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BIOL-L 312 Cell Biology (Mehta) Lecture Notes - Week One

by: Ifeoma O'Gonuwe

BIOL-L 312 Cell Biology (Mehta) Lecture Notes - Week One BIOL-L 312

Marketplace > Indiana University > Biology > BIOL-L 312 > BIOL L 312 Cell Biology Mehta Lecture Notes Week One
Ifeoma O'Gonuwe
Cell Biology
Sapna Mehta

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About this Document

This bundle of notes encompasses Professor Mehta's notes and examples presented in class. The material has been elaborated upon (based on added information from office hours) to provide a condense ...
Cell Biology
Sapna Mehta
Class Notes
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This 7 page Class Notes was uploaded by Ifeoma O'Gonuwe on Friday January 23, 2015. The Class Notes belongs to BIOL-L 312 at Indiana University taught by Sapna Mehta in Spring2015. Since its upload, it has received 153 views. For similar materials see Cell Biology in Biology at Indiana University.


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Date Created: 01/23/15
113 Notes LECTURE ONE WELCOME TO CELL BIOLOGY What is a cell 0 Lowest level of structure that can perform activities required for life 0 Activities homeostasis capacity to reproduce and grow responding to stimuli 0 Common biochemistry all cells use the same basic building blocks DNA RNA amino acids lipids carbohydrates 0 Common macromolecules and supramolecular structures and physiology lipid bilayers ribosomes use ATP as energy 0 All cells have a delimiting membrane to separate inside from out 0 Capacity for reproduction Why Study Cells 0 Form generally fits function 0 By studying a biological structure you determine what it does and how it works 0 Life emerges from interactions of structures 0 Combinations of structures components provide organization called a system What does a cell need to do 0 To live or die 0 If live then how does it produce and store energy 0 If die can it do so in a controlled way apoptosis 0 Communicate o How does information flow within the cell the environment and to neighboring cells 0 Proliferate o How does a cell divide o How does it move 0 How does a cell determine its polarity Cellular Diversity 0 Two major classes of cells based on complexity of intracellular organization 0 Prokaryotes no nucleus or nuclear envelope 0 Eukaryotes nucleus Bacteria vs Yeast o What is the difference 0 Bacteria is smaller 0 Bacteria DNA is less organized Structure of a Eukaryotic Cell 0 It is complex with many organelles discrete units of the cell necessary to carry out specific functions What does the nuclear envelope enclose 0 Nuclear envelope encloses the nucleus which contains nucleolus and DNA 0 Nucleolus production of ribosome with ribosomal RNA present The Mitochondria o It has two bilayer membranes 0 The folds inside the mitochondria is one bilayer membrane 0 It has its own genome o Remnant of evolution how a prokaryotes became a eukaryote The Chloroplasts o Thylakoids stacks of chlorophyll containing membranes 0 Has its own genome The Endoplasmic Reticulum 0 Site of lipid and protein biosynthesis o Extends from nuclear envelope 0 On the rough ER there are ribosomes where protein biosynthesis occurs 0 Smooth ER without ribosomes is where lipid biosynthesis occurs 0 Lipid biosynthesis can occur in both rough and smooth 0 Only protein synthesis occurs ONLY in the rough ER The Golgi Apparatus 0 Site of protein modification 0 Structure is a stack of membranes with vesicles 0 Sugars for modification and proteins to be modified are packaged into vesicles to enter the Golgi and leave the Golgi for exocytosis or cytoplasm from the Golgi 0 Transport center of the cell The Lysosome o Digestion with digestive enzymes to breakdown old cells and malfunctioning parts of the cell 0 Parts are recycled from lysosome for reuse in the cell 0 Microorganisms are degraded in lysosomes The Peroxisome o This has enzymes important for oxidative reactions 0 Produce and degrade H202 o Breaks down fatty acids cholesterol and bile Model Organisms o What is a model organism 0 Simple to study organisms that are used to understand different processes 0 Why do we use model organisms to study cell biology 0 They are easy to manipulate 0 Their genesprocesses