DG

Intro to Genetics

Translation – Core Mechanics

  • ribosomes: enzymes that translate the mRNA into proteins

    • A Site - where enters ribosome (‘access point’)

    • P Site- transfers amino acid bond from tRNA to for peptide bond

    • E Site- ‘exit’ site for the empty tRNA

  • nucleotides

    • mRNA

      • read in codons→ 3 nucleotides (base pairs) = 1 amino acid

      • Universal start codon – AUG (codes for methionine / “f-Met”)

        • Ethical / evolutionary angle: single start codon across all life implies a common ancestor.

        • Bases before AUG form the leader sequence (5′ untranslated region)→ molecular “ZIP code”: guides mRNA to correct ribosome

        • Never translated, but essential for proper protein targeting.

    • tRNA

      • double-stranded & far more stable than mRNA so longer life!

        • Anticodon loop ➜ complementary to the codon sit in the center of in the ribosome.

        • bound amino acid based on anticodon

Ribosome Architecture

  • Subunits

    • Small subunit (binds mRNA + tRNA anticodon).

    • Large subunit (clamps on top & performs catalysis).

  • Three Internal Sites

    • A (Amino-acyl / Access) site – incoming tRNA–AA complex docks here.

    • P (Peptidyl) site – peptide bond formation; growing chain temporarily attached to a tRNA.

    • E (Exit) site – empty tRNA is released for re-charging.

Step-by-Step Elongation Walk-Through (Class Example)

  • Initial state: mRNA threaded so \text{AUG} sits in P site with its methionine-tRNA.

  1. Ribosome shifts 3 bases ➜ next codon \text{CCG} arrives in A site.

    • Complementary anticodon \text{GGC} on a proline-tRNA binds.

  2. Peptide bond transfer: methionine detaches from its tRNA and bonds to proline.

  3. Ribosome shifts again:

    • Empty Met-tRNA exits via E site.

    • Proline-tRNA (with dipeptide Met-Pro) moves to P site.

    • New codon \text{UAC} now in A site ➜ anticodon \text{AUG} carrying tyrosine enters.

  4. Cycle continues (example codon \text{GAA} → anticodon \text{CUU} brings glutamine, etc.).

  • Energy & Directionality: each translocation consumes GTP; always 5′ ➜ 3′ along mRNA.

Termination

  • Three universal stop codons and they just have no amino acid attached

  • Stop-tRNA is “blank”; when it occupies the A site the Peptidyl-tRNA attempts bond transfer → attaches peptide to nothing ➜ chain is released.

  • Polypeptide immediately folds and/or gets post-translational modifications.

Principles of Gene Expression

  • monocistronic→ eukaryotes will have 1 mRNA for 1 protein

    • beneficial bc in nuclear envelope so can perform transcriptional modification (unless prokaryotes which get whatever they make)

    • allow them to modify the protein

  • polycistronic → prokaryotes will use 1 mRNA to make mult. proteins concurrently

    • saves time and resources and good for non-complex

    • makes up for the lack of operons

  • The genetic code

    • all organisms use the same 4 base pairs → 64 options total → only 2 amino acids

      • thus code is degenerate (has many redundancies)

      • 1st position: a little bit of flexibility

      • 2nd position: NO flexibility. if different = new amino acid

      • 3rd position: least conserved / most flexible for mutation (“wobble position”

  • overall: complementary nature of the entire process

    • DNA strands are complementary bp

    • mRNa is made as complement bp to template

    • codon is translated by complementary bp to tRNA

      • without complementary nature → not functional

Gene Regulation: Prokaryote vs. Eukaryote

Multilevel Gene Regulation

  1. Modify DNA: Chromatin supercoiling

    • Supercoiling (bacteria) or histone wrapping (eukaryotes) controls accessibility → most energy-efficient.

  2. Transcriptional Control

    • Promoter regulation → for prokaryotes mainly —> called operons

    • not so common for humans bc we only expose small portion of our DNA at on time

  3. Post-Transcriptional Control (eukaryotes only)

    • w/i nuclear envelope to edit the RNA

    • all eukaryotes will do this at some point

  4. Translational Control

    • pre translation control:

      • done from the outside usually like w meds → will turn on and off the ribosome to regulate it (erythromycin)

      • cell cannot do on its own

    • post translational control:

      • modifies proteins w/ coenzymes to make them active

        • necessary for them to function (anemic is an issue w this)

      • degrades proteins

        • a mutation w/ the gene → creates dysfunctional protein that is instantly degraded

        • not a favorable process! takes lots of energy

        • typically mutation is gene cannot turn off

    • Ribosome on/off; therapeutically targeted by antibiotics (e.g., erythromycin).

Operons – Prokaryotic Regulatory Units

  • Definition: Single promoter (operator) governs multiple genes ➜ yields polycistronic mRNA.

  • Key Components

    • Promoter – RNA polymerase binding site.

    • Operator – DNA region where repressor protein binds.

    • Structural genes – enzymes with related function.

  • Types Covered

    Repressor protein options
    - Bind operator → physically blocks RNA-polymerase → transcription OFF
    - Bind a small metabolite (inducer or corepressor) → alters repressor shape → changes operator affinity

    1. Inducible Operon (catabolic)

    • lac operon - Default transcription OFF:

    • components: operator, repressor, and inducer

      • inducer will move the suppressor to turn gene on

    • repressor normally bound to DNA. inducer molecule (lactose) inactivates repressor and will move off DNA ➜ transcription proceeds until substrate depleted

      • catabolic bc induced by outside molecule

      • repressor can bind to operator or inducer and if inducer is present will bind to inducer and thus leave and turn the gene ON and once depleted goes back

    1. Repressible Operon (anabolic)

    • trp operon - default transcription ON

      • corepressor that has a substrate attached to turn gene off

    • components: operator, repressor and corepressor

    • repressor not bound to DNA normally → gene transcribes to make bunch of tryptophan → end product comes to bind with repressor as a corepressor (instead of inducer like lac) → repressor activated and binds to DNA → stops transcription until the last substrate used

    • in order to conserve energy (fats not stored)

Summary Quick-Reference Bullets

  • \text{AUG} = universal start; \text{UAA}, \text{UAG}, \text{UGA} = universal stops (3 of them).

  • 4 bases → 64 codons → 20 amino acids; degeneracy mostly in 3rd position.

  • Complementary base-pairing underpins replication, transcription, translation, and tRNA recognition.

  • Prokaryotes: coupled transcription/translation, polycistronic mRNA, operons – regulation chiefly at promoter level.

  • Eukaryotes: nuclear envelope enables post-transcriptional processing and alternative splicing; regulation spread across multiple levels.

  • Ribosome sites: A (entry), P (peptide), E (exit) – memorize order.

  • Gene regulation hierarchy: DNA access > transcription > RNA processing > translation > protein modification > protein degradation (energy cost increases downwards).