Dr. A. Whittick's Glossary of terms

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originally at http://www.mun.ca/biology/whittick/b1001/biblio/biblio.htm
This page borrowed with minor changes by Dr. KNI Bell --report malfunctions to me (contact Dr Bell) or to Dr. Whittick, please.

Errors in Campbell & Reece 6th. Ed.

Diatom [typo: wrong def.]

A B C D E F G H I j k L M N O P q R S T U V W X Z


This glossary is for Biology 1001,  I have attempted to define the terms at a level appropriate for this course. You may find that some terms are used in a different sense in other contexts as they often have broader meaning than that defined here. While is is hoped that these definitions are of use to you they should not be seen as substitute for your lecture notes and reading of the appropriate chapters of your text book, which will provide you with more details on the topic and in context in which the terms are used.  --A.W.

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absorptive heterotroph an organism which secretes enzymes externally into its environment to digest organic materials which are then absorbed, e.g. fungi, many protists and monera. see: also ingestive heterotroph.

activation energy:  chemical reactions which release energy require the input of some energy to start the reaction, this is the activation energy. enzymes assist such reactions by lowering the activation energy required.

active site: the part of an enzyme which attaches to the substrate

active transport: the movement of a substance across a cell membrane  against its concentration gradient, which requires energy from the cell

adaptation: an evolutionary adaptation is a property of an organism produced by natural selection that fits the organism to its environment. 

adenine: one of the four nitrogenous bases occurring in DNA and RNA, also an important in many other cellular chemical such as ATP,  NADP and cytokinins

aerobic respiration: cellular catabolic reactions which require oxygen

algae: photosynthetic protists e.g. Ulva and Euglena. A useful term for a diverse group of organisms rather than a true taxonomic unit.  some scientists use the term to include the aerobic photosynthetic monerans, i.e. cyanobacteria.

alternation of generations (units 3, 4 &5): reproduction involving the repeating sequence of a  haploid (n) gamete producing generation (gametophyte) with a diploid (2n) spore producing generation (sporophyte). Seen in all plants and many protists. e.g. Ulva.  Gametes are produced by mitosis and spores by meiosis.  gametophyte---> sporophyte--> gametophyte--> sporophyte-->gametophyte-->sporophyte -->etc --> etc.

anabolism: part of metabolism which involves the build up of more complex organic molecules from more simple ones. e.g. the synthesis of  starch from sugars.

anaerobic: lacking oxygen, may refer to an organism, environment, or cellular process,  e.g. nitrogen fixation is an anaerobic process.

animal: a member of one of the five kingdoms, characterized as a eukaryotic multicellular ingestive autotroph.

annual (flowering plant): refers to a plant which completes it life cycle from seed to seed in a single year.

annual (ring): a part of the xylem in a woody perennial that is produced in a single growing season. annual rings are visible in cross sections of such stems and roots because of the cells with a narrow lumen produced at the end to a growing season contrast with the wide lumen cells produced in the spring. 

anther: the male part of a flowering plant, the end part of the stamen in which the pollen (or male gametophytes are produced)

antibiotics: chemical produced by microorganisms  e.g. fungi or bacteria, which kill or inhibit the growth of other micro-organisms. many are used in medicine in the treatment of bacterial diseases e.g. penicillin, streptomycin, tetracylines.

apical bud: bud of a plant found at the tip (or apex) of a shoot.

apical dominance: a phenomenon in plants where the presence of an an apical bud, which produced the plant hormone, auxin, inhibits the development of lateral buds beneath it.

apical meristem: tissue at the tips of shoots and roots consisting of meristomatic cells capable of division and differentiation leads to the primary growth i.e. growth in length of stems and roots. 

apoplast: the non-living parts of plants i.e. cell walls, intercellular spaces and lumen of dead cells which makes up a pathway for the movement of water and solutes 

Archeaone of the two prokaryotic domains which contains the Archaebacteria.

Archeabacteria: an ancient group of bacteria possessing ribosomes and cell membranes that distinguish them from the true bacteria. Found today in extreme environments e.g. in hot acidic environments.

ATP: adenosine triphosphate, an adenine containing nucleotide with three attached phosphate groups, these phosphate can be transferred to other chemical e.g. sugars -- phosphorylation, hydrolization of the phosphate bonds releases energy which is used to drive chemical reactions in the cell.

autogenesis: literally "self generating" one of the alternate theories to the symbiotic theory for the evolution of the eukaryotic cell. suggests that organelles developed internally in the cells from folding of membranes.

autotroph: literally a "self feeder" refers to organisms which do not require organic molecules produced by other organisms. they usually can build organic molecules from carbon dioxide or other inorganic sources e.g. a green plant is an autotroph which uses the sun energy to  "fix" carbon dioxide.

auxin: a class of plant hormones which are involved in many growth effects, e.g. apical dominance, cell elongation and fruit ripening.

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bacilli: (sing. bacillus) rod shaped bacteria

back mutation: relating to the Ames reverse histidine test for mutagens. A suspected mutagen is added to a culture of bacteria that have undergone a point mutation which renders them unable to synthesize the amino acid histidine and therefore require histidine to be provided in there culture medium. If after exposure to the mutagen they are capable of growth in histidine free medium then a "back mutation" has occurred reversing the original point mutation.

bacteria (eubacteria): prokaryotic organisms, often placed in the kingdom Monera, and sometimes divided into two domains the Archea (Archeabacteria) and the true bacteria or eubacteria. some text e.g. Campbell 6th ed. divide the monera into the Archea and the Bacteria. see. Archeabacteria.

bacteriophage: a virus which infects bacteria

bark: the outer part of a stem or root which has undergone secondary growth, it consists of the cork (=periderm) the cork cambium, any remaining cortex, the primary and secondary phloem and the vascular cambium. i.e. when the bark is removed the wood or xylem tissue is exposed. 

base insertion or deletion: a form of mutation in which a nitrogenous base in the DNA is added or deleted from the normal sequence, such changes lead to frame shift mutations and almost result in non-functional genes.

biennial: a plant which takes two growing seasons to complete its life cycle from seed to seed. e.g. turnips, grows one year stores food material and flowers and produces seed the next year. 

binary fission ( literally splitting in half)asexual reproduction by cell division,  to produce two new individuals occurs in monera and in some protists after division of the nucleus and organelles e.g. Euglena.

binomial: the latin name consisting of two word, which is uniquely associated with a species, it consists of a generic name and a specific epithet. e.g. Sarracenia purpurea, by convention the generic name is capitalized and the specific epithet is not. In printing binomials are given in italics to indicate they are latin names, when you write them they should be underlined.

biotic: pertaining to life and living organisms, the opposite is abiotic

bryophyte: a class of plants ( mosses and liverworts), lacking true vascular tissue, showing alternation of generations with a free-living dominant gametophyte generation to which the sporophyte generation is attached and nutritionally dependent on the gametophyte generation.

bulk or pressure flow: a mechanism to explain the movement of solutes in the phloem tissue of plants. 

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Calvin cycle: part of photosynthesis, in which carbon dioxide is converted into simple sugars using ATP and NADPH derived from the light reactions of photosynthesis. More accurately it should be called the Calvin-Benson cycle after the biochemists who worked it out in the early 1950's

cambium: a secondary meristem found in vascular plants, the vascular cambium contributes to growth in stem and root diameter, by producing xylem on the inside and phloem on the outside, the cork cambium is found externally to the vascular cambium and produces the cork or out part of the bark.

capsid: the protein coat of a virus, aggregation of  capsomeres, complex capsid consist of more than one type of capsomere e.g. T4 bacteriophage.

capsomere: a protein subunit which aggregates to form the capsid or  protein coat of a virus

carbohydrate: one of the four major chemical groups which characterize living organisms. a simple carbohydrate is  a sugar such as glucose, while more complex one are called polysaccharides, e.g. starch or cellulose which are polymers of glucose.

carotenoid: a pigment produced by plants, but not animals, many are used as accessory pigments in photosynthesis, they are usually yellow orange or red in colour, accessory pigments absorb light  and pass on the energy to the chlorophyll molecules. Carotenoids also may act as a "sunscreen" to protect the chlorophyll molecules from damage by excessive blue light.  Animals that have carotenoids derive them from the plant food they eat e.g. pink salmon flesh, pink feathers of flamingoes.

carpel: female reproductive part of a plant consisting of a stigma, style and ovary sometimes called a pistil.  the relationship between the terms carpel and pistil can be confusing. If a pistil is made of a single carpel then they are the same, but in many plants several carpels can fuse to form a single pistil. e.g. in tulips or daffodils examination of the pistil shows that it consists of three fused carpels. 

casparian strip: a band  of suberinized cell wall around four sides of cells of the endodermis which blocks the apoplastic route between the cortex and the stele in plant roots. The tangential walls of the endodermal cells remain un-suberinized, this means that any material moving from the cortex to the stele must go through the symplast of the endodermis.

catabolic (also catabolism): part of metabolism which involves the break down of  complex organic molecules to simple ones. e.g. the respiration of glucose to carbon dioxide, the opposite of anabolic or anabolism.

catalyst: a substance which speeds up  a chemical reactions, but emerges from it unchanged, in cells enzymes are proteins which are organic catalysts.

cell: a discrete mass of cytoplasm surrounded by a plasma membrane, the  basic unit  capable of performing all the functions of life.

cell (plasma) membrane: the outer boundary of a living cell, distinct from a cell wall, when present, which is extracellular. The cell membrane (also called the plasmalemma) is made up of a phospholipid bilayer, it prime function is to keep the cell intact and aid in regulating, and transporting material into an out of the cell. molecules associated with the cell membrane are also important in cellular communication and recognition.

cell division: the process by which a cell divides to form two new cells, this occurs after replication of the DNA and, in eukaryotes, the organelles.

cell theory:  one of the great paradigms of biology, proposed in  1839 by Matthais Scleiden and Theodor Schwann that all living organisms were composed of cells.

cell wall: a protective layer external to the cell membrane in plants, fungi, monera and some protists.  In plant cells the primary cell wall is made of cellulose.

cellulose: a polymer of glucose found in plant cell walls, also found in the walls of many protists.

Charophyceae: a class of green protists (Chlorophyceae) which show many similarities with plants, especially their mode of cell division, and the structure of their flagella. The Charophyceae are considered as having a common ancestory with land plants. includes the genera; Chara, Spirogyra and Coleochaete.

chemoautotroph: an organism that uses carbon dioxide as a carbon source, but obtains its energy by oxidizing inorganic substances. e.g. some bacteria.

chemoheterotroph: an organism that obtains both its carbon and energy by oxidizing organic materials e.g. animals, fungi, many protists and bacteria.

chitin: a polymer of a sugars, with amino groups attached, a structural component of the walls of  fungi, some invertebrates e.g. insect exoskeletons and in a very few protists cell walls.

chlorophyll: a green pigment which absorbs light energy and participates in its conversion to chemical energy in the light reactions of photosynthesis.

chloroplast: an organelle bounded by double membranes which is the site of photosynthesis in protist and plant cell.

cholesterol: a chemical found in animal cell membranes which help to stabilize them.

chromatin: the complex of DNA and proteins that makes up eukaryotic chromosomes

chromosome:  a thread like structure which is made up of DNA and associated proteins. They are multiple, linear and found in the nucleus of eukaryotic cells, while prokaryotic cells contain a single circular nucleus in their cytoplasm.

CHROMOSOME NUMBER, often represented as n: the number of chromosomes in a single set of non-homologous chromosomes, e.g. the number of chromosomes in a gamete of ploidy = n. Human haploid or n=23, diploid or 2n=46.

cilia (sing. cilium): short appendage of eukaryotic cells used in locomotion or sweeping material across the cell surface. Structurally identical to flagella in that they are made up of a inner core of two single microtubules surrounded by a 9 double microtubules. Differ from flagella principally in being shorter and more numerous on each cell.

cisternae: a fold or pouch in the endoplasmic reticulum e.g. a component of the golgi body

classification:  the act of  placing related taxa together in a higher taxon,  e.g. cats and dogs are classified in the order Carnivora, classification should not be confused with identification  which is the process of discovering the name (usually the binomial) of a specimen.

clone: a group of genetically identical cells or organisms

coacervate: a stable droplet that self assembles when a solution of macromolecules (polypeptides, poly-nucleotides or polysaccharides) is shaken. 

cocci: spherical bacteria

cohesion tension: cohesion is the binding together of some molecules by hydrogen bonds, cohesion- tension is the mechanism proposed for the movement of water in xylem tissues, the pull on the top of the water column dues to loss of water in transpiration places the column under tension, the cohesion of the water molecules means that this tension moves the whole column of water much is if it were a solid rather than a liquid.

coleoptile: leaf like protective sheath surrounding the apical meristem of  the shoot in germinating grass seed, 

collenchyma: tissue is made up of collenchyma cells, these are strengthening cells 2-3 time as long as their diameter, usually living at maturity with thick cellulose cell walls, , they work together with the turgor pressure of parenchyma cells to provide rigidity with flexibility, without restraining growth in younger parts of plants.

commensalism: a form of symbiotic association in which one partner benefits, while the other is neither helped not harmed.

companion cell: part of the phloem tissue, a sibling cell of the sieve tube member to which it is connected by numerous plasmodesmata. In contrast to the associated sieve tube member it contains a nucleus and ribosome, it is metabolically active for both itself and the sieve tube member.

complete flower: a flower with all four floral parts e.g. sepals, petals, stamens and pistils

concentration gradient: set up by the diffusion of a solute from an area of high to low concentration.

condensed chromosomes: prior to cell division the chromosomes become shortenened and thicker due to coiling of the DNA, at this time they can be stained and viewed with a light microscope, such chromosomes are said to be condensed. Some organisms e.g. Euglena and and dinoflagellates retain their chromosomes in the condensed state throughout their life cycles.

conifers: a lay term which refers to those plants which produce cones containing seeds. 

conjugation: in bacteria the transfer of DNA from one cell to another between cells which are temporarily joined for that purpose. Can also be used in protists when two apparently normal cells act as gametes and fuse to form a zygote.

contractile vacuole: an organelle found in freshwater protists that lack a cell wall. It function to remove excess water from the cell that has entered as a result of osmosis, it action requires energy provided by the cell.

cork (=periderm): the outer part of the bark of a woody plant, produced in secondary growth by the cork cambium, at maturity the cell walls are impregnated with the suberin, a waxy substance that prevents water loss and damage to the underlying tissues. Cork cells are dead at maturity. It was these "cells" to which the term cell was first used by the microscopist Robert Hooke in the 17th century, because they reminded him of a small square room or "cell"

cork cambium: the secondary meristem in the outer part of stems and roots which produces the cork or periderm.

cortex: the tissue internal to the epidermis in roots and shoots, derived from the ground meristem it is principally composed of parenchyma cells and is used for structure and food storage.

cotyledon: sometime called seed leaves, they are the embryonic leaves found in a seed, monocotyledons have one seed leaf and dicotyledons have two.

cristae: the in-foldings of the inner membrane of mitochondria.

cuticle: the outer way layer on the surface of the living cells of the epidermis of shoots and leaves, it serves to prevent water loss. 

cyanobacteria: a group of  photoautotrophic bacteria characterized by their possession of normal "plant type chlorophyll" and the ability to photosynthesize. They are structurally the most complex of the prokaryotes forming colonies and even becoming multicellular. cyanobacteria are candidates for the organisms which became chloroplasts, by symbiotic association during the development of the eukaryotic cells.  

cytokinins: a class of plant hormone, principally concerned with regulating cell division, structurally based on the nucleotide adenine. (Don't confuse it with cytokine, which is something completely different).

cytoplasm: the contents of the cell exclusive of the nucleus and the membrane bounded organelles.

cytosine: one on the four nucleotides found in DNA and RNA

cytoskeleton: a mobile frame work of  filamentous proteins found in eukaryotic cells, serves to stabilize the cytoplasm and organelles as well as serve in movement in cells e.g. in cell division, muscle cells and in cilia and flagella. 

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day neutral plant: a plant which which has no specific daylength requirement as a stimulus to flowering. i.e. will flower under both short and long days.

denatured: pertaining to enzymes- and enzyme which as lost it function due to irreversible changes in its conformation or tertiary structure. Such change can occur due to heating, or other chemical and physical changes in it environment. 

de-nitrifying bacteria: anaerobic soil bacteria with use nitrates as aerobic organisms use oxygen, this results in loss of nitrates and the generation of nitrogen gas, this results in loss of available nitrogen compounds from soils.

deoxyribose: a five carbon sugar part of the structure of DNA.

derived character: the opposite of a primitive character, one that has been derived from another more primitive character.

dermal tissue: the outer covering in plants e.g. epidermis, a product of primary growth derived from the sub-apical protoderm meristem. 

