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Lecture Notes - from January 9th to 20th, 2014

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Jon Houseman

Intro to Cell Bio January 9th Cell: fundamental unit of life, starts with single founder cell, either remains a single cell or the organisms consists of cellS The smallest unit of life with a diversity of shapes and forms Comes from other preexisting cells (cells divide to make new cells) – basic unit of reproduction Some have organelles, some don't Contains RNA and DNA (genetic material – code that controls shape, form and function and controls what the daughter cells look like) Made of organic molecules that are common to all cells Bounded by a membrane with cytosol inside (semi-aqueous fluid, jel-like) CELL THEORY a) All organisms consist of one or more cells b) The cell is the basic unit of structure for all organisms (Schwann and Schleiden) c) All cells arise only from pre-existing cells – basic unit of reproduction (Virchow) Diversity in form, function and size Similar basic chemistry (unity) – proteins, carbs, nucleic acids and lipids (chemical composition) – metabolism (all use ATP for energy, just in different ways) – DNA used for genetic info Some can survive on their own, some need others to make a multicellular organism – specific function Structure gives hint to function (ex: transport requires larger surface area, some single cells have structures to carry out all functions for life, others are specialized) From very small to big (ostrich egg, neurons in giraffes with big axons) 1 um = 10-6 m (micron) and 1 nm = 10-9 m (nanometre) 106 um (giraffe), 0.006 mm (nucleus diameter), 3 x 10-6 m (mitochondria), 30 nm (ribosome) 0.007 um (microfilament diameter) Cells are small because: Surface area to volume ratio: area determines which molecules can get into/out of the cell, volume determines how much needs to get in and out SA: 6L^2, V: L^3 therefore SA:V=6:1 SA: 24L^2, V: 8L^3 therefore SA:V=3:1 Rates of Diffusion: if no transport system, uses diffusion – diffusions distances that are long result in rates that are too slow to sustain life – diffusion distances have to be kept small to sustain the processes of life Adequate concentrations or synthetic capacity: as cells get larger, they need more molecules to reach an adequate concentration – cells can't get beyond a certain size since they can't synthesize the molecules needed for biochemical reactions Prokaryotic deal with this problem by staying small Cytoplasm lacks organelles (cytosol + ribosomes, organelles etc. So basically everything in it) No nucleus – nucleoid (genetic material is usually in a simple circular chromosome) One or more bacterial flagella Cell wall, plasma membrane Archaeans (extremophiles living in acidic conditions like the stomach, thermophiles, methanogens) and Bacteria (E. Coli – rod-shaped bacterium, mostly harmless, make up bacteria in flora of gut, can cause disease in humans, model prokaryote, easy to grow) Eukaryotes: larger than prokaryote Protists, Fungi, animals, plants Complex: membrane around genetic material (nucleus), ER, golgi complex, mitochondria, lysosomes, vacuoles, plastids in plants Solution to size: Compartmentalizing reactions rather than having to achieve the right concentration everywhere in the cell, much smaller volume for the one reaction Solution to size: Rather than diffusion, use transport systems (motor proteins) Proliferation of cell membrane to increase surface area Better at generating ATP (mitochondria) Model eukaryotes: Arabidopsis thaliana (mustard), Caenorhabditis elegans (roundworm – nematode, only 959 cells, shows development, behaviour and you can grow them in a petri dish), danio rerio (zebra fish – regenerate heart cells, small so good for storage, matures quickly, microingect genetic material , drosophila melanogaster (fruitfly – breed rapidly, keep large numbers in small bottles, genetics show as phenotypes so good for genetic studies), mus musculus (mouse – surrogate for humans, breed rapidly, lots of offspring) saccharomyces cerevisiae (baker's yeast) Relationship between Prokaryotes and Eukaryotes Endosymbiont theory: ancestral prokaryote cell formed an endosymbiosis with another – the cell engulfed the aerobic bacteria that became the mitochondria Engulfed photosynthetic bacteria (cyanobacteria) became chloroplasts Fossil record: prokaryotes first, eukaryotes later Compare mitochondria and chloroplasts to prokaryotic cells: mitochondria and chloroplast: has its own DNA, metabolism yielding ATP, double membrane (endosymbiosis – second membrane was original cell), can produce own proteins (ribosomes), mitochondria and chloroplasts come about from binary fission – reproduce from other cells, inner membrane is equivalent to original cell Mitochondria and chloroplasts showed an evolutionary history with prokaryotes through looking at ribosomal subunits January 13th Membrane bound organelles don't increase the Sa:V ratio of eukaryotic cells and make eukaryotics bigger than prokaryotics because they don't add to the cell membrane Cytosol of eukaryotics is not more complex than prokaryotic cells (just the medium) E. coli is a model prokaryote, not a protist Arabidopsis thaliana is a model species because its genome is small (for a flowering plant) Endosymbiosis: symbiotic animals containing green photobionts Solar-powered sea slugs (Elysia chlorotica is a mollusc that uses photosynthesis to supply its energy requirements – establishes a symbiosis with chloroplasts that it eats from algae) – takes in algae plastids into its gut cells – whole animal turns green from original brown due to consuming chloroplasts – the chloroplasts are functional within the cytoplasm of the sea slug cells – gene transfer from algae to sea slug - gives up feeding and simply relies on photosynthesis - not passed down to offspring Sea slug takes in chloroplast already formed, origin of chloroplast took in photosynthetic organism that became a chloroplast Gametes don't have chloroplasts in sea slugs