Gene Expression

Gene Expression

• Gene expression: The process by which DNA directs protein synthesis.

  • Stages: Two primary stages of gene expression.

  • Transcription: The process where RNA is synthesized from DNA.

  • Translation: The synthesis of a polypeptide using mRNA information.

  • Proteins: Serve as a link between genotype and phenotype.

  • Genotype: The genetic makeup of an organism.

  • Phenotype: The physical appearance of an organism.

Role of RNA in Gene Expression

• RNA: Functions as a bridge between genes and protein synthesis.

  • Transcription: Synthesis of RNA using information in DNA.

  • Location: Occurs in the nucleus of eukaryotic cells.

  • Output: Produces messenger RNA (mRNA).

  • Translation: Involves the synthesis of a polypeptide from mRNA information.

  • Sites: Ribosomes are the sites of translation.

Overall Process of Gene Expression

• Flow of Genetic Information:

  • Visual representation:

    • DNA → Transcription → Pre-mRNA → RNA Processing → mRNA → Cytoplasm → Translation → Polypeptide
      (Illustrates instances in both bacterial cells and eukaryotic cells.)

The Genetic Code

• Triplet Code: A series of non-overlapping, three-nucleotide words.

  • Usage: The DNA template strand is used to transcribe mRNA.

  • Codons: During translation, mRNA base triplets, termed codons, are read in the 5′ → 3′ direction.

  • Coding Strand: The non-template strand, also known as the coding strand, where the nucleotides are equivalent to the codons of mRNA except thymine (T) in DNA is replaced by uracil (U) in RNA.

Composition of the Genetic Code

• Codons: A total of 64 possible combinations derived from a triplet code (4^3 = 64).

  • Redundancy: The genetic code is redundant: multiple codons can encode the same amino acid.

  • Example Codon Sequence: 5’ A G U G C A C C C C U G 3’.

Transcription Process

• Catalysis: RNA synthesis is catalyzed by RNA polymerase.

  • Function: RNA polymerase unwinds the DNA strands and joins RNA nucleotides.

  • Complementarity: The RNA produced is complementary to the DNA template strand.

  • Primer Requirement: RNA polymerase does not require a primer.

  • Base-Pairing Rules: RNA synthesis follows the same base-pairing rules as in DNA, substituting uracil for thymine.

  • Example of Strands:

  • DNA Coding Strand: 5’ A T G C C T T G 3’

  • DNA Template Strand: 3’ T A C G G A A C 5’

  • mRNA: 5’ A U G C C U U G 3’

Stages of Transcription

• Initiation:

  • Process: RNA polymerase binds to a promoter region, unwinds the DNA, and commences RNA synthesis.

• Elongation:

  • Function: RNA polymerase elongates the RNA strand.

• Termination:

  • Mechanism in Bacteria: Signals marked by a terminator sequence.

  • Mechanism in Eukaryotes: RNA polymerase II transcribes the polyadenylation signal, releasing the transcript 10–35 nucleotides past this sequence.

RNA Processing in Eukaryotes

• Pre-mRNA Modification:

  • Functions: Alters ends and sequences within the RNA before cytoplasmic export.

  • 5′ Cap: A modified nucleotide added to the 5’ end for stability and ribosome attachment.

  • Poly-A Tail: Added to the 3’ end for protection from degradation.

  • Purpose: Facilitation of mRNA export, protection from hydrolytic enzymes, and assisting ribosome attachment.

Splicing of RNA

• Introns and Exons:

  • Introns: Noncoding sequences that interrupt gene sequences.

  • Exons: Coding sequences that are expressed into amino acid sequences.

• RNA Splicing:

  • Mechanism: Removal of introns by spliceosomes which comprise proteins and small RNAs that recognize splice sites.

Alternative RNA Splicing

• Definition: Some genes can produce multiple polypeptides depending on which segments are considered exons during splicing.