DIATOM: [Campbell 6th ed glossary has wrong def.] group of unicellular algae having siliceous tests that exist in two nested parts (like the two-part capsule used for some drugs).

dicotyledon: one of the two major groups of  flowering plants, named because its two embryonic leaves in the seed. Dicotyledons also usually have floral parts in multiples of 4 or 5, leaves with netted venation. Many also show secondary growth and become woody. cf. monocotyledon.

differentiation: in plant cells, when a meristomatic cell develops into another type of cell e.g. parenchyma.

diffusion: the movement of a substance from an area of high concentration to an area of lower concentration until an equilibrium is reached.

dioecious: referring to plants when male and female flowers are borne on separate individuals c.f. monoecious.

diploid: having two complete sets of homologous chromosomes.

diversity: many definitions the simplest is that an place of high diversity has a greater number of species per given area.

division of labour: referring to cells, internal compartmentalization leads to areas of the cell being used for specific purposes, e.g. a mitochondrion is the site of aerobic respiration in eukaryotic cells. cells themselves also may show division of labour i.e. parenchyma cells of the root cortex specialized for food storage, while epidermal cell with root hairs are specialized for the up take of water. 

DNA: deoxyribonucleic acid.  a macromolecule forming the genetic make up of all prokaryotes, eukaryotes, some organelles and many viruses. It consists of two long chains of four nucleotides bound to the 5 carbon sugar deoxyribose and joined by phosphate bonds.  Two chain occur together to form a double helix, which is held together by hydrogen bonds. DNA contains the genetic blue print of  a cell, which is expressed by converting the code of the sequence of nucleotides into specific proteins.

DNA triplet: the genetic code whereby a sequence of three nucleotides codes for a specific amino acid or action during protein synthesis. There are 64 way of expressing four nucleotides in sequences of three, but only 20 amino acid in proteins, the code is therefore called redundant as more than one triplet may code for one amino acid.

dormancy: in seeds, the embryo remains dormant i.e. does not grow until seed germination occurs.

double fertilization: a characteristic of flowering plants which distinguishes them from other plants. The male gametophyte (pollen grain) produced two sperm nuclei, one of which fuses with the egg to produce a zygote, which develops into the embryo, the other fuses with the polar nuclei (two or more) and the product develops into the endosperm tissue.

double helix: the structure of DNA two strands of DNA are wound together to form a helix, the two strands are held together by hydrogen bonds.

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egg: one of two types of gamete, usually referred to as the female gamete, which is large and non motile compared to the male gamete or sperm.

embryo: a multicellular structure resulting from the division of a zygote, it is not usually free living but is retained with the parent or other protective structure, for a period of development. e.g. dormant embryo found within a seed.

embryo sac: found with the ovules in the ovary they are the female gametophytes of a flowering plant. Shows a variety of structure and development, but is multicellular, among the simplest are structure of seven cells containing eight nuclei, one nucleus is the egg or female gamete, two or more nuclei are polar nuclei from which the endosperm develops, after fertilization the embryo develops within the embryo sac. 

endodermis: most commonly seen within the roots of vascular plants, it is the inner part of the cortex, the cells are partially suberinized by a casparian strip, which blocks the apoplastic pathway, by requiring that water and solute pass through the symplast of the cell it controls movement of solutes between the cortex and stele of the root.  An endodermis may also be found in other plant organs e.g. leaves of conifers.

endomembrane system: refers to the membrane system of eukaryotic cells within the cell of plasma membrane e.g. the endoplasmic reticulum and associated organelles e.g. golgi body, nuclear membrane. Excluding double membrane bounded organelles such as mitochondria and plastids.

endoplasmic reticulum: abbreviated as ER it is part of the endomembrane system serves for internal transport and compartmentalization of the cell, many metabolic processes take place on the endoplasmic reticulum, e.g. attachment of ribosomes to form rough endoplasmic reticulum is site of protein synthesis in the cytoplasm. ER without ribosome is called smooth endoplasmic reticulum.

endosperm: a nutrient storage tissue found in the seeds of  most flowering plants, it results from the development of  a cells formed by the fusion of a sperm nucleus and the polar nuclei of the embryo sac. The tissue is polyploid i.e. the cells have more than two sets of homologous chromosomes.

endo-symbiosis: symbiosis within a eukaryotic cell, a mechanism to account for the the occurrence of  mitochondria and chloroplasts within eukaryotic cells.  Sometimes stated as a theory that these organelles where once free living prokaryotes which entered into a symbiotic mutualistic relationship with another cell and over time became cellular organelles. The evidence for this is overwhelming and it is accepted by nearly all biologists.

endotoxins: toxins produced within the cells of bacteria and only released with the bacteria lyse (burst) cf. exotoxin.

enzyme: a protein catalyst found in living cells, it enhances chemical reactions by lowering their activation energy. 

epidermis: the outer layer of cells  of  produced by primary growth

equilibrium:  a state in which no net change occurs e.g.  the point in osmosis at which osmotic pressure is balanced by turgor pressure.

essential elements: in plants, these are the inorganic elements which are needed for growth and reproduction, there are about 16 in all. 

ethylene: a hydrocarbon gas (CH2CH2), which is one of the five major plant  hormones, important in fruit ripening.

euglenoid movement: a specific type of gliding movement shown by Euglena and related organism.

Eukarya: one of the three major domains of life (Archaea, Bacteria, Eukarya) distinguished by being composed of eukaryotic cells

eukaryote: one of the two major cell types (cf. prokaryota). Cells with a distinct nucleus containing multiple linear chromosomes with associated histone proteins. Cells have a cytoskeleton,  membrane bounded organelles e.g. mitochondria, and endomembrane system.

evolution: the process which combines genetic change (e.g. mutation) and natural selection to produce organisms with characters that enhance their chances of reproduction (fitness), these characters are then passed on to their offspring.

exotoxins: a toxin produced by bacteria that is excreted into its environment.

eyespot: in protists usually a red spot of carotenoid pigments, found in protists associated with plastids or the basal region of flagella, it acts as a filter or lens for blue light receptors e.g. the basal bodies of the long flagellum in Euglena.

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facultative anaerobe: a organism, which can live under anaerobic conditions, but does not require them, see obligate anaerobe.

fern: a lay term for a division of spore producing vascular plants - the Pterodophyta. The sporophyte generation has true leaves with vascular tissues, which bear the sporangia, the gametophyte generation is free living and microscopic.

fertilization: the process whereby two gametes fuse to form a zygote.

fibres: a cell of tissue type found in vascular plants, the cells are elongate, dead at maturity and  heavily lignified with a narrow lumen. They have a strengthening function and often found in the vascular tissues, e.g. in the phloem as caps on the vascular bundles.

filament: part of the stamen attaching the anther to the flower.

five-kingdom system: a highly artificial somewhat archaic system in which living organisms were placed in five kingdoms based on cell type and nutrition. Monera (prokaryotic cells), Protista (eukaryotic single cells, with related multicellular forms added later), Fungi (multicellular absorptive heterotrophs), Animalia (multicellular, digestive heterotrophs), Plantae (multicellular, autotrophs).

flaccid:  the opposite to turgid, when a cell loses turgor pressure.

flagella (eukaryotic): structurally similar to cilia i.e. 9+2 internal arrangement of microtubules, organs of locomotion usually, only a 1 to a few per cell, c.f. cilia. Found in protists and on sperm of plants. Flagella occur in some bacteria, but are simple microtubular structures.

flagella base: found in eukaryotes which link the flagella to the cytoskeleton of the cell. 

florigen: a hypothetical plant hormone, whose action in carrying the stimulus for flowering from leaves to the bud has been demonstrated, but no hormone has ever been isolated or even identified.

flower: the reproductive organ which characterizes a flowering plant in which the seeds and fruit are formed. The complete flower consists of four basic floral parts the sepals, the petals, the stamens and the carpels. 

flowering plants: vascular seed plants which produce "flowers" members of the Anthophyta or Angiosperms, distinguished from all other seed plants, by the having double fertilization. They also have true vessels which are found only on one group of non flowering plants (the Gnetales)

fluid  mosaic model: a model describing the structure of eukaryotic cell membranes, in which proteins and other chemicals, e.g. cholesterol, float in a loose association of phospholipid molecules. The model allows for the movement of the membrane constituents and its properties in a controlling the movement of substances into and out of cells. 

frame shift mutation

fruit: a mature ovary, developing after fertilization, which contains the seed, its function is in seed dispersal.

fungi: one of the putative "five kingdoms", consists of multicellular organisms with an absorptive heterotrophic mode of nutrition.

