Cell Biology Notes 1/19/16-3/1/16.pdf
Cell Biology Notes 1/19/16-3/1/16.pdf BIO 165-01
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This 25 page Bundle was uploaded by Jayme Hambleton on Friday March 4, 2016. The Bundle belongs to BIO 165-01 at University of Indianapolis taught by Dr. Daniel Scholes in Spring 2016. Since its upload, it has received 21 views. For similar materials see Introduction to Cell Biology in Biology at University of Indianapolis.
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Date Created: 03/04/16
SEMESTER II INTRO TO CELL BIO Chapter 3: Water and Life The Molecule that Supports Life Required by life mass than any other solution Cells: 70-95% water The main reason the Earth is inhabitable. Polarity Water possesses a polar covalent bonds Polarity allows for hydrogen bonds Water’s Unique Properties Cohesion o Molecules stay together because they stick to themselves Moderation of Temperature Expansion upon freezing The solvent of life o Dissolves things (breaks thing down). These all facilitate an environmental for life. Cohesion Cohesion vs. Adhesion o Adhesion is molecules sticking to things other than itself. o Adhesion causes the meniscus for water in beakers. o Leaves pull up the water up in trees because of cohesion and adhesion. Cohesion makes surface tension o Surface or film of water molecules on the surface to hold some weight. Water spiders do this. Temperature Moderation Two ways o High specific heat = the point of energy where there is a change of temp, 1g by 1 degree C. o Evaporative cooling Ex: Dog panting Water holds head so evaporation pulls it away. Kinetic Energy o Moving/action energy. Doing things. Thermal Energy Random movement of atoms/molecules Dependent of Volume. The Solvent of Life Solvent vs. Solute o Solute- things being dissolved o Solvent- thing dissolving Solution vs. Aqueous solution o Solution- two things mixed o Aqueous- dissolving done in water Water’s polarity allows it to easily form hydrogen bonds, making it a good solvent. When dealing with ions, water forms a hydration shell. o Water surrounds due to hydrogen bonds o Keep things separated, why things break down and stay Hydrophobic substances: afraid of water o Nonpolar covalent bonds Ex: C-H Ex: Tails of cell membrane Hydrophilic: likes water. Solute Concentration Most reactions are in water Rate of reaction depends on the number of collisions o Higher chance of bonding o The number of collisions depend on the concentration of the solute To have equal concentrations, there must be an equal amount of moles o 6.02 x 10^23 molecules per mole Atomic Mass Units for atomic mass is called daltons There are for finding the molecular mass, which is needed to know how big a molecule is o So then you can find the weight equal to one mole of the molecule. Creation a Solution Create 1L of solution containing sucrose o Step 1: Find the molecular mass of sucrose 342 daltons = 342 grams o Step 2: Add water up to 1L Molarity o Number of moles of solution per liter Concentration pH: Hydrogen Atoms Often, hydrogen atom will have water and it’s electron behind o Hydrogen ions (aka: proton) The molecule left behind is now a hydroxide ion (OH) The hydrogen ion (proton) can move to a new water o The molecule with the extra hydrogen makes the H O ,3a hydronium ion. + o H that doesn’t connect is the acid. pH: Changes Concentration of H and OH are equal in pure water. o Acid increases the H concentration (6-0) o Base reduces the H concentration (8-14) Acids & Bases: Acids are strong if they are not reactions that can easily be undone or redone. (Separate and come back to together is a no go) Acids are weak when the reaction can reform into the previous version. The same applies to bases. What is pH? + - A neutral solution has equal H and OH o [H ] – [OH] -7 o Both concentrations is equal to 10 o Therefore: [H ] – [OH] = 10-14 o This is why the pH goes from 0-14 Acid added lowers pH while base added increases the pH + - Each pH unit represents a tenfold difference in [H ] and [OH] Most biological fluids range from 6-8 pH Buffers are substances that minimize changes in pH in a solution. o Your body has these to help neutralize the acids and bases. Chapter 4: Carbon and the Molecular Diversity of Life CarbonChemistry Cells are 70-95% water, but rest is mostly carbon. Unparalleled it is ability to form large, complex, and diverse molecules. Proteins, DNA, carbohydrates are carbon compounds. Organic Chemistry What substances does organic chemistry study Organic compounds vary in size Organic chemistry is carbon-containing compound Most contain hydrogen in addition to carbon Carbon’s Particles Usually bonds with: o Hydrogen o Oxygen o Nitrogen Governs the architecture of living molecules Most organic molecules have multiple carbon. CarbonSkeleton Carbon chains form the skeleton and most organic molecules Vary in length and shape Prefixes show # or carbons in chain o 1= Meth o 2= Eth o 3=Prop o 4= But o 5=Pent o 6=Hex Hydrocarbons Not found in organisms, however… o If part of a larger