Bio 181 SI Session Notes

Welcome and Introduction

• Welcome to Bio 181 SI session
• Recording of session will be available 24-48 hours after conclusion
• Respectful interaction encouraged (unmute, chat, annotate)

Lipid Bilayer and Molecules

• Main Concept: Molecules passing through the lipid bilayer
• The middle part of the lipid bilayer is hydrophobic
  • This means it "fears" water due to its nonpolar fatty acid tails.
  • These tails consist primarily of carbon-hydrogen bonds, which share electrons equally, making them uncharged and insoluble in water.
• Acts as a barrier against hydrophilic molecules
  • Hydrophilic molecules "love" water because they are polar or have a net charge (like ions).
  • Their interaction with water through hydrogen bonds makes it difficult for them to pass through the nonpolar, oily interior of the lipid bilayer.

Molecules and Their Behavior

1. Oxygen ($O_2$)
   • Polar or nonpolar? Nonpolar
   • Two equal oxygen atoms share electrons equally, resulting in no partial charges (tug of war analogy).
   • Can it pass through the lipid bilayer? Yes
   • Its small size and nonpolar nature allow it to freely diffuse directly through the hydrophobic core of the membrane, following its concentration gradient.
2. Carbon Dioxide ($CO_2$)
   • Is $CO_2$ polar or nonpolar? Nonpolar
   • The molecule has two polar covalent bonds, but its linear structure ($O=C=O$) causes the two dipoles to cancel each other out, resulting in a net nonpolar molecule.
   • Can it pass through? Yes
   • Similar to oxygen, its small size and nonpolar nature enable it to easily diffuse across the lipid bilayer.
3. Water ($H_2O$)
   • Is $H_2O$ polar or nonpolar? Polar
   • Water has a bent molecular shape and oxygen is more electronegative than hydrogen, leading to unequal sharing of electrons. This creates a partial negative charge near oxygen and partial positive charges near hydrogen atoms.
   • Can it pass through? No, in theory, due to its polarity and hydrogen bonding, which make it unfavorable to interact with the hydrophobic core.
   • Osmosis: Water does move from high to low concentration. While it can pass slowly through the bilayer by simple diffusion, most water movement across cell membranes occurs rapidly through specific protein channels called aquaporins (a form of facilitated diffusion), significantly increasing its permeability.
4. Salt (NaCl)
   • Type of bond? Ionic bond
   • Formed by the attraction between positively charged sodium ions ($Na^+$) and negatively charged chloride ions ($Cl^-$).
   • Will it dissolve in water? Yes (hydrophilic)
   • When dissolved in water, it dissociates into its constituent ions ($Na^+$ and $Cl^-$), which are highly charged and readily interact with polar water molecules.
   • Can it pass through the bilayer? No
   • The strong charges on the ions prevent them from permeating the nonpolar lipid bilayer. They require specific ion channels or transporters to cross the membrane.
5. Glucose
   • Polar or nonpolar? Polar
   • It has many hydroxyl (-OH) groups, making it highly polar and soluble in water.
   • Is it large or small? Large (relative to $O<em>2$, $CO</em>2$, $H_2O$)
   • Can it pass through? No
   • Due to both its large size and polar nature, glucose cannot simply diffuse through the lipid bilayer. It requires specific membrane proteins, such as glucose transporters (GLUT proteins), to be transported into or out of cells.

Cellular Organization

• Two main groups of cells: Prokaryotes and Eukaryotes
• Prokaryotes: Bacteria, Archaea (single-celled organisms, generally simpler structure)
• Eukaryotes: Animals, Plants, Fungi, Protists (can be single-celled or multicellular, generally more complex structure with internal compartments)

Characteristics of Prokaryotes

• Lack a nucleus: DNA located in the nucleoid (a region in the cytoplasm, not a true membrane-bound organelle).
  • The DNA is typically a single circular chromosome.
• Size range: 1-10 micrometers ($ext{1-10 } imes 10^{-6} ext{ m}$).
• Less cellular organization, fewer organelles (ribosomes are present).
• Have peptidoglycan in bacterial cell walls (a polymer consisting of sugars and amino acids, providing structural support and protection).
  • Archaea have different cell wall compositions (e.g., pseudopeptidoglycan or S-layers).

Characteristics of Eukaryotes

• Contain a nucleus: A membrane-bound organelle that houses the cell's genetic material (DNA organized into multiple linear chromosomes).
• Size range: 10-100 micrometers ($ext{10-100 } imes 10^{-6} ext{ m}$).
• Organized cellular structure with membrane-bound organelles (e.g., mitochondria, endoplasmic reticulum, Golgi apparatus, lysosomes, vacuoles), which specialize in various cellular functions through compartmentalization.
• Include specialized structures (e.g., plant cells have cell walls made of cellulose, chloroplasts for photosynthesis, and a large central vacuole).

Differences Between Prokaryotes and Eukaryotes

• Diagram/Venn Diagram helps visualize differences
• Prokaryotes
  • No nucleus or membrane-bound organelles.
  • Smaller, simpler structures.
  • DNA is circular and floats in the nucleoid region.
  • Cell division by binary fission.
• Eukaryotes
  • Membrane-bound organelles, organized into functional compartments.
  • Larger, more complex structures.
  • DNA is linear, enclosed within the nucleus, and associated with histones.
  • Cell division by mitosis and meiosis.
• Both share plasma membrane (phospholipid bilayer, controlling what enters and exits the cell), cytoplasm (the entire content within the cell membrane, including organelles and cytosol), and ribosomes (complexes responsible for protein synthesis).

Ribosomes and Protein Production

• Ribosomes: Small factories for protein synthesis.
  • Composed of ribosomal RNA (rRNA) and proteins.
  • They translate messenger RNA (mRNA) into polypeptide chains (proteins).
• Found in both cell types, crucial for cellular function (protein synthesis is essential for all life).
  • Prokaryotic ribosomes ($70S$) are smaller than eukaryotic ribosomes ($80S$), but both perform the same fundamental function.

Common Cell Parts

• Plasma membrane / Phospholipid bilayer: Same fundamental structure in both cell types, acting as a selective barrier.
• Cytoplasm: Includes all contents within the cell membrane (cytosol and organelles, if present).
• Nucleus: Found only in eukaryotes; contains the cell's genetic material and controls cell activities.
• Cytosol: Only the liquid, jelly-like part of the cytoplasm, excluding organelles.

Practice Questions

1. Which structure is found in both prokaryotes and eukaryotes?
   • Answer: Ribosomes, Plasma Membrane, Cytoplasm/Cytosol
2. What is the equivalent of the nucleoid in eukaryotic cells?
   • Answer: Nucleus (both contain genetic material; nucleoid is a region, nucleus is a membrane-bound organelle)
3. Identify unique features of eukaryotic cells
   • Answer: Membrane-bound organelles, a true nucleus, linear DNA, larger size, cytoskeleton, presence of mitosis/meiosis.

Ethics and Philosophy in Biology

• Discussion on endosymbiotic theory: Mitochondria and chloroplasts (in plant cells) are believed to have originated from free-living bacteria that were engulfed by ancestral eukaryotic cells. This symbiotic relationship led to the evolution of complex eukaryotic life.
  • Evidence: Both mitochondria and chloroplasts have their own circular DNA (similar to prokaryotes), ribosomes (70S, like prokaryotes), double membranes (the inner membrane resembling bacterial membranes, the outer from the host cell), and they replicate by binary fission independent of the host cell's division.
  • This theory highlights how cooperation and integration of different life forms can drive evolutionary innovation.

Closing Remarks

• Recommended resources