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gametangia: in protists and plants, a cell or group of cells which produce the gametes.

gamete: a haploid cell which fuses with another cell to produce a diploid zygote. 

gametophyte: a plant or protist which produces gametes, gametophytes are usually haploid and produce gametes by mitosis.

gene: the basic unit of heredity, a sequence of DNA which codes for a single functional polypeptide.

generative cell: a cell found in the pollen grain (male gametophyte) which divides by mitosis to form two sperm nuclei (see double fertilization).

genome: the total of all the genetic information found in a cell. The sum of all an organisms genes.

genus: a taxon to which a species belongs, the generic name forms the first word of the binomial name. 

geometric rate of increase: e.g. in a population of cell which double with each division i.e. 1-2-4-8-16-32-64 ...

germination: the process by which dormant seeds or spores resumes growth.

gibberellin: one of the five major groups of plant hormone, implicated in many plant growth processes, e.g. seed germination, elongation of internodes

Golgi bodies: part of the endomembrane system of eukaryotic cells, function in chemically modifying proteins and packaging of substances for movement out of the cell, particularly in abundant in secretory cells. (the term dictyosome is sometimes used to describe these structures in plant cells)

grana: stacks of thylakoids in the chloroplasts of green protists and plant cells. Site of the light reactions of photosynthesis.

green tide: refers  particularly to marine bays which become choked with floating mats of  multicellular green algae (protists) such as Ulva. Usually in response to pollution leading to nutrient enrichment.

ground meristem: one of the three sub-apical meristems found in the shoots and roots of plants. In primary growth the ground meristem gives rise to the bulk of the parenchyma tissue of the plant, i.e. all except  the dermal and vascular tissues

growth: one the characteristic of living organisms, the total of cell division, enlargement and differentiation.

guanine: one of the four nitrogenous bases found in DNA, RNA and other biochemicals.

guard cell: in plant epidermal tissue, the cells immediately surrounding the stoma, the guard cells and other epidermal cells in the immediate vicinity make up the stomatal apparatus. Differential thickening of the cell walls and changes in turgor pressure of the guard cells cause opening and closing of the stoma thus regulating water loss and gaseous exchange in the plant.

guttation: a phenomenon in which liquid water appears as droplets on a leaf surface, guttation is produced by root pressure in non transpiring plants.

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halophile: literally salt loving, refers to plants such as those found in salt marshes to extreme halophiles such as members of the Archaea, which are capable of growth in saturated salt solutions.

haploid: ( see diploid) cells with one set of complementary chromosomes, in protists and plants cells of the gametophyte generation. gametes are haploid and fuse with another gamete to produce a diploid zygote.

head (virus): in virus with a complex capsid e.g. bacteriophage, the part with contains the genome.

helical: spiral shaped, e.g. the secondary structure of proteins, or the double helix of DNA.

herbaceous plant: a plant without secondary growth, i.e. a non woody plant usually an annual.

heterocyst: a special type of cell found in multicellular members of the cyanobacteria, in which nitrogen gas is "fixed" or converted into ammonium compounds. Cells are larger and paler than normal vegetative cell, they do not produce oxygen in photosynthesis and their cell walls are impermeable to oxygen. This is protect the enzyme nitrogenase, which requires a low oxygen concentration. 

heterotrophy: consuming of  organic compounds as a means of obtaining materials, chemoheterotrophs also obtain energy from these sources, while photoheterotrophs obtain energy from light.

hierarchical classification: a method of classification in which a taxon is placed in a series of taxa arranged in a  order based on increasing inclusiveness, the modern system was developed by Linnaeus.  e.g.  several genera could be placed in a family, several families in an order, several orders in a phylum and several phyla in a kingdom. 

homeostasis: One of the characteristics of living organisms is the maintainance of a stable equilibrium through metabolic processes, e.g. the maintenance of body temperature in mammals. 

hormone: in plants a regulatory substance produced in one part of the plant, but acting in another e.g. auxin is produced in the apical meristems and controls the elongation of cells in the sub-apical regions. 

hydration: in plants the uptake of water into tissues that had previously been reduced in water. e.g. in seeds the uptake of water leading to the resumption of metabolism, prior to germination.

hydrophILic: (literally water loving), refers to substances and surfaces in cells which have an affinity for water and are capable of being wetted.

hydrophobic: (literally water fearing), refers to substances and surfaces in cells which are not capable of being wetted. In cells these are usually lipid based. Hydrophobic substances in water, such as the lipid component of phospholipids tend to form into water repellant droplets. 

hypertonic: concerning osmosis, a term used to compare one solution with another, a hypertonic solution has a higher concentration of solutes, when separated by a membrane that is permeable to the solvent and impermeable to the solute. In this instance  the solvent will flow from the region of lower solute concentration (hypotonic) to the region of higher concentration (hypertonic) by the process of osmosis. e.g. most fresh water protists are hypertonic when compared with their environment.

hyphae: a term used to describe the filaments that collectively make up the body of a fungus.

hypothesis: a statement in science that is capable of being tested to see whether it is false.

hypotonic: see hypertonic for a detailed description, a solution that has a lower concentration of solutes than a hypertonic one.

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imbibition: in plants the mechanism for hydration of water uptake in seeds and other dry tissues, in which the water moves into microscopic spaces due to molecular attraction. The forces generated are sometimes large e.g. sufficient to crack open seed coats.

imperfect flower: a flower that lacks either  stamens and/or carpels (see perfect flower, complete flower or incomplete flower)

incomplete flower: a flower that lacks one or more of the four floral parts e.g. sepals, petals, stamens, carpels. Imperfect flowers are always incomplete flowers, but not all incomplete flowers are imperfect.

indeterminate growth: growth such as that of a plant which is potentially genetically unrestricted or  unlimited.

ingestive heterotroph: an animal or protist that obtains it nutrients by ingesting organic material prior to digesting it (see absorptive heterotroph)

insectivorous plant: a plant which is capable of trapping insects, some actively digest them to release inorganic nutrients, e.g. Sundew or Pitcher plant. 

inter-membrane space: the space between the inner an outer membranes of  a mitochondrion

isomorphic: identical in morphology (external appearance) see alternation of generation when morphologically similar gametophyte and sporophyte generations of the same organism are said to be isomorphic e.g. Ulva

isotonic: see hypertonic or hypotonic, when two solutions separated by a membrane permeable to the solvent but not the solutes are of equal concentration this results in no net movement of solvent across the membrane. 

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lateral bud: a bud formed between  the leaf and  a stem i.e. in the leaf axil, which may develop into a lateral branch.

lateral root: a branch root, formed in the pericycle of  a root this grows out laterally through the cortex of the root

lEAF: one of the major plant organs (see roots, stems and flowers) primarily concerned with photosynthesis and water loss through transpirations. 

lEAF PRIMORDIA: on outgrowth below the sub-apical meristems of shoots which develops into a leaf inside the terminal bud.

life cycle: the sequence of events occurring  between the formation of one organism and its production of similar offspring e.g. in protists such as Ulva the sequence of events between one stage e.g. the sporophyte and the formation of another sporophyte, these would include, spore formation by meiosis, the germination of spores to form a gametophyte generation, the formation of gametes by mitosis and the subsequent fusion of gametes to produce a zygote which would grow back into a sporophyte.

light break: in plants which show photoperiodism, the exposure to a short light period in the middle of the long dark period leads to a reversal of the photoperiodic effect. Long day plants exposed to long night  will not flower, but a short light break in the night will cause them to flower. Short day plants with grown under long night condition flower, while those given a light break in the night will not.

light reactions: part of the process of photosynthesis, occurring on the thylakoid membranes, whereby light energy is converted into chemical energy in  the form of ATP and NADPH  (see Calvin cycle).

lignin: a polyphenolic substance found in woody tissues of plants, it provides strengthening, but is still permeable to water.

lipid: a class of chemical compounds found in living organisms that includes fats, oils, phospholipids and sterols that are insoluble in water. Lipids do not include polymers (C6p68d), although some large molecules may contain several similar units (e.g. fat molecules).

liposome: an artificially produced body made up of phospholipid membranes which can be formed in water solution. their permeability to some substances, their ability to produce an internal chemical environment different from the external environment, and their ability to bud off other liposomes as they enlarge,  has lead to the suggestion that they may have been implicated in the evolution of primitive cells (see coacervate).

long-day plant: a plant which requires above a certain number of hours of daylength in order to flower, e.g. a plant which required more than 11hrs to flower would be called a long-day plant, conversely a plant that required less than a set number of hours e.g. 12hr would be a short day plant ( see photoperiodism).

lysis and Lyse: destruction of cells by the rupture of the cell membrane.