are conserved across species The information gathered can be applied to higher order organisms 0 They reproduce quickly reducing the time span of the experiment Which are the main ones 0 1 Escherichia coli bacterium o 2 Saccharomyces cerevisiae yeast 0 3 Arabidopsis thaliana weed o 4 Drosophila melanogaster fruit fly 0 5 Mus musculus mouse 0 6 Homo sapiens human Yeast A minimal model eukaryote 0 There are two types of yeast Saccharomyces cerevisiae budding yeast and schizosaccharomyces pombe fission yeast beer yeast 0 Has a very rapid life cycle 0 Generation time is 90 minutes o Is easily cultured in large amounts 0 Has a simple genome 0 Its genome is entirely sequenced 0 Has a simplified endomembrane system o Is genetically amenable 0 Has many conserved processes 0 Can survive freezing Yeast used to find key regulators of the cell cycle 0 Lee Hartwell and Paul Nurse used yeast to find key regulators of the cell cycle 0 These key regulators are highly conserved amongst the species so much so that yeast regulators can be used in humans when theirs are deficient 0 Yeast can also be used to study 0 Control of cell cycle protein secretion membrane biogenesis gene regulation chromosome structure and aging Roundworm Caenorhabditis elegans 0 Rapid generation time days 0 Whole organisms can be frozen 0 Transparent body wall 0 Useful for visualizing fluorescence 0 Simple basic multicellular organism 0 Defined cell lineage and number 929 cells per C elegans 0 Can track each cell and determine what it becomes 0 Can also study the formation of the nervous system and apoptosis 0 Was the first multicellular organism whose genome was completely sequenced Fruit fly Drosophila melanogaster 0 Rapid generation time days 0 Complex multicellular organism o Genetically amenable 0 Good developmental biology model 0 IUDrosophila stock center The genetic control of early embryonic development 0 Edward Lewis Christiane NussleinVolhard Eric Wieschus Mouse Mus Musculus 0 Complex multicellular o Biologically and genetically similar to humans 0 Cell lines can be established 0 Knockout animals possible 0 Human disease models possible Comparison of the Human and Mouse Genomes 0 Both genomes contain 25000300000 protein coding genes 0 Mouse genome 25 x 109 bp 0 Human genome of 29 x 109 bp 0 Over 908 of mouse and human genomes can be partitioned into regions of conserved synteny A Model Plant Arabdopsis thaliana 0 Small fast growing 0 Genome small and sequenced 0 Seeds can be frozen The Human Genome 0 Of the 25000 genes in the human genome 236 have unknown functions 135 control activity within the nucleus 123 allow communication inside of or between cells 102 are enzymes 50 relate to the cytoskeleton 48 are transporters for small molecules 33 are involved in cellcell adhesion 29 are tumor suppressors OOOOOOOO 09 are involved in immune functions 113 Notes LECTURE TWO CELL BIOLOGISTS TOOL KIT MICROSCOPY Name Why What Fungi S pombe and S Very rapid life cycle Cell cycle protein secretion cerevisiae Easily cultured and membrane biogenesis Simple sequenced cytoskeleton aging gene genome regulation and chromosome Simplified structure endomembrane system Genetically amenable Plants A thaliana Can be grown indoors Tissue differentiation life cycle Small fast growing flowering time plantpathogen Close evolutionary interactions tolerance to relationship between all environmental conditions flowering plants Thousands ten forty of offspring per plant after six weeks seeds Can be frozen Tools for Cell Biology 0 Can we see cells 0 Yes and no most are too small but we can see some easily 0 What are the tools of cell biology research 0 How small is small What are microscopes designed for o Magnification relative enlargement of a specimen when viewed through the microscope 0 Resolution the shortest distance between two points on a specimen that can still be distinguished by the observer or camera system as separate entities 0 Most IMP parameter influencing how much detail can be observed Microscopes A Cell Biologists Essential Tool 0 Robert Hook coined the word cell while looking at cork in 1665 0 Antoine van Leeuwenhoek Cell Doctrine o Matthias Schleden and Theodor Schwann o 1838 plant and animal tissues are made up of living cells The Path of a Light Microscope