7  The Central Dogma in Action

7.1 Learning Objectives

By the end of this chapter, you should be able to:

  1. Describe the flow of genetic information according to the central dogma of molecular biology
  2. Explain the processes of DNA replication, transcription, and translation in detail
  3. Compare and contrast prokaryotic and eukaryotic gene expression
  4. Describe post-transcriptional and post-translational modifications
  5. Explain how mutations occur and how cells repair DNA damage
  6. Analyze how information theory applies to biological information processing
  7. Describe experimental evidence supporting key concepts in molecular biology
  8. Apply understanding of the central dogma to explain genetic disorders and biotechnology applications

7.2 Introduction

The central dogma of molecular biology describes the flow of genetic information within biological systems: DNA → RNA → protein. This chapter explores how cells implement this information flow, examining the molecular mechanisms that ensure accurate transmission of genetic information from one generation to the next and its expression within each cell. We will investigate how the abstract concept of biological information, introduced in Chapter 3, manifests in concrete molecular processes that underlie all cellular functions.

7.3 The Central Dogma: Overview

7.3.1 Historical Development

Francis Crick (1958): First articulated the central dogma
Original formulation: Information flows from nucleic acids to proteins, not reverse
Modern understanding: DNA → RNA → protein, with important exceptions

7.3.2 Information Flow Pathways

General transfers (occur in all cells):

  1. DNA → DNA (replication)
  2. DNA → RNA (transcription)
  3. RNA → protein (translation)

Special transfers (occur in specific cases):

  1. RNA → RNA (replication in RNA viruses)
  2. RNA → DNA (reverse transcription in retroviruses)

Never observed:

  1. Protein → protein
  2. Protein → DNA
  3. Protein → RNA

7.3.3 Exceptions and Modifications

Prions: Protein → protein conformational change
Epigenetic inheritance: Information transmitted without DNA sequence change
RNA editing: Post-transcriptional alteration of RNA sequences
Alternative splicing: Multiple proteins from single gene

7.4 DNA Replication

7.4.1 Overview

Purpose: Duplicate genetic material for cell division
Requirements: Template DNA, nucleotides, enzymes, energy
Key features: Semiconservative, bidirectional, semidiscontinuous

7.4.2 Molecular Mechanism

Initiation:

  • Origin of replication: Specific sequences where replication begins
  • Initiation proteins: Bind origin, separate strands
  • Replication bubble: Region of separated strands
  • Replication forks: Y-shaped regions where synthesis occurs

Elongation:

  • DNA helicase: Unwinds double helix
  • Single-strand binding proteins: Stabilize separated strands
  • Topoisomerase: Relieves torsional strain ahead of fork
  • Primase: Synthesizes RNA primers
  • DNA polymerase III: Main replicase in bacteria
  • Leading strand: Continuous synthesis 5’→3’
  • Lagging strand: Discontinuous synthesis (Okazaki fragments)

Termination:

  • Termination sequences: Specific sites in bacteria
  • Telomeres: Ends of eukaryotic chromosomes
  • Telomerase: Adds repeats to telomeres in stem/germ cells

7.4.3 Enzymes and Proteins

Prokaryotic replication:

  • DNA polymerase I: Removes primers, fills gaps
  • DNA polymerase III: Main replicase
  • DNA ligase: Joins Okazaki fragments
  • DNA gyrase: Type II topoisomerase

Eukaryotic replication:

  • Multiple DNA polymerases (α, δ, ε)
  • PCNA: Sliding clamp
  • RFC: Clamp loader

7.4.4 Accuracy and Proofreading

Error rate: ~10^-9 per base pair

Mechanisms:

  1. Base pairing specificity: Hydrogen bonding geometry
  2. 3’→5’ exonuclease activity: Proofreading by DNA polymerase
  3. Mismatch repair: Post-replication correction
  4. Nucleotide excision repair: Removes damaged bases

Fidelity: Combined mechanisms achieve high accuracy

7.5 Transcription

7.5.1 Overview

Purpose: Synthesize RNA from DNA template

Types of RNA:

  • mRNA: Messenger RNA (codes for proteins)
  • tRNA: Transfer RNA (carries amino acids)
  • rRNA: Ribosomal RNA (structural component of ribosomes)
  • Other RNAs: snRNA, miRNA, siRNA, lncRNA

7.5.2 Prokaryotic Transcription

Initiation:

  • Promoter: -10 (Pribnow box) and -35 regions
  • RNA polymerase: Holoenzyme (core + σ factor)
  • Closed complex: Polymerase binds promoter
  • Open complex: DNA unwinds at start site

Elongation:

  • RNA polymerase: Synthesizes RNA 5’→3’
  • Transcription bubble: ~17 bp unwound region
  • RNA-DNA hybrid: ~8 bp

Termination:

