agarose: polysaccharide derived from the walls of red algae used to make a polymer matrix often for use in gel electrophoresis of nucleic acids

annealing:  in this context annealing refers to the formation of hydrogen bonds between complementary strands of DNA; this zips or seals the to strands together

aseptic technique: laboratory techniques used to avoid contamination of material that one is working with as well as protecting oneself from any potential pathogens; for more details visit these sites: http://www.nuffieldfoundation.org/practical-biology/aseptic-techniques, http://youtu.be/bRadiLXkqoU

biosafety cabinet”></a>biosafety cabinet (BSC):  The primary purpose of a BSC is to serve as a means to protect the laboratory worker and the surrounding environment from pathogens. All exhaust air is HEPA-filtered as it exits the biosafety cabinet, removing harmful bacteria and viruses. It also protects the materials being handled inside the cabinet from potential contaminants in the room. This is in contrast to a laminar flow clean bench, which blows unfiltered exhaust air towards the user and is not safe for work with pathogenic agents.

buffer: a solution whose pH changes little with the addition of a small amount of acid or base; composed of a weak acid and its conjugate base

caulonema: filaments of a moss with few chloroplasts and which give rise to buds that develop into gametophores

cDNA: “complementary DNA”; DNA which is synthesized from a preparation of mRNA in a reaction catalysed by the enzymes reverse transcriptase and DNA polymerase; this is a common technique use in cloning genes

cell wall: the outermost part of a cell in plants, algae, bacteria, and fungi; plant cell walls are primarily  composed of cellulose as well as additional molecules such as pectin, lignin, and hemicellulose, depending of the type of cell; the function of plant cell walls vary depeding on the type of cell. Here are some examples: maintaining cell shape; support and mechanical strength; prevent cell membrane from bursting in response to internal water pressure; control rate and direction of cell expansion; architecture of the whole plant; physical barrier to pathogens

cellulose: a polymer of glucose molecules linked by ß(1-4) linkages

cellulose synthesis complex: the complex of enzymes embedded in the plant cell membrane that builds cellulose microfibrils, formerly referred to as terminal complexes

centrifuge: a piece of equipment, generally driven by an electric motor (or, in some older models, by hand), that puts an object in rotation around a fixed axis, applying a force perpendicular to the axis. The force generated will separate  components of a heterogeneous mixture due to density differences

chloronema: filaments of a moss which contain many chloroplasts and therefore specialize in photosynthesis

complementary base pairs: In a DNA double helix, each type of nucleotide on one strand bonds with just one type of nucleotide on the other strand. This is called complementary base pairing. The nucleotides adenine and guanine are purines and have a double ring structure, and cytosine and thymine are pyrimidines, which have a single ring structure. Each pair across the DNA double helix consists of one purine and one pyrimidine, (A to T and G to C) and this results in a consistent diameter of the double helix. This arrangement of two nucleotides binding together across the double helix is called a base pair. As hydrogen bonds are not covalent, they can be broken and rejoined relatively easily. The two strands of DNA in a double helix can therefore be pulled apart like a zipper, either by a mechanical force exerted by an enzyme or by high temperature as used in PCR’s denaturation phase.

culture medium: a liquid or gelatinous material containing the nutrients, growth factors, hormones, etc. in or on which microorganisms, cells, or tissues are grown in a laboratory

denature: In this context, denaturing refers to the process of heating DNA  to a temperature that causes it to go from double stranded to single stranded by breaking the hydrogen bonds between complementary.