moleculeused for energy storage (fat) o “-ane” means just carbons and hydrogens o Fat has a hydrocarbon tail. Important Suffixes/Prefixes -ane means hydrocarbon -ene means double bonded -ol means it has an alcohol group (OH group) Cyclo- means circular shape Methyl- means it containes C3 Coefficients Number(s) in front of a molecule name indicates the carbon on which the special feature exists o Ex: 2-butene means a double bond on the second carbon o Ex: 3-Pentanol means an OH group off the third carbon Isomers Isomer: Same molecules formula but different structures and properties Three main kinds: o Structural Isomers: Have different covalent arrangement of their atoms Three structural isomers of5C 12 o Cis-Trans Isomers Have same covalent arrangements, but different in spatial arrangements Cis means the molecules on the same side Trans means the molecules are on opposite sides. o Enantiomers Isomers that are mirror images of each other. Pharmaceutical Implications Enantiomers are important in pharmaceuticals o Two enantiomers of a drug may have completely different effects. Organisms are usually sensitive to one form. Functional Groups Properties of organic molecules largely depends on the molecular components attached to the carbon skeleton. o These are known as functional groups. The number and the arrangement of functional groups give each molecule it’s unique properties. The ten function groups that are important are as follows. Hydroxyl Groups Has on OH group Polar due to electro negative oxygen. Forms hydrogen bonds with water Carbonyl Groups Double bonded oxygen Sugars with keytone groups are called ketoses; those with eldehydes Ester Group Most fat and oils have this Polyester in plastics Phosphoesters are in DNA Ether Group Often cannot form hydrogen bonds o Low boiling point Slightly polar Good solvents Carboxyl Group Have COOH group Acts as an acid Ionizes and found in cells this way (carboxylate ion) Sour taste in vinegar. Amino Group NH 2onding Acts as base Ionized form found in cells Sulfhydryl Group Sulfhydryl (-SH) Two –SH groups can react, forming a “cross-link” that helps stabilize protein structures Phosphate Group Has a –OPO 32-group Contributes negative charge. When attached, molecules are given the ability to react with water, releasing energy. Methyl Group Has a CH 3roup Effects the expression of genes as well as the shape and function of sex horomones. Alkyne Group Extremely strong bond between carbons Dominant alkyne is acetylene o Used as fuel. Facts All are hydrophilic except for sulfhydryl All but methyl are reactive. ATP Adenosine triphosphate (ATP), is the primary energy-transferring molecules in the cell. ATP is an organic molecule (adenosine) attached to the three phosphate groups ATP ADP How does ATP create energy o ATP + H2O ADP + HOPO 32- ADP Is made from a phosphate being broken off o This is an exothermic reaction, meaning it gives off energy. Chapter Five: The Molecules of Life Overview: The molecules of life Macromolecules o Large molecules composed of thousands of covalently connected atoms. All living things are made up of four classes of macromolecules: o Carbohydrates o Lipids o Proteins o Nucleic Acids Monomer vs. Polymer Monomer: a single unit Polymer: many units together o 3 or 4 macromolecules form polymers. o Lipids do not. Dehydration vs. Hydrolysis A polymer is formed when a dehydration reaction joins multiple monomers. Monomers are formed when a hydrolysis reaction breaks apart a polymer. Carbohydrates Carbohydrates (saccharides and sugars): molecules composed of carbon, hydrogen, and oxygen in the ration 1:2:1. Taste Test How do monosaccharides taste? o Major fuel for cells o Raw material for building polysaccharides. Polysaccharides are bland o Structural and support in cells o Cellulose, starch, glycogen, chitin. Lipids Lipids have long regions of C-H bonds ALL ARE HYDROPHOBIC o Consists of mostly hydrocarbons Nonpolar covalent bonds. Saturatedvs. Unsaturated Fats Which is worse for your health? o Saturated! Saturated fatty acids lack double bonds o Packed tightly o More concentrated in food o Solid at room temperature Steroids are lipids o Cholesterol, testosterone, estrogen Proteins 50% of the dry weight of cells is protein Many functions of proteins Amino Acids All amino acids have the same basic structure: o Central Carbon o Attached amino group o Attached carboxyl group o Attached variable side group (R-groups) 20 amino acid monomers. Protein Structure A three-dimensional shape gives proteins their function Four stages of protein structure o Primary Stage: a chain of amino acids o Secondary: Amino acids connected by hydrogen bonds o Tertiary: Amino acids connected by hydrogen bonds and interactions between R-Groups o Quaternary: Multiple polypeptide interacting as subunits of large protein to perform one function together. Nucleic Acids Nucleic Acids (DNA, RNA) are long chains of nucleotides Nucleotides have three parts: o A five-carbon sugar (ribose or deoxyribose) o A phosphate group o A nitrogen-containing molecule called a