1. The major groove of DNA is the larger of the two grooves described by the double helix on its external surface. Inside the groove, hydrophobic methyl groups, hydrogen atoms, and hydrogen bond donors and acceptors can be accessed by regulatory proteins attached to the helix.
2. A helix-turn-helix is a regulatory protein consisting of two alpha helices joined by a short non-helical segment. It fits into the major groove of the DNA. Homeodomains function during the development of the organism as "developmental switches," and are critical in how different body regions are assembled. A zinc-finger is a regulatory protein typically containing both an alpha helix and a _-pleated sheet, as well as one to several atoms of zinc. A leucine zipper is a Y-shaped regulatory protein consisting of two interacting alpha-helix chains; the base of the "Y" consists of the helices being held together by their hydrophobic amino acids (usually leucine, hence the name).
3. A promoter is a sequence of nucleotides at the end of a gene that tells the RNA polymerase where to begin transcribing the gene. An operon is a cluster of genes transcribed as a unit. An operator is a regulatory site on a gene to which a repressor can bind, inhibiting transcription.
4. Repressors and activators are proteins that facilitate the inhibition or stimulation of transcription, respectively, by binding to specific regions of the gene (promoter sites or operator sites).
5. When bacteria are grown in a medium containing tryptophan, they do not need to manufacture the amino acid, so their trp gene is inhibited by a repressor which binds to the trp promoter. In the absence of tryptophan, the repressor protein is not triggered, does not bind to the promoter, and transcription of the trp gene occurs, supplying the amino acid to the bacterium.
6. cAMP participates in transcription control. When glucose levels are high in the surrounding medium, cAMP levels are correspondingly low, preventing CAP from binding to DNA.
7. When lactose is present in the environment, a lactose isomer binds to the lac repressor removing it from its regulatory position on the DNA and permitting transcription of the lac gene to occur.
8. Eukaryotic transcription factors stabilize and guide RNA polymerase. Enhancers in eukaryotic cells permit regulation of transcription from a distance, often a considerable distance, whereas bacterial regulation occurs directly at the site of the gene.
9. Methylation may serve to block accidental transcription of "turned off" genes.
10. The primary RNA transcript contains both introns and exons. Primary transcripts undergo processing prior to leaving the nucleus, during which the noncoding introns are removed.
11. mRNA can be affected several ways on its way from the nucleus to the ribosome: mRNA may or may not make it out through the nuclear membrane, some mRNAs may be translated over others, and some mRNA transcripts may be degraded prior to translation.