06 Cell Bio 2024 Intro JvW PDF

Alberts Johnson Lewis Raff Roberts Walter Essential Cell Biology Fourth Edition Chapter 1 Cells: The Fundamental Units of Life tutor: Jan van Weering Copyright © Garland Science 2008  Schedule Past 3 weeks “Histo...

Alberts Johnson Lewis Raff Roberts Walter Essential Cell Biology Fourth Edition Chapter 1 Cells: The Fundamental Units of Life tutor: Jan van Weering Copyright © Garland Science 2008  Schedule Past 3 weeks “Histology” Coming 4 weeks “Cell biology”  Schedule: the teachers Past 3 weeks “Histology” Mark Verheijen Coming 4 weeks “Cell biology” Joen Luirink Jan van Weering Guus Smit Douwe Molenaar  Cell biology outline Lectures (based on Essential Cell Biology) - Cells and organelles (van Weering) - Extracellular matrix (Smit) - Intracellular transport (Luirink) - Cytoskeleton (Smit) - Cell cycle (van Weering) - Cell communication (Smit) - Systems biologie: Signal transduction (Molenaar) Practicals - From LM to EM: Organelles (van Weering) - Tissue speci c ultrastructure (van Weering) - Transport organelles (van Weering) - Cell cycle of the gut (van Weering) - Intracellular transport (Luirink) - Systems biologie: Signal transduction (Molenaar) fi  Practicals CPR1-4 are mandatory self study quizzes on Canvas. You need to score at least 6 points for each practical to pass, before its "test yourself" session (see schedule). You can start EM1 and EM2 CPRs as of today, EM3 and EM4 are available after the lecture transport II and cell cycle, respectively. You can use on-line resources to do the assignments (canvas ppts, google, pubmed, wikipedia ect.) and discuss with fellow students. CPR5 ("Signal transduction" in week 50) is on campus, see schedule. These practicals are examination material, so study these well in preparation for the exam. Deadline CPR1: Thu 28th Nov 13:00! Deadline CPR2: Fri 29th Nov 13:00!  Practicals CPR1: microscopy methods and organelles (this lecture) CPR2: tissue-speci c ultrastructure (Histo practicals and lectures) EM demo Unfortunately, EM demo on 26th Nov (11:00-12:45) is canceled EM is not working at this time fi  Learning objectives You can de ne what a cell is and to which groups it can belong. explain different microscopy methods and you can choose the best method to answer a speci c research question. identify the key-organelles of the cell and explain their prime function. fi fi From ”Histology” to “Cell biology” From tissue to cell...... to sub-cellular structure.... to sub-cellular structure. The cell  The cell What are three essential features of a cell ?  The cell... - is the essential building block of all life on Earth. - has a limiting membrane (inside/outside compartments). - contains biomolecules (e.g protein/RNA/DNA). - is an autonomous unit in performing a function. - can respond & adapt to stimuli. - can (often) reproduce itself. The cell: the corner stone of life Robert Hooke 1665: cork is consists of "small rooms" All life on Earth consists of cells.  Diversity of cells oocyte: ±150 µm in diameter, volume 4.000.000 µm3 sperm: ±1,5 µm in diameter, volume 30 µm3  Despite the obvious differences between cells, basic functions and components are highly similar. The basic ingredients of the cell DNA: deoxyribonucleic acid the language of genes proteins: from code to function From proteins to cell behaviour: organelles  Tree of life: bacteria, archaea & eukaryotes Bacteria : no nucleus or other organelles Archaea : no nucleus, often extremophiles Eukaryotes : nucleus and other organelles, sometimes multicellular life forms Tree of life: bacteria, archaea & eukaryotes  The relation between form and function Why do cells have a speci c shape? What is the function of an organelle? How does the cell contribute to the behaviour of the organism? fi The microscope: essential to study cells  the power of the lens Antonie van Leeuwenhoek (1632-1723)  the power of the lens Antonie van Leeuwenhoek (1632-1723) The microscope: essential to study cells Advanced light microscopy: uorescence microscopy fl  GFP: green uorescent protein From which organism was GFP cloned? fl  green uorescent protein Aequorea victoria fl DNA, the universal language of genes  Using GFP, you can visualise subpopulations of cells in tissue Using GFP, you can visualise living cells in multicolour  Visualise the cell beyond the resolution of light 36 Vesicle: 40 nm Green light: 500 nm  The resolution of LM (light microscopy) Schermelleh et al. 2010 JCB 38  e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e Visualise the cell beyond the resolution of light e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e e  The resolution of EM (electron microscopy) TEM 2.5 x 10-3 physical reconstructed v >1 50-300 (section) 5 (reconstruction) 0.00005 Schermelleh et al. 2010 JCB 40 A sense of scale A sense of scale A sense of scale: An animal cell: 10-500 um A cell nucleus: ~10 um Neurotransmitter vesicle: 40 nm An IgG antibody: 12 x 10 nm DNA helix width: 2.5 nm Water molecule: 0.28 nm How does an EM work? How does an EM work?  