BIOL 102 - Lecture Notes

BIOL 102 - Fundamentals of Biology: Molecular and Cell Biology

Week 2 Lecture 2

### Department of Biology, Queen's University

Plasma Membrane

  • Definition: A selectively permeable, lipid bilayer surrounding each cell.

  • Composition:

    • Inner and Outer Faces: Differ in lipid and protein composition.

    • Fluid Mosaic Model: Envisions plasma membranes as a mosaic of phospholipids, proteins, and carbohydrates (glycoproteins and glycolipids).

Membrane Proteins

  • Integral Proteins:

    • Definition: Proteins that penetrate the hydrophobic interior of the lipid bilayer.

    • Includes: Transmembrane proteins that span the membrane.

  • Peripheral Proteins:

    • Definition: Loosely bound to the membrane's surface.

    • Association: Often interact with integral proteins located within the membrane.

Cellular Membranes

  • Membrane Fluidity:

    • Influencing Factors:

    • Presence of unsaturated fatty acid tails.

    • Presence of steroids like cholesterol.

    • Dynamic Nature: Fluidity can change based on environmental factors or cellular needs.

Diffusion

  • Definition: The movement of particles that spread out across available space.

  • Process:

    • Movement occurs down the concentration gradient until reaching dynamic equilibrium.

Diffusion – Electrochemical Gradient

  • Electrochemical Gradient:

    • Definition: The diffusion gradient of an ion influenced by both the ion concentration and the membrane potential.

Osmosis

  • Definition: The diffusion of free water across a selectively permeable membrane.

  • Tonicity: Refers to the ability of a solution to affect the cell's water balance.

    • Classifications:

    • Isotonic: No net movement of water; cell size remains unchanged.

    • Hypertonic: Causes cell to lose water, leading to cell shrinkage.

    • Hypotonic: Causes cell to gain water, leading to cell swelling.

Question 1: Think – Pair – Share

  • Scenario: Consider a mammalian red blood cell (RBC) with an internal ion concentration of about 0.9 percent placed in a beaker of pure water.

  • Choices:
    A. The cell would shrink because the water is hypotonic relative to the cytoplasm of the RBC.
    B. The cell would shrink because the water is hypertonic relative to the cytoplasm of the RBC.
    C. The cell would swell because the water is hypotonic relative to the cytoplasm of the RBC.
    D. The cell would swell because the water is hypertonic relative to the cytoplasm of the RBC.
    E. The cell will remain the same size because the solution outside the cell is isotonic.

Passive Transport

  • Definition: The diffusion of molecules across a biological membrane, influenced by the electrochemical gradient.

  • Facilitated Diffusion:

    • Definition: Passive transport facilitated by highly selective transport proteins, enabling more efficient movement of molecules across the membrane.

Active Transport

  • Definition: The process that uses energy to move a compound against its electrochemical gradient.

  • Power Source: Directly or indirectly powered by ATP hydrolysis.

Active Transport - Cotransport

  • Cotransport:

    • Definition: Coupling the transport of one molecule down its electrochemical gradient with the transport of another molecule against its electrochemical gradient.

    • Types:

    • Symport: Both molecules move in the same direction.

    • Antiport: Molecules move in opposite directions.

Transport Proteins

  • Channel Proteins:

    • Definition: Provides a hydrophilic channel for specific molecules.

    • Gated Channels: Can open or close in response to signals.

    • Type of Transport: Mainly passive transport.

  • Carrier Proteins:

    • Function: Translocates molecules by changing shape, allowing movement through the membrane.

    • Type of Transport: Can facilitate passive as well as active transport.

Bulk Transport

  • Types:

    • Exocytosis: Exporting large molecules out of the cell via vesicles.

    • Endocytosis: Importing large molecules into the cell via vesicles.

    • Subtypes:

    • Phagocytosis: Engulfing solids ("cell eating").

    • Pinocytosis: Engulfing liquids ("cell drinking").

    • Receptor-mediated Endocytosis: Specific uptake of molecules based on receptor-ligand interactions.

Question 2: Think – Pair – Share

  • Scenario: The CFTR protein functions as a chloride ion channel. If the sodium ion concentration increases outside the cell and the CFTR channel is open, consider the movement of chloride ions and water across the membrane.

