Glossary | Tools | Encyclopedia

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 worm.

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 with PCR.

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 perfectly.