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LECTURE 1

1. Scientific Method

The scientific method is a systematic process for investigating phenomena, acquiring new knowledge, or correcting and integrating previous knowledge. It typically involves the following steps:

• Observation

• Question

• Hypothesis

• Experiment

• Analysis

• Conclusion

2. Rules of Strong Inferences

Strong inferences involve a systematic approach to hypothesis testing, emphasizing:

• Formulating multiple hypotheses

• Designing experiments to test these hypotheses

• Eliminating hypotheses based on experimental results

• Iterating the process to refine understanding and conclusions.

LECTURE 2

1. Phylogenetics

Phylogenetics is the study of evolutionary relationships among biological entities, often represented in a phylogenetic tree.

2. Cladogram, Phylogram, and Dated Phylogeny

• Cladogram: A tree diagram showing relationships based on shared characteristics.

• Phylogram: A tree where branch lengths represent evolutionary change.

• Dated Phylogeny: A phylogenetic tree with time scales indicating when divergences occurred.

3. Monophyly, Paraphyly, and Polyphyly

• Monophyly: A group containing an ancestor and all its descendants.

• Paraphyly: A group containing an ancestor and some, but not all, descendants.

• Polyphyly: A group that does not include the most recent common ancestor.

4. Synapomorphy and Synplesiomorphy

• Synapomorphy: A shared derived trait used to define a clade.

• Synplesiomorphy: A shared ancestral trait not useful for defining clades.

5. Mechanisms of Speciation

Speciation can occur through:

• Allopatric speciation (geographic isolation)

• Sympatric speciation (reproductive isolation without geographic barriers)

• Parapatric speciation (adjacent populations diverging).

LECTURE 3

• Basic Components of a Plant Cell:

  • Cell Wall: Provides structure and protection.

  • Chloroplasts: Site of photosynthesis.

  • Vacuole: Stores nutrients and waste products.

  • Cytoplasm: Gel-like substance where organelles are suspended.

  • Nucleus: Contains genetic material.

• Cell Wall Structure and Function:

  • Composed of cellulose; provides rigidity and support.

• Primary vs. Secondary Cell Wall:

  • Primary Cell Wall: Flexible, formed during cell growth.

  • Secondary Cell Wall: Thicker, provides additional strength, formed after growth.

• Spelling: Plasmodesmata.

• Primary Pit Field: Areas in the cell wall where plasmodesmata are concentrated, facilitating communication between cells.

• Plant Cell Growth: Involves cell expansion and division, primarily through water uptake and synthesis of new cell wall materials.

LECTURE 4

1. Structure of Chloroplast

• Outer Membrane: Smooth and permeable.

• Inner Membrane: Contains transport proteins.

• Stroma: Fluid-filled space with enzymes for the Calvin cycle.

• Thylakoids: Membrane-bound sacs where light reactions occur; stacked into grana.

2. Light Reaction and Calvin Cycle

• Light Reaction: Occurs in thylakoid membranes; converts light energy into ATP and NADPH.

• Calvin Cycle: Occurs in the stroma; uses ATP and NADPH to convert CO2 into glucose.

3. Photorespiration

A process where oxygen is consumed and CO2 is released, reducing photosynthetic efficiency, especially in C3 plants.

4. C4 and CAM Pathways

• C4 Photosynthesis: Separates initial CO2 fixation and the Calvin cycle spatially; adapted to high light and temperature.

• CAM Photosynthesis: Fixes CO2 at night and performs the Calvin cycle during the day; adapted to arid conditions.

Dark Cycle (Calvin Cycle)

• Location: Occurs in the stroma of chloroplasts.

• Process:

  1. Carbon Fixation: CO₂ is attached to ribulose bisphosphate (RuBP) by the enzyme RuBisCO, forming 3-phosphoglycerate (3-PGA).

  2. Reduction Phase: ATP and NADPH (from light reactions) convert 3-PGA into glyceraldehyde-3-phosphate (G3P).

  3. Regeneration of RuBP: Some G3P molecules are used to regenerate RuBP, allowing the cycle to continue.

• Output: Produces glucose and other carbohydrates, using energy stored in ATP and NADPH.

• Note: The cycle does not require light directly but relies on products from light-dependent reactions.

Dark Cycle (Calvin Cycle)

• Location: Occurs in the stroma of chloroplasts.

• Process:

  1. Carbon Fixation: CO₂ is attached to ribulose bisphosphate (RuBP) by the enzyme RuBisCO, forming 3-phosphoglycerate (3-PGA).

