Gene Expression

Lecture 15: Gene Expression (10/24/2025)

Overview of Gene Expression

  • Central Dogma of Molecular Biology:

    • The flow of genetic information is from DNA to RNA to Protein.

    • The processes are unidirectional:

    • Transcription: The process of synthesizing RNA from a DNA template.

      • RNA Polymerase: The enzyme responsible for synthesizing the RNA strand.

    • Translation: The process where RNA sequences direct the synthesis of proteins.

      • The RNA sequence is translated into amino acid sequences.

    • Together, transcription and translation outline the complete path of gene expression.

RNA Composition and Types

  • Ribonucleic Acid (RNA): A nucleic acid involved in various biological roles concerning coding, decoding, regulation, and expression of genes.

Comparison: DNA vs. RNA

  • Sugar Components:

    • DNA: Deoxyribose

    • RNA: Ribose

  • Nitrogenous Bases:

    • DNA: Adenine (A), Thymine (T), Cytosine (C), Guanine (G)

    • RNA: Adenine (A), Uracil (U), Cytosine (C), Guanine (G)

  • Strandedness:

    • DNA: Double-stranded (ds DNA)

    • RNA: Single-stranded (ss RNA)

Ribose vs. Deoxyribose

  • RNA contains -OH (hydroxyl group) in its sugar while DNA contains a hydrogen atom (H) instead of the -OH group.

  • The presence of -OH in RNA allows for more versatile interactions with other molecules.

  • Uracil is used in RNA as a pyrimidine base in place of thymine found in DNA.

Differences in Uracil and Thymine

  • Uracil (U):

    • Complementary to adenine (A) with 2 hydrogen bonds, unlike thymine which has a methyl group.

    • Methyl group in thymine contributes to DNA stability and serves as a checkpoint during DNA detection. The loss of this group by uracil allows RNA to attach to other molecules easily.

Types of RNA

1. Messenger RNA (mRNA)

  • Serves as a copy of the DNA that can move out of the nucleus and into the ribosome for translation.

2. Transfer RNA (tRNA)

  • Plays a critical role in translation by bringing amino acids to the ribosome.

3. Ribosomal RNA (rRNA)

  • A component of ribosomes, which facilitate protein synthesis.

The Genetic Code

  • Specifies the order in which amino acids are assembled to form proteins.

  • Each amino acid is coded by sequences of three nucleotides called codons.

    • Example: UUU codes for phenylalanine (the first amino acid determined).

    • 4 bases (A, U, C, G) can form 64 different combinations of codons (4^3 = 64) for only 20 amino acids.

Characteristics of the Genetic Code

  • Unambiguous: Each codon corresponds to only one specific amino acid.

  • Redundant: Most amino acids are specified by more than one codon (e.g., Proline can be coded by CCC, CCA, CCU, CCG).

  • Wobble Hypothesis: The third base in the codon can vary without changing the amino acid, allowing for mutation tolerance.

Reading Frame

  • Codons must be correctly grouped during translation. Changing a single nucleotide can lead to a frameshift mutation, altering the entire sequence thereafter.

    • Example: Removing the first 'T' could change “the red dog ate the bug” to “her Edd Olga test heb ug”.

Summary of Concepts Discussed

  • Flow of Genetic Information: DNA → RNA → Protein

  • Differences between DNA and RNA

  • Understanding of the genetic code including codons, wobble hypothesis, and universality

Transcription Process

  • The first step in gene expression leading to RNA synthesis, which is complementary to DNA.

  • It involves three main stages:

    1. Initiation

    2. Elongation

    3. Termination

A. Initiation

  • One DNA strand serves as a template for RNA synthesis; the other strand is not transcribed.

  • The DNA is read in the 3’-5’ direction, while RNA is synthesized in the 5’-3’ direction.

    • Promoter: A specific DNA sequence on the transcribed strand that designates the start site of transcription but is not transcribed.

    • RNA Polymerase: Enzyme that binds to the promoter, unwinds the DNA helix, and begins transcription.

B. Elongation

  • The synthesis of RNA occurs that is anti-parallel to the template strand.

  • Components of RNA synthesis:

    • RNA nucleoside triphosphates are used.

    • An example of a transcribed sequence:

    • Non-transcribed strand: 5’ A-T-G-A-C-T 3’

    • Transcribed (template) strand: 3’ T-A-C-T-G-A 5’

    • Resulting RNA: 5’ A-U-G-A-C-U 3’

C. Termination

  • A specific sequence of DNA (not a stop codon) signals RNA polymerase to release the DNA.

    • The RNA transcript dissociates from the DNA template, completing the transcription process.

mRNA Modification (Eukaryotes)

  • Transforms the initial transcript (pre-mRNA) into a usable form for translation.

  • Modifications involve:

    • Adding a 5' cap and 3' poly-A tail to enhance stability and protect mRNA.

    • These modifications aid in the export from the nucleus and recruitment of ribosomes for translation.

    • Untranslated Regions: The 5’ and 3’ UTRs, which are regions of mRNA not translated into protein.

RNA Splicing

  • Occurs in the nucleus through the removal of introns (non-coding regions) and the connection of exons (coding regions) to form a continuous coding sequence for translation.

Translation Process

  • The conversion of mRNA into a polypeptide occurs in the ribosomes, which can be either free-floating in the cytoplasm or attached to the surface of the rough endoplasmic reticulum (RER).

A. Components of Translation

  1. tRNA:

    • Transcribed from DNA and carries amino acids to the ribosome.

    • 3D Structure:

      • Forms loops due to base-pairing interactions (hydrogen bonds) within the molecule.

    • Anticodon: A region that is complementary and antiparallel to the mRNA codon.

  2. Aminoacyl-tRNA:

    • A tRNA molecule linked to its specific amino acid; considered a high energy molecule that promotes peptide bond formation.

B. Translation Initiation

  • The small ribosomal subunit binds to the mRNA along with the first tRNA, which is complementary to the start codon of the mRNA.

C. Translation Elongation

  • Characterized by cycles where each cycle adds a single amino acid to the growing polypeptide chain.

    • Ribozyme (rRNA enzyme): Catalyzes peptide bond formation.

Steps of the Elongation Cycle of Translocation

  1. Codon Recognition: Anticodon of incoming aminoacyl tRNA base pairs with the corresponding mRNA codon in the A site.

  2. Peptide Bond Formation: Between the amino group of the new amino acid in the A site and the carboxyl end of the growing polypeptide in the P site.

  3. Translocation: Moves the ribosome down one codon along the mRNA.

  4. This process repeats until the entire polypeptide chain is synthesized, producing a complete protein.