Prokaryotic transcription

• What is a gene?

  A gene is a region of double stranded DNA that encodes a peptide chain (protein).
• What do the sequences of G, A, T, and C in DNA represent?

  They represent instructions that encode the protein.
• How are instructions from DNA used to produce proteins?

  Instructions are read by copying the information to mRNA and translating it into protein.
• Do all genes encode proteins?

  No, not all genes encode proteins.
• What types of RNA do genes encode besides mRNA?

  Genes encode tRNA and rRNA, which are involved in translation to produce proteins.
• What is the role of some genes that encode RNAs?

  Some genes encode RNAs that help to process mRNA or regulate other genes.
• In which direction is RNA always synthesized?

  RNA is always synthesized in the 5’ to 3’ direction.
• Why is mRNA longer than the protein coding region?

  Because of the 5’ and 3’ untranslated regions.
• What does it mean if genes on a chromosome are not the same "way round"?

  If a gene is the other way round, then the template and coding strands will be reversed.
• Where is the promoter located in relation to the gene?

  The promoter is found at the start of the gene.
• Where is the terminator located in relation to the gene?

  The terminator is found at the end of the gene.
• In which direction is mRNA synthesized?

  mRNA is synthesized in the direction from promoter to terminator.
• What does it mean for something to be upstream of the promoter?

  It means it is against the flow of RNA polymerase.
• What does it mean for something to be downstream of the terminator?

  It means it is with the flow of RNA polymerase.
• How are genes often arranged in bacteria?

  Genes are often clustered together in operons, transcribed from one promoter.
• What is the role of RNA polymerase?

  RNA polymerase synthesizes RNA.
• Where does transcription always start for each gene?

  Transcription always starts at a particular position called a promoter.
• How does RNA polymerase know where to bind?

  It recognizes common signals in the DNA sequence from aligned promoters.
• What is the process of RNA synthesis?

  One DNA strand is used as a template, and transcription occurs in the 5’-3’ direction without a primer.
• What happens during the transcription process?

  RNA polymerase makes several abortive attempts until it produces stable RNA associated with the template DNA.
• What occurs at the active site of RNA polymerase?

  There is a hybrid of newly synthesized RNA and DNA (9 bp) at the active site.
• What is coupled transcription/translation in bacteria?

  It occurs when ribosomes latch onto mRNA while RNA polymerase is still synthesizing it.
• Where does transcription occur in eukaryotes?

  Transcription occurs in the nucleus.
• What are the two types of terminators in bacteria?

  Intrinsic and Rho-dependent terminators.
• How does an intrinsic terminator function?

  It causes the newly synthesized mRNA to fold into a hairpin structure, leading to RNA polymerase pausing and falling off the DNA.
• What is the role of the Rho factor in Rho-dependent terminators?

  Rho binds to RNA and 'chases' the RNA polymerase to terminate transcription.
• What is the rut site in Rho-dependent terminators?

  It is a sequence rich in C and poor in G that Rho recognizes in the newly synthesized mRNA.
• What happens when Rho catches up with RNA polymerase?

  Rho unwinds the DNA and RNA hybrid, leading to the release of everything and termination of transcription.