  2. Reduction Phase: 6 ATP and 6 NADPH (from light reactions) convert 3-PGA into glyceraldehyde-3-phosphate (G3P).

  3. Regeneration of RuBP: Some G3P molecules are used to regenerate RuBP, allowing the cycle to continue.

• Output: Produces glucose and other carbohydrates, using energy stored in ATP and NADPH.

• Note: The cycle does not require light directly but relies on products from light-dependent reactions.

Light Reactions

• Location: Thylakoid membranes of chloroplasts (grana).

• Process:

  • Light energy absorbed by chlorophyll.

  • Excited electrons initiate the electron transport chain.

  • Protons pumped into thylakoid lumen, creating a gradient for ATP synthesis via chemiosmosis.

  • Water split (photolysis), releasing oxygen and replenishing chlorophyll electrons.

• Products: ATP, NADPH, and oxygen (O₂).

Dark Reactions (Calvin Cycle)

• Location: Stroma of chloroplasts.

• Process:

  • ATP and NADPH convert CO₂ into glucose.

  • Phases: carbon fixation (CO₂ + RuBP), reduction (3-PGA to G3P), regeneration (RuBP).

• Products: Glucose (G3P).

Photosynthesis Process

1. Light Absorption:

   • Photosystem II (PSII) absorbs light, exciting electrons.

   • Water molecules are split (photolysis), releasing oxygen.

2. Electron Transport Chain:

   • Excited electrons move through a series of proteins, releasing energy to pump protons into the thylakoid lumen.

3. ATP and NADPH Formation:

   • Protons flow back through ATP synthase, generating ATP.

   • Electrons reach Photosystem I (PSI), where they are re-excited by light and used to reduce NADP+ to NADPH.

4. Calvin Cycle:

   • ATP and NADPH are used to convert CO2 into glucose.

This process occurs in the chloroplasts of plant cells.

Dark Cycle (Calvin Cycle) in Photosynthesis

1. Location: Occurs in the stroma of chloroplasts.

2. Phases:

   • Carbon Fixation: CO2 is fixed into a 5-carbon sugar (ribulose bisphosphate, RuBP) by the enzyme RuBisCO, forming 3-phosphoglycerate (3-PGA).

   • Reduction Phase: ATP and NADPH from the light reactions convert 3-PGA into glyceraldehyde-3-phosphate (G3P).

   • Regeneration Phase: Some G3P molecules are used to regenerate RuBP, allowing the cycle to continue.

3. Cyclic Pathway:

   • Involves PSI only, where electrons are cycled back to produce additional ATP without NADPH, helping to balance energy needs.

Summary

The Calvin Cycle synthesizes glucose using ATP and NADPH, while the cyclic pathway provides extra ATP.

LECTURE 5

1. Mitosis: A process of cell division resulting in two identical daughter cells, maintaining the same chromosome number.Meiosis: A type of cell division that reduces the chromosome number by half, producing four genetically diverse gametes.

2. Definitions:

   • Haploid: A cell with one set of chromosomes (n).

   • Diploid: A cell with two sets of chromosomes (2n).

   • Gametes: Reproductive cells (sperm and eggs).

   • Gametophyte: The haploid stage in the life cycle that produces gametes.

   • Sporophyte: The diploid stage that produces spores.

   • Alternation of Generations: The life cycle pattern alternating between haploid and diploid phases.

3. Life Cycle Differences:

   • Moss: Dominant gametophyte stage, sporophyte dependent on gametophyte.

   • Fern: Dominant sporophyte stage, independent gametophyte.

   • Flowering Plant: Dominant sporophyte, gametophyte reduced and dependent within flowers.

LECTURE 6

1. Plant Systematics, Taxonomy, and Nomenclature

• Plant Systematics: Study of plant diversity and relationships.

• Plant Taxonomy: Classification and naming of plants.

• Nomenclature: Rules for naming plants (e.g., binomial nomenclature).

2. Levels of Taxonomic Categories

• Domain

• Kingdom

• Phylum

• Class

• Order

• Family

• Genus

• Species

3. Interpretation of Phylogenies

• Phylogenetic trees depict evolutionary relationships among species.

4. Plant Speciation Mechanisms

• Allopatric Speciation: Geographic isolation leads to speciation.

• Sympatric Speciation: Speciation occurs without geographic separation, often through polyploidy or behavioral changes.