Glossary Terms 3, 4, 5, & 6

3’ end

The end of a DNA or RNA strand that has a hydroxyl group connected to the third carbon of the sugar molecule, which is deoxyribose or ribose. (The carbon number refers to the position of the carbon in the sugar molecule).

5’ end

The end of a DNA or RNA strand that terminates at the fifth carbon of the sugar molecule, which is deoxyribose or ribose. (The carbon refers to the position of the carbon in the sugar molecule).

Catalyze

To increase the rate of a reaction.

Complementary base pairs

Nitrogen-containing bases that are found opposite each other in a double-stranded DNA molecule. Complementary is the result of the size and shape in the pair (A and T form two hydrogen bonds, G and C form three). Adenine is complementary to thymine, and guanine is complementary to cytosine.

Daughter strand

In DNA replication, a new DNA strand that is created that is a complement to the original DNA strand.

Denature

To change the shape of a bio-molecule and subsequence impact its function, which is often achieved by heating. For example, a protein folds into a complex three-dimensional shape that is directly related to its function. Any process that interferes with protein folding can change its three-dimensional shape and result in inactivation of the protein.

Directionality

In biochemistry, the orientation of a strand of nucleic acid.

DNA polymerase

AN enzyme used to replicate DNA molecules.

Ligate

To join together two DNA ends.

Ligation

The reaction that chemically joins two fragments of DNA, resulting in a combinant DNA molecule.

Mutation

Change or damage occurring in a section of DNA that alters the products or processes associated with that section.

Parent strand

In DNA replication, the DNA strand that serves as a template for creating the new complementary strand.

Replica

An exact copy.

Restriction fragment

The piece of DNA that results from the cutting of the DNA molecule with a restriction enzyme. Fragments are often separated on a gel using electrophoresis.

Agar Plate

Petri plate containing agar mixed with a medium or food source named Luria Broth (LB) that supports bacterial growth.

Amino acid

The building blocks of proteins. Each of the 20 amino acids is an organic substance with two groups attached to it, an amino group (NH2) and a carboxylic acid group (COOH).

Aseptic Technique

A set of procedures and carefully controlled conditions to prevent contamination by pathogens.

Codon

A group of three mRNA bases that encode a single amino acid.

Competent

A cell that has the ability to be transformed genetically by taking up DNA from the environment.

Culture

AN isolated population of cells that have been grown in a specially prepared nutrient medium.

Eukaryote

An organism population that shelters its genes inside a nucleus and has several linear chromosomes.

Exon

The segment of a gene that codes for a protein. They are both transcribed and translated.

Heat shock

A sudden increase in temperature.

Intron

The segment of a gene that does not code for a protein. They are transcribed into mRNA but are removed before the exon (the rest of the gene) are translated into a protein.

Luria Broth

A nutritionally rich medium that supports bacterial growth.

Medium

A solution, such as Luria Broth, that contains substances that support the growth of microorganisms. The medium may be solidified by the addition of agar.

Prokaryote

A cell or organism with a single chromosome and no nuclear membrane. Bacteria are these.

Protein expression

How proteins are synthesized, modified, and regulated in living organisms.

Reverse transcriptase

An enzyme that catalyzes the formation of DNA from an RNA template in reverse transcription.

Splice

To modify messenger RNA for translation by removing introns and joining exons.

Start codon

The first codon of mRNA for translation by a ribosome; typically AUG or GUG.

Stop codon

A nucleotide triplet within mRNA that signals a termination of translation.

Transformation

A process that places foreign DNA, such as a plasmid, into a cell.

Translation

The process by which information encoded in messenger RNA is decoded and transformed into protein.

DNA Ladder

A set of known DNA fragments with different sizes in base pairs or kilo bases. These DNA fragments are separated and visualized as DNA bands on a gel, Where together they look like a ladder. They are used in gel electrophoresis to determine the size and quantity of DNA fragments.

Loading dye

A set of dyes that are added to biomolecules such as DNA for gel electrophesis. One dye moves father than the sample, which indicates that it is time to stop running the gel.

Multimer

A plasmid configuration that consists of a single plasmid that has a break in one of its two strands. The shape of this plasmid is circular.

Nicked circle

A plasmid configuration consisting of a single plasmid that has a break in one of its two strands. The shape of this plasmid is circular.

Selective breeding

When members of the same species are bred together to encourage desirable traits in their offspring.

Supercoiled

A plasmid configuration consisting of a single plasmid that has been twisted. The shape of this plasmid is more compact than the circular form.

Verify

Establish that something is true, accurate, or able to be defended.

Binding site

The area of a bio-molecule that coheres to a specific substance or part of a substance.

Buffer

A solution that resists changes in pH, which contains either a weak acid and its salt or a weak base and its salt.

Chimeric protein

A protein created by joining two or more genes that originally coded for separate proteins.

Colony

A group of the same kind of organisms living closely together, usually for mutual benefit. Within a bacterial colony, all organisms descend from a single ancestor and are genetically identical.

Column chromatography

method of separating substances, in which the substance are dissolved in a liquid that is allowed to flow through a glass column filled with small beads. The beads are coated with a material that binds the substance to different degrees.

Configuration

The three-dimensional shape or structure of something.

Death phase

The period of bacterial growth in a culture when the bacteria run out of nutrients and die.

Disulfide bridge

A single covalent bond between the sulfur atoms to two amino acids.

Eluate

The solution that washes out.

Elution

The process of extracting a substance that is bound to another by washing it with a solution.

Fusion Protein

Glycosylation

A process in which a carbohydrate is covalently attached to another molecule.

Hematopoietic growth factor

A group of proteins that promotes the growth, differentiation, and activity of blood cells.

Hormones

Substances that act as chemical messengers in the body.

Hydrophilic

Water-loving; dissolves in water; polar. Some examples are sugar and salt.

Hydrophobic

Water-fearing; doesn’t dissolve in water; non-polar. Some examples are oil, wax, and RFP.

Lage Phase

The period of bacterial growth in a culture when the bacteria adapt themselves to growth conditions; individual bacteria are maturing and are not yet able to divide.

Log Phase

The period of bacterial growth in a culture when the number of bacteria cells doubles in a fixed period of time.

Lyse

To break open

Monoclonal Antibody

A type of protein that binds two substances in the body and is made oby clones of a cell formed in the laboratory.

Phosphorylation

A process in which an organic compound takes up or combines with phosphoric acid or a phosphorus-containing group.

Polypeptide

A long linear molecule that immediately folds into a specific three-dimensional conformation, which we call a protein.

Protein folding

The process by which a polypeptide folds into its characteristic three-dimensional structure, which is essential to the protein’s function.

Resin

The material used in a chromatography column to coat the beads.

Stationary phase

The period of bacterial growth in a culture when the population stays the same because rates of cell division and cell death are equal. This is often due to a growth limiting factor such as depletion of essential nutrient.

Supernatant

The clear liquid found on top of a solid precipitate after a mixture has been centrifuged.

Suspension culture

A method of growing cells in a liquid growth medium that is moved around by shaking or stirring. The movement mixes air into the suspension and prevents bacteria from settling out of the solution.

Treatment demand

The needs of patients.

Vaccine

A mixture containing killed or weaken bacteria or viruses that cause a body’s immune system to make antibodies that will bind to a bacteria, or to make a virus to fight a disease.