Exhaustive Study Notes on Cell Structure: Prokaryotes and Eukaryotes
Overview of Laboratory Exercise 3: Cell Structure and Biology
This laboratory session, indexed as Exercise 3 for the course BSC2010L at Indian River State College (IRSC), focuses on the fundamental distinctions between prokaryotic and eukaryotic cells. The primary objectives for students include defining the specific differences between these two cell types, observing various prepared slides of prokaryotic cells, and creating wet mount slides to observe living eukaryotic cells found in pond water. Additionally, a critical component of the lab is the microscope storage check, which constitutes of the total course grade, emphasizing the importance of proper equipment maintenance.
The Three Domains and the Phylogenetic Tree of Life
Biological classification is organized into three broad taxonomic categories known as Domains. The first is Domain Archaea, which consists of unicellular prokaryotes often termed "extremophiles" because they thrive in environments where humans cannot survive; these organisms are not the focus of this specific laboratory. The second is Domain Bacteria, which includes unicellular prokaryotes that are present within the human body and all around our environment. These are microscopic and will be a major point of study. The third is Domain Eukarya, which encompasses all eukaryotes. Domain Eukarya is subdivided into four kingdoms: Kingdom Protista, Kingdom Fungi, Kingdom Plantae, and Kingdom Animalia. The latter two kingdoms will be the core focus of the subsequent laboratory session.
The Phylogenetic Tree of Life illustrates the evolutionary relationships between these groups. Within Bacteria, groups include Green Filamentous bacteria, Spirochetes, Gram-positives, Proteobacteria, Cyanobacteria, Planctomyces, Bacteroides, Cytophaga, Thermotoga, and Aquifex. Archaea includes Methanosarcina, Methanobacterium, Methanococcus, T. celer, Thermoproteus, Pyrodicticum, and Halophiles. The Eukarya branch contains Entamoebae, Slime molds, Animals, Fungi, Plants, Ciliates, Flagellates, Trichomonads, Microsporidia, and Diplomonads.
Foundations of Cell Theory
Cell Theory provides the basis for understanding biological life. It is defined by three major tenets: all living things are composed of cells, cells come only from other preexisting cells, and cells are the basic unit of life. Life is classified based on cell count: unicellular organisms are composed of a single cell, while multicellular organisms consist of multiple cells. These structures are visualized using a microscope, where a pointer inside the eyepiece is used as a reference to identify specific points of interest for other viewers.
Structural Comparison: Prokaryotes vs. Eukaryotes
There are significant structural differences between prokaryotic and eukaryotic cells. Prokaryotic cells, which include Domains Bacteria and Archaea, are generally smaller. They lack a membrane-bound nucleus; instead, their DNA is located in an unregulated region called a nucleoid. Prokaryotes do not possess membrane-bound organelles or a cytoskeleton. Structurally, they are composed of a capsule, cell wall, cytoplasmic membrane, ribosomes, cytoplasm, nucleoid, pili, and flagella.
Eukaryotic cells, found in protists, fungi, plants, and animals, are significantly larger and more complex. They feature a membrane-bound nucleus containing a nucleolus and utilize various membrane-bound organelles. Unlike prokaryotes, eukaryotes possess a cytoskeleton. The organelles involved in eukaryotic structure include microtubules, chromatin, mitochondria, centrioles, vesicles, cytosol, rough and smooth endoplasmic reticulum, ribosomes, a nuclear envelope with nuclear pores, the Golgi complex, lysosomes, flagella, and the plasma membrane.
Despite these differences, both cell types share four fundamental components: a plasma or cell membrane, DNA, ribosomes, and cytoplasm.
Comparative Examples in Microscopy
When viewing organisms under a microscope, distinct arrangements become visible. In the Domain Eukarya, the genus Allium (onion) exhibits a specific arrangement of multiple blocks of cells. In contrast, in the Domain Bacteria, the genus Bacillus appears as individual blue rods, where each rod represents a single bacterium. Bacteria in culture may appear as a mass, requiring high-power magnification to distinguish individual cells.
Within Domain Eukarya, Kingdom Protista consists mostly of unicellular organisms. These include "Protozoa," which are heterotrophic and "animal-like," and "Algae," which are autotrophic and can be microscopic (phytoplankton) or macroscopic (seaweed). Kingdom Fungi can be either unicellular or multicellular.
Taxonomic Case Studies of Simple Organisms
Several specific organisms serve as models for study. Cyanobacteria, such as Oscillatoria and Anabena, are photosynthetic bacteria within Domain Bacteria. Within Domain Eukarya, simple eukaryotic protists include Amoeba proteus, which moves using pseudopodia, and Paramecium, which moves via cilia. Ceratium is a flagellated dinoflagellate that exhibits various modes of locomotion, including flagellated, ciliary, and amoeboid movement. Volvox represents a colonial eukaryote and is a type of green algae. In Kingdom Fungi, Saccharomyces is a single-cell yeast. Kingdom Animalia includes multicellular simple eukaryotes like Planaria, which possess specialized cells for different functions but lack major organ systems.
Eukaryotic Cell Organelles and Functional Analogies
Eukaryotic cells contain specialized organelles, many of which can be understood through functional metaphors. The Nucleus serves as the "Control" or "DNA house," while the Nucleolus handles the assembly of RNA and proteins. The Nuclear Membrane or Envelope acts as a "VIP door." The Endoplasmic Reticulum acts like a "Subway" system for protein and lipid synthesis. The Golgi apparatus functions like "FedEx/UPS" for packaging and transport. Mitochondria are the "Powerhouse" for ATP production. The Cytoplasm serves as a "scaffold" for the cell, and the Cell Membrane acts as a "Revolving door."
Animal cells specifically contain Lysosomes, which act as "Janitors" for digestion via enzymes, and Centrioles, which manage the microtubule system during cell division. Plant cells possess unique structures including the Cell Wall for protection and support, Chloroplasts for photosynthesis and glucose production, and a Large Central Vacuole, compared to an "Airplane cabin" for maintaining hydrostatic pressure.
Laboratory Procedures and Post-Lab Protocol
To prepare a wet mount slide of eukaryotic cells, a specimen of pond or ocean water is placed on a clean slide. If available, a drop of "protoslo" is added to slow down motile organisms. A coverslip must be gently dropped at a angle to prevent air bubbles. Excess liquid is sopped up with a Kimwipe before visualizing with the microscope.
Students must use the Microscope Focusing Test checklist for every slide and prepare for the focal test in the following week. After completing activities, all wet mounts must be cleaned, and fixed mount slides must be stored properly. Students are required to have their microscope checked by the instructor to earn "Microscope Points" before returning the equipment to the cabinet. Post-lab responsibilities include completing Exercise 3 of the Unit 1 study guide, reviewing supplemental Canvas materials, and completing the pre-lab quiz for the next session, which will focus on Plants versus Animal cells.