Untitled Quiz

Gene Structure and Function

• A gene is a segment of DNA that provides instructions for creating proteins or functional RNA molecules.
• Genes are fundamental units of heredity, meaning they are passed down from parents to offspring.
• Genes can undergo mutations (changes in DNA sequence) and recombination (exchange of genetic material).

Coding Sequence (CDS)

• The CDS is the portion of a gene that is translated into a protein.
• It starts with a start codon (AUG) and ends with a stop codon (UAA, UAG, or UGA).
• The CDS contains specific nucleotide sequences that determine the order of amino acids in the protein.

Open Reading Frame (ORF)

• An ORF is a continuous stretch of nucleotides within DNA that potentially codes for a protein.
• An ORF starts with a start codon and ends with a stop codon.
• Not all ORFs correspond to functional proteins.

Prokaryotic Gene Structure

• Prokaryotic genes are relatively simple and organized into operons.
• Promoter: This region located upstream of the coding region controls the initiation of transcription.
  • It contains conserved sequences:
    • -10 region (Pribnow box): 5'-TATAAT-3'
    • -35 region: 5'-TTGACA-3'
• Coding Region: This region codes for the protein and does not contain introns.
  • It starts with a start codon (AUG) and ends with a stop codon (UAA, UAG, or UGA).
• Terminator: This sequence signals the end of transcription, ensuring proper regulation.
  • It can be Rho-dependent or Rho-independent.

Eukaryotic Gene Structure

• Eukaryotic genes are more complex than prokaryotic genes, containing several distinct elements.
• Promoter:
  • Core Promoter: Recognized by RNA polymerase, often containing the TATA box (5'-TATAA-3').
  • Proximal Promoter: Contains binding sites for regulatory elements.
  • Distal Promoter: Further upstream with additional regulatory elements.
• Exons and Introns:
  • Exons: Coding sequences that remain in the mature mRNA after splicing.
  • Introns: Non-coding sequences that are spliced out of pre-mRNA.
  • Signature sequences:
    • Splice donor sites: 5'-GU-3' at the beginning of introns.
    • Splice acceptor sites: 5'-AG-3' at the end of introns.
• 5' Untranslated Region (UTR):
  • The region upstream of the coding sequence that can influence translation efficiency.
• 3' Untranslated Region (UTR):
  • The region downstream of the coding sequence that plays roles in mRNA stability and translation regulation.
• Polyadenylation Signal:
  • A sequence (typically AAUAAA) that signals the addition of a poly-A tail to mRNA, enhancing stability and export from the nucleus.

Prokaryotic Gene Structure - DNA Signatures

• Promoter Region:
  • Key Elements: The promoter region in prokaryotes contains two conserved sequences:
    • -10 Box: TATAAT (Pribnow box), located about 10 base pairs upstream of the transcription start site (+1).
    • -35 Box: TTGACA, located about 35 base pairs upstream of the transcription start site.
  • DNA Signature: 5' - TTGACA (N16-18) TATAAT - 3'
• Ribosome Binding Site (RBS):
  • Shine-Dalgarno Sequence: The Shine-Dalgarno sequence is located 6-10 bases upstream of the start codon (AUG) and aligns the ribosome for translation initiation.
  • DNA Signature: 5' - AGGAGG - 3'
• Coding Sequence (CDS):
  • Open Reading Frame (ORF): The coding region starts with the start codon (AUG, which codes for methionine) and ends with one of the stop codons (UAG, UAA, UGA).
  • DNA Signature: 5' - ATG (coding region) TAG/TAA/TGA - 3'
• Terminator Region:
  • Rho-independent: Contains a palindromic sequence that forms a hairpin loop followed by a series of uracils in the RNA transcript (or thymine in DNA).
  • DNA Signature: 5' - GC-rich palindrome (stem-loop) followed by TTTTTT - 3'
  • Rho-dependent: Does not have a specific sequence but relies on the Rho protein to terminate transcription.
• Operon:
  • Multiple Genes under One Promoter: Operons like the lac operon have several genes (e.g., lacZ, lacY, lacA) transcribed from a single promoter and regulated by a single operator.
  • DNA Signature: 5' - Promoter (TTGACA...TATAAT) Operator Coding Regions (ATG...TAG/TAA/TGA) - 3'

Eukaryotic Gene Structure - DNA Signatures

• Promoter Region:
  • TATA Box: Located about 25-30 base pairs upstream of the transcription start site. Other elements such as the CAAT box or GC-rich regions may also be present.
  • DNA Signature: 5' - TATAAAA - 3' - Optional upstream elements like the CAAT Box: 5' - GGCCAATCT - 3'
• Exons and Introns:
  • Exons: Coding sequences that remain in the mature mRNA after splicing.
  • Introns: Non-coding sequences that are spliced out of pre-mRNA.
  • Splice Site Sequences:
    • 5' Splice Site (Donor Site): 5' - GU - 3' at the start of the intron.
    • 3' Splice Site (Acceptor Site): 5' - AG - 3' at the end of the intron.
    • Branch Point: A conserved "A" about 20-50 nucleotides upstream of the 3' splice site.
  • DNA Signature: 5' - Exon GU (Intron) AG Exon - 3'
• 5' Untranslated Region (5' UTR):
  • DNA Signature: The 5' UTR varies in length and sequence and contains regulatory elements that influence translation efficiency.
• Enhancers and Silencers:
  • Enhancers: Distant regulatory elements that can increase transcription.
  • Silencers: Elements that suppress gene expression.
  • DNA Signature: Enhancer and silencer sequences do not have a fixed sequence but often contain binding sites for transcription factors like NF-κB, SP1, or Oct4.
• Polyadenylation Signal:
  • Poly-A Tail Addition: A signal in the 3' untranslated region (3' UTR) instructs the addition of a poly-A tail to the mRNA transcript.
  • DNA Signature: 5' - AAUAAA - 3'
• 3' Untranslated Region (3' UTR):
  • DNA Signature: Often variable, the 3' UTR contains sequences that influence mRNA stability, localization, and translation.

Comparison of DNA Signatures: