Biology Chapter: Cell Types and Research Models

Unit 1: Overview of the Cell and Cell Research

• Biology is the study of the composition, development, functioning, links, and distribution of living things.
• A cell is the fundamental unit of living beings, capable of independent reproduction.
• Cell biology is a discipline focused on analyzing cell structure, function, components, interactions, and properties.
• Cell biology draws on knowledge from genetics, biochemistry, immunology, and other areas.
• Molecular biology studies life processes from a molecular perspective, focusing on macromolecules like nucleic acids and proteins.
• The difference between cell and molecular biology is their focus. Cell biology focuses on the overall functioning of cellular systems, while molecular biology focuses on the roles of individual molecules within a cell.

1.1 Origin and Evolution of Cells

• The cell is the fundamental unit of all living organisms.
• Different cell types exist, and multicellular organisms evolved from them.
• Robert Hooke (1635-1703) made early observations of cells in cork.
• Antoni van Leeuwenhoek (1632-1723) observed protozoa, bacteria, and other cells using microscopes.
• Cell theory, formulated in 1839, states that all organisms are made of cells, cells are the basic unit of structure and organization, and cells come from pre-existing cells.

1.2 Cells as Experimental Models

• Different types of cells, including unicellular and multicellular organisms, are used as experimental models for various studies.
• Unicellular models include Escherichia coli and Yeast.
• Multicellular models include Arabidopsis thaliana, Caenorhabditis elegans, Drosophila melanogaster, Danio rerio, and Mus musculus.
• All cells have a common ancestor with conserved fundamental properties.
• Studying one type of organism reveals insights applicable to others.

1.3 Cell Biology Instruments (a)

• Optical microscopy:
  • Magnification: a factor by which an image appears to be enlarged. The Light microscope can magnify images only up to approximately 1000 times.
  • Resolution: minimum distance between two points visible as separate points. Resolution of a light microscope is about 0.2 μm.
• Electron microscopy:
  • Much higher magnification and resolution
  • It uses beams of electrons instead of light.
  • Resolution of electron microscopes can be 1-2 nm.
• Super-Resolution Microscopy: An advanced light microscopy technique with improved resolution beyond the diffraction limit of optical microscopes.

1.3 Cell Biology Instruments (b)

• Specimen preparation
• Flow cytometry
• Subcellular separation
• Growth of animal cells in culture
• Viruses

Specimen Preparation

• Histological processing involves fixation, tissue embedding, sectioning, and staining.
• Fixation: Stops cell degradation processes by preserving protein integrity.
• Tissue embedding: Replacing water with a solid medium (like paraffin) for support during cutting.
• Sectioning: Cutting thin tissue slices with a microtome.
• Staining: Enhancing contrast with dyes or stains for easier visualization.

Fixation

• Physical: Cryofixation (-70°C), for quick freezing and avoiding ice crystal damage.
• Chemical: Using chemicals that interact with tissue molecules and stabilize them.

Tissue Embedding

• Paraffin: Primarily for light microscopy, a wax used to embed samples and support delicate cutting.
• Resins: More rigid material suitable for electron microscopy (EM) providing better structural support in sample preparation.

Sectioning

• Microtome: used for paraffin-embedded thin slicing (3-5 μm).
• Cryostat: for frozen samples, producing thicker slices (6-8 µm or more), allowing viewing of intact subcellular structures.

Other Sample Preparation Methods

• Some samples, like blood smears, are prepared directly without fixation or sectioning.

Staining

• Dyes are used in microscopy to enhance contrast among structures.
• Histological Staining: -Basic dyes (hematoxylin): bind to acidic structures (e.g., DNA). -Acidic dyes (eosin): bind to basic structures (e.g., proteins)
• Electron Microscopy: -Heavy metals (lead citrate, osmium tetroxide, uranium acetate): increase contrast by interacting with cellular materials.

Immunohistochemical Techniques

• Purpose: Identifying specific proteins in tissue sections using specific antibodies
• Direct technique: Primary antibody is directly labeled.
• Indirect technique: A secondary antibody recognizes the primary.
• These techniques are crucial in diagnostics (e.g. viral proteins, oncogene overexpression).

Flow Cytometry

• Analyze cells in a suspension.
• It quantifies cells, differentiates cell types, and measures cellular complexity
• Instruments include fluidic sample transport system, optical laser illumination, and electronic detectors.

Subcellular Separation

• Isolating specific organelles and other subcellular particles.
• Physical Methods: Osmotic shock, ultrasound, mechanical grinding
• Enzymatic Methods: Lysozyme to degrade the cell wall.

Differential Centrifugation

• Separating cellular components by varying speeds and forces exerted on the sample using centrifugation. This separates components based on their differential densities and sizes.

Density Gradient Centrifugation

• A technique involving applying a dense gradient in a centrifuge tube in order to separate biological components based on their density.

Cell Cultures

• In vitro cell growth and maintenance.
• Primary cultures: derived directly from tissue samples.
• Secondary cultures: derived from primary cultures allow more convenient study by controlling the culture conditions.
• Immortalized cells: derived from tumors, that continue to proliferate indefinitely within a cell culture.

HeLa cells

• Example of an immortalized cell line widely used in research.
• Derived from a cervical tumor patient in 1951
• Enables investigating various cellular processes, including development of polio vaccine.

Cell Culture Media

• A crucial component for successful cell culture.
• Composed of salts, glucose, amino acids, vitamins, and growth factors.
• Required for cell survival, growth, and division in a laboratory environment.

Viruses

• Viruses are obligate intracellular parasites needing a host for their lifecycle.
• Laboratory research relies on virus cultured in suitable host cell lines for studying viral functions, molecular mechanisms, genetic potential, and oncogenes.

Other Model Organisms:

• A. thaliana (Plant): plant biology, agricultural applications, stress response, etc.
• C. elegans (Nematode): animal development, aging, cell death, genetics, nervous system.
• D. melanogaster (Fruit fly): animal development, genetics (especially for gene function).
• D. rerio* (Zebrafish): Vertebrate development, regeneration of tissues, genetics of human diseases, etc.
• M. musculus (Mouse): Neuroscience, pharmacology, physiology, transgenic research, and genetic studies in mammals.

The Choice of Model Organisms

• Choosing appropriate organisms for research depends on the research question.
• Specific characteristics, such as ease of culture, size, and genetic accessibility, of different species allow scientists to understand a wider array of biological phenomena.

Trends in Cell Biology

• New model organisms are being discovered, including cnidarians.

Human Organoids

• Sophisticated model systems created using human cells to study diseases and cellular mechanisms in a three-dimensional, more realistic structure.

Test your knowledge on the classification of organisms, the unique features of various algae, and the complexities of plant and animal cells. This quiz also delves into important model organisms used in scientific research and advancements in genetic studies. See how well you understand the diverse world of cellular biology and its applications.