Introduction to Genetics, Evolution, and the Cellular Basis of Inheritance

Course Introduction: 1042SCG Genetics and Evolution in Biology

Lecturer and Convener Information:
- Dan Bock: Course convener and lecturer for Nathan campus. He specializes in evolutionary biology and will lead Module 1 (The Chromosomal Basis of Inheritance) and Module 4 (Evolutionary Biology).
- Maggie: Course convener and lecturer for the Gold Coast campus.
- Professor Jeremy Brownlee: A long-time convener and lecturer taking students through Module 2 (The Molecular Basis of Inheritance).
- Senior Lecturer Jean Giacomoto: Lead for Module 3 (Advanced Molecular Biology Techniques).
Course Structure and Logistics:
- Duration: The course spans twelve weeks.
- Enrollment Issues: Due to high demand, a parallel online version is operating. Content is identical to the in-person offering.
- Recordings: All in-person sessions are recorded and available via the Echo360 link on Canvas for students who cannot attend live.
- Communication: Students should use the dedicated course email address provided in Canvas announcements. Announcements on Canvas will trigger email notifications to Griffith University accounts.
Weekly Learning Components:
- Lectures: Two-hour on-campus sessions held weekly.
- Workshops: Interactive two-hour sessions focusing on assessment-style questions. Nathan workshops occur on Fridays. Note: There is no workshop in Week 1; they commence in Week 2.
- PASS (Peer Assisted Study Sessions): Statistical data shows that students attending PASS sessions achieve better marks and higher pass rates. An introduction from the PASS team occurs in the Week 2 workshop.
Laboratory Session (Week 8):
- Weighting: The laboratory experience accounts for $20\%$ of the final grade.
- Duration and Venue: A single three-hour session in Week 8, held in room N 78.
- Activities: DNA extraction, quality checking DNA extracts, and interpreting a Restriction Fragment Length Polymorphism (RFLP) experiment.
- Capacity Limits: Due to health and safety regulations, the lab is capped at $80$ students per session. Switching sessions is generally not possible as most are full.
- Requirements:
  - Mandatory completion of the Lab Induction on Canvas.
  - Personal Protective Equipment (PPE): Safety glasses, lab coat, and enclosed shoes.
  - Miscellaneous: Long hair must be tied back; students must bring a printed lab manual.
- Lab Primer: Conducted on the Friday of Week 7 to prepare students for the following week.
Curriculum Overview (Four Modules):
- Module 1: Cellular reproduction, the cell cycle, and the chromosomal basis of inheritance.
- Module 2: The Central Dogma of molecular biology, focusing on the connection between nucleic acids and proteins (DNA to RNA to Protein).
- Module 3: Recombinant DNA technology, including cloning, PCR, and DNA sequencing.
- Module 4: Evolutionary biology, covering population genetics, natural selection, adaptation, Charles Darwin, and genetic diversity in ecosystems.
Recommended Textbooks:
- Primary: Campbell Biology, 12th Edition (10th Edition onwards is acceptable). An eTextbook is available via Canvas.
- Alternate Resources: Various recommended textbooks are suggested for different illustrations or examples, though they cover identical core topics.

Cellular Organization and the Domains of Life

Bio-molecular Focus: Biology consists of four main classes of molecules: carbohydrates, nucleic acids, proteins, and lipids. This course focuses primarily on nucleic acids.
The Three Domains of Life:
- Bacteria: Abundant and diverse; found in environments ranging from the human gut to deep ocean trenches.
- Archaea: Extreme survivors found in high-salinity lakes or deep-sea vents. Evolutionarily, they are more closely related to Eukarya than Bacteria, despite their prokaryotic cellular organization.
- Eukarya (Eukaryotes): Organisms with complex cells containing a nucleus. This includes animals, plants, fungi, and protists.
Comparison of Prokaryotes and Eukaryotes:
- Similarities: Both possess ribosomes, DNA (chromatin arranged in chromosomes), a cell membrane, and often a cell wall or flagella.
- Prokaryotes (Bacteria and Archaea):
  - No nucleus; genomic DNA is located in a region called the nucleoid.
  - Lack membranous organelles.
  - Significantly smaller in size.
  - Genome consists of a single circular chromosome.
  - Division occurs via binary fission.
- Eukaryotes:
  - DNA is encased in a membrane-bound nucleus.
  - Contain membranous organelles (e.g., Endoplasmic Reticulum, Golgi apparatus, mitochondria, vesicles).
  - Larger and more complex.
  - DNA organized into several linear chromosomes.
  - Division occurs via mitosis and meiosis.

