Campbell Biology Chapter 17: Gene Expression

Gene Definition & Genome Overview

• Human karyotype: 46 chromosomes per somatic cell.

  • Total DNA content ≈ $6\times10^{9}$ nucleotides (= $3\times10^{9}$ base pairs).

  • Each chromosome harbors thousands of genes.

• Historical / functional descriptions of a gene

  • Discrete unit of inheritance.

  • Specific nucleotide sequence on a chromosome.

  • DNA sequence coding for a specific polypeptide chain.

• Modern definition

  • Region of DNA that can be expressed to produce a final functional product, either a polypeptide or an RNA molecule.

Proteins & Amino-Acid Basics

• Proteins = long polymers (polypeptides) of the 20 standard amino acids.

• Amino acids are connected by peptide bonds; many peptide bonds → one polypeptide.

• Analogy: amino acids = 20-letter “alphabet” vs. 26-letter English alphabet.

Flow of Genetic Information

• Relationship genotype → phenotype is mediated by proteins.

• Canonical pathway: DNA → RNA → Protein → Phenotype.

• Term “Central Dogma” coined by Francis Crick; depicts one-way flow of hereditary information (with known exceptions such as retroviruses).

Basic Principles of Transcription & Translation

• RNA serves as the molecular bridge between stored DNA information and functional protein products.

• Transcription: DNA-templated synthesis of RNA (produces pre-mRNA, tRNA, rRNA, etc.).

• Translation: mRNA-directed synthesis of polypeptide on ribosomes.

• Cellular compartmentation

  • Prokaryotes: transcription and translation are coupled; mRNA is translated while still being transcribed (no introns, no nuclear envelope).

  • Eukaryotes: transcription in nucleus, translation in cytoplasm; RNA processing separates the two stages.

Genetic Code – Core Properties

• Triplet (codon) system: $3$ nucleotides specify $1$ amino acid (3∶1 ratio).

  • Total permutations: $4^{3}=64$ codons encode 20 amino acids.

• Redundancy (degeneracy): several codons can specify the same amino acid (e.g., GAA & GAG → Glu) but the code is not ambiguous (each codon → one amino acid only).

• Wobble: 3rd codon position tolerates non-Watson–Crick pairing, enhancing speed & resilience.

• Special codons

  • Start: AUG (also codes Met).

  • Stops: UAA, UAG, UGA (no amino acid, terminate translation).

• Nearly universal across all life forms and thus evidence for common ancestry; genes can often be expressed across species boundaries.

Exons & Introns (Eukaryotes)

• Exon: DNA segment retained in mature mRNA; encodes protein information.

• Intron: non-coding intervening sequence removed during RNA splicing; absent in prokaryotic genes.

RNA Types & Specific Roles

• mRNA (messenger)

  • Single-stranded, relatively short-lived, carries genetic message from nucleus to ribosome.

  • Only RNA species that is translated.

  • Codons read 5′→3′ during translation.

• tRNA (transfer)

  • Cloverleaf structure; dozens of genes encode distinct tRNAs.

  • 3′ end carries specific amino acid; anticodon loop base-pairs with mRNA codon (antiparallel orientation, e.g.
    AUG ↔ UAC).

• rRNA (ribosomal)

  • Combines with proteins to form large & small ribosomal subunits.

  • Confers catalytic peptidyl-transferase activity and structural framework.

Reading Frames & Importance

• mRNA must be read in correct, non-overlapping triplets.

• Frameshifts (caused by insertions/deletions) scramble message:

  • Demonstrated by phrase analogy: “the red dog ate the bug” → shifting letters produces gibberish.

Transcription Mechanics (Prokaryotes & Eukaryotes)

• Enzyme: RNA polymerase (no primer needed); synthesizes RNA 5′→3′ using DNA template (read 3′→5′).

• Key DNA elements

  • Promoter (contains TATA box in both domains): binding site for RNA polymerase.

  • Terminator (prokaryotes) / polyadenylation signal (eukaryotes): signals RNA release.

  • Transcription unit: region between promoter & terminator that is transcribed.

• Stages

  1. Initiation
     • Transcription factors bind promoter (Eukaryotes) → recruit RNA Pol II.
     • Promoter + TFs + RNA Pol = transcription initiation complex.

