DNA Structure and Gene Expression

Chapter 25: DNA Structure and Gene Expression

25.1 DNA Structure

  • In the mid-twentieth century, geneticists and biochemists were uncovering DNA as the genetic material, leading to significant advancements in modern molecular biology.
  • Key Qualities of Genetic Material:
    • Capability to store information essential for development, structure, and metabolism of cells or organisms.
    • Stability that allows for high-accuracy replication and transmission across generations.

Structure of DNA

  • Discovery: James Watson and Francis H. C. Crick elucidated the structure of DNA in 1953.
    • DNA is composed of a chain of nucleotides, with each nucleotide consisting of three subunits:
    • Phosphoric acid (phosphate).
    • A pentose sugar (deoxyribose).
    • A nitrogen-containing base.
  • Types of Bases in DNA:
    • Four possible bases:
    • Purines (double ring):
      • Adenine (A).
      • Guanine (G).
    • Pyrimidines (single ring):
      • Thymine (T).
      • Cytosine (C).
  • Polynucleotide Structure:
    • Each DNA strand is a polynucleotide with a backbone composed of alternating phosphate and sugar groups, with the bases attached to the sugar and projecting sideways.
  • DNA Double Helix:
    • Made up of two polynucleotide strands held together through hydrogen bonding between complementary bases:
    • Complementary Base Pairing:
      • Adenine (A) pairs with Thymine (T) via two hydrogen bonds.
      • Guanine (G) pairs with Cytosine (C) via three hydrogen bonds.
  • Antiparallel Orientation:
    • The two DNA strands are antiparallel, meaning they run in opposite directions:
    • One strand has its 5′ carbon atom at the uppermost position, while the other has its 3′ carbon atom at the uppermost position.
  • Visual Representation:
    • When unwound, DNA resembles a ladder where:
    • The sides are sugar-phosphate backbones.
    • The rungs are complementary base pairs.

25.2 DNA Replication

Overview of DNA Replication

  • Definition: DNA replication is the process of copying one DNA double helix into two identical double helices.
    • The double-stranded structure allows each original strand to serve as a template for a complementary strand.
    • Semiconservative Replication: Each daughter DNA helix contains one new strand and one old strand from the parent molecule, ensuring identical daughter molecules.
  • Enzymatic Roles in DNA Replication:
    • Several enzymes and proteins play a role in replication:
    • DNA Helicase: Unwinds the double-stranded DNA at the replication fork by disrupting hydrogen bonds between paired bases.
    • DNA Polymerase: Positions new complementary DNA nucleotides along the separated strands, using the original strands as templates.
    • DNA ligase connects Okazaki fragments on the lagging strand and seals gaps in the sugar-phosphate backbone, ensuring the integrity of the DNA.
  • Orientation and Synthesis Directions:
    • DNA strands are antiparallel, and DNA polymerase can only add nucleotides to the free 3′ end. Therefore, the synthesis occurs in opposite directions:
    • Leading Strand: Synthesized continuously in the same direction as the helicase unwinds.
    • Lagging Strand: Synthesized in segments (Okazaki fragments) away from the replication fork.

Implications of Chemotherapeutic Drugs

  • Some cancer treatments target DNA replication by using nucleotide analogs which are mistakenly incorporated into DNA by cancer cells, halting replication and leading to cell death.

25.3 Gene Expression

Overview of Gene Expression

  • Gene expression involves turning a gene sequence into a protein through different types of RNA:
    • Messenger RNA (mRNA): Carries genetic information from DNA to the ribosomes.
    • Transfer RNA (tRNA): Brings amino acids to the ribosome during protein synthesis.
    • Ribosomal RNA (rRNA): Component of ribosomes, facilitating translation.
  • Process of Gene Expression:
    • Transcription: Occurs in the nucleus, where a segment of DNA serves as a template to form mRNA.
    • Translation: Occurs in the cytoplasm, where mRNA codons determine the amino acid sequence of a polypeptide with aids from tRNA and rRNA.
  • Historical vs. Proposed Gene Definition:
    • Historical: A gene was defined as a nucleic acid sequence coding for amino acid sequences in proteins.
    • Proposed: A gene represents a segment of genetic material coding for functional products, which can be either DNA or polypeptides (proteins).

