3.2 Gene structure and organization

Genes are the blueprints of life, containing instructions for making proteins. They're made up of coding regions called exons and non-coding regions called introns. Understanding gene structure is key to grasping how genetic information is stored and used.

Genes aren't just about coding sequences. They also have regulatory regions that control when and how much a gene is expressed. These include promoters, enhancers, and silencers. In bacteria, genes can be organized into operons, allowing for coordinated expression of related genes.

Gene Components

Exons and Introns

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• Exons are coding regions of genes contain sequences that are present in the mature mRNA after splicing
• Exons code for amino acids in the final protein product
• Introns are non-coding regions of genes that are transcribed but removed from the pre-mRNA through splicing before translation
• Introns can contain regulatory sequences that influence gene expression (alternative splicing)

Open Reading Frame and Coding Sequence

• Open reading frame (ORF) is the portion of a gene that has the potential to code for a protein
• ORF begins with a start codon (usually AUG) and ends with a stop codon (UAA, UAG, or UGA)
• Coding sequence (CDS) is the portion of the ORF that actually codes for the protein
• CDS begins with the start codon and ends with the codon immediately before the stop codon

Untranslated Regions (UTRs)

• UTRs are portions of the mRNA that are not translated into protein
• 5' UTR is located at the beginning of the mRNA before the start codon
  • Plays a role in regulating translation and mRNA stability
  • Contains the ribosome binding site (Shine-Dalgarno sequence in prokaryotes)
• 3' UTR is located at the end of the mRNA after the stop codon
  • Influences mRNA stability, localization, and translation efficiency
  • Contains polyadenylation signal for adding the poly(A) tail

Regulatory Regions

Promoter and Regulatory Elements

• Promoter is a region of DNA located upstream of the gene's transcription start site
• Promoter contains binding sites for RNA polymerase and transcription factors
• Core promoter elements include the TATA box and initiator (Inr) sequence
• Regulatory elements are DNA sequences that influence gene expression
  • Can be located within the promoter or at more distant locations (enhancers, silencers)
  • Provide binding sites for transcription factors and other regulatory proteins

Enhancers and Silencers

• Enhancers are regulatory elements that increase gene expression
  • Can be located upstream, downstream, or within introns of the gene they regulate
  • Function independently of their orientation and distance from the promoter
• Silencers are regulatory elements that decrease gene expression
  • Act by binding repressor proteins that inhibit transcription
  • Can be located near the promoter or at more distant locations

Gene Organization

Operons

• Operons are functional units of gene expression found in prokaryotes
• Consist of multiple genes that are co-regulated and transcribed as a single mRNA
• Genes in an operon typically encode proteins with related functions (metabolic pathways)
• Lac operon in E. coli is a well-studied example
  • Encodes enzymes for lactose metabolism
  • Regulated by the presence or absence of lactose and glucose
• Trp operon in E. coli is another example
  • Encodes enzymes for tryptophan biosynthesis
  • Regulated by the levels of tryptophan in the cell