BIO 201 Set 1 Notes - A Preview of Cell Biology PDF

BIO 201 Set 1 Notes A Preview of Cell Biology  Contents (1.1) – Ye Olde Microscopes: Robert Hooke & Antonie Van Leeuwenhoek (1.2) – Compound Microscopes: Robert Brown and Theodor Schwann (1.3) – Rudolf Virchow (1.4) – The 3 Strands of Modern Cell Biology (1.5) – Cytology: Micr...

BIO 201 Set 1 Notes A Preview of Cell Biology  Contents (1.1) – Ye Olde Microscopes: Robert Hooke & Antonie Van Leeuwenhoek (1.2) – Compound Microscopes: Robert Brown and Theodor Schwann (1.3) – Rudolf Virchow (1.4) – The 3 Strands of Modern Cell Biology (1.5) – Cytology: Microscopes (1.6) – Biochemistry: The Chemistry of Biological Structures/Functions (1.7) – Genetics: Information Flow in the Cell (1.8) – Review: The Scientific Method  1.1 – Ye Olde Microscopes: Robert Hooke & Antonie Van Leeuwenhoek Robert Hooke built a microscope in 1665 that examined dead cells from an oak tree (called cork cells). He discovered that the cork cells looked like tiny little boxes, which he called “cells”, the place where monks stayed in a Monastery. Latin: cellula = “little room” Q1. Why was Hooke not actually looking at real “cells”? Q2. When have you previously looked at a microscope with 30X Cork Cells (30X) magnification? Tube full of lenses Hooke’s microscope was only able to magnify objects up to 30X total magnification and he was therefore, unable to see the details of any cellular structures. Hooke was interested in many of the branches of sciences and even got into disputes with Sir Isaac Newton, claiming that Newton’s ideas were influenced by him (Hooke). FYI: Hooke discovered the “Law of Elasticity” Hooke’s constant = k [Know Robert Hooke’s Scientific Contributions] Hooke’s Microscope  1.1 – Ye Olde Microscopes: Robert Hooke & Antonie Van Leeuwenhoek Nobody actually knows what Robert Hooke looked like as any self-portraits of Newton Hooke were destroyed (perhaps by Newton)! Hooke? Image of Robert Hooke?? Image from “The wacky history of the cell theory” https://www.youtube.com/watch?v=4OpBylwH9DU Antonie van Leeuwenhoek was a Dutch textile merchant. He was also interested in microscopes and produced a microscope made of small lenses, which could magnify objects ~300X their size. Q3. Which microscope have you previously used in BIO 111/112 lab that can magnify objects up to 300X? [Know van Leeuwenhoek’s Scientific Contributions]  1.1 – Ye Olde Microscopes: Robert Hooke & Antonie Van Leeuwenhoek Antonie van Leeuwenhoek’s microscopes were not very large and about the size of a lens (found on glasses). Van Leeuwenhoek’s microscopes on display at Boerhaave (Dutch national museum history of science) Van Leeuwenhoek became the first person to view: 1. Blood cells. 2. Single-celled organisms (algae and protists). 3. Sperm cells. 4. Bacteria (looked at dental scrapings from other people). [Know van Leeuwenhoek’s Scientific Contributions]  1.1 – Ye Olde Microscopes: Robert Hooke & Antonie Van Leeuwenhoek Antonie van Leeuwenhoek didn’t call the single-celled organisms when he witnessed bacteria or protists, but coined the term “animalcules because they looked like little animals. All of the microscopes produced in the 1600’s-1700’s were limited by their resolution (resolving power). Resolution = The shortest distance between two points on a specimen that can still be distinguished by the observer as 2 separate entities. Poor resolution – Image is magnified, but the objects are not distinguishable as separate entities. Good resolution – Image is magnified, and the objects are distinguishable as separate entities.  1.2 – Compound Microscopes: Robert Brown and Theodor Schwann Compound Microscope (1831) Today’s Compound Microscope By the 1830’s compound microscopes were used. This greatly increased the magnification of objects and the resolving power of the microscope. The compound microscope included 2 lenses: Q4. How does one calculate the total magnification on a compound microscope? Objective Lens and Ocular Lens The limitation however was that structures only 1 μm in size could be seen.  1.2 – Compound Microscopes: Robert Brown and Theodor Schwann ~1831, Robert Brown used a compound microscope and discovered the plant nucleus found from the epidermis of an orchid. Brown named the rounded structure the Robert Brown “nucleus” which is derived from the Plant cell nucleus from an orchid Latin word kernel. In 1838, Matthias Schleiden came up with the conclusion that all plant tissues are composed of CELLS. He also came to the conclusion that an embryonic plant always arises from a single cell. Plant cells! Schleiden is a CO-FOUNDER of the Matthias Schleiden German Professor of CELL THEORY. Botany [Know Brown’s and Schleiden’s Scientific Contributions]  1.2 – Compound Microscopes: Robert Brown and Theodor Schwann In 1839, Theodor Schwann came to the conclusion that all animal tissues are composed of CELLS. It was more difficult to come to this conclusion because plant cells have cell Theodor walls, which easily show boundaries Schwann Animal Cells between each cell. Schwann had to look at animal cells from Q5. What other discovery was made by cartilage to see boundaries between each Theodor Schwann regarding neurons? cell, because there was thick deposits of collagen fibers between them. Q6. In 1839, Schwann postulated 2 basic principles of the cell theory. What are these 2 basic principles? [Know Schwann’s Scientific Contributions]  1.3 – Rudolf Virchow In 1855, Rudolf Virchow began to observe cell division, and contributed the 3rd principle of the modern cell theory: Rudolf 3. All cells arise only from pre- Virchow existing cells. Advancements in microscopy has allowed us to see the large physical differences between different cells. Top-Left: Filamentous fungi Bottom-Left: Villi found in small intestine Bottom-Right: Neuron Does cell structure relate to function? [Know Virchow’s Scientific Contributions] 1.4 – The 3 Strands of Modern Cell Biology DO NOT MEMORIZE THIS DIAGRAM! 