  • These cells protect plants from loosing too much water.
• Epigenetic Change
  • A change which alters the expression of the information in the genome at the transcriptional, translational, or post-translational levels.
• Episome
  • A factor like F which can either be present as a free cytoplasmic element, or be intergrated into the chromosome
• Epistatic
  • description of a gene which suppresses another.
• Epistasis
  • the phenomenon that the effect of different enzymes are not additive. eg. a process may require all enzymes to be there before it will happen at all, rather than just happening a little if only some are there.
  • (GP) the degree of dependance between mulitple genes in a chrmosome
• Epithelial Cells
  • Outer cells of a body or organ.
• Erythrocytes
  • Red blood cells, move oxygen round the body
• ESI
  • Electrispray ionization - method used within LCMS
• Euchromatin
  • The poorly stained regions in heterochromatin patterns.
• Euploid
  • Organisms with some multiple of their monoploid number of chromosomes.
• Eutherian
  • mammals which have a placenta.
• Evaluation Function
  • function which given the genotype for an individual returns a value relating to how 'fit' the individual is.
• Exconjugants
  • Describes cells which were involved in mating when interupted.
• Exergonic
  • Describes a reaction which frees energy for use elsewhere.
• exogenote
  • When there is interrupted mating and so the recipient cell ends up with an incomplete genome derived from the donor cell.
• Exon
  • A coding region of a gene.
• Exon Shuffling
  • A theory that exons encode discrete domains of proteins and hence exon shuffling allows recombination and faster evolution of proteins.
• Expressivity
  • The extent to which a genotype is expressed phenotypically in an individual.

F

• Faculative Heterochromatin
  • non-permanent heterochromatin, as opposed to constitutive heterochromatin.
• F'-duction
  • see sexduction
• Fertility
  • fitness measure of organism based on function of the number of offspring the organism has
• Fertility Factor (or F)
  • a cytoplasmic entity with these properties:
    • F can replicate its DNA
    • Cells carrying F can produce pili.
    • Cells can then transfer replicated F DNA to new cells
    • Cells carrying F only attach to cells not carrying F
    • Sometimes F intergrates with the cell's own chromosome
• Fibroblasts
  • They secrete protein fibres to form connective tissue.
• Fibrous
  • Protein's which are fibrous are insoluble, composed of long parallel polypeptide chains which are cross-linked at many points. These help compose structures in the body, eg. hair, nails, tissue and muscles.
• Filtration Enrichment
  • A technique for finding auxotrophic mutants in conidia.
• Fine Structure (or ultra structure)
  • Structure of a cell as seen through an electron microscope.
• Fingerprint (of a protein)
  • The result of two dimensional chromatography on the protein.
• Fisher Ratio
  • The between group variance divided by the within group variance
• Fission
  • A method of assexual reproduction whereby an organism divides into 2 or more equally sized parts.
• Fitness Function
  • given the results from the evaluation function, for an individual it returns the likelihood that individual will breed.
• Fitness Landscape
  • representation of the search space (all possible genotypes) along with their respective fitness
• Flagella
  • A micro tubule which is longer than a cilia and is used for movement.
• Fluctuation Test
  • A mesure of the numbers of adapted cells in different cultures and hence due to variation you can calculate mutation rates.
• Fluid-Mosaic Model
  • A theory that the cell membrane is viscose and proteins in it are arranged like a mosaic.
• Forward Mutation
  • A change away from a wild type allele.
• Fragmentation
  • A method of asexual reproduction whereby an orgnaism is broken into two (or more) pieces which each regenerate into new organisms. Sucessful regeneration relies on the organism having large numbers of undifferentiated cells which can be turned into whatever is needed.
• Functional proteomics
  • The use of proteomics to study protein function. So use protein micro-arrays to study expression levels in large sets of proeins between diseased and control states.

G

• Gamete
  • a haploid cell formed by genes exchanged from a pair by crossover within one parent
• Gametogenesis
  • Production of gametes
• Gametophyte
  • The haploid stage of orgnaisms which undergo alternation of generations.
• Gene Locus
  • The place on the map where the gene is located.
• Gene Pool
  • The sum total of all the different genes present in the population.
• Generalised Transducing phage
  • A phage which can carry any part of the chromosome. See also specialised transducing phage.
• Generation Gap
  • fraction of new individuals in each generation.
• Genes
  • functional blocks of DNA that a chromosome can be conceptually divided into
  • in GA, single bits or short blocks which encode a particular element of the candidate solution
• Genetic Death
  • A failure to pass your genes onto the next generation
• Genetic Load
  • The total of the dangerous alleles found in a population. Often due to them conferring some advantage when present in a heterozygote
• Genetic Map Unit
  • The distance between genes for which 1 percent are recombinant.
• Genome
  • collection of all genetic material for an organism
• Genomics
  • Studies the genetic complement
• Genotype
  • particular set of genes in a genome.
  • in GA; configuration of bits in that individuals chromosome
• Germinal Mutation
  • A mutation which occurs in the tisue which will ultimately form sex cells.
• Ghost
  • An empty phage carcass.
• Glandular Cell
  • Cell responsible for secretion.
• Globular
  • protein's which are globular are tightly folded polypeptide chains which form a spherical shape. The are relatively soluble and easily go into colloidal suspensio n. They occur in blood plasma and all cells and they maintain the composition of protoplasm in cell membranes and form enzymes.
• Glycogen
  • Storage carbohydrate for animals
• Glycoprotein
  • A carbohydrate conjugated with a protein.
• Gogli Body
  • Structure with lots of smooth endoplasmic reticulum, concerned with the production of substances in a cell. Used for adding carbohydrates to glycopr oteins.
• Gonads
  • Where the formation of gametes takes place in humans.
• G-Protein
  • A protein which binds with the intracellular parts of a G-protein Coupled Receptor.
  • G proteins are heterotrimetic which means they have three subunits, called alpha, beta and gamma.
• G-Protein Coupled Receptor (GPCR)
  • The biggest single class of receptors in biology.
  • They are often split into two subclasses Gi/o, Gs/q.
  • It is possible some GPCRs are in both classes.
  • GPCRs have parts outside the cell, within the membrane and inside the cell.
  • G-proteins bind with the bits inside the cell.
  • They bring signals from outside the cell into it, without the ligands needing to enter the cell.
  • Stands for Guanine nucleotide binding proteins
  • Structurally GPCRs are made up of...
    • An N-terminus outside the cell
    • 7 transmembrane loops
    • Some extracellular loops
    • Some intracellular loops
    • A C-terminus inside the cell
    • Filler peptides(?what?)
  • GPCRs are central to vision, smell, taste and perception
  • They are found in all Eukaryotes
  • About half of all known drugs work through GPCRs
  • Many other proteins also bind to GPCRs and regulate activity
  • Biggest single class of receptors in Biology
  • Abnormalities in GPCR regulation can lead to cancer, cardiovascular disease, alzheimers and parkinsons
• Gradient of Transfer
  • Refers to the fact that as there is a fixed origin there is certain information in the cell which is always transfered first, and therefore most likely to get through and certain information which is transfered last and therefore less likely to get through.
• Guanosine Diphosphate (GDP)
  • A complex found in the alpha subunit of a G-Protein before activation.
• Guanosine Triphosphate
  • A complex which replaces GDP in the Alpha subunit of a G-Protein once activation has occured.