  • Rho-dependent: ρ protein binds rut site, terminates
  • Rho-independent: Hairpin formation in RNA

7.5.3 Eukaryotic Transcription

RNA polymerases:

  • RNA Pol I: rRNA (except 5S)
  • RNA Pol II: mRNA, snRNA, miRNA
  • RNA Pol III: tRNA, 5S rRNA, other small RNAs

Transcription factors:

  • General TFs: Required for all Pol II transcription
  • Specific TFs: Regulate specific genes
  • Enhancers: Distant regulatory sequences
  • Mediator complex: Bridges TFs and polymerase

Initiation complex: >50 proteins at promoter

7.5.4 RNA Processing (Eukaryotes)

5’ capping: 7-methylguanosine cap added immediately

3’ polyadenylation: Poly-A tail added (100-250 A’s)

Splicing: Removal of introns, joining of exons

  • Spliceosome: snRNP complex catalyzes splicing
  • Alternative splicing: Different exons combined

RNA editing: Base modification (A→I, C→U)
Nuclear export: Mature mRNA exported through nuclear pores

7.6 Translation

7.6.1 Overview

Purpose: Synthesize protein from mRNA template

Components: mRNA, ribosomes, tRNA, amino acids, factors

Genetic code: Triplet code, degenerate, nearly universal

7.6.2 Genetic Code Properties

Triplet code: 3 nucleotides = 1 amino acid
Degenerate: Multiple codons for most amino acids
Non-overlapping: Read in consecutive triplets
Commaless: No gaps between codons
Universal: Same in nearly all organisms (minor variations)

Start codon: AUG (methionine)
Stop codons: UAA, UAG, UGA

7.6.3 Transfer RNA (tRNA)

Structure: Cloverleaf secondary structure, L-shaped tertiary

Anticodon: Base pairs with mRNA codon

Amino acid attachment: Covalent bond to 3’ end

Aminoacyl-tRNA synthetases: Attach correct amino acid to tRNA

  • Accuracy: High specificity prevents errors
  • Proofreading: Some synthetases have editing sites

7.6.4 Ribosomes

Prokaryotic: 70S (50S + 30S subunits)

Eukaryotic: 80S (60S + 40S subunits)

Components: rRNA and proteins

Functional sites:

  • A site: Aminoacyl-tRNA binding
  • P site: Peptidyl-tRNA binding
  • E site: Exit site

7.6.5 Translation Mechanism

Initiation:

  • Prokaryotic: Shine-Dalgarno sequence, initiation factors
  • Eukaryotic: 5’ cap scanning, Kozak sequence, more factors

Elongation:

  1. Aminoacyl-tRNA binding: To A site (EF-Tu in bacteria)
  2. Peptide bond formation: Catalyzed by peptidyl transferase
  3. Translocation: Ribosome moves one codon (EF-G in bacteria)
  • Rate: ~15-20 amino acids per second

Termination:

  • Release factors: Recognize stop codons
  • Polypeptide release: From ribosome
  • Ribosome recycling: Subunits separate

7.6.6 Post-translational Modifications

Folding: Assisted by chaperones

Cleavage: Removal of signal peptides, propeptides

Chemical modifications: Phosphorylation, glycosylation, acetylation

Disulfide bonds: Stabilize tertiary structure

Proteolytic processing: Activation of zymogens

Targeting: Signals for specific cellular locations

7.7 Regulation of Gene Expression

7.7.1 Prokaryotic Regulation

Operon model (Jacob and Monod):

  • Operon: Cluster of genes with related functions
  • Promoter: RNA polymerase binding site
  • Operator: Repressor binding site
  • Structural genes: Code for enzymes

Lac operon: Inducible system for lactose metabolism

  • Lactose absent: Repressor bound, no transcription
  • Lactose present: Allolactose binds repressor, transcription occurs
  • Glucose effect: Catabolite repression via cAMP-CAP

Trp operon: Repressible system for tryptophan synthesis

  • Tryptophan absent: No repression, transcription occurs
  • Tryptophan present: Corepressor binds repressor, transcription blocked

7.7.2 Eukaryotic Regulation

Transcriptional control:

  • Chromatin remodeling: Histone modifications, nucleosome positioning
  • DNA methylation: Typically represses transcription
  • Transcription factors: Activate or repress transcription
  • Enhancers/silencers: Distant regulatory elements

Post-transcriptional control:

  • Alternative splicing: Different mRNA isoforms
  • RNA stability: Control of mRNA degradation
  • RNA interference: miRNA, siRNA regulation

Translational control:

  • Initiation factors: Phosphorylation regulates activity
  • mRNA secondary structure: Affects ribosome binding
  • microRNAs: Block translation or cause degradation

Post-translational control:

  • Protein modification: Affects activity, stability, localization
  • Protein degradation: Ubiquitin-proteasome pathway

