Ch4 Regulation

• Regulated genes


  Genes whose activity is controlled in response to the needs of a cell or organism
• Constitutive genes/Housekeeping genes


  Genes whose products are essential to the normal functioning of a growing and dividing cell, no matter what the conditions are
• All genes are regulated on some level
• Operon


  Genes that encode proteins that work together in the cell are organized into operons, with the genes adjacent to each other and transcribed together onto a polycistronic mRNA
• Inducible gene


  A gene that is transcribed in response to a regulatory event occurring at a specific regulatory DNA sequence adjacent to or near the protein-coding sequence, typically involving an inducer and a regulatory protein
• Inducer


  A regulatory substance that brings about gene induction
• Effectors/Effector molecules


  Small molecules that help control the expression of many regulated genes
• Regulation of inducible gene expression

  1. Regulatory event at regulatory DNA sequence

  2. Inducer and regulatory protein involved

  3. RNA polymerase initiates transcription at promoter

  4. Gene turned on, mRNA made, protein produced
• Lac Operon


  • Genes for enzymes required to metabolize lactose are organized into an inducible operon
  • Allolactose is the inducer molecule
  • Lac repressor binds to operator to repress transcription in absence of inducer
  • Inducer binds to repressor, causing it to dissociate from operator, allowing transcription
• Regulation of lac operon by glucose (catabolite repression)

  1. Glucose metabolism produces high ATP

  2. High ATP inhibits adenylate cyclase, reducing cAMP

  3. Low cAMP prevents cAMP-CAP complex from enhancing RNA polymerase binding to lac operon promoter

  4. Transcription of lac operon genes repressed
• trp Operon


  • Encodes enzymes for tryptophan biosynthesis
  • Repressed by Trp repressor when tryptophan is abundant
  • Regulated by attenuation - ribosome position on leader transcript determines transcription termination or antitermination
• Regulation of trp operon by tryptophan (corepressor)


  1. Tryptophan binds to aporepressor, converting it to active Trp repressor

  2. Active Trp repressor binds to operator, preventing transcription initiation
• Regulation of trp operon by attenuation

  1. Leader transcript has regions that can form secondary structures

  2. Ribosome position on leader determines if termination or antitermination signal forms

  3. Low tryptophan causes ribosome stalling, allowing antitermination signal to form

  4. High tryptophan allows ribosome to translate past termination signal
• Region 3 synthesis


  1. Region 3 paired with region 2

  2. Region 3 cannot pair with region 4

  3. 2:3 pairing is an antitermination signal

  4. Termination signal of 3 paired with 4 does not form

  5. RNA polymerase continues past the attenuator and transcribes the structural genes
• Ribosome translation of Trp codon

  1. Ribosome continues to the stop codon for the leader peptide

  2. Ribosome covers part of RNA region 2

  3. Region 2 unable to pair with region 3

  4. Region 3 able to pair with region 4
• Bonding of region 3 with region 4

  Transcription termination signal
• Eukaryotic gene expression regulation


  • More complex
  • Happens at many different levels
  • Eukaryotic genes not organized into operons
  • Each gene must be regulated independently
  • Eukaryotic cells have many more genes than prokaryotic cells
• Levels of regulation of gene expression in eukaryotes

  • Epigenetic
  • Transcriptional
  • Post-transcriptional
  • Translational
  • Post-translational
• Epigenetic regulation


  Changes that alter the chromosomal structure so that genes can be turned on or off
• Mechanisms of chromatin remodeling

  • ATP-remodeling complexes
  • Histone chaperones
  • Histone modifications (methylation, acetylation, phosphorylation)
  • DNA modifications (methylation)
• Histone modification


  Chemical modifications (acetylation, methylation, phosphorylation, ubiquitination) that alter the structure of histone proteins, relaxing or condensing chromatin structure
• Chromatin remodeling


  ATP-dependent complexes that move, eject, or restructure nucleosomes, modulating accessibility of genomic regions to transcription factors and RNA polymerase
• DNA methylation


  Addition of methyl groups to cytosine residues in CpG dinucleotides, leading to gene silencing
• Histone chaperones


  Proteins that facilitate the assembly and disassembly of nucleosomes, regulating gene expression by controlling access to DNA and modulating chromatin structure
• Transcriptional regulation


  Control of whether or not an mRNA is transcribed from a gene in a particular cell
• Promoter region


  Immediately upstream of the coding sequence, where transcription factors bind to control transcription initiation
• TATA box


  Repeat of thymine and adenine dinucleotides within the promoter region, where transcription factors bind to assemble the initiation complex
• Enhancers


  Regions that help increase transcription, can be located thousands of nucleotides away from the gene, binding sites for activators
• Transcriptional repressors


  Bind to promoter or enhancer regions and block transcription
• Post-transcriptional regulation


  Occurs after the mRNA is transcribed but before translation begins, can happen at the level of mRNA processing, transport, or binding to ribosomes
• Alternative RNA splicing


  Mechanism that allows different combinations of introns and exons to be removed from the primary transcript, producing different protein products from one gene
• mRNA stability


  Factors like poly-A tail length contribute to how long an mRNA exists in the cytoplasm and can be translated
• Types of eukaryotic RNA editing

  • Deamination (adenosine to inosine or cytidine to uridine)
  • Guide RNA-directed editing (insertion/deletion of uridine residues)
• Polyadenylation


  Addition of a polyadenine (poly(A)) tail to the 3' end of the mRNA molecule, important for stability, export from the nucleus, translation efficiency, and regulation of alternative polyadenylation