11-22

• How do expression levels of genes vary?

  Each gene is uniquely regulated

  
• At what levels can gene expression be regulated?

  At transcription or translation levels
• What does mRNA carry?

  The 'sense' of the information
• What defines the DNA strands in relation to mRNA?

  Non-template strand is the 'sense' strand

  
• What is the direction of the non-template strand?

  5' to 3'
• What is the direction of the template strand?

  3' to 5'
• How does RNA synthesis differ from DNA synthesis?

  Uracil substitutes for thymine in RNA
• How do sense strands depend on context?

  They vary for different genes
• Why is uracil not found in DNA?

  Cytosine can deaminate to uracil
• What happens during DNA replication after deamination?

  A C-G pair is replaced with a U-A pair

  
• How does DNA repair uracil in DNA?

  Uracil is removed by uracil-DNA glycosylase
• What are the three major classes of bacterial RNA?

  mRNA, rRNA, tRNA
• What is the function of mRNA?

  Encodes proteins

  
• What is the role of rRNA?

  Constituents of ribosomes

  
• What is the function of tRNA?

  Adapters between mRNA and amino acids

  
• How many RNA polymerases are in Escherichia coli?

  One single RNA polymerase
• What is a bacterial transcription unit composed of?

  5' promoter, coding sequence, 3' terminator

  
• What is the role of the 5' promoter?

  Attracts and binds RNA polymerase

  
• What does the 3' terminator signal?

  Signals the stop point for transcription

  
• What is the directionality of transcription?

  5' to 3' is downstream
• What is the composition of bacterial RNA polymerase?

  α, β, β', and ω subunits

  
• What does the addition of a σ subunit do?

  Converts the enzyme to holoenzyme

  
• How does RNA polymerase bind to DNA?

  Binds non-specifically and can slide

  
• What is the purpose of DNA foot printing?

  Identifies where RNA polymerase binds DNA

  
• What are the conserved elements of bacterial promoters?

  • 10 sequence TATAAT and -35 sequence TTGACA
• What is the significance of the +1 position in bacterial promoters?

  It is usually A or G

  
• How does RNA polymerase transcribe RNA?

  Uses the antisense strand as a template

  
• What are the three stages of transcription?

  Initiation, elongation, termination

  
• What happens during initiation of transcription?

  RNA polymerase binds the promoter and opens DNA

  
• What occurs during elongation of transcription?

  Core enzyme continues to make new RNA

  
• What is required for termination of transcription?

  Specific signals for RNA polymerase to dissociate
• What is the role of σ factors in E. coli?

  Provide specificity for different promoters
• What is scrunching in transcription initiation?

  Polymerase pulls downstream DNA towards itself

  
• What is the error rate of RNA polymerase during transcription?

  About one mistake every 10,000 to 100,000 nucleotides
• What are the two mechanisms of transcription termination in bacteria?

  Rho-independent and Rho-dependent mechanisms

  
• What is Rho-independent termination?

  Involves a palindromic GC-rich sequence
• What is Rho-dependent termination?

  Requires Rho protein to disrupt RNA:DNA hybrid
• What is the role of Rifampicin?

  Inhibits prokaryotic transcription initiation

  
• How does bacterial transcription differ from eukaryotic transcription?

  Transcription and translation occur simultaneously in bacteria

  
• What happens to eukaryotic transcripts after transcription?

  They are processed and transported to the cytosol