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Dalhousie University
BIOL 1010

LECTURE 1- TOUR OF THE CELL Discovery of Cells 1660 – microscopes! Robert Hooke coined the term “cells” 1670’s – Anton van Leeuwenhoek, Made many microscopes and looked at EVERYTHING! Cell Theory • 1838 • Schleiden and Schwann All organisms composed of one or more cells. The cell is the structural unit of life. • 1855 • Virchow • added: Cells can only arise by division from a pre-existing cell Two types of Cells: 1. Prokaryotes BEFORE Nucleus No membrane-bound nucleus No membrane-bound anything! Bacteria, Archaea 2. Eukaryotes Compartmentalized, Protists, Fungi, Animals, Plants A bit about sizes. There are 1000 microns (µm) in 1 mm Most eukaryotic cells are between10 and 100 microns (µm) Most prokaryotic cells are about 5 microns (µm) Eukaryotic Cells- Endomembrane System Regulates protein traffic and performs metabolic functions in cell. Nucleus Genetic info = Chromatin Chromatin = DNA + Protein Nuclear envelope Have nuclear pores, stuff goes in and out. Nuclear pores facilitate movement, allows only certain things to enter. Nucleolus Makes ribosomes. DNA --> RNA --> PROTEINS Transription Translation in nucleus in cytoplasm Nuclear Lamina Made of lamin proteins, give shape and stability. Fibres breakdown during mitosis. Ribosomes Function: PROTEIN SYNTHESIS! • Large and small subunits • rRNA and protein Where are Ribosomes found in the Cell? Free in cytosol, Attached to membranes (ER and nucleus). In Mitochondria and Chloroplasts (different structurally) Rough Endoplasmic Reticulum “Rough” because ribosomes attached Protein synthesis Proteins to be exported out of cell Proteins to be incorporated into membranes Proteins to be imported into other organelles Smooth Endoplasmic Reticulum NO ribosomes! Stores calcium. Two main functions: Lipid synthesis Detoxification Golgi Functions • Acisternae comprises a flattened membrane disk that makes up the Golgi apparatus -Manufacturing/modifying (add sugars) • Sorting • Storing • Shipping Cisternal Maturation Model Cisternae is formed off th ER, vesicles bud off. Lysosome Lysosomes come from the Golgi, digestive compartments, work best in acidic environment. RER-->Golgi-->Vesicle Hydrolytic enzymes Intracellular digestion Intracellular Digestion 1. Phagocytosis (“cell eating”)- cell eating, engulphs food. 2. Autophagy (“self eating”) - a damaged organelle becomes surrounded by a double membrane and a lysosome fuses with outer membrane of vesicle, self eating. Lecture 2- Endomembrane system organelles Mitochondria (Mitochondrion), Role in the cell is to make ATP! Outer and Inner membranes Cristae (inner) Matrix, Intermembrane Space, and Ribosomes Mitochondrial DNA • Circular • All maternal! Endosymbiont Theory Mitochondria used to be bacteria and the eukaryotic cells did not have them. The cell ate a bacteria and storied it in a vacuole and did not eat it right away. Bacteria made atp so eukaryotic cell didnt eat it and eventually this arrangement became permanent. Cytoskeleton Microfilaments Microtubules Intermediate filaments Cytoskeleton Functions • Mechanical support • Movement/motility Microfilaments Made of actin and protein Functions of Microfilaments (often working with motor protein myosin) -Move (cilia back and forth motion, flagella snake like motion, anchored by a basal body, structurally similar to centriole) -Cell division(cytokinesis) -Muscle contraction -Change cell shape actin and myesin work together to do these things. Microtubules (Hollow cylinders) Tubulin, Very dynamic, grow out of centrosome. α-tubulin β-tubulin Microtubules act as railway tracks for motility within the cell. Molecular Motors Kinesin: Move towards outside of cell, “+” end directed movement Dynein: Move towards inside of cell, “-” end directed movement -The centrosome is the microtubule organising center of the cell Microtubules form cilia and flagella (attach to basal body at 9+0 pattern. ) dynein allows them to move. It reaches out and walks along the other. Causes bend and makes them move. Internal Structure of Cilia/ Flagella is called the Axoneme “9+2” pattern Nine doublet microtubules+Two single microtubules in center Cilia and Flagella attach to the cell at the Basal body “9+0” pattern Intermediate Filaments • Intermediate in size • Stabilize cell structure • Very strong, resist tension • No motility, no motor molecules • Variety of different proteins Neurofilaments They are a major component of the cell's cytoskeleton, and provide support for normal axonal radial growth (i.e. increases in axon's diameter). Neurofilaments are composed of polypeptidechains or subunits that are related structurally to the intermediate