  • Choices:
    A. Chloride ions will move out of the cell, and water will move into the cell.
    B. Both chloride ions and water will move out of the cell.
    C. Chloride ions will move into the cell, and water will move out of the cell.
    D. Both chloride ions and water will move into the cell.
    E. Movement will not be affected by sodium concentration outside the cell.

Endosymbiont Theory

  • Definition: A theory that explains the evolutionary origins of mitochondria and chloroplasts in eukaryotic cells.

  • Mechanism:

    • Engulfing of a non-photosynthetic prokaryote leading to mitochondrion development.

    • Engulfing of a photosynthetic prokaryote leading to chloroplast formation.

  • Question: Can new endosymbionts be generated?

Synthetic Biology

  • Definition: A scientific discipline that involves engineering life forms for human benefit.

  • Core Concept: Most life functions are driven by proteins, which are synthesized by cells.

    • Methods: Altering DNA to create new proteins enhances existing abilities or introduces new capabilities.

    • Components: Other cellular components influencing protein production can also be modified or replaced.

  • Applications:

    • Medicine and Pharmaceuticals:

    • Drug discovery and antibody production.

    • Vaccine development (e.g., mRNA vaccines).

    • Biofuels and Sustainable Energies:

    • Fermentation processes.

    • Production of ethanol by thermophilic organisms.

    • Biodiesel from sugarcane-cultured yeast.

    • Environmental:

    • Bioremediation for cleaning chemical wastes.

    • Development of biosensors for detecting toxins (e.g., arsenic).

    • Food and Agriculture:

    • Improving nutrient content in food products (e.g., yogurt).

    • Enhancing crop resistance to diseases.

    • Space Systems and Exploration:

    • Applications in medicine, food, and material production.

Designer Endosymbionts Hypothesis

  • Hypothesis: New organelles with desired properties can be engineered by imitating the origins of mitochondria and chloroplasts.

  • Key Requirements for Symbiosis:

    • Syntrophy: Mutual dependence; essential for survival.

    • Tolerance: Neither partner harms the other.

  • Challenge: The engineered endosymbiont must avoid degradation by lysosomal pathways.

Engineering Yeast Endosymbionts

  • Study Reference:

    • Research on creating new organelles resembling mitochondria through engineering yeast cells.

    • Authors: Angad P. Mehta et al.

    • Affiliations: Various research institutions and universities.

Experimental Strategy

  • Objective: Insert an ATP-exporting E. coli auxotroph into a yeast cell, which lacks an electron transport chain, and utilize glycerol as a carbon source for growth.

Selection of Yeast Strain

  • Description: Selection of a mutant yeast strain that lacks complex IV of the electron transport chain.

Initial Engineering of E. coli

  • Modifications:

    • A gene for thiamine biosynthesis was deleted and replaced with green fluorescent protein (gfp).

    • Introduced ADP/ATP translocase (antiport); however, this did not support yeast growth on glycerol.

  • Confirmation of Thiamin Auxotrophy: Ensured dependency on external sources of thiamine.

Failure of Initial E. coli Engineering

  • Reasons for Failure:

    • Likely killed by yeast through lysosomal degradation pathways.

    • Potential role of bacterial pathogens with SNARE-like proteins inhibiting eukaryotic vesicle fusion.

E. coli Engineering - Round 2

  • Further Modifications: E. coli was engineered to express three SNARE-like proteins.

    • Outcome: Yeast cells were able to catabolize glycerol, albeit at a slower growth rate than the wild type.

  • Results: Observations of yeast colonies under selective and non-selective conditions, with PCR amplification confirming gene presence.

Microscopy of Engineered Yeast

  • Observations: Confocal fluorescence micrographs showcasing yeast with and without synthetic E. coli endosymbionts.

Conclusions from Research

  1. New synthetic organelles can be engineered and remain stable for over 120 days.

  2. Escape from lysosomal degradation is crucial for establishing new endosymbioses.

  3. Using various nutrients might enable the establishment of syntrophy, allowing for potential genome reduction.

  4. The initial environment may not have favored the acquisition of mitochondrial precursors but could allow for niche expansion.