H

• Hairpin Loop
  • A double stranded bit of RNA formed by transcribing a G and C rich area of DNA so that RNA forms complementary bonds with itself.
• Halogenated
  • To have an halogen introduced to.
• Haploid
  • organisms or cells where the chromosomes are unpaired
• Haploidization
  • The process of a diploid nucleus becoming haploid.
• Heat Capacity
  • The amount of energy needed to raise the temperature of 1 gram of the substance by 1 degree Celsius.
• Helicase
  • An enzyme which disrupts the bonds which hold the two DNA strands together, so that replication make take place.
• Hematopoietic
  • Associated with the formation of blood cells
• Hemisect
  • like bisect.
• Hemizygous
  • Term used to describe the genes located on the differential region.
• Hepatic
  • To do with the liver
• Hermaphroditic
  • Species where each individual has both male and female organs on the same flower.
• Heterochromatin
  • The densely stained regions in heterochromatin patterns.
• Heterochromatin Patterns
  • The patterns formed when you stain chromosomes.
• Heterogametes
  • Gametes which differ in size and structure from male to female (eg. sperm and egg).
• Heterozygous
  • Describes a species which is not homogametic
• Heterokaryon
  • In conidia if 2 haploid strains are mixed then things fuse and both nuclei stay in a common cytoplasm.
• Heterotrimetic
  • A protein(?or other thing?) with three parts, for instance G-proteins have 3 subunits, alpha, beta and gamma.
• Heterozygous
  • chromosomes which differ eg. the organism has one recessive gene and one dominant gene for that characteristic. Also known as hybrids.
• Hexose Sugars
  • Sugars which contain 6 carbon atoms.
• High Frequency of recombination
  • describes strains of bacteria where F has been encorporated into the chromosome.
• Histology
  • The study of tissues
• Histones
  • Basic proteins which mask genes in higher organisms.
  • Special chromosome proteins which make up nuclesomes
• Histopathology
  • The study of microscopic anatomical changes in diseased tissue.
• Hoist
  • operations in GA's which creates a new individual which is a copy of a subtree of the parent.
• Holoenzyme
  • A single RNA polymerase with a sigma factor, as opposed to a core enzyme.
• Homeologous
  • only partially homologous.
• Homogametic
  • Describes a speices where there is only one kind of sex chromosome.
• Homolog
  • A member of a homologous pair
• Homologous Pair
  • A pair of identical chromosomes
• Homozygous
  • chromosomes which are the same. Eg. the genes are either both dominant or both recessive. Pure bred.
• Host Range
  • Refers to the range of bacteria a phage will attack.
• Hot Spots
  • Sites on a chomosome which are more likely to get mutated than others.
• H-PLS
  • Hierarchical PLS
• Human Embryonic Stem Cells (hES)
  • Cells isolated from early stage human embryos (blastocysts) with the potential for unlimited self-renewal
• Hydrogen Bonding
  • a form of non-covalent bonding whereby a bond is formed between a hydrogen atom and another atom, given that the hydrogen atom is already covalently bonded to some more electroneg ative atom and the atom it is now bonding with is also more electronegative.
  • a positive Hydrogen atom in molecule 1 is attracted to a negative oxygen atom in molecule 2 and a bond forms between them.
  • the type of bonding used to hold together the two chains in the double helix.
• Hydrophilic Interaction
  • an umbrella term for non-covalent bonding with water by other molecules.
• Hydropic
  • Something which is swollen or taking up fluid.
• Hydrophobic
  • molecules which are non-soluble in water.
• Hypermorph
  • An organism which does the same thing as the wild type but does it more efficiently.
• Hyphae
  • A thread of cells joined end to end found in some fungi.
• Hypomorph
  • An organism which does the same thing as the wild type but does it less efficiently.
• Hypostatic
  • A gene which is being suppressed by another.
• Hypoxia
  • Being in a state of lacking oxygen.

