MD7 Genetic and Gene expression

• Genome


  The entire collective instructions of an organism
• Genotype


  The individual genes that make up the genome
• Phenotype


  The collective traits that each individual organism carries with it and passes on to future generations
• Cells don't always express all of their genes simultaneously, even in organisms with smaller genomes like bacteria
• It is wasteful for cells to be constantly making enzymes they don't absolutely need
• Gene regulation


  Cells can turn on or express genes in response to environmental signals, and turn off or repress gene expression
• Constitutive genes


  Genes that need to always be kept on because they are essential for basic cell functions
• Housekeeping genes

  Another term for constitutive genes
• Prokaryotic chromosomes are circular DNA molecules, as opposed to the linear chromosomes in eukaryotes
• Bacteria and archaea typically have one single large chromosome within the nucleoid
• Plasmids


  Extra smaller independent circular pieces of DNA that carry a few extra genes
• Conjugation

  Transfer of a plasmid from a donor cell to a recipient cell using a sex pilus
• F plasmid


  Plasmid that allows a cell to express a sex pilus for conjugation
• F+ cell


  Donor cell that carries the F plasmid
• Plasmids can carry genes for novel metabolic capacity, antibiotic resistance, or the use of new resources
• Recombinant plasmid

  Plasmid that has been engineered to carry a gene of interest, using restriction enzymes and ligase
• Natural transformation

  Bacteria taking up plasmids present in the environment
• Electroporation


  Using an electrical charge to introduce DNA into cells
• Heat shock method


  Incubating cells with DNA on ice, then briefly heating to 42°C to induce DNA uptake
• Transduction


  Transfer of genetic material via a virus
• Horizontal/lateral gene transfer


  Transfer of genetic information between cells that are not related, as opposed to vertical transfer from parent to offspring
• Topoisomerases


  Enzymes that help relieve strain from DNA supercoiling
• DNA gyrase


  A bacterial-specific topoisomerase that relaxes positive supercoils in circular DNA
• DNA gyrase is an attractive target for antibiotics
• Operons


  Groups of related genes organized together in the prokaryotic genome, under shared control
• Promoter


  DNA sequence recognized by RNA polymerase to initiate transcription of an operon
• Operator

  DNA sequence upstream of an operon that can be bound by a repressor protein to stop transcription
• Polycystronic RNA


  Single mRNA transcript in prokaryotes that codes for multiple proteins
• In prokaryotes, transcription and translation are coupled, as mRNA is produced directly in the cytoplasm
• Polycystronic RNA


  RNA that codes for more than one protein
• Polycystronic RNA in bacteria


  • Ensures important proteins in a pathway are produced in the right ratios and at the same time when they are needed
  • One single messenger RNA serves as a template for the ribosome to make more than one protein
• In eukaryotic cells, messenger RNA is synthesized as pre-messenger RNA molecules that then have to be processed
• Processing of pre-messenger RNA in eukaryotes

  • Involves removing of intervening sequences or introns that are non-coding
  • Involves addition of the five prime cap and the poly A tail
• In eukaryotes, the process of transcription and translation are separated in space and time
• Levels of gene expression regulation in bacteria

  • Transcriptional level
  • Translational level
  • Post-translational level
• Regulation at the transcriptional level in bacteria

  Controlling how readily something gets transcribed or not
• Regulation at the translational level in bacteria

  Modifying the RNA to have secondary structure elements that make it harder for the ribosome to access or take longer to melt out
• Rare codons

  Incorporate rare codons in the message to stall the ribosome while it finds the appropriate tRNA, slowing the rate of translation
• Post-translational regulation

  Activating or inhibiting proteins by adding chemical groups like phosphorylation, or adding cofactors and coenzymes
• Sigma factors

  Subunits of the bacterial RNA polymerase enzyme that bind to the promoter region and help recruit the core RNA polymerase