7.8 Mutations and DNA Repair

7.8.1 Types of Mutations

Point mutations:

  • Silent: No amino acid change (same codon)
  • Missense: Different amino acid
  • Nonsense: Stop codon introduced
  • Frameshift: Insertion/deletion not multiple of 3

Chromosomal mutations:

  • Deletion: Loss of chromosome segment
  • Duplication: Repeat of segment
  • Inversion: Segment reversed
  • Translocation: Segment moved to different chromosome

7.8.2 Causes of Mutations

Spontaneous:

  • Replication errors: Polymerase mistakes
  • Tautomeric shifts: Rare base forms
  • Depurination: Loss of purine base
  • Deamination: C → U conversion

Induced:

  • Chemical mutagens: Base analogs, alkylating agents
  • Radiation: UV light (pyrimidine dimers), ionizing radiation
  • Intercalating agents: Insert between bases

7.8.3 DNA Repair Mechanisms

Direct reversal:

  • Photolyase: Repairs pyrimidine dimers (light-dependent)
  • MGMT: Removes methyl groups from guanine

Excision repair:

  • Base excision repair: Removes damaged bases
  • Nucleotide excision repair: Removes oligonucleotides (bulky lesions)
  • Mismatch repair: Corrects replication errors

Double-strand break repair:

  • Non-homologous end joining: Error-prone, direct ligation
  • Homologous recombination: Error-free, uses sister chromatid

Translesion synthesis: Error-prone bypass of lesions

7.9 Information Theory Applications

7.9.1 Information Content of DNA

Maximum information: 2 bits per base (4 equally likely bases)
Actual information: ~1.8-1.9 bits/base (non-random distribution)
Coding regions: Lower entropy (conserved sequences)
Non-coding regions: Higher entropy (more variable)

7.9.2 Error Rates and Channel Capacity

DNA replication: Error rate ~10^-9 per base
Transcription: Error rate ~10^-4 per base
Translation: Error rate ~10^-4 per amino acid

Channel capacity: DNA → protein information transmission

  • Noise sources: Polymerase errors, environmental damage
  • Error correction: Multiple repair mechanisms
  • Redundancy: Genetic code degeneracy provides error buffering

7.9.3 Evolutionary Information

Sequence conservation: Indicates functional importance

Information gain: Natural selection increases information about environment

Molecular evolution rates:

  • Synonymous substitutions: Higher rate (neutral)
  • Nonsynonymous substitutions: Lower rate (subject to selection)

7.10 Experimental Foundations

7.10.1 Key Experiments

Avery-MacLeod-McCarty (1944): DNA is transforming principle
Hershey-Chase (1952): DNA is genetic material of phage
Meselson-Stahl (1958): Semiconservative DNA replication
Nirenberg-Matthaei (1961): Deciphering genetic code
Jacob-Monod (1961): Operon model of gene regulation

7.10.2 Modern Techniques

DNA sequencing: Sanger, next-generation, third-generation

Gene expression analysis: Microarrays, RNA-seq

Protein detection: Western blot, immunofluorescence, mass spectrometry

Gene editing: CRISPR-Cas9, TALENs, zinc finger nucleases

7.11 Chapter Summary

7.11.1 Key Concepts

  1. Central dogma: DNA → RNA → protein information flow
  2. DNA replication: Semiconservative, requires multiple enzymes
  3. Transcription: RNA synthesis from DNA template
  4. Translation: Protein synthesis from mRNA template
  5. Genetic code: Triplet, degenerate, nearly universal
  6. Gene regulation: Controls expression at multiple levels
  7. Mutations: Changes in DNA sequence, repaired by multiple mechanisms
  8. Information theory: Applies to accuracy and evolution of biological information

7.11.2 Comparison: Prokaryotes vs. Eukaryotes

Process Prokaryotes Eukaryotes
Transcription/Translation Coupled Separated (nuclear/cytoplasmic)
mRNA processing Minimal Extensive (capping, polyA, splicing)
Gene organization Operons Individual genes with introns
Regulation Mainly transcriptional Multiple levels

7.11.3 Accuracy of Information Transfer

Step Error rate Correction mechanisms
DNA replication ~10^-9/base Proofreading, mismatch repair
Transcription ~10^-4/base Lower fidelity acceptable
Translation ~10^-4/amino acid Proofreading, kinetic selection
Overall Very high Multiple redundant systems

7.11.4 Information Flow Summary

DNA (replication) → DNA
      ↓
    RNA (transcription)
      ↓
  Protein (translation)
      ↓
Cellular function

7.12 Review Questions

7.12.1 Level 1: Recall and Understanding

  1. State the central dogma of molecular biology and its three general transfers.
  2. Describe the semiconservative model of DNA replication.
  3. List the three types of RNA involved in protein synthesis and their functions.
  4. What are the properties of the genetic code?
  5. Name three types of DNA repair mechanisms.