I

• Immortalisation
  • A resistance to apoptosis and a blockage of terminal differentiation.
    • A hallmark of cancer cells
    • Stem cells are naturally immortal.
• Incomplete Dominance
  • Heterozygotes are intermediate in phenotype eg. Pure white X Pure red = pink
• Induce
  • An organiser can induce adjacent cells to develop in a particular way.
• Inhibitor
  • A substance which slows or stops an enzyme controlled reaction
• Initiation
  • The first stage of trnascription
• Inorganic
  • Anything which is not organic
• Insertion
  • A type of gene mutation whereby a nucelotide is insered into the DNA.
• Instance (of a schema)
  • strings which fit the template
• Interference
  • The fact that having a crossover in one region affects the probability of crossover occuring in other regions.
• Intermediate Population
  • the selection of individuals from the current population who have been chosen to be used with crossover and mutation (breed).
• Interphase
  • The 'resting' stage of about 1 hour in between cycles of mitosis when daughter cells grow and prepare for division. The DNA replicates and chromosomes are in the form of chromatin threads. The cell also builds up a store of energy and ressembles a non-dividing cell. Finally, it also forms new cytoplasmic organelles.
• Interrupted Mating
  • Describes the process of putting cells in a kitchen blender to disrupt mating pairs mid mating.
• Interstitial deletion
  • A deletion from the middle of a chromosome caused by two breaks.
• Intragenic Recombination
  • Recombination within a gene.
• Introns
  • non-coding areas of the genes.
• Inversion
  • an operator which reverse a random section of the chromosome. Best used on position independent encodings.
  • A chromosome mutation whereby the chromosome breaks in two places and the code in the middle turns round before reattachment.
  • A gene mutation whereby one or more nucleotides are deleted from the DNA seuqence.
• Inversion Loop
  • The loop an inverted piece of DNA must form to pair up with a normal piece.
• Ionic Bonding
  • occurs when one of the pair is so electronegative that it attracts all the electrons from the other atom. (Less stable)
• Island Model
  • a genetic algorithm where the population is split into distinct subpopulations. Swap a few strings every n generations between populations. This can be used for exploiting parallelism (eg. many processors) efficiently.
• Isoaccepting tRNA's
  • If two different tRNA molecules accept the same amino acid.
• Iso electric point
  • The pH at which the molecule carries no electric charge.
• Isoenzymes
  • Sets of enzymes which have different sequences but which catalyze the same reaction (seen in tumour cells).
• Isogametes
  • Gametes which are identical (eg. one's produced by green algae and fungi).
• Isomerase
  • Enzymes which move atoms from one part of a molecule to another.

J

• Jacob Monad Theory of Gene Action
  • A theory of how genes work, based on there being a structural gene, an operator gene and a regulator gene.
• Jelly Coat
  • The coating outside the membranes of a human egg cell.
• Juxtamedullary
  • Near the medulla of the kidney

K

• Kinetics (of a reaction)
  • Measure the rate of the reaction via a reaction velocity function, the parameters of this function depend on the enzyme and the status of the cell.
• Knowledge Base
  • A set of concepts which each partition all the objects in the universe into categories. Eg. in a universe of coloured blocks of different sizes and shapes, the concepts of colour, size and shape could all appear in a knowledge base.

L

• Lagging Strand
  • The strand of DNA which is synthesised in short bursts, as opposed to the leading_strand
• Lambda
  • The name of a particular temperate phage
• Lariat Model
  • A model of how introns are cut out and exons joined together.
• LC-MS
  • Liquid Chromatography Mass Spectrometry - a coupling of a chromotographic method and mass spec, don't need to purify samples and since you only need small amounts of sample it is good for measuring things in low abundance.
• LDA
  • Linear Discriminant Analysis
• Leading Strand
  • The strand of DNA which is synthesised continuously in replication.
• Leptotene
  • A stage of prophase 1 in meiosis whereby, chromosomes become visible and contract and chromomeres develop.
• Lethal Allele
  • An allele which if present in both chromosomes causes a failure of the orgnaism to be able to survive.
• Lethal Mutation
  • A mutation which dertrimentally affects the survival of the organism.
• Leukocytes
  • White blood cell, port of the immune system
• Level of Transcription
  • Gene control from DNA.
• Level of Translation
  • Gene control from cytoplasm.
• Ligand
  • A molecule which binds to a target site.
• Lignification
  • the covering of a plant cell in wood.
• Linkage
  • Used to describe the phenomenon that two genes are not selected independantly of each other. Often caused by them being on the same chromosome.
• Linkage Map
  • map of where genes are in relation to each other on the chromosome, generated by the data on the percentage of recombinants and other more sophisticated techniques.
• Lipids
  • Includes fats and oils (NB. fat is solid at room temperature).
• Lipogenesis
  • The production of fat
    • Essential for tumour growth
    • Locus
      • position of a gene on a chromosome
    • LV
      • Latent Variable
    • Lyophilisation
      • A method for drying a substance without destroying its physical structure.
    • Lysis
      • The breaking open of bacterial cell walls to release many phage descendants.
    • Lysogenic Bacteria (or lysogens)
      • resistant bacteria which induce lysis in other cells.
    • Lysogenic Cycle
      • The phage exists as a prophage in the bacteria cell for a while.
    • Lysosomes
      • contain enzymes for splitting complex chemical compounds up and destroy worn out organelles in cells or the whole cell if needed.
    • Lytic
      • Describes a phage for whom there are no lysogenic bacteria.
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    M

