Glossary of Terms
16S rRNA, Ribosomes This
is covered in more detail in the lab. Ribosomes are cellular organelles
that are the site of protein synthesis. They comprise various protein molecules
as well as associated RNA molecules (known as ribosomal RNA or rRNA). 16S
rRNA is one of the three RNA molecules associated with the ribosomes of
procaryotes. 16S signifies its size.
Adenine, Cytosine, Guanine, Thymine Nitrogen-containing bases that
are part of nucleotides in DNA. They are often referred to by the letters
A, C, G, and T. The sequences of these bases in a DNA molecule comprise
the genetic code. Because of the structure of the bases, adenine can form
two hydrogen bonds with thymine while cytosine can form three hydrogen bonds
with guanine. A-T and C-G pairs are thus termed complementary, and this
property of the bases is fundamental for allowing DNA to self-replicate.
Anneal, Melt, Extend These are the three status indicators that appear
during PCR. In the context of PCR, annealing refers to the cooling phase
following a melting phase. During the melting phase, DNA's double strands
separate. During the annealing phase, single strands that are complementary
come together to reform double strands (this process is called hybridizing).
During PCR, instead of the two original strands coming together, a primer
molecule, which is present in a much higher concentration than the DNA,
will bind to the single strand DNA. Then, during the extend phase, DNA polymerase
extends the 3' end of the primer molecule, making a copy of the DNA.
BLAST BLAST (Basic Local Alignment Search Tool) is a set of tools
for comparing sequence information in proteins or DNA by using all available
public sequence databases. It is designed to find matches in sequence information
by looking for close matches of a small portion of DNA or protein within
a larger whole sequence. The tool is available publically from the National
Library of Medicine. (Check
the BLAST site for more details.)
DNA Polymerases Enzymes that accurately copy a DNA template by polymerizing
nucleotides to form a DNA that is complementary to the template. Different
DNA polymerases are responsible for replication and repair of DNA. Polymerases
extend the chain by adding nucleotides to the 3' end of the growing DNA.
DNA/RNA (Deoxy)ribonucleic acid. First discovered in nuclei
of cells (thus, they are also called "nucleic acid"), DNA together with
RNA are molecules that carry genetic information. DNA consists of double
chains of nucleotides. RNA usually consists of a single chain. DNA/RNA are
polymerized chains of nucleotides. The polymerization of the nucleotide
chain occurs by joining the hydroxyl group on the 3' carbon of the sugar
to the phosphate of an adjacent nucleotide. Thus, at one end of the chain,
there is an unjoined hydroxyl or phosphate group at the 5' carbon (5' end
of the chain); at the other end, there is an unjoined hydroxyl group at
the 3' carbon (3' end of the chain).
Gene The definition of a gene is a tricky one. Often, it is defined
as a segment of DNA that codes for a functional product, the functional
product being either a polypeptide chain or an RNA molecule. But more broadly,
a gene can be defined as the fundamental unit of heredity which carries
information from one generation to the next. In that sense, it can also
include segments of DNA such as those that do not code for any product but
rather have specific sequences for binding other regulatory molecules.
Nucleotides Constituent components of DNA and RNA. Each nucleotide
has three parts: a nitrogen-containing base, a five-carbon sugar, and a
phosphate group. The bases are adenine, cytosine, guanine, thymine (in DNA),
and uracil (in RNA).
Oligonucleotide A short chain of a small number of nucleotides.
Pathogenic agent A disease-causing organism. It could be anything
from a virus, bacteria, to a multicellular organism such as a parasitic
Phylogenetic Relating to the evolutionary relationships of organisms.
A phylogenetic tree, for example, refers to a graphic representation of
the evolutionary history of organisms described in a branching pattern.
Such trees are made with a variety of information, but for bacteria, a powerful
technique is to use the similarity of DNA sequences to deduce relatedness.
An assumption is that close relatives share more DNA similarity than distant
ones. However, there are complications with this method, which is described
in detail in the last part of the lab.
Polymerase Chain Reaction (PCR) A method for creating a large number
of copies of a specific piece of DNA. It uses a version of DNA polymerase
that can function at high temperatures together with an automated temperature-controlled
device known as a thermocycler. See the PCR section of the lab for details.
Primers Oligonucleotides that have been designed and manufactured
to bind to a specific part of a known segment of DNA. DNA polymerase can
then extend the oligonucleotide and replicate the DNA. The process allows
replication of the specific known segment of DNA, particularly in conjunction
Supernatant Floating on the surface, or relates to the clear fluid
over a sediment or precipitate. In this lab, used to describe the layer
of fluid that is over the centrifuged particulate matter.
Thermocycler A device with an incubation well whose temperature can
be programmed to change very rapidly, accurately, and in repetitive cycles.
An incubation well is a metal block into which special sample tubes fit