How does an EM work? e e Nature: e e Element #protons e H 1 e e C 6 e N 7 e O 8 e e S 16 e e + e Elektron Microscopist: e Element #protons e Ru 44 e Os 76 e e Pb 83 e e e e eeeeeeeeeeeeeeeee U 92  LM vs EM Advantage of EM over LM: - Superior resolution (up to 0.5 nm!, atoms!) - Visualise the whole cell, not only a uorescent probe (e.g. GFP). - Huge magni cation range (30x-300.000x: 104) Disadvantages of EM compared to LM: - requires xation of cells (operates under vacuum). - Only small pieces of tissue can be imaged. - Time-consuming method fi fi fl  Summary 1: cells & microscopes All life on Earth consists of cells A cell is a compartment containing biomolecules (DNA, RNA, protein) that are surrounded by membrane and can react to stimuli. All cells have the same basic ingredients but the show a huge diversity in shapes and specialised functions. To study the form-function relationships, microscopes are essential: Light microscopy Fluorescence microscopy Electron microscopy Using these methods in combination, you can study processes in cells at a 1 000 000 magni cation range. fi Tree of life: bacteria, archaea & eukaryotes Organelles The nucleus : form and function? The nucleus : form and function? Chromatin: a complex of DNA and protein that forms chromosomes DNA storage in chromosomes Translation of RNA to protein in the endoplasmic reticulum (ER) Translation of RNA to protein in the endoplasmic reticulum (ER)  2 compartments: inside and outside/cytosolic and luminal What does the Golgi apparatus do? protein modi cation & protein sorting Man: mannose Gal: galactose GlcNAc: n-acethylglucosamine NANA: N-acetylneuraminic acid fi The Golgi morphology Sorting station: Golgi complex Sorting station: Golgi complex Post-translational modi cation of proteins Man: mannose Gal: galactose GlcNAc: n-acethylglucosamine NANA: N-acetylneuraminic acid fi Intracellular transport system Transport and many other processes in the cell require energy The mitochondrion: energy supply Burning glucose yields energy in the form of adenosine triphosphate (ATP) Mitochondria contain their own DNA The chloroplast: energy supply in plants photosynthesis  Plants still need mitochondria to burn the glucose provided by photosynthesis. What critical cell compartment have we not yet discussed? The "soup": cytoplasm cytoplasm is not uid, but a jelly matrix of proteins fl cytoplasm is not uid, but a jelly matrix of proteins fl  processes of the cytoplasm transport protein synthesis protein break-down signal transduction membrane fusion ionic homeostasis form and transport: the cytoskeleton  The cytoskeleton comprises 3 types of laments: intermediate microtubules actin laments fi fi Intracellular transport system The dynamic microtubule network  Summary 2: organelles Cells in the tree of life comprise bacteria, archaea and eukaryotes. Only eukaryotes contain organelles and a nucleus, these cells can form multicellular organisms. The basic organelles and their function: The nucleus: store DNA and transcription of DNA to RNA. The endoplasmic reticulum: translation of RNA to protein and protein folding. Golgi apparatus: post-translational modi cation and sorting of proteins. Mitochondrion: energy supply in the form of ATP Chloroplast: photosynthesis Cytoskeleton: cell shape and transport Cytoplasm: multifunctional protein gel and homeostasis fi  EM Practicals These are mandatory self study quizzes on Canvas. The CPR rooms in your personal schedule do no longer apply, we follow the schedule on Canvas only. You need to score at least 6 points for each practical to pass, before its "test yourself" session (see schedule). You can start EM1 and EM2 CPRs as of today, EM3 and EM4 are available after the lecture transport II and cell cycle, respectively. You can use on-line resources to do the assignments (canvas ppts, google, pubmed, wikipedia ect.) and discuss with fellow students, CPR rooms are available (see schedule) These practicals are examination material, so study these well in preparation for the exam. Deadline CPR1: Thu 28th Nov 13:00! Deadline CPR2: Fri 29th Nov 13:00!  Learning objectives You can de ne what a cell is and to which groups it can belong. explain different microscopy methods and you can choose the best method to answer a speci c research question. identify the key-organelles of the cell and explain their prime function. fi fi  Cell biology outline Lectures (based on Essential Cell Biology) - Cells and organelles (van Weering) - Extracellular matrix (Smit) - Intracellular transport (Luirink) - Cytoskeleton (Smit) - Cell cycle (van Weering) - Cell communication (Smit) - Systems biologie: Signal transduction (Molenaar) Practicals - From LM to EM: Organelles (van Weering) - Tissue speci c ultrastructure (van Weering) - Transport organelles (van Weering) - Cell cycle of the gut (van Weering) - Intracellular transport (Luirink) - Systems biologie: Signal transduction (Molenaar) fi