  2. Elongation
     • RNA Pol adds complementary ribonucleotides; DNA rewinds behind enzyme.

  3. Termination
     • Prokaryotes: terminator sequence forms hairpin or rho-dependent stop.
     • Eukaryotes: RNA Pol II passes AAUAAA signal; pre-mRNA cleaved & released.

Post-Transcriptional Processing (Eukaryotes)

• Pre-mRNA → mature mRNA via three main modifications:

  1. 5′ Capping: addition of 7-methyl-G cap; assists ribosome binding & mRNA stability.

  2. 3′ Polyadenylation: poly-A tail (~50–250 $A$ residues); enhances nuclear export, translation, stability.

  3. Intron Splicing
     • Spliceosome (snRNA + proteins) excises introns and ligates exons.
     • Ribozymes (catalytic RNAs) participate.

• Alternative Splicing

  • Regulatory proteins allow different exon combinations, generating multiple proteins from one gene; drives proteomic diversity & evolution (exon shuffling).

Translation Overview

• Occurs on ribosomes in cytosol or on rough ER.

• Ribosome anatomy

  • Small subunit: mRNA binding.

  • Large subunit: catalytic peptidyl-transferase center.

  • Sites: A (aminoacyl), P (peptidyl), E (exit).

• Activation of amino acids

  • Aminoacyl-tRNA synthetase (20 enzymes) uses ATP to attach amino acid to corresponding tRNA → “charged” tRNA (aminoacyl-tRNA).

• Three translation phases (all GTP-dependent factors)

  1. Initiation
     • Small subunit binds mRNA at Shine-Dalgarno (prokaryotes) or 5′ cap (eukaryotes); locates AUG.
     • Initiator tRNA $\text{Met–tRNA}^{\text{i}}_{\text{Met}}$ enters P site.
     • Large subunit joins → initiation complex.

  2. Elongation (cyclic)
     • Codon recognition at A site.
     • Peptidyl transferase forms peptide bond between P-site chain & new amino acid in A site.
     • Ribosome translocates 5′→3′; deacylated tRNA moves to E site and exits.

  3. Termination
     • Stop codon reached; release factor binds A site.
     • Hydrolysis adds H₂O, releasing completed polypeptide; ribosomal subunits dissociate.

• Multiple ribosomes translating the same mRNA form a polyribosome, greatly amplifying protein output.

Protein Folding & Post-Translational Modifications (PTMs)

• Polypeptide often requires further steps to become functional:

  1. Covalent additions: sugars (glycosylation), lipids, phosphate groups, etc.

  2. Proteolytic cleavage of leading methionine or signal peptides.

  3. Assembly of multiple subunits → quaternary structures.

• Chaperone proteins may guide folding.

• Ribosome targeting

  • Free ribosomes → cytosolic proteins.

  • Bound ribosomes (RER) → endomembrane system proteins or secreted proteins; signal peptide directs ribosome to ER.

Antibiotic Targets on Bacterial Translation

• Tetracycline: blocks A site → prevents tRNA binding → inhibits codon recognition (elongation stops).

• Chloramphenicol: inhibits peptidyl transferase → prevents peptide-bond formation → halts protein chain growth.

Mutation Types & Consequences

• Mutagens: physical (radiation) or chemical agents; many are carcinogenic.

• Point Mutations (single-nucleotide substitutions)

  • Silent: codon change but same amino acid (redundancy).

  • Missense: different amino acid (e.g., sickle-cell anemia).

  • Nonsense: converts codon to stop; creates truncated non-functional protein.

• Frameshift Mutations (insertions/deletions not in multiples of 3)

  • Shift reading frame; generally severe (cystic fibrosis, Crohn’s disease).

• Comparison summary

  • Point: substitution only, reading frame intact.

  • Frameshift: indel, reading frame altered, often larger phenotypic impact.

Retroviruses – Exception to Central Dogma

• Carry single-stranded RNA genome.

• Reverse transcriptase converts RNA → DNA (error-prone).

• Viral DNA integrates into host genome; host machinery transcribes & translates viral genes.

• HIV (causative agent of AIDS) is the canonical human retrovirus.

• Coronaviruses are not retroviruses (lack RT).

DNA Sense vs Antisense Strands

• Sense (coding, non-template, $+$): sequence identical to mRNA (except T ↔ U); written 5′→3′.