In sea slugs, not really a “symbiosis” since chloroplast does not gain any benefit Sea slug is a multicellular organism taking in an organelle whereas the origin of chloroplasts was just a cell taking in another cell CELL MEMBRANES Fluid Mosaic Model: 1972 Singer and Nicolson – fluid lipid molecuels in which proteins are embedded and freely floating – unique complement of proteins that carry out the specific functions of the membrane Functions: a) Define boundaries; selectively permeable barrier b) Localisation and organisation of proteins – ex: presence of ribosomes on RER for protein synthesis, mitochondria c) Regulation of solute transport – transport proteins control what solutes get in and out, with diffusion gradient or against it d) Responses to external signals – receptors and signal transduction that allow the cell to respond to stimuli, detects the stimuli e) Cell-cell communication – recognition, adhesion, exchange of materials, gap junctions allow transfer of material between cells, plasmodesmata Chemical composition: inner mitochondrial membrane is 76% protein and 24% lipid, Schwann cells are 82% lipid forming the myelin sheath that act as an insulator Standard membrane is usually 50/50 protein/lipid MEMBRANE STRUCTURE Membrane is a fluid double layer of lipids – lipid bilayer has proteins that carry out specific functions of membrane – forms basic boundary and permeability – water- soluble compounds can't get through very easily Two fluid lipid layers – structural backbone Membrane is held together by NONCOVALENT interactions – allow them to move Lipids can move quite freely Experiment: fused mouse cell and human cell and membrane proteins spread across membrane, mixing – ability of molecules to move around this fluid membrane FRAP – Fluorescence Recovery After Photobleaching: Cover cell surface with fluorescent dye, laser beam bleaches an area, since membrane is mobile the fluorescent labeled molecules diffuse into bleached area GFP – green fluorescent protein In a graph of Intensity of Fluorescence vs. Time, deep decrease and then exponential increase that levels off to slightly lower than original THE LIPID BILAYER Gorter and Grendel, 1925 – calculated the area of the cell and how many lipids would be required and measure how many lipids in membrane – proposed it was a BIlayer Key component of permeability barrier – water soluble things don't cross it easily Phospholipids – amphipathic (molecule that has both polar and non-polar regions) Phosphoglycerides - head group attached to phosphate is polar Sphingolipids – built on a sphingosine molecule that has a long hydrocarbon chain on one side that behaves very much like a fatty acid would – sphingosine is a backbone, fatty acid is a tail – polar head region is a head group with a phosphate group (ex: head group could be choline) Hydrophobic interactions are a kind of noncovalent interactions Polar heads on outside, hydrophobic tails facing inward Glycolipids: remove polar head and phosphate and replace them with carbohydrates Can have glycosphingolipids (carb attached to sphingosine and a fatty acid tail) Carbohydrates sticks outward – act as recognition signals ABO Blood Groups – on outside of red blood cells, have different type of glycolipids that determine your blood type Sterols (steroids) Mostly non-polar – made up of four hydrocarbon rings with a hydroxyl group at ring end and a hydrocarbon tail attached to rings on other end Animal cells typically have cholesterol (and some protists) Plants have phytosterols Fungi have ergosterols Sterols present in outer membrane of mitochondria (eukaryotic origin) but not in inner membrane (prokaryotic origin) Lipids can move within their leaflet but they rarely flip-flop (turn upside down into the other layer) – hard to go through the hydrophobic core Lipids distributed unequally between the two leaflets Glycolipids only stick out into the extracellular environment (receptors) Cholesterol is evenly distributed between the outside of the cell membrane and the inside of the cell membrane If membrane is too fluid, it's not organized – not fluid enough so can't carry out functions Ex: when skin is cold, it becomes numb – cell membranes have become too cold for the receptors to function properly so you don't feel things As temperature goes up, it becomes more fluid (don't pack tightly) – falls, less fluid (membranes pack tightly together) Length of fatty acid chains/hydrocarbon chains – when all long, they pack together nicely and give low fluidity – mix of long/short chains don't pack together well and you get higher fluidity Unsaturation (double bonds) leads to kinks in the chain – rather than long straight chains, have bends that don't pack together tightly resulting in higher fluidity Type of head group – polar head groups repel each other and they pack together less tightly – less polar pack more tightly together (less repulsion) – PC vs. PE Sterols: cholesterol is built on a four ring hydrocarbon structure that is quite rigid – at high T's, sterols provide stability to the membrane (lower fluidity) due to rigid nature – at low T's, the rigid nature of the sterol grouping prevents them from packing tightly (increase fluidity) Sterols - buffer effect on fluidity and stability Exotherms – at high T's, more fluidity and vice versa Homeoviscous adaptation: cells alter composition of the lipid membrane to counter effects of Temperature on membrane fluidity – alters ratio of PC/PE – net effect is constant fluidity January 16th POP QUIZ Fry and Edidin proposed the fluid mosaic model of membrane structure in 1970. (False) A cell membrane is 0.010 mm thick. (False -10 nm) Membrane structure depends on the amphipathic nature of membrane lipids which allows hydrogen bonds forms to form to hold the membrane together. (False - hydrophobic bonds) The inner layer of the nuclear envelope, the inner mitochondrial membrane and the inner boundary membrane of chloroplasts lack sterols. (False – inner membrane of nuclear enve
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