gene expression

• Shine Dalgarno sequence

  • Ensures mRNA is read in correct reading frame
• what are plasmids


  extra chromosomal dna which is highly mobile
• what is the start codon


  AUG.
• What is the function of amino acetyl tRNA syntheses 


  binds to amino acid and uses AMP to generate a link between tRNA and amino acid
• what is a reading frame 


  the order in which the sequence of bases on mRNA must be read
• what are frame shift mutations


  when triplet of bases is read in a different way so the wrong bases
• what are the three sites on ribosomes

  E site, P site and A site
• Transcription


  1. Enzymes use a strand of DNA as a template to generate tRNA

  2. RNA polymerase binds to the promoter within the gene, splitting the strands apart and moving along the gene synthesizing mRNA as it moves along

  3. RNA polymerase is the enzyme responsible for making RNA

  4. Sigma factor is an initiator protein involved in protein recognition

  5. Sigma factor has affinity for RNA polymerase

  6. RNA polymerase needs a promoter to know where to bind, and it locates the promoter when bound with sigma factor which gives it this identifying attribute
• Bacteria and prokaryotes

  • Have a single RNA polymerase
  • Bacteria have multiple sigma factors (sigma factor 70 for housekeeping genes, sigma factor 32 for heat shock genes, sigma factor F for sporulation genes)
• Bacteria's genes are organised onto operons

  1. An operon is a group of closely linked genes which produces a single messenger RNA molecule in transcription

  2. A cluster of genes that is transcribed together to give a single messenger RNA molecule which encodes for multiple proteins
• E. coli operon

  • Lac operon of E. coli contains genes involved in lactose metabolism
  • It is only expressed when lactose is present and glucose is absent
• Terminators

  • Stem loops are signals for transcription termination
  • Bacteria have two types of terminators: rho dependent and rho independent
  • Rho is a protein involved in the termination of transcription
  • Rho-dependent termination often occurs in genes that are not translated
  • Rho-independent termination is located after the end of the open reading frame, forms a stem loop which terminates translation, and often occurs in genes that aren't translated
• Function of anti-termination

  1. prevent termination of tRNA and rRNA which are not translated so need anti-termination systems to prevent termination by rho
• Regulatory proteins - repressors and activators

  • Dimeric proteins Interact with DNA via DNA binding motifs like helix turn helix, zinc finger, and leucine zippers
• what do repressors do


  bind to operator to block RNA polymerase and generation of mRNA
• Gene activation - maltose

  1. RNA polymerase cannot bind unless the activator is bound

  2. The activator protein only binds when maltose is present
• Activation at a distance

  • Activator sites can be distant from the promoter
  • Common in eukaryotes
  • Often called enhancers
  • Can be bound by activator protein which causes a u bend in the DNA to bring activator site closer to promoter
• Catabolite repression

  1. Bacteria need to decide what nutrients to utilise

  2. Bacteria have a preference for glucose as a carbon source until it is exhausted

  3. Only when the glucose is exhausted then the bacteria will induce lactose catabolism genes

  4. The lactose operon is controlled by two different regulators: Catabolite activator protein (CAP) - glucose sensor, Lactose repressor - lactose sensor

  5. When glucose runs our cAMP levels increase which binds to CAP helping RNA polymerase initiate transcription
• Attenuation

  1. Controls expression of genes for amino acids and nucleoside synthesis

  2. The leader peptide senses the level of amino acids in the cell
• Tryptophan regulation

  1. Tryptophan leader peptide sequence

  2. Excess tryptophan: Ribosome can translate leader mRNA, stem loop forms

  3. Limited tryptophan: Ribosome stalls on leader mRNA allowing anti-terminator to form

  4. Specific to tryptophan biosynthetic genes
• Regulation by small RNA's

  • Antisense RNA which can bind to mRNA to block translation
  • staphylococcus aureus using small non-coding RNA to regulate factors allowing it to be a successful pathogen
• Riboswitches

  • A part of an mRNA molecules that can bind and target small molecules regulating gene expression
  • Has the ability to regulate RNA by responding to concentrations of its target molecule
  • Associated with gene clusters that encode biosynthetic enzymes
  • Controlled by final product of biosynthetic pathway
• Cell signalling by quorum sensing

  1. Bacteria can secrete a signal molecule at a constant rate

  2. Regulation of gene expression in response to cell popularity density