    • MA
      • Moving Average Model
    • Macromolecules
      • Large molecules eg. lipids, proteins and Nucleotides.
    • Mapping Function
      • The mapping function takes recombination frequencies and turns them into map distances, taking double, triple... crossovers into account.
    • Maximal Clique
      • A clique which cannot be extended by adding more nodes.
    • Meiocyte
      • A cell destined to become a gamete.
    • Meiosis
      • nuclear division in special cells which are designed to produce gametes.
      • Cell division where the daughter cells end up with half the number of chromosomes the parent had
    • Meiospores
      • Products of meiosis in plants.
    • Meiotic Recombination
      • Any meiotic process which generates a haploid product with a different genotype from both the haploid genotypes which made up the diploid cell.
    • Memetic Algorithm
      • An evolutionary algorithm combined with local search
    • Merodploidy
      • partial diploidy
    • Merozygote
      • A partial diploid.
    • Messenger RNA (mRNA)
      • It is produced from the dna template and contains the information which is translated into proteins.
    • Metabolic Fingerprinting
      • Like metabolomics or metabonomics, but does not attempt to identify or quantify all metabolites, just to produce a viable 'fingerprint' for classification.
    • Metabolic Pathway
      • A series of gentle reactions which turn a metabolite into the desired end product.
    • Metabolic Profiling
      • Measures levels of particular metabolites.
    • Metabolism
      • word describing the chemical reactions which take place in cells.
    • Metabolites
      • Molecules which participate in the chemical reactions which happen in cells.
    • Metabolomics
      • studies the metabolic regulation and fluxes in individual cells or cell tyoes
    • Metabonomics
      • The quantative measurement of the dynamic multi-parametric metabolic response of living systems to pathophysiological stimuli or genetic modification.
      • determines systematic biochemical profiles and regulation of function in whole organisms by looking at biofluids and tissues
    • Metabotropic Glutamate Receptors
      • Another kind of GPCR which also has a distinctive 7TM signature
    • Metacentric
      • Describes a chromosome where the centromere is positioned in the middle.
    • Metaphase
      • A stage of mitosis where the nuclear membrane disrupts and chromosomes move to the centre plane of the cell. Sister chromatids get orientated towards opposite pole s.
    • Metastasis
      • Process by which tumor cells are spread throughout the body in cancer.
    • Micropinocytic Vessels
      • Found on the surface of cells, they turn into vacuole, used for taking large molecules into cells.
    • Micro tubule
      • a general name for a small bit of cell which can be taken apart easily then later reassembled in a different bit of the cell. eg. cilia and flagella
    • Microvilli
      • the folds in cell membranes which provide the necessary surface area for reaction/exchange of materials
    • Mineral Salts
      • a compound of a metal and a non-metal eg. NaCl.
    • Mitochondria
      • There are 1000 per cell and most chemical reactions of respiration in cells take place in them with help from enzymes. Cells which need to expand large amounts of energy tend to have more.
    • Mitosis
      • Nuclear division between somatic cells of an eukaryotic body.
      • Cell division where the daughter cells end up with the same number of chromosomes as the parent had.
    • Mitotically inactive
      • Non-dividing/replicating
    • Mitotic Non-Disjuction
      • When non-disjunction occurs in mitosis.
    • Mixed Infection
      • Occurs when cells are simultaneously infected by more than one phage
    • Messenger RNA (mRNA)
      • bits of DNA which have been left after the introns have been cut out and copied to RNA form.
    • Modifier Genes
      • Genes which hide or accentuate the action of other genes.
      • Genes which change the way other genes are expressed (eg. making a colour more milky in an animals coat.)
    • Monocistronic
      • An mRNA molecule which codes for only one cistron.
    • Monoecious
      • Like hermaphroditic except the male and female organs are in different flowers on the same plant.
    • Monohybrid Inheritance
      • The pattern of inheritance observed when there are a pair of contrasting charictaristics for a particular allele.
    • Monoploid Number
      • The number of chromosomes in a basic set.
    • Monosomic
      • when the chromosome number is 2n-1
    • Morphological Mutation
      • A mutation which affects the outward appearance of an organism.
    • Mosaic
      • desription of an individual whose phenotype is made up by mixing more than one genotype (eg. some cells show one genotype and some another). All females are mosaic due to the barr body.
    • Multimeric
      • Describes a structure composed of several separate polypeptide chains or monomers.
    • Multiple allelism
      • when there are more than 2 possible alleles for a particular gene.
    • Multiplicity of Infection
      • The phage to bacteria ratio.
    • Multi-Variate Design (MVD)
      • a combination of multi-varaite characterisation, principal components analysis and statistical experimental design
    • Muscle Fibres
      • Cells which form our muscles, they work by responding to electricity by contraction
    • Mutant
      • An organism whose changed phenotype is attributable to the possession of a mutation.
    • Mutagen
      • A compound which causes DNA damage
    • Mutation Event
      • When the mutation actually occurs.
    • Mutation Frequency
      • Proportion of a population which have a particular mutation.
    • Myc
      • A gene
        • Involved in cell cycle progression
        • Related to energy metabolism
        • Virutally all glytotic enzymes are induced by Myc.
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    N

    • Native State
      • 3d structure of polypeptides which makes up a protein.
    • Necrosis
      • Death of tissues or cells in a localised part of the body.
    • Neomorph
      • An orgnaism which does something completely different from the wild type.
    • Nephron
      • A filtering unit in the kidney which removes waste from the blood.
    • Nephropathy
      • Any disease of the kidney
    • Neuropeptide
      • An important group of short proteins.
      • They act as neurotransmitters helping the passage of signals within the central nervous system and between the central nervous system and the rest of the body.
      • Neuropeptides are ligands.
      • The sequences for Neuropeptides are subsequences of those for Neuropeptide Precursors.
    • Neuropeptide Precursor (NPP)
      • A seqeunce which contains one Signal Peptide and a number of neuropeptides.
      • They are highly variable in length.
      • They undergo Proteolysis before the neuropeptides are released.
    • NIPALS
      • Non-linear Iterative PArtial Least Squares - an algortihm for performing PLS
    • Node Replacement Mutation (Point Mutation)
      • randomly changes one node of the tree. (In GP)
    • Non-Competitive Inhibition
      • The inhibitor attaches permanently to the active site of the enzyme. This can stop the reaction if there is enough inhibitor present and it is irreversible.
    • Non-Covalent Bonding
      • occurs between molecules rather than atoms.
    • Non-Disjunction
      • Addition or loss of one or more chromosomes due to them not separating properly during meiosis.
    • Nonsense codon
      • Another name for a stop codon.
    • Norm of Reaction
      • a table of the possible phenotypes resulting from a particular genotype.
    • N-Terminus
      • The end of the secondary structure of a GPCR which lies outside the cell
    • Nuclear Spindle
      • see spindle.
    • Nucleolar Organiser Region
      • Part of a cell's nucleus which contains the genes responsible for ribosomal RNA coding.
    • Nucleoli
      • Large intra-nuclear spherical structures which disappear from view during prophase.
    • Nucleoside
      • A nucleotide without the phosphate.
    • Nucleosomes
      • beads on the necklace seen when viewing chromosomes in certain conditions.
    • Nucleotides
      • The building blocks of nucliec acid consisting of a 5-carbon sugar, an organic base and a phosphoric acid linked together.
    • Nullisomic
      • When the number of chrosomes is 2n-2.
    • Nullo-X Nucleus
      • A nucleus which contains no X-chromosome due to non-disjunction.
    • Nutrigenomics
      • how diet influences gene transcription, protein expression and metabolism and how individual genetic disposition affects susceptibility to diet.
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    O