The Central Dogma: Information Flow

Transcription:
- Occurs in the nucleus.
- DNA is transcribed into precursor messenger RNA (pre-mRNA), which then matures into messenger RNA (mRNA).
- The nuclear membrane is NOT impermeable; mRNA must exit through the nuclear envelope to reach the cytoplasm.
Translation:
- Occurs in the cytoplasm.
- Ribosomes (consisting of a small and large subunit) assemble on the mRNA to synthesize proteins using amino acids as building blocks.
Ribosome Localization and Protein Destination:
- Free Ribosomes: Occur in the cytoplasm; the proteins they produce typically remain inside the cell.
- Bound Ribosomes (Found on the Rough Endoplasmic Reticulum): Produce proteins destined for export (secretion) from the cell.
- Pathway for Secretion: Rough ER $\rightarrow$ Golgi apparatus (shipping and receiving center) $\rightarrow$ Plasma membrane $\rightarrow$ Exocytosis.

DNA Structure and Genomic Organization

Chemical Composition of DNA:
- DNA is a double-stranded helix made of building blocks called nucleotides.
- Each nucleotide consists of:
  1. A phosphate group.
  2. A sugar (deoxyribose).
  3. A nitrogenous base (Adenine, Cytosine, Guanine, or Thymine).
Genomic Dimensions:
- Genome: The total DNA content of a cell.
- Physical Length: If unwound and pieced together, human DNA would reach $1.8$ to $2.0\,m$ in length.
- Compaction: The DNA strand diameter is only $2\,nm$ . Through proteins, it is packed into chromosomes with a diameter of $700\,nm$ ( $10,000 \times$ to $50,000 \times$ compaction).
Genes: Discrete units of hereditary information consisting of specific nucleotide sequences. Each eukaryotic chromosome contains thousands of genes.

The Eukaryotic Cell Cycle and Mitosis

Functions of Cell Division:
- Reproduction: Primary mechanism for unicellular eukaryotes (e.g., amoeba).
- Growth and Differentiation: Human bodies contain approximately $30$ - $40$ trillion cells ( $3.0 \times 10^{13}$ to $4.0 \times 10^{13}$ cells), all originating from a single fertilized egg.
- Tissue Renewal: Rapid division occurs in areas like the bone marrow to replace damaged or aging tissue.
The Cell Cycle Phases:
- Interphase ( $\approx 23\,hours$ in humans):
  - G1 (Gap 1): Normal cell function, metabolic activity, and growth.
  - S (Synthesis): Replication of the entire genome.
  - G2 (Gap 2): Final growth, duplication of centrosomes, and DNA repair/correction.
  - G0 Phase: A non-dividing state for highly specialized cells like neurons or cardiac muscle cells.
- Mitotic Phase ( $\approx 1\,hour$ in humans): The process of dividing the genome and the cell.
Stages of Mitosis (PPMAT):
- Prophase: Chromosomes condense; centrosomes migrate to opposite poles; mitotic spindle begins to form.
- Prometaphase: Nuclear envelope fragments; chromosomes attach to spindle microtubules via kinetochores (protein structures on the centromeres).
- Metaphase: Chromosomes align along the metaphase plate in the center of the cell due to a ‐tug-of-war‐ between spindle fibers.
- Anaphase: Cohesin proteins holding sister chromatids together break; sister chromatids separate and migrate toward opposite poles.
- Telophase: Nuclear membranes reform around two new sets of chromosomes; mitotic spindle breaks down.
- Cytokinesis: Physical division of the cytoplasm. In animal cells, actin microfilaments pinch the cell into two identical daughter cells.
Centrosomes: A region near the nucleus containing two centrioles (each made of nine triplets of microtubules). They act as the microtubule-organizing centers (MTOC).

Karyotypes and Ploidy

Karyotype: A visual representation of the genome where chromosomes are stained, imaged, and organized by size and banding patterns (a characteristic ‐fingerprint‐).
Human Somatic Cells: Contain $46$ chromosomes arranged in $23$ pairs (one maternal set and one paternal set).
Chromosomal Anatomy:
- Sister Chromatids: Identical copies of a chromosome produced during the S phase.
- Centromere: The narrow region where sister chromatids are most closely attached.
Ploidy Variation (Chromosomes per species):
- Humans: $46$ ( $23$ pairs).
- Social Ants: $1$ or $2$ .
- Peas: $14$ .
- Dingoes: $78$ .
- Certain Butterflies: Up to $450$ chromosomes.
- Polyploidy: Some organisms are not diploid ( $2n$ ); for example, certain plants are hexaploid ( $6n$ ), possessing six copies of each chromosome.

Binary Fission in Prokaryotes

Prokaryotic division is simpler than mitosis.
DNA replication begins at a single origin of replication.
As the DNA replicates, the two origins move toward opposite ends of the cell.
The cell elongates and the plasma membrane pinches inward, dividing the parent cell into two daughter cells.