Mechanism of Transcription (HL) (HL IB Biology)

• The synthesis of mRNA occurs in three stages:
  • Initiation
  • Elongation
  • Termination
• During initiation, RNA polymerase binds near the promoter, causing the DNA strands to separate to form an open complex
• During elongation, RNA polymerase moves along the template strand
  • RNA polymerase adds the 5‘ end of the free RNA nucleotide to the 3’ end of the growing mRNA molecule
  • Elongation occurs in a 5’ to 3’ direction, synthesising a single strand of RNA
• Termination occurs when RNA polymerase reaches a terminator sequence
  • Which triggers the detachment of the polymerase enzyme and mRNA strand
• When the mRNA is translated at the ribosome it is also read in the 5’ to 3’ direction

Direction of transcription diagram

The template strand of the DNA molecule is the one that is transcribed

Gene expression varies in different cells

• Genes are not expressed equally in every cell
  • Essential genes needed for the survival of an organism are expressed all the time
    • e.g. Genes for the main enzymes in the respiratory pathways or ATP synthase
  • Other genes are only expressed when needed and at levels that make specific amounts of protein
    • e.g. The gene for rhodopsin that is only expressed in light-sensitive receptor cells of the eye
• Regulatory mechanisms exist to ensure the correct genes are expressed at the correct time
  • These mechanisms are different between prokaryotes and eukaryotes but both employ transcription factors and other proteins that bind to specific sequences in DNA

The function of the promoter

• Only some DNA sequences code for the production of polypeptides, these are called coding sequences
• Non-coding sequences produce functional RNA molecules like transfer RNA (tRNA) or are involved in the regulation of gene expression such as enhancers, silencers and promoters
• The promoter is a non-coding sequence located near to a gene
  • The promoter is not itself transcribed
• The promoter acts as the binding site for RNA Polymerase during the initiation of transcription
• Binding of RNA Polymerase to the promoter is under the control of various regulatory proteins

Regulation of gene expression in eukaryotes

• Eukaryotes regulate gene expression in response to variations in their environment
• Specific proteins bind to DNA to regulate transcription and ensure that only the genes required are being expressed in the correct cells, at the correct time and to the right level
  • This is key to how processes of cellular differentiation and development in multicellular organisms are controlled
• General transcription factors are a type of transcription factors that bind directly to the promoter to help initiate transcription
  • This helps RNA polymerase to attach to the promoter and start transcribing the gene
  • In eukaryotes, several general transcription factors are needed for transcription

Transcription factor binding to promoter diagram

A transcription factor binding to the promoter region of a gene which allows RNA polymerase to bind and for transcription to occur

• DNA molecules are very long but only certain regions code for the production of polypeptides
  • These are called coding sequences
• In humans only 1.5% of the genome contains coding sequences
• The majority of a eukaryotic genome contains non-coding regions of DNA that do not code for polypeptides but have other important functions
• Non-coding gene regulatory sequences are involved in the control of gene expression by enhancing or suppressing transcription
• Non-coding sequences can produce functional RNA molecules like transfer RNA (tRNA) or ribosomal RNA (rRNA) 
• Introns are non-coding sequences of DNA found within genes of eukaryotic organisms
  • Different proteins can be produced from a gene depending on how introns are removed
• Telomeres are regions of repeated nucleotide sequences at the end of chromosomes that provide protection during cell division
  • The repeated sequence facilitates binding of an RNA primer at the end of the chromosome leading to synthesis of an Okazaki fragment
  • Without telomeres, DNA replication could not continue to the end of the DNA molecule and chromosomes would become shorter after every cell division
  • Nonetheless, telomeres shorten with age due to oxidative damage within cells
    • Loss of telomeres during ageing can be accelerated by smoking, exposure to pollution, obesity, stress and poor diet
    • Antioxidants in the diet are claimed to reduce the rate of telomere shortening

mRNA splicing diagram

The RNA molecule produced from the transcription of a gene contains introns that must be removed before translation can occur