Agarose 0.7 - 2% gel used in gel electrophoresis.

It is a thick gelatinous substance

derived from seaweed, which we prepare from a powder.
Agarose gel electrophoresis -- a method used to separate a mixed population of DNA or
proteins in a matrix of agarose. A current is passed through the gel, and DNA, which is
negatively charged, is drawn in a direction. DNA sections separate according to size
(length in base pairs), because longer sections have a larger mass, and therefore move
slowly. Conversely, short sections move quickly through the agarose, and over time the
DNA becomes organized by length.
BAC (bacterial artificial chromosome) a large constructed piece of DNA (typically
150-350 kbps) that is used in transformation and cloning processes.
Buffer a mixture of salts used to stabilize biochemical various reactions.
Electroporation the process of increasing the electrical conductivity and permeability
of a cells plasma membrane in order to introduce a new substance (typically DNA) into
the cell.
Enzyme any protein that acts as a catalyst in a specific biochemical reaction. In lab, we
use enzymes to cut, combine and change DNA. They are kept in the -20C freezer, and
can only be removed in a mini cooler for short periods of time.
Ethidium bromide -- Ethidium bromide is an intercalating agent commonly used as a
fluorescent tag in techniques such as agarose gel electrophoresis. The chemical inserts
itself into the physical structure of the DNA helix, acting as a marker. It is a mild
carcinogen, which is why we keep the gel benches separate from the rest of lab. When
working with ethidium bromide, or anything it may have touched, change your gloves
before using items from the rest of the lab.
DNA nucleic acid that encodes the genetic instructions used in the development and
functioning of all (known) living organisms. The cross-sectional structure of the DNA
double helix is made up of four chemicals: guanine (G), adenine (A), thymine (T), and
cytosine (C). Various arrangements of these four letters denote different DNA sequences
these arrangements can be determined through a form of gel electrophoresis, and can
analyzed on a computer. In lab, DNA appears in different forms:
cDNA (complimentary DNA) synthetic form of DNA complimentary to the
RNA of a cell. It is created through a process called reverse transcription and can
be replicated via PCR.
gDNA (genomic DNA) natural chromosomal DNA
mDNA (mitochondrial DNA) -- DNA located in organelles called mitochondria,
structures within eukaryotic cells that convert chemical energy from usable
cellular food. Mitochondrial DNA is only a small portion of the DNA in a
eukaryotic cell; most of the DNA can be found in the cell nucleus.
rDNA (recombinant DNA) -- DNA sections formed by laboratory methods
of genetic recombination (such as molecular cloning) in order to bring together
genetic material from multiple sources, creating sequences that would not
otherwise be found in biological organisms.
DNA polymerases -- enzymes that create DNA molecules by assembling nucleotides, the
building blocks of DNA. DNA polymerases read existing DNA strands to create two
new strands that match the existing ones.
dNTP (deoxyribonucleotide) the DNA building blocks used in a PCR reaction.
DNTPs are comprised of a sugar and phosphate group (the backbone), along with a
nitrogenous base (which forms G, A, T, or C).
Heterozygous cells contain two different alleles of a particular gene. On gels this
manifests as a combination of wildtype and homozygous bands
Homozygous -- cells contain two identical alleles for a particular gene. On gels this
manifests as a unique set of bands (different sized sections of a cut DNA strand)
Insert -- a piece of DNA that is inserted into a larger DNA section (the vector) via
a recombinant DNA technique, such as ligation or recombination.
LB & SOC liquid cultures for growing bacteria. SOC is more nutritious and more
easily contaminated. When working with either, turn on a flame and keep your area as
sterile as possible.
Ligation the process of joining two nucleic acid fragments (typically DNA) through the
action of an enzyme.
Nanodrop a machine used to measure the concentration (ng/microliter) of different
DNA solutions (and other types of samples).
Nucleotide A portion of a DNA molecule one phosphate group, a sugar, and a
nitrogenous base.
PCR (polymerase chain reaction) a biochemical technique used to amplify a few copies
of a piece of DNA across several orders of magnitude, generating thousands to millions
of copies of a particular DNA sequence. PCR typically consists of six steps: initialization,
denaturation, annealing, extension/elongation, final elongation, and final hold. In-depth
descriptions of these steps and their appropriate temperatures can be found online.
Plasmid a generally circular piece of double-stranded DNA that only occurs in
bacteria. In lab, plasmids are essential tools because they are stable, easy to work with,
simple to replicate, and widely useful. We use bacterial plasmids to clone and store
various sections of DNA.
Primer -- a strand of nucleic acid that serves as a starting point for DNA synthesis. It is
required for DNA replication (PCR reactions) because the enzymes that catalyze this
process, DNA polymerases, can only add new nucleotides to an existing strand of DNA.
Restriction enzyme (restriction endonuclease) -- an enzyme, produced chiefly by certain
bacteria, that has the ability to cleave DNA molecules at or near a specific sequence of
bases. Ajay calls them molecular scissors.
RNA a nucleic acid similar to DNA. It is typically single stranded, and is used to carry
short-term messages within a cell.
mRNA (messenger RNA) a type of RNA that conveys genetic information from
the nucleus to the ribosome in shorthand.
RNase an enzyme that degrades RNA. It is everywhere: in your body, on your skin, in
the air. Because of this, RNA work in lab is easily contaminated, and must be kept
separate from the rest of our equipment.
Spin column a purification tool used to quickly clean nucleic acid samples.
Taq polymerase (abbreviated as taq) -- a thermostable DNA polymerase named after
the thermophilic bacterium Thermus aquaticus. The enzyme is frequently used in PCR
reactions, because it is able to withstand the protein-denaturing conditions (high
temperatures) required for the process. Taq's optimum temperature for activity is 75
80C, where it is highly efficient. However, it has relatively low replication fidelity,
meaning it makes a high number of replication errors (about 1 in 9,000 nucleotides),
compared to other polymerases.
Transformation -- the process of inserting/incorporating exogenous DNA into a cell
through its membrane
Vector see definition of Insert