Microbiology and Cell Biology Lecture Notes

Page 1:

  • Date: 9/16/87

  • Date: 11/24/83

  • Early Microbiologists:

    • Mention of a "mammoth."

    • Reference to an Early Microscope.

Page 2:

  • Date: Larson 5/1/91

  • Character's Exclamation: "Oh no!..It's Professor Labuznik--that yussie* over in Research…Trying to get me to notice his new car microscope."

  • Additional Date: 3/2/88

  • Quote: "No, wait! That's not Uncle Floyd! Who is that? … Crimony, I think it's just an air bubble!"

    • *Young Urban Scientist (yussie): Potentially a term of endearment or familiarity used informally.

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  • Introduction to Unit 2 – Cell Biology (SL)

    • Topics Covered:

    • Microscopes and Cells: Chapter 8; IB microscope lab (measuring cell sizes).

    • Functions and Origins of Organelles: Chapter 8; organelle functions assignment.

    • The Cell Membrane and Cell Transport: Section 8.3; Venom Cure clips; Osmosis lab.

    • Cell Division and Differentiation: Cloning and Stem Cells: Chapter 11; Mitosis lab; Clone video; Personhood assignment.

    • Access to Lectures 3 – 6 available on Google Classroom.

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  • Development of the Light Microscope and the Cell Theory:

    • First Compound Light Microscopes:

    • Built in the mid 1600s by Anton van Leeuwenhoek (Dutch) and Robert Hooke (English).

    • Both discovered a previously unknown world and corresponded via letters.

    • Robert Hooke coined the term “cell” based on observations of cork and published Micrographia.

    • Anton van Leeuwenhoek was the first to see living cellular structures termed “pond animalcules.”

    • The Cell Theory (established in the mid-1800s by Schleiden, Schwann, and Virchow):

    1. All organisms are composed of cells (one or many).

      • Matthais Schleiden (botanist) observed plant cells.

      • Theodor Schwann (zoologist) observed animal cells.

    2. The cell is the basic unit of structure and function in living systems (e.g., movement of body results from movement of muscle cells).

    3. All cells come from pre-existing cells (Rudolph Virchow).

    • Spontaneous Generation:

    • Disproved by Francisco Redi and Louis Pasteur.

    • Current conditions (oxygenated atmosphere and omnipresent bacteria) result in degradation and loss of free organic materials.

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  • Cellular Domains:

    • DOMAIN BACTERIA: Representing one of the fundamental classifications of life.

    • DOMAIN ARCHAEA: Another fundamental classification, distinct from bacteria.

    • DOMAIN EUKARYA:

    • Protists.

    • Kingdom Fungi.

    • Kingdom Plantae.

    • Kingdom Animalia.

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  • Modern Microscopes:

    • Compound Light Microscope:

    • Magnification is a product of the two lenses (eyepiece and objective lens).

    • Lowest objective lens is known as scanning lens (4X).

    • Images are inverted; resolution is limited by the relatively large size of photons.

    • Parfocal Lens: An object placed in the center of the field of view prior to changing objective lenses; field of view decreases but the object remains in view.

    • Dissecting Microscope (Stereomicroscope):

    • Images are not inverted; preferred for dissections.

    • Electron Microscopes (in use since the 1950s; significantly greater resolution):

    • Scanning Electron Microscope: Provides images of the surfaces of objects; magnification up to approximately 60,000x.

    • Transmission Electron Microscope: Produces images of sections, displaying internal structures (such as organelles); magnification up to approximately 200,000x.

    • Scanning Tunneling Microscopes (Atomic Force Microscopes): Allows for imaging of large molecules with multiple technologies; magnifications up to approximately 100 million x.

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  • Staining with Light Microscopy:

    • Brightfield (unstained specimen) vs. stained specimen.

    • (a) Brightfield (unstained specimen) results in a clear view of internal structures.

    • (b) Brightfield (stained specimen) enhances visibility of structures.

    • Phase-contrast: Technique enhances contrast in unstained, transparent specimens.

    • Differential-interference-contrast (Nomarski): Technique providing a three-dimensional appearance.

    • Fluorescence: Shows specific structures tagged with fluorescent markers.

    • Confocal Microscopy: Provides high-resolution images by eliminating out-of-focus light.