base. Polymer has a backbone of sugar-phosphate with bases as appendages. **THIS IS ALL THE INFO FOR EXAM I** Chapter 6: Tour of the Cell Cell Size Why are cells so small? The Surface-to-volume ratio restricts cell size by limiting transport of nutrients and wastes. All cells need to bring materials in and push materials our o It is best to build with lots of little cells than one giant one for this reason; things move quicker through small cells than large ones due to radius and volume. Surface area increases while total volume remains constant Most cells are measured in micrometers o One micrometer (µm)is one-thousandths of a milliliter. What are the smallest cells in the world? o Prokaryotic cells (0.5 µm) What are the largest in the world? o Nerve cells in large organisms (12m) Cell Properties What do all cells have? o Plasma membrane o Cytoplasm o DNA Nucleus in eukaryotic cell Nucleoid region in prokaryotic cells o Ribosomes Sites of protein creation Plasma Membrane What are plasma membranes made out of? o Lipids o Phospholipids Phospholipid bilayer o The lipid bilayer has two layer of lipids, the tails of which are sandwiches between the heads. Proteins typically intermingle. o The hydrophilic heads of the phospholipid bathe in the watery fluid on both sides of the bilayer. o Hydrophobic Cytoplasm Mostly water Contains parts of the cell o Ribosomes o Organelles o Cytoskeleton o DNA (prokaryotes only) DNA How is DNA stored in the cell? o Chromosomes Humans have 46 of them in 23 pairs Chromosomes o DNA + Histones (storage proteins) o Condenses DNA for easier storage DNA wraps around the histones which condense near others. Ribosomes: Protein Factories Ribosomes o Particles made of RNA and proteins NOT organelles Ribosomes create proteins Activity takes place in two locations: o Free ribosomes in the cytoplasm o Ribosomes on the outside of the endoplasmic reticulum or the nucleus where ribosomes are bound to it. Diversity of Life Every organism belongs to one of two taxonomic group o Prokaryote o Eukaryotes Prokaryotes Prokaryotes have… o No nucleus o DNA stored in open regions of the cytoplasm called the nucleoid o No membrane-bound organelles o Smaller cells compared to eukaryotes o All have cell walls. Eukaryotes Eukaryotes are characterized by having… o DNA in an nucleus, bound by a nuclear envelope o Membrane which has bound organelles o Being larger than prokaryotic cells o Some have cell walls (plants) while others don’t Organelles of a Eukaryotic Cells What are some major organelles of eukaryotes o Nucleaus o Mitochondrion o Chloroplast o Endoplasmic reticulum o Ribosomes o Golgi Body o Lysosome o Vesicles Peroxisome Vacuole The Nucleus What is the main job of the nucleus? o To keep the DNA away from damaging reactions in the cytoplasm Nuclear Envelope o Two lipid bilayers pressed together as a single membrane Outer bilayer is continuous with the ER Nuclear pores allow certain substances to pass through the membrane (but not DNA!) The Endoplasmic Reticulum Endoplasmic Reticulum (ER) o An extension of the nuclear envelope that forms a continuous, folded compartment. Makes and folds polypeptides (using ribosomes to do so) making lipids, breaking down carbs and lipids, and detoxifies poisons. Golgi Body (Apparatus) Golgi Body o Folded membrane that modifies polypeptides and lipids from the ER Packages and finishes products into vesicles that carry them to their final destination. Lysosomes Lysosomes o Vesicles containing enzymes that fuse with and digest waste materials. Mitochondrion Makes energy molecule, ATP, through aerobic respiration. Two membranes Has its own DNA and ribosomes Resembles bacteria; probably evolved through endosymbiosis. Chloroplasts Specialized for photosynthesis Creates energy (ATP) and eventually sucrose. Two membranes Has its own DNA and ribosomes Resembles photosynthetic bacteria; probably evolved through endosymbiosis like the mitochondria The Center Vacuole Central Vacuole o Vesicle o 50%-90% of plant cell o Stores amino acids, sugars, ions, waste, and toxins. o Fluid pressure keeps plant cells firm Eukaryotic Cell Walls Plant, Protist, and Fungal cells Cell Wall= carbohydrates Cellulose= carbohydrates Primary Cell Wall o Thin, Pliable walls around the cell Secondary Cell Wall o A strong wall composed of ligin. Chapter 7: Organization of the Cell Organization of Cell Selectively permeable Embedded proteins Revisiting the Lipid Bilayer Phospholipid molecules in the plasma membrane have two parts: o Hydrophilic heads o Hydrophobic heads Proteins Cell membranes WORK using proteins o No proteins=cell membrane does nothing! Six types of membranous proteins based on their function: o Transport proteins o Enzymatic action proteins o Signal Transduction proteins o Cell-to-Cell recognition proteins o Intercellular joining proteins o Attachment to the cytoskeleton proteins The Cytoskeleton Eukaryotic cells have an extensive internal protein framework called a cytoskeleton. Three main parts: o Microtubules Moving scaffoldings o Microfilaments A mesh under the