3 historical strands are woven together to form the concept of modern cell biology. Each strand is important because it gives us a better understanding of cells. 1. CYTOLOGY: Focuses mainly on structure and emphasizes optical techniques. Observation of cell physiology. 2. BIOCHEMISTRY: The strand that focuses mainly on cellular function (especially at the molecular level) – Krebs’ cycle, Glycolysis, etc. 3. GENETICS: The strand that focuses on information flow and heredity. DNA sequencing, chromosomal inheritance, etc.  1.5 – Cytology: Microscopes 1. CYTOLOGY: Focuses mainly on cell structure and emphasizes optical techniques. LIGHT MICROSCOPE: Earliest tool used by cytologists. Allows for identification of membrane-bound organelles within cells as well. Q7. What is the smallest organism you have been able to see clearly (in a light microscope) in first-year BIO at UFV? Q8. Why is the light microscope used in the UFV lab known as a “brightfield’ microscope? Slides that are used for the light microscope are prepared using a microtome.  1.5 – Cytology: Microscopes Microtome MICROTOME: First started to be used in the mid 1800’s. A device used to create very thin sections of a specimen. These thin slices are called “sections”. When creating sections, it is often useful to use dyes and stains in order to distinguish different parts of the cell.  1.5 – Cytology: Microscopes It is must easier to see details in the stained specimen vs. the unstained specimen. Later on in the course, you will be performing staining of various slides. Staining improves the limit of resolution of the microscope. Limit of resolution = How far apart objects must be to appear distinct. Q9. What is the ‘limit of resolution’ of a typical light (compound) microscope that we use in the Bio 111/112 lab? The smaller the limit of resolution a microscope, the greater its resolving power (higher resolution). Q10. What is a major disadvantage in using stained specimens in a brightfield microscope? 1.5 – Cytology: Microscopes Phase Contrast Microscope and Differential Interference Contrast When light passes through the specimen, some wavelengths of light pass through the specimen more slowly. This is called a phase shift. The human eye can not detect this, but a phase contrast microscope can exploit these differences and create different brightness patterns, resulting in a better defined 3D object. Brightfield Phase-Contrast Microscope Microscope (unstained) (unstained)  1.5 – Cytology: Microscopes Fluorescence Microscope: Detects fluorescence dyes or labels and shows the locations of substances or structures inside a cell. Liposomes (lipid-based drugs) that contain a fluorescent label show up as RED. Cell nuclei (Hoescht) labeled in BLUE. This was how I demonstrated that my liposomes accumulated in the tumor. Lee et al. (2012)  1.5 – Cytology: Microscopes Fluorescence Microscope: Antibodies that target certain proteins (such as microtubules) can be added to cell/tissue samples. The antibodies have strong binding and specifically bind to these proteins. A fluorescent secondary antibody can be added and will attach to the first (primary antibody) that you added to your sample. GREEN = Microtubules BLUE = Nuclei Your sample can then be taken to a fluorescent microscope where images can be taken highlighting specifically labeled sections of the Q11. Draw a diagram of how fluorescent cell. microscopy works with primary and secondary fluorescent antibodies.  1.5 – Cytology: Microscopes Confocal Microscope: Similar to fluorescent microscopy except that only a single plane of a fluorescently labeled specimen is visualized. Software can be used to compile all of the images of each single plane to create a complete 3D image. This can be especially useful for fluorescently labeled drugs and can determine how far the drugs can penetrate into a tumor site for example.  1.5 – Cytology: Microscopes The Electron Microscope: The electron microscope uses a beam of electrons rather than light. It was a major breakthrough for cell biology! - The limit of resolution of an electron microscope is around 0.1-0.2 nm. - Electron microscopes can magnify images up to 100,000X. Transmission Electron Microscopy (TEM): Electrons are transmitted through the specimen. Scanning Electron Microscopy (SEM): The surface of the specimen is scanned. Electrons A SEM produced images in (a) and (b) are deflected from the outer surface of the Note only the surface is seen! specimen. A TEM produced images in (c) and (d) Note internal structure can be seen!  1.5 – Cytology: Microscopes Electron microscopes can help visualize cell structures that are too small to be seen with a light microscope: - Ribosomes - Membranes - Microtubules (fine structure) - Microfilaments - DNA double-helix!  