Glossary

Agarose - A long chain polysaccaride isolated from seaweed. It is similar to collagen (used in Jello) in that when it is heated (to dissolve it) and then cooled it forms a matrix (gel) with buffer solution trapped inside.

Anneal - When primers anneal to the template, they stick to the DNA strand in a specific way due to base pairings.

Associated proteins - Proteins like histones adhere to the DNA and allow it to fold up into tight bundles. DNA is very negatively charged. In the purified state, these negative charges repel each other, making the helix rigid. The positive charges on the histones help to neutralize these charges, allowing the helix to have more flexibility and compactness. Unfortunately, this inhibits the actions of enzymes in in vitro experiments.

Autoradiography - during the polymerase reaction, a small concentration of radioactive nucleotide is added. After the gel is run it is used to expose X-ray film. When the film is developed an image of the radioactive DNA strands can be seen.

Bacteriophage - a virus that attacks bacteria

Base pairs - Since double stranded DNA is a very large molecule, it's awkward and relatively uninformative to talk about its size in terms of molecular weight (i.e., g/mole or kilodaltons). However, an excellent understanding of the size of the molecule can come from knowing how many consecutive base pairings (base pairs or bp) are lined up in the molecule. A piece of double stranded DNA that is 10 bp has one strand with 10 consecutive bases paired with another strand with the complimentary bases:

5 'A-G-G-T-C-A-A-T-T-G3 '
3 'T-C-C-A-G-T-T-A-A-C5 '

 

Endonuclease - a DNA enzyme that cuts DNA inside the strand, not from an end

Extraction - This involves equilibrating an aqueous solution that contains many different molecules with an organic solvent. The more polar molecules will stay in the aqueous solution and the more non-polar molecules will be exteacted into the organic layer.

Gene of Interest - Any gene that you wanted to study

Genetically Engineered - A fancy term for taking out the genes you don't want and putting in the ones you do.

Homogenate - The solution made when cells are lysed in a buffer. This involves grinding the tissue up to break (lyse) all the cell walls and homogenize the entire mixture.

Lac Z - One of the three genes in the Lac operon, it is the enzyme beta-galactosidase. This enzyme breaks down lactose into glucose and galactose. Transformed bacteria are grown on media containing the chemical X-Gal, which turns blue when cleaved by beta-galacosidase. If the bacteria has taken up a plasmid without an insert, the colony will be blue. If the bacteria has taken up a plasmid with an insert, the enzyme will be non-functional and the colony will be white. This provides a selection mechanism to detemine if your gene of interest is in the plasmid.

Kilobases - one thousand base pairs

Labile - unstable - easily killed

Lattice - A solid matix- kind of like if you put monkey bars in a pool, and then tried to swim through them underwater. The bars would slow you down.

Lytic Cycle The lambda phage has two different life cycles. In the lysogenic cycle, it's genome inserts itself into the host cell's genome and lies dormant until the host cell experiences stress. When this happens, it goes into the lytic cycle, which involves massive replication leading to amplification of the virus and lysis of the cell.

Marker - Something that is experimentally measureable. This could be an enzyme activity, a radioactive label, a protein that you have an antibody against, etc.

Melt - When DNA is heated, the two strands (which are only held together by H bonds) fall apart. This is called melting.

Negative control - This is an experiment that you expect to fail (like using water instead of a protein sample in a protein assay). This shows that you have the conditions controlled and a positive result is truly a positive result.

OD600 - Optical Density (light scatter by suspended cells) at 600nm - a spectrophotometric measure of the number of cells/ml

Other Methods - Cheap, fast, or good. Pick any two.

PAGE - polyacrylamide gel electrophoresis functions similarly to agarose gel electrophoresis, except it uses polymerized acrylamide to produce the lattice. Acrylamide produces a lattice with smaller size holes and provides better separation of small length fragments. For example, in agarose electrophoresis, the best separations are in the 3000 bp and 300 bp and the resolution is, at best, 50 bp. In PAGE, the best separation is in the 20 base pair to 300 base pair range and the resolution is 1 bp. This kind of resolution is necessary for sequencing.

Polylinker - This is a short stretch of nucleotides inserted into a vector plasmid which has ten to twenty restriction enzyme sites. These sites only exist in this place in the vector. They make it easy to clone inserts into the vector and take them back out.

Positive control - This is an experiment that should definitely work. It's important to set one of these up so that if your test experiment doesn't work, you know that it's because of the thing that you're testing and not because of some other factor (like the cells being dead).

Rate - Change in concentration per change in time.

Radioactive Nucleotide - In a radioactive nucleotide, one of the phosphorous atoms (the one esterified directly to the 5' carbon of the ribose) is replaced with either radioactive phosphorous (32P) or radioactive sulfur (35S). Any DNA strand that has this incorporated in it is "labeled" and can be easily detected with a geiger counter, scintillation counter, or by autoradiography.

Resolution - the smallest distinction that can be accurately determined

Selective Pressure - The same as in evolution - only the organisms that have a particular trait (in this case antibiotic resistance) will survive.

Specific Purpose - Each commercial plasmid will contain sequences designed for a specific purpose. For example, some make it easy to make RNA from the inserted DNA, make it possible for eukaryotic cells to express the gene, or include enhancer sequences to increase expression of the gene. pBluescript has sequences that make it capable of converting from a bacterial plasmid into a bacteriophage, which can be really handy for some applications. A molecular biologist will choose a vector plasmid that is most useful for his/her particular application based on these extra functions.

Structural information - In this case, stuctural information includes an approximation of its length in base pairs and the location of restriction enzyme sites within the DNA. The information on the location of the sites can then be used for later manipulations of the DNA.

Subclone - This involves taking a fragment out of a large piece of DNA (a clone) and inserting it into a different plasmid.

Vector - Something that is used to transfer something else (e.g., a mosquito is a vector of the plasmodium that causes malaria). A plasmid is a "vector" or carrier for getting a piece of DNA into a cell in a usable form. A phage can also be used as a vector to get DNA into a cell.