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macronutrient: relating to inorganic nutrition of plants, these are elements required in relatively large amount e.g. carbon, nitrogen, phosphorus, calcium , they are important in the chemicals which make up the structure of the plant. 

matrix: in cell biology it refers to the fluid part of a mitochondrion inside the inner membrane.

megasporangium: a cell in plants which divides to form the megaspores.

megaspore: in plants these are spores formed by meiosis which will develop into the female gametophyte.

meiosis: some time called reduction division because the offspring cells have half the number of chromosomes as the parent. Normal diploid cells have two sets of homologous chromosomes, meiosis is a form of division which ensures each offspring cell has one of the two sets of chromosomes.  

membrane proteins: proteins embedded, or on the surface of cell membranes, they may be structural, involved in cross membrane transport, cell recognition  or be enzymes.

meristem: a tissue made up of meristematic cells whose function is to divide to produce new cells. 

meristEmatic: cells whose function is to divide to produce new cells.

messenger RNA (mRNA): produced by transcription of a DNA strand this provides the template for the synthesis of proteins on the ribosomes.

metabolism: the total of all the chemical reactions which occur in a cell or organism.

methanogen: a member of the Archaea which grows anaerobically and produces methane.

microfilament: part of the cytoskeleton of a eukaryotic cell.

micronutrient: relating to the inorganic nutrition of plants, these are inorganic elements required in small amounts, they are usually associated with metabolic processes often associated with particular enzymes, e.g. the enzyme nitrogenase contains molybdenum.

microsphere: aggregations of abiotically produced peptides which are capable of growth by absorption of other peptides. Thought to be one of the  possible precursors of cellular life on earth.

microsporangium: part of a plant in which the microspores are formed.

microspore: in plant reproduction the microspore divides by meiosis to produce the male gametophytes..

microtubules: proteinaceous part of the cytoskeleton of eukaryotic cells.

middle lamella:  the outer layer of  plant cell walls , made up of calcium pectate, it serves to "stick" one cell to another.

mitochondria: a organelle found in eukaryotic cells which is bounded by a double membrane, it is the site of aerobic respiration. Mitochondria initially arose by the capture and development of endosymbiosis of a free living aerobic bacterium.

mitosis: a form of eukaryotic cell division in which the offspring cells are genetically identical to the parent cell.

mixotrophic: applied to protists such as Euglena which are capable of both autotrophic and heterotrophic growth.

molecular biology: basically the study of genes and there associated proteins, structure, expression and regulation. The science of molecular biology id often stated to have started with the discovery of the structure of DNA by Crick and Watson in 1952.

Monera: one of the five kingdoms, comprising those with prokaryotic cells. 

monocotyledon: see dicotyledon, one of the two groups of flowering plants, there seeds only contain a single cotyledon or seed leaf, monocotyledons also have other diagnostic characteristics, e.g. leaves with parallel veins, floral parts arranged in groups of three or multiples of three, monocotyledons do not show  secondary growth and most are non woody.

monoecious:: literally meaning one house, applies to plants which have either male or female flowers, i.e. are male or female (see dioecious)

monomer: one of the constituent parts (building blocks) of macromolecules e.g. amino acids are the monomers of proteins, monosaccharides are the monomers of carbohydrates.

MONOsaccharide: a single sugar, e.g. glucose, fructose. Chemical names for sugars (or categories of sugars) usually end in -ose. [sugars: structural, storage, and importance to osmosis]

morphological diversity: diversity of a group of organisms as shown by there external appearance rather than based on any evolutionary of genetic basis. e.g. protists may show great morphological diversity while many monerans show little morpholigical diversity. 

mRNA codon: the triplet code carried on the mRNA which codes for a specific amino acid i.e. the complementary code of the DNA, e.g. UUU codes for the amino acid phenylalanine.

multicellularity: an organism made up of more than one cells, in which the cells are closely associated into a tissue rather than being a lose association of unicells which might make up a colonial protist.

mutagen: a chemical or physical agent which interacts with DNA and produces mutations e.g. ultraviolet light.

mutation: a change in the sequence of nucleotides in the DNA of a gene.

mutualism: a form of symbiosis from which both partners derive benefit.

mycorrhizae: symbiotic fungal hyphae associated with the roots of plants, they often are mutualistic with the fungus deriving organic material from the plant and providing the plant with inorganic nutrients.  

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NADP: nicotinamide adenine dinucleotide phosphate an important substance involved in electron transport in plants, as a substrate in the light reactions of photosynthesis, it is reduced to NADPH.

NADPH: reduced NADP it is produced in the light reactions of photosynthesis as well as ATP, it serves as a source of electron for reduction reactions in the Calvin cycle.

natural selection: the principle mechanism of evolution. Given the diversity of organisms making up a population some will be better fitted to their environment and are more likely to reproduce and pass on their genes than those less fitted to the environment. 

nitrifying bacteria: part of the nitrogen cycle, nitrifying bacteria convert ammonium compounds to nitrite and then to nitrates.

nitrogen fixation: the process by which an organism converts atmospheric nitrogen N2 to ammonium compounds using the enzyme nitrogenase. Only prokaryotic organisms are capable of  nitrogen fixation which also must take place under anaerobic conditions.

nitrogenase: an enzyme found in some bacteria which is capable of catalyzing the conversion of gaseous nitrogen found in the atmosphere to ammonium compounds. It is found in some cyanobacteria as well as Rhizobia inhabiting nodules of leguminous plants. Nitrogenase contains iron and molybdenum and only functions in an anaerobic environment.

nitrogenous base: adenine, thymine, cytosine, guanine  are the four  nitrogenous bases found in DNA with a fifth, uracil substituting for thymine in RNA they are linked to sugars, ribose in RNA, deoxyribose in DNA to form nucleotides.

nucleic acid: polynucleotides, two naturally occurring forms DNA and RNA. 

nucleoid: an aggregation of DNA in prokaryotes, mitochondria and chloroplasts of eukaryotes, lacks a nuclear membrane and histone proteins.

nucleotide: nitrogenous bases in nucleic acids linked with sugars, ribose in RNA, deoxyribose in DNA.

nucleus: a major organelle typical of eukaryotic cells, it is surrounded by a membrane which is part of the cells endomembrane system and contains the chromosomes.

nutrient cycle: an ecological process by which chemicals involved in nutrition are cycled between the environment and living organisms, e.g. carbon cycle whereby carbon dioxide is converted into organic substances in the Calvin cycle and then these are subsequently converted back to carbon dioxide in respiration.

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obligate anaerobe: an organism which requires an oxygen free environment.

optimum: the "best" conditions for something, e.g. enzymes have optimum conditions of temperature and pH at which they function at maximum efficiency.

organ: a functional and anatomical unit of most multicellular organisms, consisting of a number of tissue types combined to perform one or more recognized functions e.g. a plant leaf functions in photosynthesis and transpiration.

organelle: structural and functional part of a cell, often, but not always, membrane bound e.g. a mitochrondion or chloroplast (membrane-bounded) or a ribosome (not membrane-bounded).

osmoregulation: the ability of a cell or an organism to regulate its internal concentration of  water or salts in order to maintain it self in a an specific environment  e.g. the contractile vacuole of Euglena actively expels water from the cell which enters as a result of the cell being hypertonic in comparison with the fresh water environment.

osmosis: the phenomenon whereby water flows across a selectively permeable membrane from an hypertonic environment to a hypotonic environment.

ovary: (in plants) part of the flower at the base of the pistil in which ovules are found. The ovules become the seeds and the ovary at maturity becomes the fruit of the plant.

oxidizing atmosphere: an atmosphere containing oxygen. The original atmosphere of the earth under which life evolved was anaerobic (oxygen free), the oxygen in the atmosphere was formed as a result of photosynthesis of aerobic bacteria (cyanobacteria)

ozone and the ozone layer: oxygen gas in the atmosphere is found in the form of the diatomic molecule O2, under the influence of radiation in the upper atmosphere oxygen is converted into the triatomic form O3 or ozone.  This layer in the upper atmosphere is called the ozone layer.