filaments of other tissues such as keratin subunits.. The Extracellular Matrix is found on the OUTSIDE of the cell The ECM is mainly composed of glycoproteins (proteins attached to long sugar chains) Collagen is an example of a glycoprotein. Proteoglycan--> small core protein with many carb chains covalently attached. Extracellular Matrix Functions: Cell Migration Coordinate cell behaviour Cells are connected to other cells via Junctions -Tight junctions -Desmosomes -Gap junctions 1. Tight Junctions Two membranes almost fused 2. Desmosomes Fasten cells together, Connected to keratin 3. Gap Junctions Small hole between cells so tiny signalling molecules can move between the two cells Macromolecules- Chapter 5 Lecture 3 Polymers- make all different sorts of finalized products. Monomers- small units, like lego pieces, slightly different colors/sizes, can be assembled Many macromolecules are formed from condensation reactions. regardless of carbs, fat, proteins they all assemble somewhat similarly. one hydrogen from monomer one forms with one OH from monomer two making water and leaving you with polymers When you put them together. condensation reaction/dehydration reaction, loss of water. Condensation reactions are catalysed by enzymes. Long Polymer Broken Down: does not happen spontaneously. enzymes grab monomers and pull them together. hydrolysis reaction- long polymer breaks down into shorter polymer or monomer water is necessary for this reaction, water comes in and splits it.. one monomer and one shorter polymer are the result. Lysosome Vesicles Hydrolytic enzymes - acidic pH Intracellular digestion CARBS these are sugars also called saccharides. every carb is formed similarly (c, h, o) when those atoms come together they do so in a predictable ratio. 1 carbon: 2 hydrogen: 1 oxygen. they end in ose Two mono-saccharides linked = disaccharide Glucose Glucose + Fructose Sucrose Glucose + Galactose Lactose Polysaccharides = hundreds or thousands of mono-saccharides linked together Example 1: Glycogen Used to STORE carbohydrates Example 2: Starch good food source, filling, long term source of energy Cellulose: not used for storage so much as it is used for structure. Polysaccharides. alpha - OH on bottom beta- OH on top when cellulose is formed its using beta isomers, they switch, every second glucose is upside down, we don't have an enzyme that can break up beta glucose monomers. other eukaryotes eat cellulose, cows technically do not digest the grass, the bacteria in their gut does it for them. Lipids They are Hydrophobic -Fats (triglycerol) -Phospholipids -Steroids within the middle water molecule, there is a slight difference in charge, the oxygen is slightly negative, hydrogen's are slightly positive. water is a polar molecule meaning one end of the molecule has a different charge than the other end. things that are polar like other things that are polar, causing an electrostatic attraction. Hydrocarbon chains are NOT charged. Therefore they are non-polar, or hydrophobic. A hydrocarbon chain with a carboxy group on end is called a fatty acid. fatty acids are monomers for storage fats, they are variable in their length. 13-20 carbons long Hydrophobic and Hydrophillic molecules do not mix i.e salad dressing. Storage Fats = 3 fatty acids + 1 glycerol Triglycerols a condensation reaction occurs and a hydrocarbon tail attaches. They are called triglycerols because there are three fatty acids that have attached. How lipids are stored in cell... human adipose cell (fat cell) Saturated vs. Unsaturated Fats Saturated = no double bonds Unsaturated = double bonds Refers to whether there are double bonds in the hydrocarbon chain or not. Saturated No double bonds! Solid at room temp. I.E butter. Food labels have to tell you if something is mostly saturated or not. Most animal fats are saturated, steak, bacon, the hard white fat. Unsaturated Double bonds! Liquid at room temp. fatty acids are in the molecules that have double bonds, double bond kinks that fatty acid and makes a bend..they don't pack tightly because there is space in between the bend. As a result these are liquid at room temp. Can either be CIS or Trans.. CIS will form a bend, trans will not. Plants and fish generally have cis unsaturated fats. (e.g. Olive oil) adding hydrogen's artificially saturates the molecule. i.e margarine, shortening. you could take oils, and do this process called hydrogenation to make them solid which was convenient. trans fat survive for a really long time. Phospholipids = Glycerol + 2 Fatty Acids + phosphate and another small molecule almost the same as a storage lipid. instead of three fatty acids they only have two plus a phosphate group and another group