    • Oceanic Islands
      • Islands which have never been connected to the mainland.
    • Ochre codon
      • One of the stop codons, UAA.
    • Octad
      • A double tetrad formed by an extra meiotic division.
    • Oligonucleotide
      • A short sequence of single stranded cDNA. They are often used in microarrays (although not in all platforms), since they readily bind to their mRNA complements.
    • Oligosaccharide
      • A carbohydrate which contains a relatively small number of monosaccharides.
    • Oncogenes
      • Genes for cancer.
    • One gene one enzyme Hypothesis
      • A theory that each gene on the genome controls a specific enzyme
    • One Point Crossover
      • the point where crossover takes place is the same in both parents and is chosen from the bits of the trees that are geometrically the same.
    • Oogenesis
      • Production of egg cells in humans.
    • Opal codon
      • One of the stop codons, UGA.
    • Open Promoter Complex
      • After a closed promoter complex has been formed it causes denaturation of the DNA duplex and so froms an open promoter complex.
    • Operator Gene
      • In the jacob monad theory of gene action the operator gene is the one which is close to the structural gene and activates it when needed.
    • Orthogonal PLS
      • A adaption of PLS where the variation in X is split into those parts which are correlated to Y and those parts which are orthogonal to it.
    • Order (of a schema)
      • number of defined bits
    • Organelles
      • Small parts of cells which do different functions.
    • Organic
      • All complex compounds of carbon are organic.
    • Organisers
      • Tissues which can influence neighbouring tissues during development.
    • Origin
      • The fixed point, in bacteria, where gene transfer starts.
    • Osmolality
      • Concentration of an osmotic solution
    • Osmomtetry
      • The measurement of osmotic pressure.
    • Osmotic
      • An osmotic solution can pass through a semi-permeable membrane (by osmosis)
    • Osteoblasts
      • Cells which make bone
    • Oxidase
      • Enzymes which add oxygen to hydrogen.
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    P

    • P site
      • A site on a ribosome for a tRNA carrying a growing polypeptide chain.
    • Pachytene
      • A stage of prophase 1 during meiosis which is characterised by thick fully synapsed threads. The nucleoli are pronounced and chr omomeres align precisely in homologous pairs.
    • Pangaea
      • The one massive continent supposed to be in existance before continental drift.
    • Paracentric
      • Describes an inversion where the centromere is outisde the inverted region.
    • Parenchymn Cells
      • These cells fill the spaces between tissues in organisms
    • Parental Combination
      • The original arrangement of alleles on the 2 chromosomes.
    • Pareto Optimality
      • a method for comparing individuals on several scales for fitness.
    • Parthenogenesis
      • The development of a new individual from an unfertilized egg. In diploid parthenogenesis eggs are formed by mitosis instead of meiosis. In haploid part henogenesis the new creatures are haploid.
    • Partial Dominance
      • Off spring don't resemble either parent, but are similar to each other.
    • Pasteur Effect
      • The inhibition of glycolysis by oxygen, provoking the oxidation of pyruvate in mitochondria, seen in normal (non-malignant) cells, and clashes with the Warburg Effect which malignant cells shw instead.
    • Pathology
      • Study of diseases
    • PCA
      • Principal Component Analysis - a dimension reduction data modeling technique which takes sequential components by maximising the remaining variance of the data described by each component.
    • Penecillan Enrichment
      • Like filtration enrichment but for bacteria.
    • Penetrance
      • The percentage of individuals with a genotype who express the associated phenotype
    • Pericentric
      • Describes an inversion where the centromere is inside the inverted region.
    • Permissive Condition
      • The condition, that when satisfied will mean that a wild type is expressed despite a conditional_mutation.
    • PCR
      • Principal Components Regression - another PLS-like technique for regression.
    • Phage
      • A virus specific to bacteria.
    • Phage Lysate
      • progeny phage.
    • Phenotype
      • physical and mental characteristics of an organism arising from the genotype
      • In GA's often not used (same as genotype) although not always.
      • derived from Greek, literally means "the form that is shown".
    • Phosphate Salts
      • A compound which acts as a buffer in humans.
    • Phosphodiester Bonds
      • The bonds that holds together the chains of nucleotides in the double helix.
    • phosphokinase
      • Enzymes which add phosphate groups to molecules.
    • Photosynthetic Cells
      • Cells which build complex molecules in plants.
    • Phylogenetic Relationship
      • the relationship species have in evolutionary terms.
    • Pili
      • minute proteinaceous tubules that allow cells to attach and stay attached to other cells.
    • Pinocytosis
      • Liquid is transported into the cell by ending up in a fold in the cell membrane and then being encompased in a sac or vesicle and then brought into the cytoplasm.
    • Plaque
      • A clear area presnt on the opaque lawn of bacteria on the surface of a solid medium????
    • Plaque Morphology
      • The shape and characteristics of the plaques formed by phages
    • Plasma Membrane
      • The inner membrane of a human egg cell.
    • Plasmids
      • Smaller extra chromosomes which bacteria have. They contain things like the sex factor and resistance to drugs.
    • Plating
      • The process of spreading liquid with bacteria in onto a petri plate with agar gel so that the cells will be spread around and immobilised by the gel and have to reproduce by fission, creating colonies of copies of themselve s.
    • Pleiotropic
      • Describes genes which have more than one distinct phenotypical effect.
    • PLS
      • Partial Least Squares - a modeling technique which minimises the covariance between X an Y matrices in each component
    • PLS-DA
      • Partial Least Squares-Discriminant Analysis - PLS done with a dummy Y matrix based on classes, to allow for classification using PLS.
    • Pluripotent
      • Has developmental plasticity so it could develop into more than one type of cell or tissue.
    • Polar Bodies
      • The waste products from oogenesis. Each primordial germ cell is split into 4, but only one of them become an egg, the other three beccome polar bodies.
    • Polar Molecule
      • The distribution of electric charge in a polar molecule, is such that there are centres of positive and negative charge separated by a short distance.
    • Polycistronic
      • An mRNA molecule which codes for several cistrons.
    • Polygenic
      • A characteristic controlled by the cumulative effect of a number of genes.
    • Polymorphism
      • a set of two or more common, alternative, normal phenotypes.
    • Polypeptide
      • sequence of amino acids linked together by peptide bonds.
    • Polyploidy
      • Having some integer multiple of the number of chromosomes which a haploid gamete of the species would have. Common in plants.
    • Polytene Chromsomes
      • A bundle of replicas of a single chromosome found in some tissue.
    • Position Effect Variegation
      • Occurs when a gene near the tip of a chromosome and a translocation causes the dominant allele on one chromosome to be lost, so the recessive allele on the other shows through.
    • Primary Structure
      • The lowest of the four layers of structure of a protein in which the protein is viewed as a sequence of amino acids in a polypeptide chain.
    • Primase
      • The enzyme which synthesises RNA primers.
    • Primordial Germ Cells
      • The original diploid cells from which gametes are formed.
    • Prognostic (biomarker)
      • a test or set of tests which indicates the likely progression of a specific disease (something in between a surrogate and a diagnostic).
    • Promiscuity
      • When applied to a GPCR it means that the same receptor may belong to more than one class, this may occur because they will behave differently in different environments - over 20 GPCRs are promiscuous.
    • Promoter
      • A region of DNA which signals initiation in single celled organisms.
    • Prophage
      • the factor which causes lysogenic behaviour, but occasionally gives rise to infective phage.
    • Prophase
      • The stage of mitosis where things are mobilised for action. The chromatin threads condense to form distinct chromosomes which gradually become shorter and fatter. Also protein fibres are formed in the cytoplasm and span the cell from end to end.
    • Prosthetic Group
      • The other compound in a conjugated protein.
    • Proteins
      • A compound which contains nitrogen, hydrogen, carbon and oxygen as well as often sulphur and sometimes potassium or other elements. They are built up from amino acids in chains.
    • Proteolysis
      • Specific Enzyme dregradation
    • Proteolytic enzyme
      • Enzymes which can break peptide bonds only between specific amino acids in proteins.
    • Proteomics
      • analyses protein synthesis and cell signalling
    • Protoplast
      • A cell stripped of its cell wall.
    • Prototrophic
      • A nutritionally self-sufficent organism whic can feed only on inorganic matter.
    • Pseudoautosomal Inheritance
      • Inheritance patterns shown by genes on the homologous parts of the X and Y chromosome.
    • Pseudo Dominance
      • The expression of a recessive allele when it is present in only a single dose.
    • Puffs
      • Regions of a polytene chromosome which appear to be swollen.
    • Pulse Chase
      • The name of an experiment which allows you to track RNA molecules.
    • Punnett Square
      • A table of the parents genes showing the possible children they could have.
    • Pure Line
      • a population which breeds true for, or shows no variation in the characteristic being studied.
    • Purine
      • The bases A and G
    • Pyramidine
      • The C and T bases.
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    Q