  • Electron Microscopy:

    • (a) Scanning Electron Microscopy (SEM): Detailed surface imaging, e.g., cilia at 1 μm.

    • (b) Transmission Electron Microscopy (TEM): Displays internal structures, e.g., longitudinal and cross-section imaging of cilia at 1 μm.

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  • The Chemical Structure of a Molecule Resolved by Atomic Force Microscopy:

    • Authors: Leo Gross, Fabian Mohn, Nikolaj Moll, Peter Liljeroth, Gerhard Meyer.

    • Objective: Resolve individual atoms using surface microscopy techniques.

    • Key Findings:

    • Utilizing noncontact atomic force microscopy to image molecules with unprecedented atomic resolution by interrogating short-range chemical forces using a CO-functionalized tip apex.

    • Experimental results corroborated by ab initio density functional theory calculations.

    • Theory indicates Pauli repulsion contributes to atomic resolution, while van der Waals and electrostatic forces provide a diffuse attractive backdrop.

    • Reference: Science 325: 1110 (28 Aug 2009).

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  • Figures Detailing STM and AFM Imaging of Pentacene on Cu(111):

    • (A) Ball-and-stick model of the pentacene molecule.

    • (B) Constant-current STM and (C/D) constant-height AFM images showing variations in imaging parameters.

    • Noted imaging conditions include current and voltage settings.

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  • Cell Types and Shared Structures:

    • Prokaryotic Cells (Prokaryotes: Eubacteria and Archaea):

    • Typically 1-10 μm; appear in fossil records dating back 3.5 billion years ago; lack a nucleus and other membrane-bound organelles (with DNA freely located in a nucleoid region).

    • Eukaryotic Cells (Eukaryotes: Fungi, Protists, Plants, and Animals):

    • Typically 10-100 μm; appear in fossil records dating back 2.2 billion years ago; contain nuclei and other membrane-bound organelles.

    • Common Features of All Cells:

    • Cell (plasma) membrane: Acts as a boundary, allowing micelles to form naturally.

    • Ribosomes: Composed of proteins and RNA; bacteria possess different ribosome sizes and structures compared to eukaryotes.

    • DNA, RNA, and the Genetic Code: Bacterial chromosomes are simple rings; eukaryotic DNA is organized with proteins.

    • Other molecules/structures: Include membrane proteins (e.g., ATP synthase) and various metabolic enzymes and cytoskeletal components.

Page 11:

  • Figure 8-5: Bacterium Characteristics:

    • (a) Depicts a typical rod-shaped bacterium with features like fimbriae, nucleoid, ribosomes, and plasma membrane.

    • (b) Shows a thin section through the bacterium Bacillus coagulans (using TEM).

    • Indication of bacterial chromosome within the 'nucleoid' region.

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  • Eukaryotic Cells - Figure 8-5:

    • Key organelles include:

    • Endoplasmic Reticulum (ER): Divided into rough ER (with ribosomes) and smooth ER.

    • Nucleus: Surrounded by a nuclear envelope containing nucleolus, chromatin, and ribosomes.

    • Cytoskeleton: Composed of microfilaments, intermediate filaments, and microtubules.

    • Peroxisomes, Mitochondria, Lysosomes, Golgi Apparatus.

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  • Size Hierarchy, Figure 8-4:

    • Displays different biological scales, showcasing dimensions from the human height down to atoms:

    • 10 m: Human height.

    • 1 mm: Most plant and animal cells.

    • 1 μm: Most bacteria including mitochondria.

    • 10 nm: Proteins.

    • 1 nm: Small molecules.

    • 0.1 nm: Atoms.

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  • Eukaryotic Structures and Organelles:

    • Structures like the Nucleus, Nucleolus, and Ribosomes are crucial for cellular function.

    • The Nucleus: Bound by a porous nuclear membrane containing DNA, which organizes chromatin.

    • The Nucleolus: A prominent, dense area where ribosomes are formed.

    • Ribosomes: Primary sites for protein synthesis located in the rough ER and cytoplasm.

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  • Endoplasmic Reticulum (ER):

    • Extends throughout the cell, integral for transport systems:

    • Rough ER: Ribosome-studded, involved in synthesizing proteins.

    • Smooth ER: Lipid synthesis and detoxification processes.

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  • Figure 8-7: Nuclear Envelope Structure:

    • Highlights the inner and outer membrane structures and nuclear pore complexes.