1.6 – Biochemistry: The Chemistry of Biological Structures/Functions Biochemistry is the study of looking at the chemical processes occurring in living organisms. It is vital in understanding how cells work! Much of Biochemistry dates back to the work of Fredrich Wohler* (1828), who demonstrated that urea could be synthesized in a laboratory setting. Note: When amino acids are catabolized (broken down) in the body, ammonia is released. To prevent any toxic effects of ammonia on the blood (i.e. causes pH to increase), your body uses a series of enzymes to convert the ammonia into a non- Molecule of Urea toxic end product called urea that is excreted in the urine. Louis Pasteur* (1860’s) demonstrated that living yeast cells could ferment sugar into alcohol. [Do not need to know scientist’s names beyond this point i.e. slide 21 or later]  1.6 – Biochemistry: The Chemistry of Biological Structures/Functions Eduard and Hans Buchner* (1897) discovered that isolated yeast extracts (not live yeast) could also perform fermentation of sugar into ethanol. Q12. Why would yeast extracts be able to perform fermentation? Eduard Buchner* was awarded the Nobel prize in Chemistry (1907) for his work on fermentation. His work helped to initiate the discoveries of biochemical pathways, which utilize enzymes. Gustav Embden* and Otto Meyerhof* described the metabolic pathway of GLYCOLYSIS in the early 1930’s. We will study this process in detail in Ch 9. Hans Krebs* discovered the metabolic cycle known as the Krebs’ Cycle/TCA Cycle/Citric Acid Cycle shortly after. We will study this process in detail in Ch 9 as well! Q13. What are glycolysis and the Krebs’ Cycle important for in the cell?  1.6 – Biochemistry: The Chemistry of Biological Structures/Functions Other advancements in Biochemistry: Radioactive isotopes: 3H, 14C and 32P can be used to trace where atoms and molecules end up when molecules are transformed by enzymes in the cell. Examples will be given later in the course. Subcellular Fractionation: Centrifugation (shown to the right) spins test tubes at a high speed causing more dense organelles/cell structures to sediment to the bottom of the test tube and less dense organelles/cell structures to stay near the top of the test tube. Covered in Lab #3.  1.6 – Biochemistry: The Chemistry of Biological Structures/Functions Other advancements in Biochemistry: Chromatography: Biochemical technique to separate molecules based on size, charge, or different chemical properties (like polarity) Recall Thin-Layered Chromatography (TLC) in BIO 111?? Electrophoresis: Uses an electrical field to move proteins, DNA or RNA molecules through a medium based on size/charge. Covered in BIO 202, not BIO 201! Mass Spectrometry: To determine the size and composition of individual proteins. Covered in BIO 320, not BIO 201! The main point is that Biochemistry is needed in order to understand how a cell functions at the molecular level!  1.7 – Genetics: Information Flow in the Cell The last “strand” of cell biology incorporates genetics, which is the study of genes, heredity of genes and the variation of inherited characteristics. BIO 220 (genetics) and BIO 202 (cell signaling and regulation of gene expression) cover most of the this “strand” of cell biology, which is why it will only be covered briefly in BIO 201. Gregor Mendel’s experiments with peas (1866) laid the foundation for understanding the passage of “hereditary factors” (now known as genes) from parents to offspring. Walther Flemming* (1880) saw threadlike bodies in the nucleus that he called chromosomes. Also coined the term mitosis for the process of cell division. Wilhelm Roux* (1883) and August Weisman* suggested that chromosomes carried the genetic material.  1.7 – Genetics: Information Flow in the Cell Other advancements in Genetics: 1953: Watson and Crick proposed the double helix model for DNA 1960s: Understanding of DNA replication, transcription and the genetic code (codon table). Nucleic acid hybridization: A variety of techniques that use the ability of nucleic acid bases to bind to each other. Covered in BIO 202. Recombinant DNA technology: Using restriction enzymes to cut DNA at specific places allowing scientists to create recombinant DNA molecules with DNA with different sources. i.e. GMO’s. covered in BIO 202.  1.7 – Genetics: Information Flow in the Cell Other advancements in Genetics: DNA sequencing: Methods for rapidly determining the base sequences of DNA molecules. i.e. The human genome project. Covered in BIO 202. Bioinformatics: Merges computer science with biology to organize and interpret enormous amounts of information (DNA sequencing, proteomes, etc.) i.e. You can find the DNA sequence or amino acid sequence of a specific protein simply by doing a search! Covered in BIO 202.  1.8 – Review: The Scientific Method The scientific method is used to assess new information found in cell biology (just like in any field of other science as well!) This should be review from first-year Biology. - Scientists make observations about the world around them. They formulate a question/problem. - Scientists formulate a hypothesis (tentative explanation or model that can be tested). - Data are collected and interpreted. - Hypothesis is accepted or rejected. - The experiment is normally modified and repeated numerous times to better understand the question/problem at hand.