    • QSAR
      • Quantitative structure-activity relationship
    • QSPR
      • Quantitative structure-property relationship
    • Quadrivalent
      • A pairing of four chromosomes.
    • Quarternary Structure
      • The final level of strcuture in a protein formed when two or more folded structures bind together.
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    R

    • Random Coil
      • the parts of the polypeptide chain in a protein where no specific pattern of structure emerges.
    • Recessive Mutation
      • A change to a non-wild type recessive allele.
    • Recipient
      • One of the two participants in bacterial conjugation the other being the donor.
    • Reciprical Translocation
      • When two parts of different chromosomes are swapped.
    • Recombinants
      • See crossover products
    • Recombinant Frequency (R.F)
      • percentage of recombinants present in the cross.
    • Regression
      • Building a model to predict a matrix of Y values from a matrix of X values.
    • Regulator Gene
      • In the jacob monad theory of gene action the regulator gene inhibits the operator gene when the structural gene isn't needed.
    • Release Factors
      • A protein factors which recognises a stop codon.
    • Renal Cortex
      • The outer portion of the kidney where ultrafiltration occurs.
    • Repulsion Conformation
      • When the dominant alleles are not together in the parental combination.
    • Resistant Mutation
      • A mutation which confers on the mutant the ability to grow in the presence of an inhibitor.
    • Restrictive Condition
      • The condition which if true means that a conditional mutation will show.
    • Reverse Mutation
      • A change back to a wild type allele.
    • Rho
      • An additional protein factor sometimes used to find termination points in transcription
    • Rhodopsin-like GPCR
      • a wide protein family which includes hormones, neurotransmitters and light receptors.
      • They all transduce extracellular signals through interaction with G-proteins
      • Their ligands vary wildly in structure and character but the amino acid sequences of receptors are very similar and adopt a comon strcutural framework comprising of 7 transmembrane helices
      • Rhodposin receptors are receptors for light.
    • Ribosomal RNA (rRNA)
      • RNA which combines with proteins to form ribosomes
    • Ribosomes
      • they are attached to the matrix side of nuclear membranes and are rich in ribonucleic acid (RNA).
      • Bioloogical machines used for protein synthesis.
    • Ribozyme
      • An RNA molecule with enzyme properties.
    • RMSEP
      • Root mean squared error of prediction
    • RNA polymerase
      • the enzyme which catalyses transcription.
    • Rough Endoplasmic Reticulum
      • Endoplasmic reticulum which is covered in ribosomes. It is used to transport proteins from ribosomes (where they are made).
    • Rough Set
      • Take a 'Knowledge Base', K of partitions of all objects in the universe, if a set of objects from the universe can be described exactly using K - then the set is exact. If this is not possible then the set is Rough in K. eg. If your universe contains blocks of different sizes and colours, and pictures on them, but your knowledge base only describes the sizes and colours, then the set of all blocks with a pciture of a duck on them will (probably) be rough, since unless by luck it is also describeable by info on the colours and sizes, it can't be described.
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    S