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palisade  mesophyll: palisade mesophyll is a form of parenchyma tissue rich in chloroplasts and found predominantly in dicotyledon leaves towards the upper surfaces. The cells are arranged in rows rather like the boards on a fence or palisade, hence the name. The cells are  primarily involved in the absorption of light.

paramylum: a polysaccharide made of glucose monomers, it a food storage product of Euglena. It differs from starch in being a smaller molecule and in the way in which the glucose units are joined. Paramylum is structurally more similar to the food storage products of brown seaweeds.

parasitism: a form of symbiosis in which one partner benefits to the detriment of the other.

parasitic plant: a plant such as Indian pipe (Monotropa uniflora) which lacks chlorophyll, and lives a heterotrophic existence deriving its materials from organic material obtained from its associated fungal mycorrhizae. 

parenchyma cell: the basic living cell which makes up much of the ground tissue of plants. It functions as a source of bulk, for food storage and for support of the plant through its turgor pressure. It also gives rise to cells like sieve tube members.

passive transport: a form of transport which requires no energy from the organism, i.e. diffusion of a substance from an area of high concentration to one of a lower one.

pectin: the substance which makes up the mid lamella of a plant cell walls, it serves to stick the cell walls to each other. Pectin is Calcium pectate which is soluble in hot water but forms a gel in cold water. It is the gelling agent in jams.

pellicle: a layer of proteinaceous plates below the cell membrane in Euglena, it gives some strengthening to the cells while retaining flexibility and allowing cellular movement.

peptidoglycan: an amino-acid -glucose polymer, which is found in the cell walls of  bacteria. The antibiotic, penicillin , inhibits peptidoglycan formations. 

perennial: a plant which persists in the vegetative stage over several years and usually flowers and produces seed each year, see annual and biennial.

perfect flower: a flower which has both male (stamens) and female (pistils) parts.

pericycle: in a plant root with primary growth, this is the layer of undifferentiated cells in the stele which gives rise to the cork and vascular cambia as well as being the point of origin of the lateral roots.

petal: one of the parts forming part of a flower, often brightly coloured to attract insects to aid in pollination.

phloem: along with xylem one of the two vascular tissues, a complex tissue with a number of cell types, in flowering plants the unique cells are the sieve tube elements and the companions cells, phloem tissue is involved in the movement of organic materials in the plant, it may also be modified for food storage e.g. phloem parenchyma in some roots such as parsnips.

phospholipid: phosphate groups attached to lipid groups, has the features that one part of the molecule is hydrophilic (attracted to water) while the other is hydrophobic ( repelled by water) these  properties make it an important component of cell membranes.

phospholipid bilayer: when phospholipids are placed in a water environment they spontaneously form bilayers, with the hydrophilic phosphate groups external and the lipids internally arranged. 

photoautotroph: an organism which obtains its carbon from carbon dioxide and its energy from light e.g. a plant, photosynthetic protist or moneran.

photodetector: a receptor in protists such as Euglena, usually associated with the base of a flagellum,  in combination with the eyespot, which serves as a lens and/or filter allows the organism to detect the intensity and the direction of light source and respond appropriately.

photoheterotroph: an organism which obtains it energy from light but its carbon from preformed organic carbon compounds.

photoperiodism: in plants is the ability of a plant to detect and respond to varying daily periods of light and dark, which are used a cue for the plant to perform a specific function such as flowing or seed germination. etc.

photosynthesis: the process in which an organism converts physical energy of light  into chemical energy. In photoautotrophs there are two processes one requires light and produces ATP and NADP, the other is light independent (Calvin cycle)

phototaxis: occurs when an organism such as Euglena responds by moving either towards of away from a light source.

phylogenetic tree: a diagram representing the phylogeny of a group of organisms, showing their evolutionary relationships

phylogeny: an evolutionary history of a group of  related organisms, ancestor- descendent relationships.

phytochrome: a blue-green protein which serves as the detector of daylength in plants which show photoperiodism

pili: protein filaments protruding from the walls of some bacteria they may have a role in cell recognition or in the transfer of  DNA in bacterial conjugation.

pith: the central part of plant stems, made of parenchyma cells.

pits: holes in a plant cell wall which connect the lumen of  one dead cell to another dead cell.

plant: one of the supposed five kingdoms (Plantae) multicellular autotrophs in which the zygotes develop within the parent plant.

plasmid: found in prokaryotic organisms, a small circular strand of DNA separate from the main genome, plasmid are frequently moved from on cell to another in conjugation, allowing the movement of genetic information from one cell to another.

plasmodesmata: holes in the primary cell walls of plant cells allowing cytoplasmic continuity between the cells, important part of the symplastic route in plants.

plasmolysed: when  a living cell with a cell wall is placed in a hypertonic solution it loses water by osmosis, if sufficient water is lost the cell membrane is pulled away from the cell wall and the cell is said to be plasmolysed.

plasmolysis: the act of becoming plasmolysed, see above.

PLOIDY: the number of complete sets of chromosomes, e.g. a diploid organism has (2n) = one paternal set (n) and one maternal set (n). Diploid is literally "two-ploid", gametes of all organisms are called haploid ("half-ploid") but in 2n organisms haploid=n.

point mutation: where one nucleotide in a nucleic acid is substituted for another, because of the redundancy in the code this may frequently cause no changes in the resulting protein or minor changes due to the substitution of  a single amino acid. 

pollen grain: male gametophyte of a seed plant

pollination: the act of moving pollen from the anther of a flower to the stigma of the pistil (note this is not the same as fertilization, which is the fusion of two gametes)

polyhedral capsid: the elaborate multifaceted capsid of some viruses e.g. T4 bacteriophage.

polymer:  the product of  the chemical linking of many monomers e.g. starch is a polymer of glucose.

polypeptide: a polymer of amino acids, also usually assumed to be the product of  the code of a single gene. a functional protein, may be made of  single polypeptide or of more than one.

polysaccharide: a polymer of monosaccharides, e.g. cellulose, chitin [sugars: structural, storage, and importance to osmosis]

primary cell wall: the first cell wall of a protist, plant of fungus, usually the cell is alive at maturity, the cell wall and the is important in resisting turgor pressure and thus giving strength and shape to the cell. Primary cell wall are flexible and allow the cell to grow and differentiate.

primary growth: in plants is essentially growth produced by division and differentiation of cells produced in the apical meristems, it gives length to the plant but does not usually result in an increase in girth.

primary meristem: a group of meristomatic cells, usually situated at the apices of stems and roots which give rise to primary growth.

primary structure of root: the structure of a mature root, which is the result of cells produced from the primary meristems, in dicotyledons.

primitive character: a character present in an early ancestral organism, which has remained relatively unchanged in its descendents.

procambium: one of the three sub-apical meristems in plants, which gives rise to the vascular tissue and to the secondary cambia( see protoderm & ground meristem)

prokaryote: a member of the kingdom Monera, made of prokaryotic cell, cells which lack the features of  eukaryotic cell no nucleus, single circular chromosome, no cytoskeleton, no membrane bounded organelles such as mitochondria or chloroplasts.

protein: made of one of more polypeptides, has a specific three dimensional structure which determines it function in the cell, proteins are usually structural or catalytic (enzymes), while other are important in cell signaling and recognition.

Protista: one of the supposed, five kingdoms, originally all unicellular eukaryotic organisms were placed in the protista, then it became a "dumping ground" for others that could not be placed clearly placed in the Fungi, Plants or Animals. It is a highly artificial group.

protobiont:  an aggregate of abiotically produced molecules, which may have developed into simple cells.

protoderm: one of the three sub-apical meristems in plants, gives rise to the outer layers of the plant body e.g. epidermis..

provirus: a sequence of  viral DNA inserted into the host cell DNA which when expressed will give rise new viruses e.g. the HIV virus has a RNA genome, this is reverse transcribed to a single strand of DNA by reverse transcriptase, the single strand of DNA serves as a template to produce a double strand which is then inserted into the host cell DNA, this viral fragment is called a provirus.

pyrenoid: a body found in some primitive plant and protist cell, always associated with the chloroplasts and frequently with starch synthesis in the main it is composed of the enzyme RUBISCO.