7.12.2 Level 2: Application and Analysis

  1. Compare transcription and translation in prokaryotes and eukaryotes.
  2. Explain how the lac operon is regulated in response to lactose and glucose.
  3. A mutation changes a codon from UUU to UUA. What type of mutation is this, and what are its potential effects?
  4. How does alternative splicing increase proteomic diversity?
  5. Calculate the information content of a DNA sequence with base frequencies: A=0.25, T=0.25, C=0.30, G=0.20.

7.12.3 Level 3: Synthesis and Evaluation

  1. Design an experiment to determine whether a newly discovered virus has DNA or RNA as its genetic material.
  2. Evaluate the statement: “The central dogma needs revision in light of modern discoveries like prions and epigenetics.”
  3. How does information theory help explain why some DNA sequences evolve faster than others?
  4. Propose a mechanism for how a cell might coordinate the expression of genes involved in a metabolic pathway.

7.13 Key Terms

  • Central dogma: DNA → RNA → protein information flow
  • Replication: Process of copying DNA
  • Transcription: Synthesis of RNA from DNA template
  • Translation: Synthesis of protein from mRNA template
  • Codon: Three-nucleotide sequence specifying an amino acid
  • Anticodon: Three-nucleotide sequence on tRNA complementary to codon
  • Operon: Cluster of prokaryotic genes with related functions
  • Promoter: DNA sequence where RNA polymerase binds to initiate transcription
  • Intron: Non-coding sequence in eukaryotic genes, removed by splicing
  • Exon: Coding sequence in eukaryotic genes, retained in mature mRNA
  • Mutation: Change in DNA sequence
  • DNA repair: Mechanisms correcting DNA damage
  • Genetic code: Correspondence between nucleotide triplets and amino acids
  • Ribosome: Cellular structure where translation occurs
  • RNA polymerase: Enzyme that synthesizes RNA from DNA template
  • Transcription factor: Protein regulating transcription

7.14 Further Reading

7.14.1 Books

  1. Watson, J. D., et al. (2014). Molecular Biology of the Gene (7th ed.). Pearson.
  2. Lodish, H., et al. (2021). Molecular Cell Biology (9th ed.). W. H. Freeman.
  3. Berg, J. M., et al. (2015). Biochemistry (8th ed.). W. H. Freeman.

7.14.2 Scientific Articles

  1. Crick, F. H. C. (1970). Central dogma of molecular biology. Nature, 227(5258), 561-563.
  2. Meselson, M., & Stahl, F. W. (1958). The replication of DNA in Escherichia coli. PNAS, 44(7), 671-682.
  3. Nirenberg, M. W., & Matthaei, J. H. (1961). The dependence of cell-free protein synthesis in E. coli upon naturally occurring or synthetic polyribonucleotides. PNAS, 47(10), 1588-1602.

7.14.3 Online Resources

  1. NCBI Molecular Biology Resources: https://www.ncbi.nlm.nih.gov/guide/molecular-biology/
  2. DNA Learning Center: https://dnalc.cshl.edu
  3. Protein Data Bank: https://www.rcsb.org

7.15 Quantitative Problems

  1. Information Content:

    1. Calculate Shannon entropy for a DNA sequence with equal base frequencies.
    2. For a sequence with A=0.2, T=0.2, C=0.3, G=0.3.
    3. Which sequence has higher information content? Why?

  2. Mutation Rate Analysis:

    The human genome is 3.2 × 10^9 bp. Mutation rate is 10^-8 per base per generation.

    1. How many new mutations per genome per generation?
    2. If only 2% is coding DNA, how many affect protein sequences?
    3. What percentage of these are likely deleterious?

  3. Translation Rate:

    A protein has 300 amino acids. Translation rate is 15 amino acids/second.

    1. How long does synthesis take?
    2. If ribosome footprint is 30 nucleotides, how many ribosomes can be on an mRNA simultaneously?
    3. Calculate protein production rate if mRNA half-life is 2 hours.

7.16 Case Study: Thalassemia and Gene Expression Defects

Background: β-thalassemia results from reduced or absent β-globin synthesis.

Questions:

  1. How could mutations in promoter, splice sites, or coding sequence cause thalassemia?
  2. Why do some mutations affect RNA processing while others affect translation?
  3. How might understanding transcription factors help develop therapies?
  4. Design experiments to determine which step in gene expression is affected by a new thalassemia mutation.

Data for analysis:

  • β-globin gene: 3 exons, 2 introns
  • Normal hemoglobin: 2 α-globin + 2 β-globin chains
  • Mutations: >200 known in β-globin gene
  • Symptoms: Anemia, organ damage, bone deformities

Next Chapter: Cell Communication and Signaling