    • Images depict essential functionalities involving the nucleolus and chromatin.

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  • Figure 8-8: Endoplasmic Reticulum:

    • Displays the smooth and rough ER with associated ribosomes, emphasizing the transitional regions within the ER structure.

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  • Golgi Apparatus (Complex) and Vesicles:

    • Modifications of products from the ER occur in Golgi apparatus.

    • Vesicles are employed for transportation to cell membranes, allowing products to leave the organelle.

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  • Golgi Apparatus Faces:

    • Cis Face: Receiving side.

    • Trans Face: Shipping side.

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  • Lysosomes and Vacuoles:

    • Lysosomes:

    • Membrane-enclosed sacs of digestive enzymes, primarily in animal cells.

    • Function in digestion, immunity, and cellular waste degradation.

    • Vacuoles: Membranous sacs for storage (food, water), with the central vacuole being particularly notable in plant cells.

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  • Autophagy Mechanism:

    • Displays cellular processes involving lysosomes and vacuoles in cellular maintenance and recycling mechanisms.

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  • Cell Structure:

    • Central vacuole, cytosol, cell wall, and chloroplast identified in a plant cell.

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  • Golgi Apparatus Structure:

    • Shows connections to smooth and rough ER with observable vesicle distributions.

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  • Plastids:

    • Chloroplasts: Responsible for photosynthesis in plants.

    • Chromoplasts: Contain pigments; e.g., melanin.

    • Mitochondria: Critical for cellular respiration, termed the cell's energy factories.

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  • Structure of Mitochondria:

    • Detailed anatomical structures including intermembrane spaces, ribosomes, and cristae.

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  • Cytoskeleton and Cytosol:

    • Provides structural support, cell shape maintenance, and movement; dynamic reassembly potential.

    • Cytosol described as the semi-fluid medium of the cytoplasm.

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  • Microtubules and Centrioles:

    • Central role in cellular mechanics and transport. Morphological analysis through figures demonstrates vesicular transport mechanisms involving these structures.

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  • Motile Appendages - Flagella and Cilia:

    • Discussed with respect to function in sediments, mucus clearance, and mechanosensitivity in particular systems (e.g., cochlea).

    • Flagella: Longer, singular structures that exhibit a whiplike motion for cell movement.

    • Cilia: Shorter and often found in groups, moving in unison.

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  • Flagella vs. Cilia Motion:

    • Motion dynamics illustrated comparing organism movement directed by flagella vs. cilia.

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  • Ciliary Structure:

    • Examines dimensions and components essential for structural integrity and function at microscopic levels.

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  • Cilia in Airways:

    • Studied showing role in sensing and mechanically clearing foreign materials.

    • Cilia noted to have sensory receptors influencing rhythmic beating based on environmental cues.

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  • Extracellular Matrix:

    • Describes composition involving collagen, fibronectin, and proteoglycan; critical for cell stability and communication within tissues.

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  • Cell Junctions:

    • Tight Junctions: Prevent fluid passage between cells; structural implications discussed.

    • Desmosomes: Provide strong adhesion between cells.

    • Gap Junctions: Allow for intercellular communication.

Page 34:

  • Evolution of the Eukaryotic Cell:

    • Outlining Serial Endosymbiotic Theory by Lynn Margulis which posits acquisition and incorporation of other genomes leading to speciation.

    • Examples include transition from aerobic bacteria to mitochondria and cyanobacteria leading to chloroplasts.

    • Evidence noted for plastid origin based on similarities with bacteria including a similar membrane structure and replication process (binary fission).

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  • Figures on Eukaryotic Evolution:

    • Visual representation detailing ancestral prokaryotes giving rise to key organelles through symbiotic relationships.

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  • Evolution of Multicellular Organisms:

    • Describes the transition from unicellular to multicellular life via colonial organisms. Specialization of cells for specific functions characterized early multicellular entities.

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  • Cell Signaling and Adhesion in Evolution:

    • Evolutionary insights derived from choanoflagellates as precursors to animals indicate the foundations of cell signaling and adhesion systems emerged prior to true multicellularity.

    • Choanoflagellates express proteins integral to signaling pathways significant within metazoan evolution, indicating a common genetic pool predating animal lineage.

    • Reference: Science 301: 361 (18 July 2003).