mRNA Formation

  • mRNA is synthesized when RNA polymerase binds to a promoter region on the DNA, resulting in a sequence complementary to the DNA template, using uracil (U) in place of thymine (T).
  • mRNA Processing:
    • Involves removing introns and splicing exons together with the help of spliceosomes prior to mRNA's exit from the nucleus.

Translation Overview

  • Genetic Code:
    • The triplet code consists of three nucleotide units (codons) in mRNA. There are 64 different codons:
    • 61 encode specific amino acids.
    • 3 serves as stop codons (UAA, UGA, UAG) signaling termination of polypeptide synthesis.
    • It is generally universal across all living organisms.

Role of tRNA

  • Transfer RNA Structure:
    • tRNA has a boot-like shape with an amino acid attached at one end and an anticodon at the other, complementary to the mRNA codon.
  • Codon-Anticodon Pairing:
    • The order of mRNA codons directs the sequence of tRNA bringing in amino acids, influencing the amino acid sequence in proteins.

Ribosomes and rRNA

  • Composition: Ribosomes consist of proteins and rRNAs with two subunits that bind to mRNA during translation.
  • Function: Ribosomes facilitate the complementary base pairing between tRNA anticodons and mRNA codons, crafting polypeptides as new tRNAs arrive.
  • Polyribosomes: On mRNA, multiple ribosomes can synthesize several copies of the same polypeptide simultaneously.

Steps of Translation

  1. Initiation: Assembles all translation components (small ribosomal subunit, mRNA, initiator tRNA, and large ribosomal subunit).
    • Initiator tRNA pairs with the start codon (AUG).
  2. Elongation: Involves peptide bond formation, elongating the polypeptide chain. Two tRNAs can be present at a time.
  3. Termination: Occurs at stop codons where a release factor hydrolyzes the bond, freeing the completed polypeptide.

Genetic Disorders and Proteins

  • Proteins link genotype to phenotype. Abnormal genes can lead to genetic disorders or contribute to cancer due to faulty protein synthesis affecting physiological functions.

25.4 Control of Gene Expression

  • Gene activity regulation contributes to cell specialization.

25.5 Gene Mutations and Cancer

Types of Mutations

  • Germ-Line Mutations: Occur in sex cells and can be inherited.
  • Somatic Mutations: Non-inherited and can lead to cancer development.

Causes of Mutations

  • Spontaneous Mutations: Occur during normal biological processes.
  • Induced Mutations: Result from environmental factors like radiation and chemicals.
  • DNA Replication Errors: Minimally occur due to proofreading by DNA polymerase, typically resulting in one error per billion nucleotides.

Effects of Mutations

  • Point Mutations: Involve single nucleotide changes, ranging from no effect to producing abnormal proteins (e.g., sickle-cell disease).
  • Frameshift Mutations: Results from insertion/deletion, altering downstream codon sequences and protein functionality.

Cancer Development and Characteristics

  • Cancer arises via accumulated mutations affecting tumor suppressors and oncogenes, leading to uncontrolled cell growth.
  • Well-known tumor suppressor gene: p53.
  • Cancer cells are characterized by:
    • Genomic instability and multiple mutations.
    • Lack of regulation of cell cycle.
    • Ability to escape apoptosis signals.
    • Metastatic capability due to altered adhesion mechanisms.
  • Malignant tumors can invade surrounding tissues, forming new tumors (metastasis).

Summary

  • Understanding DNA structure and function is critical for grasping gene expression and the implications of mutations in disease mechanisms, particularly cancer.
  • Biochemical pathways and mechanisms governing DNA replication and protein synthesis are vital for comprehending genetic continuity, organismal development, and disease pathology.