CHAPTER 9

• Gene


  A segment of DNA that is used to make a functional product, either an RNA molecule or a polypeptide

  
• Transcription


  Synthesizing RNA from a DNA sequence

  
• The Central Dogma of Genetics


  The process by which the information in a gene is used to make a functional product, often a polypeptide

  
• Transcription of structural genes produce an RNA molecule known as messenger RNA (mRNA)

  
• Translation


  The synthesis of polypeptide from mRNA molecule

  
• The sequence of nucleotides within mRNA determines amino acids sequence of a particular protein

  
• Transcriptional unit


  • Contains base sequences that have different functions during transcription
• Promoter


  Provides the site to begin transcription

  
• Terminator


  Signals the end of transcription
• The RNA transcript is complementary to the template strand

  
• Regulatory sequence


  Site for the binding of regulatory proteins, which influence the rate of transcription

  
• Ribosome-binding sites


  Occur within the mRNA (in bacteria) and provide a site for ribosome attachment to begin translation

  
• Codon


  A series of three bases read during translation
• Start codon


  The first codon
• Stop codon


  Signals an end to translation
• Stages of Transcription


  1. Initiation

  2. Elongation (or synthesis)

  3. Termination

  
• All three stages of transcription involve protein-DNA interactions

  
• Closed promoter complex


  When the DNA is in the form of a double-helix

  
• Open promoter complex


  The RNA polymerase separates the DNA into template and non-template strands

  
• Termination signals the RNA polymerase to dissociate with the DNA
• Promoter


  Directs the exact location for the initiation of RNA transcription

  
• Promoters are located upstream of the start site
• Transcriptional start site


  The first base used as a template for RNA is denoted +1

  
• Promoter sequence elements


  • Crucial for promoter recognition

  
• • 10 region


  Also called the Pribnow box
• The sequence within the -10 and -35 regions may vary slightly but typically have a consensus sequence of bases

  
• RNA polymerase holoenzyme


  Composed of core enzyme (5 subunits) and sigma factor (1 subunit)

  
• Roles of RNA polymerase subunits

  • Alpha subunits involved in polymerase assembly and DNA binding
  • Beta subunits involved in DNA binding and catalytic processes
  • Sigma factor recognizes the promoter

  
• Binding of RNA polymerase holoenzyme at the promoter

  1. Binds loosely to DNA

  2. Sigma factor recognizes -10 and -35 regions

  3. Sigma factor promotes tighter binding

  4. DNA unwinding at -10 region

  
• Elongation stage of transcription

  1. RNA polymerase moves along DNA, causing it to unwind

  2. Template strand used as template

  3. Coding strand has same sequence as RNA transcript except U replaces T

  4. Open complex is 17 bp long

  5. RNA polymerase moves at 43 bp/sec

  6. RNA polymerase connects bases according to AT/GC rule

  7. RNA synthesized in 5' to 3' direction

  
• Multiple transcript events can occur in close proximity, and both strands of DNA can contain genes

  
• Termination of transcription


  1. Rho-dependent termination

  2. Rho-independent (intrinsic) termination
• Rho-dependent termination


  Involves rho protein, rho utilization site, and stem-loop in RNA
• Rho-independent termination


  RNA forms uracil-rich stem-loop structure, causing pause and dissociation of RNA from DNA

  
• Eukaryotic promoter


  • Contains transcriptional start site, TATA box, and regulatory elements

  
• TATA box


  Core promoter sequence, usually at -25 bp, determines transcription start site

  
• Basal transcription


  Low level of transcription produced by core promoter alone

  
• Regulatory elements


  Short DNA sequences that affect binding of RNA polymerase to promoter

  
• Enhancers


  Stimulate transcription
• Silencers


  Inhibit transcription