    • Saturated
      • When a fatty acid contains the maximum possible number of hydrogen atoms it is saturated.
    • Scaffold
      • The central core of a chromosome.
    • Schema
      • a set of bit stings made up of 1's 0's and *'s (wild cards)
    • SDEP
      • Standard Error of prediction
    • Secondary Structure
      • The second layer of structure in a protein refering to the interelationships of close amino acids.
    • Secreted Proteins
      • proteins which are made in the cell for 'export'
    • Secretin-like GPCRS
      • Another type of GPCR which has no significant sequence identity with the Rhodopsin-like GPCRs and also has its own distinctive 7TM signature.
    • SECV
      • Standard Error of cross validation
    • Segregation
      • The separation of 2 alleles in a heterozygous genotype into two phenotypically distinguishable individuals or cells.
    • Selective Predation
      • When a predator is more likely to get individuals with one characteristic than another.
    • Self
      • often used to mean self pollinate.
    • Self Incompatibility
      • The phenomenon that some plants, despite producing male and female gametes are unable to produce seeds from just their own gametes.
    • SELDI-TOF-MS
      • A form of time-of-flight mass spectrometry. Good for high throughput analysis of complex mixtures. Separation is based on the physcial properties of the protein.
    • Semiconservative Replication
      • Produces two daughter duplex consisting of one strand of parental DNA and one new strand each.
    • Semilethal
      • see subvital.
    • Semisterility
      • When 50% of products are viable.
    • Senescence
      • Getting old.
    • Sense Strand
      • the DNA template for mRNA
    • SEP
      • see SDEP
    • 7 Transmembrane Helices
      • A common structural framework shared by many/all(?) GPCRs, however it has not been shown that everything with this framework is a GPCR.
    • Sexduction
      • Creation of meroploids by F' elements.
    • Sex Factor
      • A piece of DNA found in bacteria which allows them to become donors in bacterial conjugation.
    • Sex Linkage
      • Inheritance pattern for all genes found on the sex chromosomes
    • Sexual Spores
      • Haploid products of meiosis.
    • Shrink
      • replaces a randomly chosen subtree with a random terminal.
    • SIMCA
      • Soft Independant Class Modeling - build a PCA model separately for each class, then can predict in new samples by examining their distance to each model.
    • Sister Chromatids
      • The two chromatids of one chromosome.
    • Signal Peptide
      • A short prefix of about 20-30 amino acids in length which is found in Neuropeptide Precursors.
    • Smooth Endoplasmic Reticulum
      • This is not joined to the rough endoplasmic reticulum and is thought to be connected with the synthesis and transport of lipids and steroids.
    • Solenoid
      • The bead necklace form of a chromosome when coiled.
    • Somatic Cells
      • Cells which will not become gametes.
    • Somatic Cell Hybridization
      • A technique for mapping genes in humans using cell growth in a culture.
    • Somatic Mutation
      • a mutation in developping somatic tissue can lead to a population of identical mutant cells all descended from the original mutated cell.
    • SPC
      • Statistical Process Control
    • Specialised Transducing phage
      • A phage which can only carry restricted parts of the chromosome. See also generalised transducing phage.
    • Spermatogenesis
      • Production of sperm in humans.
    • Spermatozoon
      • Posh word for sperm.
    • Spindle
      • Structure of protein fibres which span the cell during prophase.
    • Spore Formation
      • A method of assexual reproduction whereby unicellular bodies which were formed in the parrents are released and if conditions are favourable they will germinate.
    • Sporophyte
      • The diploid stage of an organism which undergoes alternation of generations.
    • SS
      • Sum of Squares
    • Starch
      • Storage carbohydrate for plants.
    • Steady State Population
      • instead of using generations you continually add new children to the population and remove some individuals to make room. The total size of the population remains constant.
    • Stoichiometry
      • The proportion (or quantities) of substrate and product molecules involved in a reaction
    • Striated Border
      • see brush border.
    • Structural Gene
      • In the the structural gene is the one which actually codes for an enzyme.
    • Substitution
      • A type of gene mutation whereby 1 or more nuleotides are substitued into the DNA.
    • Subtree Mutation
      • replaces a randomly selected subtree by another randomly created subtree.
    • Subvital (or Semilethal)
      • An allele which in some way 'disables' the organism so less of them are present in the population than might be expected.
    • Supernatant Fluid
      • Liquid containing lighter organelles resulting from differential centrifugation
    • Suppression
      • When one gene stops anothers effects from showing in the phenotype
    • Surrogate
      • A test or set of tests which idicates teh progression or regression of a specific human pathology - ideally this surrogate should correlate both with improvement and worsening of the condition and should appear before or be easier to measure than actual disease progression.
    • Synapis
      • When homologous chromosomes lie side by side in Prophase 1 during meiosis and become paired as if by a zipper.
    • Synaptonemal Complex
      • An elaborate structure composed of DNA and protein which is found sandwiched between homologs during synapis
    • Syngamy
      • Union of gametes in sexual reproduction.
    • Synthetic
      • A type of reaction in a cell where A + B -> AB. It is anabolic and endergonic.
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    T

