Structures and Function of the Cell: Comprehensive Study Notes

Augustinian Opening Prayer

• Leader: When we live in unity.
• Response: How good and how pleasant it is.
• Leader: Pray for us Holy Father Augustine.
• Response: That we may dwell together in peace.
• Leader: Let us pray.
• Response: God our Father, Your Son promised to be present in the midst of all who come together in His Name. Help us recognize His presence among us and experience in our hearts the abundance of Your grace, Your mercy and Your peace, in truth and in love. We ask these through Christ our Lord. Amen. Our Father…
• Leader: Our Lady of Grace.
• All: Pray for us.

Introduction to Microscopy and Cell Discovery

• Microscope Definition: An instrument used to see objects that are too small to be seen by the naked eye.
• Microscopy: The science of investigating small objects and structures using a microscope.
• Microscopic: Term used for objects or structures that remain invisible to the eye unless aided by a microscope.
• Historical Development of the Microscope and Cell Studies:
  • $1590$ (Hans and Zacharias Janssen): Developed the Single Microscope (tube format); discovered single-cell animals.
  • $1609$ (Galileo Galilei): Developed the Compound Microscope utilizing a combination of convex and concave lenses.
  • $1625$ (Giovanni Faber): Coined the term "microscope" to refer to Galilei's compound microscope.
  • $1665$ (Robert Hooke): An English physicist who published Micrographia. He was the first to see plant cells (using thin slices of cork) under a single lens microscope and coined the term "cell" because the empty spaces reminded him of small rooms or cells.
  • $1675-1676$ (Antonie Van Leeuwenhoek): Improved the microscope with high-quality lenses ($300\times$ magnification). He pioneered observations of protozoa, red blood cells ($RBC$), the capillary system, yeast, life cycles of insects, and discovered the existence of bacteria (which he called "animalcules").
  • $1830$ (Joseph Lister): Reduced spherical aberration by using several weak lenses together at specific distances to achieve high magnification without distortion.
  • $1830-1850$ (Robert Brown): Made detailed observations on the cell nucleus and was the first to name it the "nucleus."
  • $1838$ (Matthias Schleiden): Stated that all plants are composed of cells.
  • $1839$ (Theodor Schwann): Proposed that the cell is the basic unit of life and stated that animal tissue is composed of one or more cells.
  • $1855$ (Rudolf Virchow): Stated that all cells come from pre-existing cells, refuting spontaneous generation.
  • $1874$ (Ernst Abbe): Developed a mathematical formula correlating resolving power to the wavelength of light, allowing for the calculation of theoretical maximum resolution.
  • $1880-1890$ (Robert Koch): Developed staining techniques to improve the visibility of bacteria under the microscope.
  • $1931-1942$ (Max Knoll and Ernst Ruska): Constructed the first Electron Transmission Microscope ($TEM$). Unlike optical microscopes, it uses electron beams rather than light to visualize objects as small as the diameter of an atom.
  • $1932$ (Fritz Zernike): Invented the first phase-contrast illumination, allowing for the imaging of transparent samples without staining.
  • $1957$ (Marvin Minsky): Developed the principle of confocal imaging, providing higher resolution than conventional light microscopy.
  • $1967$ (Lynn Margulis): Proposed the Endosymbiont Hypothesis regarding the origin of eukaryotic organelles.
  • $1972$ (Godfrey Hounsfield and Allan Cormack): Developed Computerized Axial Tomography ($CAT$) scanners to generate cross-sectional and $3-D$ images of internal organs.
  • $1978$ (Thomas and Christopher Cremer): Developed the first confocal laser scanning electron microscope.
  • $1981-1986$ (Gerd Binnig and Heinrich Rohrer): Developed the Scanning-Tunneling Microscope ($STM$), which visualizes individual atoms. They received the Nobel Prize for this work.
  • $1992$ (Douglas Prasher): Cloned Green Fluorescent Protein ($GFP$) used in fluorescent microscopy.
  • $1993-1996$, $2014$ (Stefan Hell, Eric Betzig, William Moerner): Developed super-resolution microscopy, allowing visualization of matter smaller than $0.2 \text{micrometers}$. Stefan Hell pioneered the first super-resolution microscopy in the early $90s$, and the group received the Nobel Prize in Chemistry in $2014$.
  • $2010$ (University of California Researchers): Used the cryoelectron microscope to visualize atoms and viruses.