that is named "group" because it could be tons of things. this forms membranes. They have a amphipathic region that is hydrophobic and hydrophillic region. the fatty acid tails are hydrophobic and the top part (group) like water making them hydrophillic. any molecule that has both sections on same molecule is ampthipathic. Steroids they do not look anything like other fats. they are hydrophobic. example:cholesterol. They make four carbon/hydrogen rings. OH group on one end and C and H on other end. Testosterone and oestrogen are made from cholesterol. Proteins Polymers of amino acids linked end-to-end in a specific sequence. I.E enzymes, hormones, structure, movement, storage, receptors. Etc. the proteins are the work horses of the cell, many functions monomer: amino acid Amino acids link together from condensation reactions to form proteins. Structure every amino acid has a carbon in middle. one bond to AMINO group, bottom bond to hydrogen, third bond to a carboxle group, fourth bond is to side chain, identity to specific amino acid depends on what the side chain is. Non polar side chains are HYDROPHOBIC. Polar side chains are HYDOPHILLIC. Electrically charged side chains; hydrophillic these are electrically charged side chains that are acidic or basic. fully charged, negatively (acidic) or positively (basic). when amino acids join together they do so in a condensation reaction resulting in a bond between two amino acids which is a peptide bond. Four Levels of Protein Structure.... Primary= Amino Acids in order Secondary Structure = Hydrogen bonds between atoms of the polypeptide backbone. 3D shape that is in a small localized area. This little section coils up and between coils are hydrogen bonds that hold it together. (alpha) OR... the beta pleated sheet. small areas of the peptide line up so they are parallel with each other and hydrogen bonds hold its shape. Tertiary Structure = 3D shape Due to interactions between side chains. the bigger 3d shape of entire protein functionality is very dependent on 3d shape. van der waals (no charge) forces fold proteins together in areas that are hydrophobic. this course is weak. ionic bonds. I.E R groups. Fourth Level- interacts between different proteins. come together and form finished functional protein. Collagen is in extracellular matrix, each individual protein is one of those fibres. Comes together with two other collagen proteins and wrap themselves around each other and make bonds. LECTURE 4- Membranes 1.Composition (physical structure and biological activity) 2. Selective Permeability (passive and active transport) Membrane Composition Lipids (phospholipids and cholesterol!) Proteins Carbohydrates cell membranes contain about a 50/50 ratio between lipids and proteins. the lipid that makes up cell membrane is primarily a phospholipid. phospholipids are amphipathic molecules (hyrophobic and hydrophillic). this is critical in how they are able to form a membrane. Phospholipids = Glycerol + 2 Fatty Acids + phosphate + another small molecule Phospholipid Bilayer they turn and wiggle and move around to organize themselves into two rows so that the fatty acid tail (hydrophobic) and the hydrophillic tale are on the outside interacting with water. mostly water on inside of cell, also mostly water on outside of cell. because it is two layers it is called a phospholipid Bilayer. also when we talk about these we will refer to two different leaflets. top row is one leaflet bottom row is other leaflet. They will form spontaneously in water. mitochondria have 4 rows of phospholipids Unsaturated vs Saturated hyrdocarbon tails unsaturated- increased fluidity saturated- decreased fluidity Different membranes have different proportions. Cholesterol affects membrane fluidity. hydrophobic molecules each one has a tiny OH group. these molecules are not even or straight and this affects all the other molecules around. it disrupts them. cholesterol comes from our diet also the smooth ER makes cholesterol along with making phospholipids for the membranes phospholipids move side to side rapidly but almost never flip-flop. they are constantly in motion, if you could tag and follow one phospholipid you will see that it will zip around left and right but on the other hand they can not go from top to bottom or flip. the hydrophillic head does not want to go into the middle part so switching/flipping is not possible there are times when a phospolipid has to flip because it may be needed on the other leaflet, the enzymes help with this the enzyme is called flippase. proteins are another important component of membranes. they can be either integral or peripheral. these names refer to where abouts in the membrane that the