• Antisense (template, non-coding, $-$): strand read by RNA polymerase; complementary to mRNA.

Information Transfer Summary Diagram

• DNA (triplets) → transcription → pre-mRNA → processing (cap, poly-A, splicing) → mature mRNA (codons) → translation (tRNA anticodons, ribosome sites) → amino acid sequence (peptide bonds) → functional protein (after folding & PTMs).

Numerical / Formula Highlights

• $4^{3}=64$ codons encode 20 amino acids.

• Human genome ≈ $3\times10^{9}$ bp (diploid nucleotide count $6\times10^{9}$).

• Ribosomes read mRNA 5′→3′; RNA Pol synthesizes RNA 5′→3′.

• Energy: aminoacyl-tRNA formation consumes $1$ ATP; many elongation steps consume GTP.

Gene Definition & Genome Overview

• The human karyotype has 46 chromosomes, containing $3\times10^{9}$ base pairs of DNA across thousands of genes. A gene is a DNA region expressed to produce a functional polypeptide or RNA molecule.

Proteins & Amino-Acid Basics

• Proteins are long polypeptides composed of 20 standard amino acids linked by peptide bonds.

Flow of Genetic Information

• The Central Dogma (DNA

→ RNA

→ Protein

→ Phenotype) describes the flow of genetic information, with retroviruses as an exception.

Basic Principles of Transcription & Translation

• RNA serves as a bridge, with Transcription being DNA-templated RNA synthesis and Translation being mRNA-directed polypeptide synthesis on ribosomes.

• Prokaryotes couple transcription and translation due to no nuclear envelope, while eukaryotes separate them (nucleus for transcription, cytoplasm for translation).

Genetic Code – Core Properties

• The genetic code is a triplet codon system ($4^{3}=64$ codons specifying 20 amino acids), demonstrating redundancy (multiple codons for one amino acid) but no ambiguity.

• Key codons include AUG (start/Met) and UAA, UAG, UGA (stops).

• The code is nearly universal, supporting common ancestry.

Exons & Introns (Eukaryotes)

• In eukaryotes, exons are coding segments retained in mature mRNA, while non-coding introns are removed during splicing.

RNA Types & Specific Roles

• mRNA carries genetic messages and is translated.

• tRNA carries specific amino acids and has an anticodon that pairs with mRNA codons.

• rRNA forms ribosomal subunits, providing catalytic and structural functions.

Reading Frames & Importance

• mRNA must be read in correct, non-overlapping triplets; frameshift mutations (insertions/deletions) severely alter the message.

Transcription Mechanics (Prokaryotes & Eukaryotes)

• RNA polymerase synthesizes RNA 5′→3′ from a DNA template.

• Key elements include promoters (RNA Pol binding) and terminators (prokaryotes) or polyadenylation signals (eukaryotes).

• Stages are Initiation (RNA Pol recruitment), Elongation (nucleotide addition), and Termination (RNA release).

Post-Transcriptional Processing (Eukaryotes)

• Pre-mRNA in eukaryotes undergoes 5′ capping, 3′ polyadenylation, and intron splicing by spliceosomes.

• Alternative splicing allows one gene to produce multiple proteins, contributing to proteomic diversity.

Translation Overview

• Translation occurs on ribosomes (with A, P, E sites) and involves charged tRNAs formed by aminoacyl-tRNA synthetases.

• Phases: Initiation (ribosome binds mRNA, initiator tRNA enters P site), Elongation (codon recognition, peptide bond formation, translocation), and Termination (stop codon, polypeptide release).

• Polyribosomes allow efficient amplification of protein output.

Protein Folding & Post-Translational Modifications (PTMs)

• Polypeptides often require folding (guided by chaperones) and PTMs (e.g., glycosylation, cleavage) to become functional.

• Ribosomes are targeted to the cytosol for cytosolic proteins or to the rough ER for endomembrane/secreted proteins via a signal peptide.

Mutation Types & Consequences

• Point mutations (single-nucleotide changes) can be Silent (no amino acid change), Missense (different amino acid), or Nonsense (premature stop codon).

• Frameshift mutations (insertions/deletions not in multiples of 3) shift the reading frame, leading to severe consequences.