Dave Gray's Build-A-Gene Class Notes Glossary

• 5' - The "upstream" end of DNA. The end of the DNA or RNA strand that has the fifth carbon in the sugar-ring of the deoxyribose or ribose at its end. If the 5' end is missing, the DNA cannot be extended by joining additional neucleotides beyond that point.
• 3' - The downstream end of DNA. Can attach to a 5' end.
• Anneal - Bind two strands of DNA. This happens at a temperature of around 55°C.
• Amplify - Make copies of a DNA template.
• Denature - Separate the two strands of DNA. This is done by heating the DNA to near the boiling point of water.
• Enzyme (e.g. Taq polymerase) - Biological molecules (mostly proteins) that catalyze chemical reactions needed for life. In this case, the enzyme facilitates the replication of DNA.
• Extension - The process of adding DNA nucleotides when making a copy. The enzyme binds to the end of the primer and synthesizes DNA by attaching nucleotides. (Error rate is about 1/1,000,000 for Taq. We are using Herculase - somewhat lower error rate.)
• GFP – Green Florescent Protein - A coding sequence that yields a protein that fluoresces green under UV light. Originally isolated from the DNA of florescent jellyfish. GFP variants contain about 750 nucleotides. We ordered 60 NT sets (about 20 pieces)
• Nucleobases - These are the coding components of DNA and only come in four flavors – A C T and G (adenine, thymine, cytosine and guanine). A always binds with T and C with G. A fifth nucleobase U (uracil) replaces T (thymine) in RNA and lacks the 5' methyl group. A and G are called purines. C T and U are pyrimidines.
• Nucleotides – A building block of DNA consisting of a nucleobase, a five-carbon sugar (either ribose or 2-deoxyribose), and one or more phosphate groups. The 5-carbon sugar and phosphate group(s) make up the “backbone” of the DNA.
• Vector - A DNA molecule used as a vehicle to artificially carry foreign genetic material into another cell.
• PCA – Polymerase Cycling Assembly (A.K.A. Template Independent PCR) – A process for assembling segments single-strand DNA into a full double-strand.
• PCR – Polymerase Chain Reaction (A.K.A. Template Dependent PCR) – A process for replicating (“amplifying”) DNA or a portion of a DNA molecule. With each cycle, the copies of DNA double.
• Polymerase - So called because it makes a polymer.
• Primer - A short single strand of DNA (= oligonucleotide) that the enzymes can build on to replicate the entire strand we want. It is the starting point of the new strand. It contains a combination of nucleotides that will allow it to uniquely bind to the right starting point because the complementary sequence to the primer appears only one place in the DNA. The enzymes that drive this process, DNA polymerases, can only add new nucleotides to an existing strand of DNA. The polymerase starts replication at the 3'-end of the primer, and copies the opposite strand.
• Promoter – A region of DNA that initiates transcription of a particular gene into RNA. Can be strong, weak or function only in the presence of a certain chemical. Note the distinction - the primer determines the starting point for DNA replication whereas the promoter defines the starting point for RNA transcription.
• RBS - Ribosome Binding Site - Point at which protein synthesis starts.
• Terminator - Stops MRNA synthesis.

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