DNA replication: process of copying DNA

dNTPs: deoxyribonucleotide triphosphates, the monomers used to build DNA, including ATP, TTP, GTP, and CTP

elongation step:  A step in PCR when the reaction is then heated to 72° C, the optimal temperature for DNA polymerase to act. DNA polymerase extends the primers, adding nucleotides onto the primer in a sequential manner, using the target DNA as a template.

ethidium bromide: a dye that is used to visualize bands of DNA or RNA in gels or in some centrifugation preparations; it is known as an “intercalating agent”; remember that “inter-” means between, so in this context, an intercalating agent is something that inserts itself between nucleotides in DNA and RNA; since ethidium bromide fluoresces in UV light, this intercalating agent helps us to see where the nucleic acids have migrated to in a gel or a clear centrifuge tube when illuminated with UV light; CAUTION: intercalating agents are mutagens and therefore you must wear appropriate personal protective equipment (PPE) in the laboratory when using this substance; know the protocols for handling and disposal of this substance in your laboratory

fume hood:  a type of local ventilation device that is designed to limit exposure to hazardous or toxic fumes, vapors or dusts. Two main types exist, ducted and recirculating (aka ductless). The idea is the same for both types: air is drawn in from the front (open) side of the cabinet, and either expelled outside the building or made safe through filtration and fed back into the room.

gametophore: a structure that bears gametes

gel electrophoresis: a technique used to separate a mixture of molecules such as DNA, RNA, or proteins based on their size and charge through a porous matrix (agarose in the case of nucleic acids and polyacrylamide in the case of proteins) using an electric field

glycoproteins: proteins that have oligosaccharide side chains

homogenized tissue:  tissue that has been ground up to release cells and/or their components

laminar flow hood:  (or tissue culture hood) a carefully enclosed bench designed to prevent contamination of biological samples (also sometimes used with sensitive electronics to avoid contamination by dust). Air is drawn through a HEPA filter to eliminate spores and cells and blown in a very smooth, laminar flow towards the user.

lignin:  complex polymer of aromatic alcohols; lignin helps give added strength to woody tissues; lignin is like the concrete in reienforced concrete where the cellulose microfibrils are like the rebar: lignin fills the spaces in the cell wall between cellulose, hemicellulose, and pectin components, especially in the xylem of woody plants

microfibril: a very fine fiber-like strand of cellulose

pathogenic: capable of causing disease

PCR: Polymerase Chain Reaction; this is a technique used in molecular biology to make thousands to millions of copies of specific DNA sequences

pectins: a complex set of polysaccharides in the primary cell walls of terrestrial plants; it influences the mechanical properties of cells and tissues

pH: a measure of the acidity or basicity of a solution; pH = -log [H+]

phenotype: an observable characteristic

pipette: a tool commonly used in the laboratory to measure and deliver specific volume of liquids

plasmid: a small circular chromosome found in many bacteria and used by molecular biologists to clone genes and to move small segments  of DNA of interest into different types of organisms in recombinant DNA technology

polymerase: an enzyme that puts many nucleotides together to build a polymer of DNA or RNA

primers: a strand of nucleic acid that serves as a starting point for DNA synthesis. It is required for DNA replication because the enzymes that catalyze this process, DNA polymerases, can only add new nucleotides to an available 3’-hydroxyl group on an existing strand of DNA. In most cases of natural DNA replication, the primer for DNA replication is a short strand of RNA (which can be made by Primase, the enzyme whose job it is to build primers). Many of the laboratory techniques of biochemistry and molecular biology that involve DNA polymerase, such as DNA sequencing and the polymerase chain reaction (PCR), require DNA primers. These primers are usually short, chemically synthesized oligonucleotides, with a length of about twenty bases. They are hybridized to a target DNA (where they are sufficiently complementary), which is then copied by the polymerase.

protoplast:  in plants, a protoplast is a cell that has had its cell wall removed

rotor:  the rotating unit in a centrifuge; these often contain holes into which balanced tubes containing mixtures are placed to be spun at high speeds; some have sleeves that hold the tubes which are allowed to swing out as the rotor spins and the centrifugal force increases

sporophyte: a structure that generates haploid spores

TAQ Polymerse: a heat-stable enzymed that puts deoxyribonucleotide triphosphates together to build DNA, commonly used in PCR

UV transilluminator: a light box that emits UV light instead of visible light for use in visualizing DNA or RNA that has been separated on a gel and stained with a fluorescent dye that binds to nucleic acids; SAFETY NOTE: be sure to protect your eyes from the UV when using this piece of equipment with a safety shield that absorbs UV light and/or safety gasses which absorb UV light