What is a Gene?

  • A gene is defined as a sequence of DNA that codes for a protein.
  • Gene expression allows visibility of traits in organisms.

Molecular Biology

  • Definition: The study of gene structure and function at the molecular level.

Central Dogma of Molecular Biology

  • The central dogma describes the flow of genetic information from DNA to RNA to protein.
  • Two major steps involved in gene expression:
    • Transcription: The process of making mRNA from DNA.
    • Translation: The process of translating mRNA into a protein.

Inheritance of Genes

  • Genes are inherited from parents to offspring.
  • DNA replication occurs during cell division so that each somatic cell contains identical DNA.
  • GAMETES (reproductive cells) undergo meiosis, resulting in half the DNA content.

Historical Context of Genetics

Domestication and Cultivation

  • Evidence exists that prehistoric humans recognized inheritance through:
    • Domestication of animals around 8000-1000 BC, understanding traits could be inherited (e.g., breeding dogs).
    • Specific pollination practices in plants since 5000 BC (shown in Egyptian art).

Particulate Theory of Inheritance

  • Supported by Aristotle: Suggested that "particles" were passed from parents to offspring, explaining traits.

Modern Genetics Pioneer

Gregor Mendel
  • Recognized as the father of modern genetics.
  • Discovered the concept of "factors" (genes) being passed from parents to offspring.
  • Worked with pea plants, establishing foundational principles of inheritance.

Linkage Between Genes and Chromosomes

Thomas Hunt Morgan
  • Linked gene inheritance to chromosome inheritance using fruit flies.
  • Conducted experiments mating red-eyed females with white-eyed males:
    • Observed all progeny in the first generation (F1) had red eyes (dominant trait).
    • In the F2 generation, white eyes appeared only in males, demonstrating sex-linked inheritance.

Genetic Linkage

  • Definition: Genes located on the same chromosome are "linked" and usually inherited together.
  • Crossing over interrupts linkage during prophase I of meiosis.

Discovery of DNA

Friedrich Miescher

  • Discovered DNA while studying proteins; termed it "nuclein."
  • Isolated it from pus and identified it was different from proteins because it precipitated in acid and dissolved in alkali conditions.

Griffith Experiment

  • Studied pneumonia-causing bacteria (S strain - pathogenic, R strain - non-pathogenic).
    • Treatment outcomes:
    • Mice with live S strain died.
    • Mice with live R strain survived.
    • Mice with heat-killed S strain survived.
    • Mice with heat-killed S strain and live R strain died, implying R strain transformed into S strain.

Avery's Contribution

  • Showed that DNA is the hereditary material by transforming R strain into S strain using isolated DNA from S strain.

Hershey and Chase Experiment

  • Investigated inheritance in bacteriophage; determined DNA, not protein, is the hereditary material.
    • Labeled DNA with P-32 and protein with S-35.
    • Found P-32 inside infected bacteria, confirming DNA was responsible for the inheritance of traits.

Linking Genes to Proteins

Beadle and Tatum

  • Studied Neurospora and concluded that one gene produces one enzyme, leading to the one gene-one polypeptide hypothesis.

Differences in DNA Structures

B-DNA, A-DNA, Z-DNA
  • B-DNA: Most common form under physiological conditions; right-handed helix with 10 base pairs per turn.
  • A-DNA: Found in low humidity; more compact; base pairs tilted 20 degrees from horizontal; 11 base pairs per turn.
  • Z-DNA: Alternating purines and pyrimidines; left-handed helix; least compact form, function unknown.

DNA Structure and Characteristics

Linear, Circular, and Supercoiled DNA

  • Linear DNA: Held looped out on a protein scaffold.
  • Circular DNA: Found in bacterial and viral genomes; often in large loops in eukaryotic cells.
  • Supercoiled DNA: Twisted more tightly around its axis; occurs in closed structures.

Importance of GC Content

  • Indicates the difficulty of separating DNA strands; G-C pairs form three hydrogen bonds, whereas A-T pairs form two.

Denaturation and Melting Temperature (Tm)

  • Denaturation: The process of separating the two strands of DNA, typically done using heat.
  • Tm: Melting temperature at which half of the DNA strands are denatured. Influenced by GC content, length of DNA, and salt concentrations.

Aspects of DNA Renaturation

  • Annealing: Bringing together two strands of DNA.
  • Factors influencing renaturation include temperature and DNA concentration.
  • Cot curves: Describe reassociation of DNA, representing time and concentration required for half the DNA to renature.

Complexity of DNA Sequences

  • Complexity influences renaturation time and concentration; less complex sequences have lower Cot1/2 values.

Techniques in Molecular Biology

Hybridization Techniques

  • Southern Blots: Detect DNA sequences using tagged ssDNA probes.
  • Northern Blots: Detect RNA sequences similarly but targeting RNA.
  • Conditions during hybridization affect probe binding; low stringency allows for more mismatching.

C-value Paradox

  • Some organisms with greater complexity do not necessarily have higher DNA content.

Levels of DNA Packaging

First Level: Nucleosomes

  • DNA wraps around histone proteins, creating a "beads on a string" structure.

Higher Levels of DNA Packaging

  • The nucleosome fiber coils into a 30 nm chromatin fiber.
  • Further compaction forms looped domains anchored to protein scaffolds.
  • Final condensation seen during mitosis with fully packed chromosomes.

DNA Replication Initiation

Prokaryotic Replication

  • Initiation starts at oriC with AT-rich regions that are easier to unwind.
  • Key proteins involved are DnaA (initiator), DnaB (helicase), single-stranded binding protein (SSB), and DnaG (primase).

Eukaryotic Replication Initiation

  • Multiple origins of replication characterized by ARS sequences recognized by the Origin Recognition Complex (ORC).

Leading vs. Lagging Strand Synthesis

  • Leading Strand: Synthesized continuously with one RNA primer.
  • Lagging Strand: Synthesized discontinuously; multiple RNA primers are needed for each Okazaki fragment.

DNA Polymerases

Prokaryotic DNA Polymerases

  • Pol III: Main enzyme for DNA synthesis.
  • Pol I: Involved in primer removal and DNA repair.
  • Pol II: Backup function primarily for repair.

Eukaryotic DNA Polymerases

  • At least five distinct polymerases serving different roles.

What is Telomerase?

  • An enzyme extending telomeres to prevent shortening during cell division, essential for immortal cancer cells.

Cancer and Telomerase

  • Cancer cells often activate telomerase, avoiding replicative senescence and allowing indefinite division.

Significance of Telomeres

  • Protect chromosome ends from degradation and fusion, addressing the end-replication problem in linear DNA.

Replicative senescence and the Hayflick limit

  • Represents the maximum number of divisions normal somatic cells can undergo before halting.

Summary of DNA Functionality

Genetic Material Requirements

  1. Must provide information for traits.
  2. Must allow for organism replication.
  3. Must be able to replicate itself.