  • Benefit: Increases the diversity of proteins an organism can produce, significantly outstripping the number of genes.

Protein Structure and Domains

• Modular architecture: Most proteins have discrete regions called domains, with different exons coding for different protein domains.

Translation Process

• Mechanism: mRNA is translated into protein.

  • tRNA (Transfer RNA): Transfers specific amino acids to the growing polypeptide chain.

  • Each tRNA carries an amino acid and has an anticodon to pair with mRNA codons.

Structure of tRNA

• Shape: The tRNA adopts a flattened cloverleaf primary structure that folds into an L-shaped tertiary structure.

  • Ends: The 5′ and 3′ ends are positioned near one end for amino acid attachment at the 3’ end.

Accuracy in Translation

• Steps for Accuracy:

  1. Correct matching of tRNA to amino acid by aminoacyl-tRNA synthetase enzyme.

  2. Correct pairing of the tRNA anticodon to the corresponding mRNA codon.

• Wobble Hypothesis: Flexible pairing at the third codon position allows some tRNAs to bind to multiple codons.

Ribosomes and Their Function

• Structure: Comprise two subunits (large and small) of ribosomal proteins and rRNA.

  • Binding Sites: Ribosomes have three tRNA binding sites: the P site (growing polypeptide), A site (next amino acid), and E site (exit for discharged tRNA).

Initiation of Translation

• Process: Starts with small ribosomal subunit binding to mRNA and initiator tRNA carrying methionine, reading until the start codon (AUG).

• Formation: The assembly of the large ribosomal subunit results in the formation of the translation initiation complex.

Termination of Translation

• Stop Codons: Specific sequences (UAA, UAG, UGA) signal the termination of translation.

  • Key Steps:

  1. Ribosome reaches a stop codon.

  2. Release factor binds to the A site, promoting hydrolysis of the polypeptide from the tRNA.

  3. Ribosomal components dissociate following release of the newly synthesized polypeptide.

Post-Translational Modifications of Proteins

• Definition: Changes to proteins after translation that may affect shape or function and facilitate targeting to specific locations in the cell.

  • Differences:

  • Free ribosomes synthesize cytosolic proteins.

  • Bound ribosomes synthesize proteins for secretion, marked with a signal peptide.

• Pathway to ER:

  • Signal recognition particle (SRP) binds the signal peptide, leading the ribosome to an ER receptor for translocation and processing of the protein.

RNA Translation in Bacteria

• Polyribosomes: Multiple ribosomes can simultaneously translate a single mRNA, enabling rapid production of polypeptides.

Mutations in Genetic Information

• Definition: Mutations are changes in the genetic material of an organism.

  • Types of Mutations:

  • Point Mutations: Changes in a single nucleotide pair, leading to potential abnormal protein production. If negative, may result in genetic disorders.

  • Examples:

    • Sickle-Cell Disease: A specific point mutation affecting hemoglobin structure and function due to a single nucleotide change.

Detailed Types of Point Mutations

• Nucleotide-Pair Substitution: Replaces one nucleotide pair with another, which can manifest in different ways:

  • Silent Mutation: No effect on amino acid output due to redundancy.

  • Missense Mutation: Codes for a wrong amino acid but still produces a protein.

  • Nonsense Mutation: Converts an amino acid codon into a stop codon, usually leading to a nonfunctional protein.

Insertions and Deletions of Nucleotides

• Impact: Cause frameshift mutations, which disrupt the reading frame and are often more detrimental than substitutions.

• Frameshift Mutations: Can result from either insertion or deletion, resulting in significant changes in the resulting polypeptide.

Causes of Mutations

• Spontaneous Mutations: Occur naturally during replication, recombination, or repair processes. Can have neutral, beneficial, or harmful effects.

  • Mutagens: Agents causing mutations, including physical agents (e.g., UV rays, X-rays) and chemicals (e.g., components of tobacco smoke).

  • Most carcinogens are mutagens, linked to cancer development.