protein is found. integral proteins penetrate into the hydrophobic region of the bilayer. they are also called trans-membrane proteins. The reason they are so stuck in the structure is because in the middle area it has positioned itself so that the amino acids with hyrophobic side chains are all in the middle area. top and bottom have hydrophillic side chains hydrophobic interact in the middle of bilayer. Integral protiens have a lot of alpha helixes. most of these proteins are asymmetrical. peripheral proteins- not embedded, on surface of membrane. these do not fit into membrane instead they sit on the edge of membrane. carbs attach to both proteins and lipids. when attached to lipids they are called glycolipids and attached to protein they are called glycoproteins. carbs only live on the outside of the cell, they act as flags for signalling Fluid Mosaic Model lipid-fluid bilayers -proteins - intergral and peripheral -asymmetric carbs - glycolipids - glycoprotiens all of this together is the fluid mosaic model Membrane Transport Biological membranes are barriers to solute movement Selective permeability passive transport happens on its own. when molecules are moving from a high concentration to a low concentration. down gradient. active transport needs energy, normally atp. low concentration to high concentration. up gradient. passive: simple diffusion, facilitated diffusion in both cases there is no energy and moving down concentration gradient. molecules move right through bilayer in SIMPLE DIFFUSION. molecule has to be tiny, big will not fit. no proteins involved. the molecules have to be hydrophobic and non polar, has to be able to pass through. CO2 or O2 charged molecules will not go through bilayer, water will not diffuse through membrane Aquaporin, integral membrane protein (goes all the way through). has an alpha helixes second structure. its a channel or tunnel where water molecules can freely move from inside to outside of cell. facilitated diffusion in facilitated diffusion we rely on channel transport proteins and carrier transport proteins channel proteins are just like tunnels. carrier proteins are a bit more difficult, they open at top, take in molecule then open at other end. facilitated diffusion: passive, specific, saturable Active transport usually uses ATP, transport may be against concentration gradient, transport proteins involved, can be primary or secondary in primary active transport the ATP is directly involved sodium potassium pump is a protein and it is probably the best example of primary active transport. its function is to maintain a high concentration of pottassium ions on inside of cell and high conc of sodium ions outside cell. Integral membrane glycoprotein four subunits conformational changes a conformational change is a fairly dramatic change. if another molecule comes and touches it it has a "freak out". pumps job is to pump sodium out and potassium into cell. 3:2 ratio ATP is hydrolysed and the phosphate group attaches to the pump. that phosphate group is the nudger, the pump now will have a "freak out". The binding of the phosphate causes a conformational change in the protein, and the three Na+ are released to the outside of cell. Two K+ are now able to bind on the exoplasmic side. The phosphate is released, causing another conformational change. When K+ ions bind, yet another conformational change in pump, so now open to cell side again. Cycle repeats. Secondary Active Transport ATP participates indirectly, Ion gradients Amino acids and sugars, Cotransport Final way things get across the membrane… BULK TRANSPORT (Endocytosis) Intracellular Digestion- Phagocytosis (engulphs) (cell eating) Pinocytosis (cell drinking) Receptor-mediated Endocytosis Ligand will bind to a receptor on the cell membrane. Lecture 5- Metabolic Pathways metabolism is the sum total of all the chemical reactions happening in cell. 2000 chemical reactions all happening at once. most reactions can be classified as being catabolic or anabolic. catabolic break stuff down and release energy anabolic reactions build up stuff and consume energy. condensation reaction is an example of an anabolic reaction. Gibb’s Free Energy (G) if the gibbs free energy is negative that describes a reaction that is called exergonic, it releases energy. they do not need energy. a positive describes a reaction called endergonic, it needs energy absorbed not energetically favourable the cell will couple together the two types of reactions. one produces energy coupled with a reaction that needs that energy. Adenosine triphosphate (ATP) Currency for the cell our cells use the hydrolysis of ATP as our
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