o What does the eyepiece do 0 Has a lens to magnify but it s not as much as the objective Doesn t add more detail but refocuses onto the detector and the eye 0 What does the objective do close to the object 0 Contains the lens to magnify the image o What does the condenser do 0 Focus the light unto the specimen Resolution 0 Ernest Abbe deduced that smallest resolvable distance between two points may never be smaller than half the wavelength of the imaging light 0 Today s Light microscopes farther than 200nm 0 Why is it difficult to see detailed information just using BrightField Microscopy o Brightfield microscopy plain light 8 magnification regular microscope to look at tissue samples etc Contrast using cell stains or interference 0 Advantages of staining allows for different parts of the specimen to be easier visualize generate contrast 0 Pick a different stain to highlight what you are looking for o What are the disadvantages of staining 0 Not sure what will be stained 0 Must fix the cell to allow for staining 9 might alter ultrastructure of the cell I The cell must be dead so no live cell imaging Light Microscopy Techniques to Generate Contrast 0 You can stain Image Enhancement Digital 0 Using a camera at the eyepiece instead of looking at it o Advantage you can digitize the image and then do quantitative you can also do it in the dark 0 In most microscopes images are captured on highly sensitive cooled CCD chargecoupled device cameras 0 Allows us to see details within cells at low light 0 Images can be digitized and processed with help of a computer 0 Increase contrast 0 Remove latent information o Attain theoretical limit of resolution 0 Can detect very small objects The Power of Fluorescence Microscopy o Fluorescent molecules absorb light at one wavelength and emit it at an another 0 Are we still limited by the wavelength of light for detection of a fluorescent molecule I No the fluorophores have different wavelengths than light 0 What about resolution I No because you can t resolve them You can t know how many molecules are close together because the diffraction of light means you will detect a halo of light not a pinpoint of light unless they are more than 200 nm apart REWORD plz How Can We Convert the Light Microscope to a fluorescent scope o 1 Ask the microscope to make sure that the light that touches the specimen if it is a fluorophores is of the absorption of the specimen 0 How to do that place a filter colored glass by the light to only allow the wavelength of light that the fluorophores absorbs at 2 Ask the microscope to make sure that the light emitted by the specimen is the only light that comes through the detection Using Antibodies in dead cells Primary antibody rabbit antibody direct against antigen A o Antibody generated is coupledwith a fluorophore Secondary antibodies markercoupled antibodies directed against rabbit o Antibody that won t recognize antigen the molecule of interest 0 Example primary antibody is a rabbit antibody AntiX binds to protein X What is the advantage of using a secondary antibody instead of labeling the primary antibody with a fluorophore 0 Many more secondary antibodies can attach to a primary antibody Only one primary antibody can attach to one antigen There will be an enhanced signal by labeling secondary antibodies The cell will be dead because you have to introduce the synthetic antibodies made using an animal not in a test tube but not natural to the cell into the cell through fix Can be used for localization of proteins 0 Detect the secondary antibodies fluorescently tagged that attach to the primary antibody AntiX that is attached to protein X the protein of interest Disadvantage 0 Specificity make sure that the secondary antigen will bind to multiple primary antigens The Discovery of GFP Osamu Shimomura Martin Chalfie Roger Tsien Is There a Way to Get a Direct Readout Commonly called proteintagging Addition of DNA encoding fluorescent protein to the DNA encoding the protein of interest Fluorescent signal provides a direct readout about the state of the your particular protein Expression can be controlled through a specific promoter Fluorescence can be visualized and followed in living cells NOW ROUTINE


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