The Cell Theory

• Organization: Formulated approximately $150$ years after the initial discoveries of Hooke and Van Leeuwenhoek.
• Classic Postulates:
  1. Cells are the basic unit of life. All known living things are made up of cells.
  2. The cell is the structural and functional unit of all living things.
  3. All cells come from pre-existing cells by cell division. Spontaneous generation does not occur.
• Modern Cell Theory Addition: Cells contain hereditary information ($DNA$) which is passed on to new cells during cell division.

Endosymbiotic Theory (Endosymbiont Hypothesis)

• Proposed by: Lynn Margulis ($1967$).
• Concept: This theory posits that specific organelles (mitochondria and chloroplasts) were once free-living bacteria that began living inside larger host cells.
• Process:
  1. Infoldings in the plasma membrane of an ancestral prokaryote gave rise to endomembrane components, including the nucleus and endoplasmic reticulum.
  2. First Endosymbiotic Event: The ancestral eukaryote consumed aerobic bacteria, which eventually evolved into mitochondria.
  3. Second Endosymbiotic Event: The early eukaryote consumed photosynthetic bacteria (cyanobacteria), which evolved into chloroplasts.
• Supporting Evidence: Phylogenetic analyses show that mitochondrial $DNA$ is similar to Typhus bacterium $DNA$, and chloroplast $DNA$ is similar to cyanobacteria $DNA$.

Cell Diversity and Size Constraints

• Surface Area to Volume Ratio: As a cell grows, its volume increases much faster than its surface area. If a cell becomes too large, its surface area-to-volume ratio ($SA:V$) becomes too small to efficiently maintain life functions (nutrient intake and waste export).
• Diversity examples:
  • Human Sinus Cells: Approximately $10 \text{μm}$.
  • Onion Cells: Approximately $50 \text{μm}$.
  • Bacterial Cells: Approximately $500 \text{nm}$.

Prokaryotic Cells

• General Characteristics: Small, simple structure with a high surface area per volume ratio. They lack a nuclear envelope and membrane-bound organelles. Reproduction occurs via binary fission.
• Types:
  • Bacteria: Unicellular organisms involved in nutrient cycling.
  • Archaea: Obligate anaerobes living in extreme environments (e.g., hot springs, soil with low oxygen).
• Structures and Functions:
  • Capsule: A sticky outer layer that provides protection and aids in adherence.
  • Cell Wall: Confers rigidity and maintains the cell's shape. In bacteria, this is composed of Peptidoglycan (Murein).
  • Plasma Membrane: Acts as a permeability barrier.
  • Nucleoid: Area in the cytoplasm containing the circular $DNA$.
  • Plasmid: Small, extra-chromosomal circular $DNA$ molecules.
  • Ribosomes: Smaller than eukaryotic versions ($70S$ type); site of protein synthesis.
  • Pili (Pilus): Hair-like appendages used for adhesion.
  • Flagellum: Facilitates movement; in prokaryotes, it is a single submicroscopic fiber.
• Specific Examples:
  • Streptococcus pneumoniae: Causes pneumonia, meningitis, and septicemia.
  • Lactobacillus acidophilus: Beneficial bacteria found in dairy that converts lactose into lactic acid.
  • Staphylococcus aureus: Found on skin and in noses; can cause staph infections.
  • Cyanobacteria (Blue-green algae): Photosynthetic prokaryotes containing thylakoids; produce oxygen and possess a mucoid sheath, carboxysomes, and RuBisCO.

