Exam 3: Molecular Regulation

  • Promoter: A specific DNA sequence where RNA polymerase binds to initiate the transcription of a gene.

  • Pribnow box: A specific consensus sequence (TATAAT) found within the bacterial promoter, located about 10 base pairs upstream from the transcription start site, essential for initiating transcription.

  • Leader sequence (5′ UTR): The region of an mRNA molecule that precedes the coding sequence; it is involved in regulating gene expression and ribosome binding.

  • Shine-Dalgarno sequence: A ribosomal binding site in bacterial mRNA that helps align the ribosome with the start codon to correctly initiate protein synthesis.

  • Start codon: The first codon of a messenger RNA (mRNA) transcript translated by a ribosome (typically AUG), signaling the start of protein synthesis.

  • Termination: The final step of transcription where the RNA polymerase dissociates from the DNA template and releases the newly synthesized RNA.

    • Rho-dependent termination: Requires the Rho protein, which binds to the nascent RNA and uses ATP to pull the RNA away from the RNA polymerase.

    • Rho-independent (Intrinsic) termination: Does not require an extra protein; it relies on a G-C rich hairpin loop followed by a string of uracil residues to stall and release the polymerase.

  • Introns: Non-coding sections of an RNA transcript (or the DNA encoding it) that are spliced out before the RNA is translated into a protein.

  • Exons: The sections of DNA or RNA that code for proteins and remain in the final mature mRNA molecule.

Gene Regulation & Operons

  • Constitutive expression: Refers to "housekeeping" genes that are transcribed continuously at a relatively constant rate regardless of environmental conditions.

  • Operon: A cluster of genes under the control of a single promoter, allowing for coordinated regulation of a specific metabolic pathway.

    • Operator sequence: A DNA segment within an operon where a regulatory protein binds to inhibit or facilitate transcription.

    • Regulatory gene: A gene involved in controlling the expression of one or more other genes, often by coding for a repressor protein.

    • Regulatory protein: A protein (like a repressor or activator) that binds to DNA to control the transcription of specific genes.

  • Inducible operon: An operon that is usually "off" but can be stimulated ("on") when a specific small molecule (an inducer) interacts with a regulatory protein (e.g., the lac operon).

  • Repressible operon: An operon that is usually "on" but can be inhibited ("off") when a specific small molecule (a corepressor) binds to a regulatory protein (e.g., the trp operon).

RNA Interference & Advanced Regulation

  • Short interference RNA (siRNA): Small, double-stranded RNA molecules that interfere with the expression of specific genes by degrading mRNA after transcription.

  • RISC (RNA-Induced Silencing Complex): A multiprotein complex that uses a single strand of siRNA to recognize and cleave complementary mRNA molecules.

  • Dicer: An enzyme that cleaves long double-stranded RNA (dsRNA) or pre-microRNA into short fragments like siRNA.

  • Riboswitch: A regulatory segment of a messenger RNA molecule that binds a small molecule, resulting in a change in production of the proteins encoded by that mRNA.

Genetic Transfer & Variation

  • Recombinants: Organisms or cells that contain a new combination of genes produced by crossing over or genetic engineering.

  • Horizontal gene transfer (HGT): The movement of genetic material between unicellular and/or multicellular organisms other than by the transmission of DNA from parent to offspring.

  • Vertical gene transfer: The transmission of genes from an organism to its offspring during reproduction (e.g., cell division).

  • Transduction: The process by which DNA is transferred from one bacterium to another by a virus (bacteriophage).

    • Generalized transduction: Any bacterial gene can be transferred to a recipient cell.

    • Specialized transduction: Only specific bacterial genes (those near the viral integration site) are transferred.

  • Conjugation: The transfer of genetic material between bacterial cells by direct cell-to-cell contact or a bridge-like connection (pilus).

  • Competent cells: Bacterial cells that are in a physiological state which allows them to take up extraneous DNA from their environment via transformation.

  • Bacteriophage: A virus that parasitizes a bacterium by infecting it and reproducing inside it.

Biotechnology & Molecular Tools

  • Endonucleases (Restriction endonucleases): Enzymes that cut the DNA phosphodiester backbone at specific internal sequences.

  • Phosphodiester backbone: The structural framework of nucleic acids, consisting of alternating sugar and phosphate groups linked by covalent phosphodiester bonds.

  • Vector: A DNA molecule (like a plasmid or virus) used as a vehicle to artificially carry foreign genetic material into another cell.

  • CRISPR: A technology (Clustered Regularly Interspaced Short Palindromic Repeats) that allows for highly specific genome editing.

    • Spacers: Short segments of "DNA memory" from previous viral infections stored within the CRISPR locus.

    • Cas9 endonuclease: A specific enzyme associated with CRISPR that acts as "molecular scissors" to cut DNA at a targeted location.

    • crRNA (CRISPR RNA): RNA derived from the spacers that guides the Cas9 enzyme to the matching viral DNA.

    • Guide RNA (gRNA): A synthetic or natural RNA molecule that directs the Cas9 nuclease to a specific target DNA sequence for editing.