    • Tandem
      • A duplication like ABCBCD
    • TCA cycle
      • A metabolic pathway involved in cancer, related to the Warburg effect and takes in pyruvate and glucose and cycles round through citrate, succinate, malate and others.
    • Telocentric
      • describes a chromosome where the centromere is postioned at the end.
    • Telomere
      • The ends of chromosomes thought to remain anchored in the nuclear membrane and hence homologous pairs are thought to locate each other during zygotene by their telomeres being anchored close together.
    • Telophase
      • Phase of mitosis whereby chromatids become densely packed at the ends of the spindle and cell starts to divide into two.
    • Temperate Phage
      • A phage which has a lysogenic cycle
    • Temperature Sensitive Period
      • Sometimes the restrictive and permissive conditions are related to temperature and when it udergoes the change from one to another it experiences a termperture sensitive pe riod.
    • Teratogen
      • A drug or other substance which interferes with development causing birth defects
    • Teratoma
      • A tumour made up of different tissue types (such as is obtained if you xeno-graft pluripotent cells into an immuno-deficient mouse.)
    • Terminal Deletion
      • A deletion of the end of a chromosome caused by a single break.
    • Termination
      • The final stage of transcription
    • Tertiary Structure
      • The third layer of structure of a protein whereby it is viewed in terms of its 3d architecture.
    • Test Cross
      • crossing an organism with a similar homozygous recessive one. Allows experimenter to study the recessive genes in the original organism.
    • tetrads
      • groups of 4 cells which are all the product of a single meiotic division.
    • tetraploid
      • An individual who develops from 2 diploid gametes, or in other words, someone who has 4 sets of chromosomes.
    • Thiol
      • A compound which contains an -SH group
    • Three Point Test Cross
      • Studying 3 genes by crossing a completely dominant organism with a completely recessive one.
    • Topoisomerase
      • Enzymes which control the supercoiling of DNA.
    • Topology (of a gene)
      • The manner in which the parts are interconnected.
    • Tournament Selection
      • parents are selected by randomly choosing two individuals and then selecting the 'fittest' one to breed.
    • Trait
      • very roughly, each gene encodes a trait.
    • Transanimase
      • Enzymes which transfer amino groups from one molecule to another.
    • Transamination
      • Process of getting amino acids for use in proteins from other amino acids found in food.
      • The transfer of an amino group from one compound to another
    • Transcriptomics
      • studies the gene expression
    • Transcription
      • The process of synthesising RNA from a DNA template.
    • transduction
      • the process of picking up DNA from one cell and injecting it into another.
    • Transfer RNA (tRNA)
      • a group of small RNA molecules which each have a specificity for an amino acid and they carry that amino acid to the ribosome so it can be attached to the polypeptide c hain.
    • Transferase
      • Enzymes involved in reactions which transfer atoms or groups of atoms from one molecule to another.
    • Transformation
      • The process whereby a prokaryotic cell picks up DNA from the environment and encorporates it into its own chromosome.
      • The conversion of one genotype into another by the introduction of exogenous DNA
    • Translocation
      • A chromosome mutation whereby a section of chromosome breaks off and reattaches to another chromosome.
    • Triploid
      • An individual which develops from a diploid gamete joining with a normal haploid one, will be triploid, in other words have 3 sets of chromosomes.
    • Trisomic
      • When the chromosome number is 2n+1
    • Trisomy
      • When a person has 3 chromosomes to code for something due to non-disjunction.
    • Trivalent
      • A pairing of three chromosomes.
    • Trophectoderm
      • Cells from the outermost layer of a blastocyst that normally attach to the uterine wall.
    • Tubulorrhexis
      • Necrosis of the cells in the lining of the kidney tubules.
    • Turnover Number
      • A measure of an enzyme's performance based on the number of substrate molecules which 1 molecule of enzyme can turn into product per minute.
    • Turns
      • sharp bends in the polypeptide chain consisting of 3 or 4 amino acids.
    • Two dimensional Chromatography
      • A method for identifying proteins
    • 2-D gel Electrophoresis (2DGE)
      • A spearation method for complex protein mixtures. Separates based on mass and iso electric point. It is one of the oldest and most used methods, but it is easy to miss proteins present in low quantities.
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    U

    • Ultra Structure
      • see fine structure
    • Unequal Crossover
      • When the crossover point is at different places in both homologs and so one deletion and one duplication takes place.
    • Uniform Crossover
      • for each position in the chromosome randomly pick the value from one of the two parents. (no linkage)
    • Unit Membrane
      • Membrane found round each organelle, it is essentially the same no matter what type of organelle is examined.
    • Univalent
      • An unpaired chromosome.
    • Unselected Marker
      • A marker from which you are measuring the distance to another specific selected marker, by measuring linkage.
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    V

    • Valency
      • How many bonds an atom will naturally form.
    • Variant
      • Organisms which differ in a particular charicter.
    • Variegation
      • The coexistance of different looking sectors in somatic tissue.
    • Vegetal Pole
      • The end of a human egg which contains inert yolky stuff.
    • Vegetative Propagation
      • The method of asexual reproduction used in plants when part of the body gets detached and develops into a new plant.
    • Vestigal
      • Structures which have been reduced by the process of evolution.
    • Viability
      • probability organism will live to reproduce
    • VIP
      • Variable Influence on Projection
    • Virulent Phage
      • Has an infective cycle which is always lytic
    • Vitelline Membrane
      • The outer membrane of a human egg cell.
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    W

    • Warburg Effect
      • An effect seen in many cancer cells, where high rates of glucose consumption and lactate production are seen despite oxygen being available, so that the glucose could be oxidised completely providing a more efficient form of energy.
      • This effect is also seen in non-transformed (non-cancerous) cells during rapid proliferation.
    • Wild Type
      • The 'normal' allele found in the wild.
    • Wobble
      • A loose base pairing at one end of a codon, which gives rise to redundancy in the coding for an amino acid eg. GC* = Ala.
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    X

    • Xenobiotic
      • A chemical or other substance foreign to the organism
    • X-linkage
      • inheritance pattern of hemizygous genes located on the X chromomsome.
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    Y

    • Y-Linkage
      • inheritance pattern of hemizygous genes located on the Y chromomsome.
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    Z

    • Z DNA
      • The backbone zigzags and the helix is left handed.
    • Zygote
      • A sperm and egg united to form something which has the potential to turn into an adult organism.
    • Zygotene
      • A stage of prophase 1 of meiosis whereby the active pairing of threads occurs and chromosomes are synapsed.
    • Zygotic Induction
      • The entry of lambda prophage into a non-immune cell triggers a lytic cycle.
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    Please note - these definitions may not necessarily be accurate, any mistakes please report them to Rachel