Eukaryotic Cells

• General Characteristics: Large and complex structure with extensive compartmentalization via membrane systems. They possess a true nucleus where $DNA$ is enclosed in a nuclear membrane.
• Major Parts: Cell Membrane, Cytoplasm, and Nucleus.
• Eukaryotic Organelles and Components:
  • Cell Membrane (Plasma Membrane): Composed of a phospholipid bilayer with hydrophilic (water-loving) heads and hydrophobic (water-fearing) tails. It regulates the entrance and exit of substances.
    • Davson-Danielli Model: Described the membrane as a simple phospholipid bilayer.
    • Singer-Nicolson Model (Fluid Mosaic Model): Describes the membrane as a mosaic of proteins embedded in or attached to a fluid lipid bilayer.
  • Nucleus: The command center of the cell.
    • Nucleolus: Site of ribosome production.
    • Nuclear Envelope: Double membrane with nuclear pores to regulate passage.
    • Chromatin: Composed of nucleic acids and proteins. Chromosomes are chromatin wrapped around histone proteins.
  • Cytoplasm: Jelly-like substance where organelles (membrane-bound) and inclusions (non-membrane bound) are located.
  • Endoplasmic Reticulum (ER):
    • Rough ER: Studded with ribosomes; involved in protein processing.
    • Smooth ER: Tubular and non-granular; involved in lipid synthesis and steroid hormone biosynthesis.
  • Ribosomes: Sites of protein synthesis. Composed of a large and small subunit ($80S$ type in eukaryotes). They use $mRNA$ (messenger), $rRNA$ (ribosomal), and $tRNA$ (transfer) to assemble amino acids.
  • Golgi Apparatus: Composed of sets of cisterna and vesicles. Responsible for processing, packaging, and sorting secretory materials.
  • Mitochondrion: The "powerhouse of the cell." Contains enzymes for chemical oxidation of food to produce $ATP$ (energy). Possesses its own $DNA$, an inner membrane with folds called Cristae, and an internal space called the Matrix.
  • Lysosomes: Common in animal cells; contain hydrolytic digestive enzymes to break down waste, worn-out cell parts, and invading pathogens.
  • Peroxisomes: Contain oxidative enzymes involving energy metabolism and detoxifying hydrogen peroxide ($H_{2}O_{2}$) into water and oxygen.
  • Vacuoles: Membrane-bound sacs for storage and waste. They are large in plants (maintaining turgor pressure) and small in animals.
  • Chloroplasts: Specialized plant organelles containing chlorophyll for photosynthesis. Structures include the Stroma (fluid) and Thylakoids stacked into Grana.
  • Plastids: Double-membrane organelles in plants/algae. Types include Chloroplasts (green), Chromoplasts (yellow/red), and Leucoplasts (non-pigmented; store starch/lipids).
  • Cytoskeleton: Network of protein filaments responsible for maintain shape and cell motility.
    • Microtubules: Largest; tubes of protein molecules; found in centrioles, cilia, and flagella.
    • Intermediate Filaments: Provide support and strength.
    • Microfilaments (Actin): Smallest; responsible for cell movement.
  • Centrioles/Centrosome: Known as the Microtubule Organizing Center ($MTOC$). Centrioles are rings of nine groups of fused microtubules (three per group). They replicate and guide chromosome separation during cell division via "spindles."
  • Cell Wall (Plants): Composed of cellulose, pectin, and lignin. Primary wall forms during growth; secondary wall forms after growth ceases.

Comparative Analysis of Organelles

Cell Reproduction and Human Biology

• Mitosis: Process for somatic cell division resulting in two identical daughter cells. Stages include Interphase, Prophase, Prometaphase, Metaphase, Anaphase, and Telophase/Cytokinesis.
• Meiosis: Two-stage division ($Meiosis I$ and $II$) to produce four haploid gametes (sperm and egg).
• Spermatogenesis: The production of sperm cells; normal sperm have a head (with acrosome/nucleus), neck, middle piece (mitochondria), and tail. Abnormalities can include giant, micro-sperm, double heads, or long heads.
• Oogenesis: The production of the egg (ovum). Includes the follicular phase, ovulation, and luteal phase (Corpus luteum).
• Hormonal/Thermal Context: During the menstrual cycle, the ovarian cycle is influenced by $Estradiol$, $LH$, $FSH$, and $Progesterone$. Basal body temperature fluctuates between $36^{\circ}C$ and $37^{\circ}C$.

Questions & Discussion

• How did the discovery of the microscope help in the development of cell theory? The microscope allowed scientists to see the previously invisible structures of life, leading to the identification of the cell as the basic unit and the observation of cell division.
• Who are the scientists that contributed to the development of the microscope? Key figures include Hans and Zacharias Janssen, Galileo Galilei, Robert Hooke, Antonie Van Leeuwenhoek, Joseph Lister, Ernst Abbe, Max Knoll, and Ernst Ruska.
• How important is the development of the cell theory in the study of biology? Cell theory provided the fundamental framework for understanding biological organization, reproduction, and the continuity of life through genetics.
• What are the three postulates of Cell Theory? 1. Cells are the basic unit of life. 2. Cells are the structural and functional unit of living things. 3. All cells come from pre-existing cells.
• How does cell size affect the ratio of volume to surface area? As cell size increases, volume grows faster than surface area, decreasing the ratio and limiting the cell's ability to transport materials efficiently.

Augustinian Closing Prayer

• Leader: Our help is in the name of the Lord.
• Response: Who made Heaven and Earth.
• Leader: Let us pray.
• Response: God, the desire of every human heart, you moved Saint Augustine to seek restlessly for truth and peace. Touch our hearts with his burning desire for wisdom, for the word made flesh. We ask this through Christ our Lord. Amen. Glory be…
• Leader: St. Augustine.
• All: Pray for us.