Prokaryotic and Eukaryotic Gene Structure PDF

Gene A gene is a segment of DNA that contains the necessary information to produce proteins or functional RNA molecules. Genes are fundamental units of heredity and can undergo mutations and recombination. Coding Sequence (CDS) The coding sequence (CDS) is the portion of a gene that is translated in...

Gene A gene is a segment of DNA that contains the necessary information to produce proteins or functional RNA molecules. Genes are fundamental units of heredity and can undergo mutations and recombination. Coding Sequence (CDS) The coding sequence (CDS) is the portion of a gene that is translated into protein. It begins with a start codon and ends with a stop codon. The CDS includes specific nucleotide sequences that dictate the amino acid sequence of the resulting protein. Open Reading Frame (ORF) An open reading frame (ORF) is a continuous stretch of nucleotides that starts with a start codon and ends with a stop codon. An ORF may or may not correspond to a functional protein-coding sequence. Prokaryotic Gene Structure Prokaryotic genes are typically simpler and organized into operons. Key components include: Promoter: A sequence located upstream of the coding region that initiates transcription. Common signature sequences include: -10 region (Pribnow box): 5'-TATAAT-3' -35 region: 5'-TTGACA-3' Coding Region: This region encodes the protein and is continuous without introns. The sequence starts with an initiator codon (AUG) and ends with a stop codon (UAA, UAG, or UGA).  Terminator: A sequence that signals the end of transcription. It can be Rho-dependent or Rho-independent. Function of Each Element Promoter: Controls transcription initiation by providing binding sites for RNA polymerase. Coding Region: Responsible for synthesizing proteins through transcription and translation. Terminator: Signals RNA polymerase to stop transcription, ensuring proper regulation. Eukaryotic Gene Structure Eukaryotic genes are more complex, containing several distinct elements: Promoter: Includes: 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: Eukaryotic genes consist of exons (coding sequences) and introns (non- coding sequences). Signature sequences include splice donor sites (5'-GU-3') at the beginning of introns and splice acceptor sites (5'-AG-3') at the end. 5' Untranslated Region (UTR): The region upstream of the coding sequence that may 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. Function of Each Element Promoter: Regulates when and where transcription occurs through binding transcription factors. Exons: Code for amino acids in proteins after splicing. Introns: Non-coding regions that may play roles in gene regulation and alternative splicing. 5' UTR & 3' UTR: Influence translation efficiency and mRNA stability; they do not code for proteins but are crucial for post-transcriptional regulation.  Polyadenylation Signal: Ensures proper mRNA processing and stability, facilitating transport to ribosomes for translation. Supporting Figures 1. Prokaryotic Gene Structure This figure illustrates how prokaryotic genes are organized in operons, showing promoter regions, coding sequences, and terminators. 2. Eukaryotic Gene Structure This figure depicts eukaryotic genes with exons, introns, promoter regions, UTRs, and polyadenylation signals, highlighting their complexity compared to prokaryotic genes. These figures provide visual context to better understand the structural differences between prokaryotic and eukaryotic genes while emphasizing their functional components. I. Prokaryotic Gene Structure - DNA Signatures 1. Promoter Region: o 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. o DNA Signature: ▪ 5' - TTGACA (N16-18) TATAAT - 3' o Example: In E. coli, this signature is found in several housekeeping genes. 2. Ribosome Binding Site (RBS): o 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.  o DNA Signature: ▪ 5' - AGGAGG - 3' o Example: Found in E. coli genes, ensuring correct mRNA-ribosome alignment. 3. Coding Sequence (CDS): o 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). o DNA Signature: ▪ 5' - ATG (coding region) TAG/TAA/TGA - 3' o Example: The lacZ gene in the lac operon starts with ATG and ends with TAA. 4. Terminator Region: o 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). o DNA Signature: ▪ 5' - GC-rich palindrome (stem-loop) followed by TTTTTT - 3' o Rho-dependent: Does not have a specific sequence but relies on the Rho protein to terminate transcription. 5. Operon: o 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. o DNA Signature: ▪ 5' - Promoter (TTGACA...TATAAT) Operator Coding Regions (ATG...TAG/TAA/TGA) - 3' o Example: The lac operon sequence contains regulatory regions like the CAP site and operator sequences. II. Eukaryotic Gene Structure - DNA Signatures 1. Promoter Region: o 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. o DNA Signature: ▪ 5' - TATAAAA - 3' ▪ Optional upstream elements like the CAAT Box: 5' - GGCCAATCT - 3' o Example: In the human globin gene, the TATA box precedes the transcription start. 2. Exons and Introns: o Exons: Coding sequences that remain in the mature mRNA after splicing. o Introns: Non-coding sequences that are spliced out of pre-mRNA. o 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. o DNA Signature: ▪ 5' - Exon GU (Intron) AG Exon - 3' o Example: The β-globin gene in humans has a well-defined intron-exon structure with conserved splice site sequences. 3. 5' Untranslated Region (5' UTR): o DNA Signature: The 5' UTR varies in length and sequence and contains regulatory elements that influence translation efficiency. o Example: In eukaryotes, the 5' UTR can include sequences that regulate mRNA stability and translation.  4. Enhancers and Silencers: o Enhancers: Distant regulatory elements that can increase transcription. o Silencers: Elements that suppress gene expression. o 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. o Example: The enhancer sequence upstream of the immunoglobulin gene helps regulate antibody production. 5. Polyadenylation Signal: o 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. o DNA Signature: ▪ 5' - AAUAAA - 3' o Example: The AAUAAA sequence in the 3' UTR of many eukaryotic genes signals polyadenylation. 6. 3' Untranslated Region (3' UTR): o DNA Signature: Often variable, the 3' UTR contains sequences that influence mRNA stability, localization, and translation. o Example: The 3' UTR in the β-globin gene influences mRNA stability. III. Comparison of DNA Signatures: Element Prokaryotic Signature Eukaryotic Signature Promoter -35 TTGACA -10 TATAAT TATAAAA (TATA Box) Ribosome Binding No specific sequence, but Kozak sequence: Shine-Dalgarno: AGGAGG Site ACCAUGG Start Codon ATG ATG Rho-independent: GC-rich + No fixed terminator, polyadenylation: Terminator TTTTTT AAUAAA Intron/Exon No introns 5' GU...AG 3' Poly-A Signal Not present AAUAAA These DNA signatures define essential components of gene expression regulation in both prokaryotes and eukaryotes. While prokaryotes tend to have simpler, more straightforward sequences (like operons and Shine-Dalgarno), eukaryotes feature more complex mechanisms (like enhancers, intron-exon splicing, and poly-A tails). Alternative Splicing Alternative Splicing