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radicle: the embryonic root found in a plant seed.

ray: in plants, there are several rays, in primary stems it refers to the parenchyma between the vascular bundles, rays also occur in secondary xylem and phloem initially they are made of living parenchyma cells and are important in lateral transport of materials.

recombination: an process other than  mutation by which an organism produces gene combinations different from the ones that it inherited. This a major source of variation and is most commonly brought about in eukaryotic organisms by sexual reproduction.

reducing atmosphere: the early earths atmosphere lacked oxygen and was known as a reducing atmosphere in contrast to the modern oxygen rich, oxidizing atmosphere, current theories concerning the evolution of life on earth require a reducing atmosphere. 

redundancy (in triplet code): there are 64 ways of arranging four nucleotides in sequence of three but proteins are made up of only twenty amino acids. This means that some amino acids have more than one triplet code, this is called redundancy. Another name for this redundancy is to say the code is degenerate.

replication: applied to DNA means that the double helix unwinds and each strand serves as a template to produce a new complementary strand, the new strands then coil up in a new DNA molecule, this is  replication.

reproduction: one of the characteristics of life where an organism is capable of producing new copies of itself. 

reservoir (a.k.a. gullet, ampula): a sac like structure at the front of a Euglena cell, in which the flagella bases are found, there is not pellicle lining the reservoir and this allow discharge of the contractile vacuole.  

responsiveness: one the characteristics that define living organisms, sometimes called irritability, i.e. showing a response to a stimulus.

reverse transcriptase: an enzyme found in retroviruses such as HIV which catalyze the production of a DNA strand from a RNA strand i.e. reverse transcription.

Rhizobium: the generic name of a bacterium that is found symbiotically associated with legume roots where it produces nodules in which nitrogen can be fixed ( conversion of gaseous dinitrogen (N2) to ammonium compound and amino acids.

ribosome: a body, within a cell or organelle, that attaches to an mRNA molecule and also attaches sequentially to a series of tRNAs matched by their anticodons to the mRNA codons, and assembles into a polypeptide the amino acids carried by the tRNAs. (In short, ribosomes make the polypeptides specified by mRNA code.) Ribosomes of prokaryotic cells, chloroplasts and mitochondria are smaller than those of eukaryotic cells. Ribosomes are sometimes called organelles, but they are not membrane-bounded.

root: one of the major plant organs, (leaf, stem flower etc) primarily concerned with absorption of water, inorganic materials an anchorage, roots can have other secondary modification e.g. food storage.

root cap: a group of parenchyma cells formed on the apical side of the apical meristem in a root, they serve to protect the apical meristem and to lubricate the passage of the growing root in the soil, as cells of the outer surface are lost they are replaced from beneath by new cells formed be the apical meristem. In some plants the root cap cells are important in detecting the stimulus of gravity.

root hair: an out growth of the epidermis of a primary root, found near the tip in the zone of differentiation, important in increasing the surface areas of the roots to allow for more efficient uptake of water and minerals.  

root nodule: (see Rhizobium) an outgrowth of roots of  leguminous plants in which are found symbiotic Rhizobia bacteria which are capable of fixing nitrogen. Nitrogen fixation only occurs under anaerobic conditions and root nodules may appear pink in colour due to the presence of  leghaemoglobin, which remove oxygen.

root pressure: pressure generated by osmotic flow of water from the cortex of a roots into the stele, water is then forced up the xylem. Root pressure is unimportant in actively transpiring plants as it cannot account for a great deal of water flow, it is probably more important in seedlings and in plants growing in still air in 100% humidity. Under such conditions guttation may occur, in which liquid water is forced out on the the leaf surfaces by water pressure. The "dew" sometimes seen on plants is due to guttation rather than condensation of external water vapour.

rough ER: part the endoplasmic reticulum with abundant attached ribosomes. 

RUBISCO: ribulose carboxylase, the enzyme involved in the first step of the Calvin cycle, wherein CO2 is attached to RuBP, ribulose biphosphate.

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sap: the "liquid" part of plant, e.g. cell sap is primarily the contents of the vacuole, sap my also refer to the liquid moved  in the xylem and the phloem. e.g. aphids are used to sample the phloem sap.

sclereids: like fibres, heavily lignified  cells making up  sclerenchyma tissue, unlike fibres they are usually non elongated, but may have very elaborate shapes, there functioning is in strengthening parenchyma tissue e.g. stone cells in the flesh of the fruit of pears.

sclerenchyma: type of stengthening tissues made up of cells with thick lignified cell walls, there are two main cells types fibres which are elongated and stone cells which are more spherical.

secondary cell wall: the outer layer of a plant cell wall, made up of closely woven cellulose fibres, which may also be impregnated with lignin. Cells with secondary cell wall are show no further growth in size and are usually dead at maturity.

secondary meristem: in plants, the cork cambium and the vascular cambium are secondary meristems derived from the protoderm, which add to the girth of the plant in secondary growth.

seed: produced by seed plants, an agent of dispersal and perennation, consists of a dormant embryo (sporophyte) associated food material e.g. endosperm, all enclosed by a seed coat or testa.

selectively permeable: applies to membranes which allow one substance to pass, but impede another.

semi-conservative: in DNA replication it means that in each replication one strand of the parent DNA and one newly synthesized strand is found in the two new DNA molecules formed. Shown to be correct by the Meselson and Stahl experiment.

sepal: outer floral layer of  flower, sepals are often  leaf like and serve to protect the petals and other floral parts as the outer layers of the bud.

short-day plant: a plant which requires stimulus of a daylength shorter than some value in order flower e.g. Poinsetta.

sieve plates: the end walls of sieve tube members, they have a number of perforation which connect one tube member to another allowing continuous cytoplasmic connection.

sieve tubes: part of the phloem, made of sieve tube members connected end to end specialized for the transport of organic solutes in plants.

sieve tube member: a cell which makes up the sieve tubes of the phloem tissue, an elongate cell which at maturity is still alive, but lacks a nucleus and mitochondria, it has a sibling companion cell to which it is connected by many plasmodesmata. Sieve tube members are specialized for the transport of organic solutes in plants and have perforations in their end walls which are linked to other sieve tube members to form the sieve tubes.

single celled: when an organism is made of a single cell e.g. many protists such as Euglena.

smooth ER: the endoplasmic reticulum part of the endomembrane system, distinguished from rough ER by the absence of ribosomes, involved internal transport in the cell and chemical modification of proteins.

solute: something that is dissolved in a solvent to form a solution

solution: formed when a solute is dissolved in a solvent e.g. sugar (solute)+ water (solvent)=syrup (solution)

solvent: the liquid in which a solute is dissolved to form a solution.

source and sink: a concept in phloem transport whereby sugars flow from a source of high concentration to a sink of lower concentration. 

species: members of the same species show similar characteristics and have the ability to interbreed.

sperm: a male gamete, a sperm fuses with an egg to form a zygote.

spirilla: a morphological form of a bacterium (see rods and cocci) in which the cells have a spiral shape.

spongy mesophyll: specialized parenchyma cells found in leaves, they are rich in chloroplasts and have many intercellular spaces giving a spongy appearance. In many dicotyledon leaves they are located toward the lower surface of the leaf. They  are important in uptake of carbon dioxide and also in water loss in transpiration.

spontaneous mutation: a mutation which occurs in the structure of  a DNA molecule without any obvious cause, such as chemical or physical stress.

sporangia: a cell or a group of cells of a protist or plant in which spores are formed.

spore: a haploid (1n) reproductive cell produced by plants and protists (and some monerans) which develops directly into a new individual. In organisms showing alternation of generations spores may be produced by meiosis from the sporophyte generation and develop into the gametophyte generation. A zoospore is a spore that is motile. In algae and plants, the spore gives rise to a gametophyte in/on which gametes are produced by mitosis.

sporophyte:  the diploid (2n) generation (of protists, macroalgae, and plants) that produces haploid spores (n) (in sporangia in which diploid spore-mother-cells undergo meiosis).

sporepollenin: a protein found in cells walls of  some spores and pollen grains which is very resistant to decay.

stamen: the male part of the flower, consisting of the filament and the anther at the tip in which the pollen is produced.

starch: a polymer of glucose, used as a food storage in the majority of plants and many autotrophic protists and moneran's.

stele: in a plant root it refers to the tissues internal to the endodermis.

stem: a plant organ, which connects the roots to the leaves and flowers, its primary function is support and transport, actually the most primitive of the plant organs, from which the others are derived. 

stigma:  the tip of the pistil, which receives the pollen

stoma: in plants, literally a hole, the opening in the stomatal apparatus surrounded by the guard cells.

stomata: in plants, more accurately should be called the stomatal apparatus, consisting of  at least two guard cells and in many plants the adjacent epidermal cells, involved in the opening and closing of the stoma.

stroma: the fluid constituent of  a chloroplast which surrounds the grana, the site of the Calvin cycle.

stromatolite: aggregations of minerals such as calcite laid down as a result of the metabolic processes of some cyanobacteria, very common in the ancient fossil record though there still are living stromatolites.

style: the "stalk" part of the pistil which connects the ovary to the stigma.

sub-apical meristem: primary meristems found below the apical meristem  in shoots and roots, usually divided into three type, the protoderm which gives rise to the epidermal tissue, the procambium which gives rise to the vascular tissue, and the ground meristem which gives rise to the parenchyma bulk of the plant tissue.

suberin: a waxy water proofing substance found in some plant cell walls,  e.g. the Casparian strip of the endodermis, the cork cells of the bark of a woody plant.

substrate: in enzyme catalyzed reactions it is the substance on which the enzyme acts.

sucrose: a disaccharide sugar, made of  one molecule of  glucose and one of fructose, the most abundant sugar in phloem translocation.

suGar: generally, a molecule with a molecular formula that is some multiple of CH2O. In earlier days they were sometimes thought of as "hydrated carbon" which was not really the case but it may help to remember. (see also: monosaccharide, polysaccharide, starch, chitin, cellulose; these words have relevance to: osmosis)
    Sugars are very important. [sugars: structural, storage, and importance to osmosis] Monosaccharides or simple sugars (e.g. glucose) are key proximate energy sources used to generate ATP in most cells. Polysaccharides are important as energy and structure. Key structural polysaccharides: cellulose (most plants), chitin (many arthropods). A wooden chair is mostly cellulose, i.e. mostly big structural molecules made of sugar (but the chair won't dissolve in water, and stirring your tea with a wooden stick doesn't make it sweet). Cellulose is not easily broken down into monosaccharides, and that's why cow dung burns nicely when dry (it still has lots of cellulose). Key energy storage polysaccharides: starches (in plants) and glycogen (in animals) can be readily converted into monosaccharides. Starches are nearly insoluble in water, which is why they are suitable as storage: they have little effect on osmolarity. Therefore, the assembly and disassembly of given quantity of simple sugars into polysaccharides and vice versa directly affects osmolarity and therefore is a way of controlling osmosis (water flux). For example, a ripening fruit swells because sucrose is transported into the fruit and once in the fruit it is split into monomers, thus increasing osmolarity and creating the conditions under which water will move by osmosis into the fruit, causing it to swell. Similarly, translocation in the phloem operates by managing osmosis in a similar way: sugars produced by photosynthesis cause uptake of water in the leaf symplast (living tissues), from the apoplast (xylem and inercellular spaces); this generates pressure that causes flow through the interconnected phloem cells, and near the roots simple sugars can be transported into 'sink' cells and assembled into insoluble storage polysaccharides, which reduces osmolarity allowing water to move out of the symplast into the apoplast and be carried back up to the leaves.

symbiosis: the act of living together for a greater part of  there life cycle of two different species. If both benefit the symbiosis is called mutualism, if one benefits to the detriment of the other it is parasitism.

symplast: the living part of a plant, everything inside the cell membranes, the plasmodesmata linking on living cell to another ensures continuity of the symplast throughout the plant.

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T4 bacteriophage: a virus which infects E. coli bacteria, it has a complex capsid. The "T-even" phages (T2, T4, & T6) coincidentally have very similar structure.

taxon: a named taxonomic unit of any level e.g.  Canis  is a taxon,  Carnivora is a taxon, Mammalia is a taxon.

template: a mold from which a complementary structure may be formed, in biology it usually refer to one strand of a DNA molecule, which can be used to produce a complementary DNA strand or by transcription form a RNA strand.

thermophile: literally "heat loving" usually applied to organisms which grow at temperature significantly above normal for life e.g. some members of the Archaea are found in boiling water springs.

three domain system: a classification system based on cell and molecular biology which divides living organisms in to three groups, Archaea, Bacteria (prokaryotic cells) and the Eukarya (eukaryotic cells)

thylakoids: the membrane systems of  chloroplasts on which the pigments are found, involved in the light reactions of photosynthesis in green protists and in plants the thylakoids may be stacked to form grana.

thymine: one the nitrogenous bases found in DNA, but replaced by uracil in RNA.

tissue: a collection of cells with a common function. Tissues may be simple i.e. made of a single cell type e.g. parenchyma tissue or complex made of several cell types e.g. phloem, with sieve tube members, companion cell, fibres and parenchyma. 

tonoplast: a single membrane, similar in structure to the cell membrane, which surrounds the vacuole in a plant cell, another name is the vacuole membrane. 

tracheids: one of  the characteristic cell types of the xylem tissue, involved in water transport and strengthening,  compared to vessels tracheids have a narrow lumen and have end walls, usually the walls contain numerous pits.

transcription: the production of mRNA using a DNA template.

transduction: the process in which a bacteriophage picks up a piece of DNA from one bacterial cell and transfers it to another bacterial cell where it is incorporated in the bacterial genome.

transfer cells: specialized parenchyma cells associated with vascular bundle of leaves they function in the loading of phloem sieve tube members with sugars produced in photosynthesis.

transfer RNA: (tRNA) specialized small RNA molecules  which bring specific amino acids to the ribosomes for assembly  into peptides. There is a specific tRNA for each amino-acid, these are characterized by a specific triplet anticodon, which matches the triplet code on the mRNA. 

transformation: in Monera, the uptake and incorporation of DNA from the environment leading to the insertion of new genes in the organism and thus the acquiring of new characteristics.

translation: the process by which the triplet codes of the mRNA are translated by the ribosomes into a sequence of amino acids. 

translocation: the movement of organic materials in plants, usually specifically refers to the movement of solutes in the phloem sieve tubes.

transpiration: water loss from the surface of a plant, most occurs through the stomata. This loss of water through transpiration creates the pull which moves water into the roots and up thought the xylem of the plant.

transposon: a small fragment of DNA encoding for a few genes which is capable of moving from one site on the genome to another, or possibly to another genome.

turgid: means firm, the opposite of flaccid, cells with wall become firm as a result of the uptake of water by osmosis,

turgor: (pressure) the force exerted on a cell wall by a cell membrane as a result of osmotic uptake of water. 

two kingdom system: an old classification system for organism in which they were classified either as plants or animals.

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uracil: one of the four nitrogenous bases found in RNA, in DNA it is replaced by thymine.  

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vaccine: a harmless variant or non-virulent part of a pathogen that when it is introduced into a host stimulates the host immune system to mount defenses against the pathogen.  

vascular cambium: a secondary meristem which adds xylem tissue to its inner surface and phloem tissue to its outer surface.

vascular tissue: the xylem and phloem tissues of plants, which function in transport of water and materials.

vernalization: in plants, the process by which a cold treatment will initiate the flowing process, or seed germination.

vesicles: in cells a term given to an infolding, pouch like structure,  of the endoplasmic reticulum e.g. golgi bodies..

vessel elements: a cell type found, with a single exception, only in flowering plants, they are part of the xylem tissue, at maturity they are elongated, lignified, dead cells, which lack end walls, or whose end walls have large perforations. Vessel elements are joined end to end to provide an open pipe like structure the vessels.

virulent: usually applied to disease causing organisms, e.g. a virulent bacterial has the associated toxins to cause disease whereas a non virulent strain will not cause disease. 

viral envelope: the membrane which surrounds the capsid in some viruses, it is derived from the host cell membrane. 

virus: an infective agent which has no inherent metabolism and can only reproduced when introduced into a host cell, the simplest viruses consist of a protein capsid surrounding a nucleic acid genome.

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white light: a combination of the wavelengths of the electromagnetic spectrum visible to the human eye, in plants it usually refers to the photosynthetically active range of  of the electromagnetic spectrum i.e. between 400 and 700nm.

wood: a laypersons  term for secondary xylem and associated lignified tissues.

woody plant: a plant showing secondary growth characterized by the formation of wood.

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xylem: one of the two vascular tissues, primary xylem is formed from the procambium, secondary xylem from the vascular cambium, xylem is a complex tissue made of, in flowering plants, vessels and tracheids together with associated fibres and parenchyma cells. 

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zone of differentiation (or maturation)

zone of elongation: the area behind the subapical meristems and in front of the zone of differentiation in stems and roots. It is the regions where the cells are elongating.

ZOOSPORE: a spore that is motile, having flagella. The prefix "zoo-" (zoe-oh-) comes from the Greek and means animal-like, referring to motility.

zygote: the immediate result of the fusion of two gametes.