Molecular

• Regulatory elements


  Parts of the gene expression process that control and regulate it

  
• Traditional view of gene expression


  1. Chromatin

  2. Transcription

  3. Translation

  4. Protein folding

  
• The traditional view saw the steps of gene expression as independent, but they can actually occur simultaneously

  
• Contemporary view of gene expression

  1. Processes can take place at the same time

  2. RNA polymerase II coordinates transcription and processing

  
• Gene expression


  Process from DNA sequence to proteins

  
• Gene regulation


  All the mechanisms to control gene expression, including different modifications and steps

  
• The genes expressed depend on the function of the tissue

  
• Chromatin

  • Can be tightly packed by histones
  • Chromatin modifiers help modify the chromatin

  
• Heterochromatin


  Tightly packed chromatin
• Euchromatin

  Relaxed chromatin
• Chromatin regulators need to recognize both histones and DNA
• RNApol II activation


  1. Binding of RNA to promoter

  2. Promoter binds RNA polymerase, initiates transcription, controls gene expression

  
• Promoters


  • Have an RNA polymerase binding site
  • Different types: core, proximal, tissue-specific, ubiquitous, inducible, constitutive
• Core promoter


  Sequences near the coding region, repeated (TATA)

  
• Proximal promoter


  Sequences far from the coding region (CAAT)

  
• Tissue-specific promoter


  Directs gene expression in a specific tissue or stage of development

  
• Ubiquitous promoter


  Directs gene expression in all tissues

  
• Gene expression


  Not all the genes are expressed at the same time, depending on the needs of the cell the gene expression will be one or another, meaning that the genes will be on or off

  
• Inducible promoter


  Directs gene expression in response to an inducer, modulated by repressors or activators

  
• Gene expression control


  1. Transcription

  2. Splicing

  3. Translation

  4. Protein folding

  
• Constitutive promoter


  Always expressed, regardless of environmental conditions
• Regulation levels in prokaryotes


  Less levels of regulation, transcription and translation overlap, can control transcription, translation and post-translational modifications

  
• Housekeeping genes

  Genes that are always expressed as they regulate essential functions for life, e.g. actin, GAPDH

  
• Transcription regulation in prokaryotes


  1. Codify initiation

  2. Codify termination

  3. Inhibit elongation

  
• Prokaryotic operons


  • DNA sequence with different genes that code for different proteins, have a same promotor region for every gene, several genes that code for the same proteins implied in the same pathway

  
• Transcription factors


  Proteins that help with the binding of RNA polymerase

  
• RNApol II activity modification


  Modifications can favor or disfavor the attachment of RNA polymerase
• Operon regulation


  Repressive operons are normally expressed and can be inhibited, inducible operons are genes that are normally not expressed but can be induced

  
• Operon regulation


  1. Operator DNA sequence where repressor can bind

  2. Activator can bind to operator and activate transcription

  
• Enhancer

  DNA sequences that bind activators and help position the polymerase at the promoter, can be far away

  
• Operon regulation types


  • Negative inducible: Lac operon
  • Negative: Repressor binds to operator
  • Positive: Regulated by activator
  • Inducible: Operon normally off, activated by substrate
  • Repressible: Normally on, inhibited by product

  
• Silencer


  DNA sequences that bind repressors and favor the detachment of the polymerase

  
• High glucose levels


  cAMP not bound to CAP, no transcription of lac operon

  
• Insulator


  DNA sequences that differentiate euchromatin from heterochromatin regions, bound by CTCF proteins

  
• Low glucose levels


  cAMP binds to CAP, allows transcription of lac operon

  
• Tryptophan operon regulation


  Tryptophan acts as corepressor, binds to repressor and helps it bind to operator, inhibiting expression

  
• Regulation levels in eukaryotes

  Some steps in nucleus, some in cytoplasm, more complex regulation

  
• Chromatin remodeling


  Alters structure of chromatin, packing, methylation of histones
• Transcriptional control


  Depends on transcription factors binding to transcription factor binding sites (promoters, enhancers, silencers, insulators)

  
• Transcription factor binding sites

  • Short DNA sequences (6-20bp), often have direct repeats or palindromic sequences, regulate transcription processes