plasma membrane o Intermediate filaments Most stable, never moving, strengthening structures. Motor Proteins Move filaments on tracks of microtubules & microfilaments Use ATP Membrane Permeability Selective permeability All cells need to interact and exchange materials with their environment. What can normally cross, what can’t? o Large, polar objects can NOT cross without help o Small, nonpolar objects CAN with no help usually Concentration Gradients Concentration o The number of molecules (or ions) of substance per unit volume of fluid Concentration gradient o The difference in concentration between two adjacent regions. Modes of Transportation Most solutes use diffusion Water, ions, and large polar molecules require other mechanisms to cross: o Osmosis o Passive Transport o Active Transport o Endocytosis and exocytosis Diffusion Net movement of molecules down a concentration gradient During diffusion, the solute moves from a region of higher solute concentration to one of lower solute concentration. Rate of diffusion depends on many factors: o Solute size o Temperature o Steepness of concentration gradient o Pressure/Movement Osmosis The movement of water down its concentration gradient through a selectively permeable membrane. Water always moves from a region of lower solute concentration to a region of higher solute concentration. Tonicity For two fluids separated by a semipermeable membrane, the one with lower solute concentration. o The one with higher solute concentration is hypertonic Lots of sugar = hyper! Water moves from hypotonic to hypertonic Isotonic fluids have the same solute concentration. Passive Transport Facilitated diffusion o Requires a transport protein, but does not require ATP Moves specific solute WITH its concentration gradient across the membrane. Active Transport Requires a proteins AND ATP Moves a specific solute AGAINST its concentration gradient, to the concentrated side of the membrane. Endocytosis & Exocytosis By these processes vesicles take in (endocytosis) and expel (exocytosis) particles. Transport proteins that are too big for proteins Chapter 8: Metabolism Metabolism All the chemical reactions in an organism to sustain life. Emergent property of the cell. Pathways Metabolic pathways has multiple reactions and a final product. o Intermediate products o Enzyemes are always used. Two kinds: o Catabolic pathways release energy (complex molecules are made simple) o Anabolic pathways consume energy (simple molecules are made complex) Ex: Protein creations Forms of Energy Energy o The capacity of cause change Two Main Forms: o Kinetic Energy concerns the motion of objects Ex. Heat (thermal energy) o Potential Energy concerns energy pressed by an object due to its location or structure. Ex. Chemical energy The Study of Energy: Transformation Thermodynamics o Study of energy transformations that occur in matter Isolated vs. Open Systems o Organisms are open systems Laws of Thermodynamics First law of thermodynamics o The principal of conservation of energy: “No energy can be created or destroyed.” Second law of thermodynamics o Entropy= disorder o Natural systems go from low disorder to high disorder. Entropy Matter/forms of energy tend to change from ordered to disordered states. Increased entropy means physical disintegration or less ordered forms of matter. o Spontaneous process No energy input; just what naturally happens Ex: Rust. Biological Order and Disorder Cellular processes create ordered structures o Disorganized small molecules are made into large, complex molecules and structures o Life Order from disorder Cells and organisms create order from disorder…is this a violation of the second law? o No. Creation of order isn’t spontaneous, but requires interactions with energy and matter from outside the organism o This is known as metabolism. Energy G = Energy Δ G = Gproductsreactants If the difference is 0 or a positive ΔG, then the reaction was nonspontaneous, meaning it required energy o This is also called endergonic If the difference is a – ΔG, then the reaction was spontaneous, meaning it didn’t need energy. o This is called exergonic It’s All About Stability Matters and forms of energy tend to change from ordered (which is unstable) to disordered (which is stable) states. ΔG is really a measure of reactions more to stability (-ΔG) or instability (+ΔG). Types of Reactions Types are decided by whether the reaction will put out energy or need energy to happen. Two types: o Exergonic reactions - ΔG Spontaneous/put out energy instead of taking it in Is a catabolic pathway that creates simpler molecules. o Endergonic reactions 0 or + ΔG Nonspontaneous/ requires energy to take place. Is an anabolic pathway that creates complex molecules. Linking Reactions Energy from breaking down C 6 12c6n be used to add phosphate to an adenosine molecules o AKA: making ATP or energy for your body ATP can be transported around the cell When the phosphates are broken off the ATP (to make ADP), the energy is released again and can be used in a reaction that requires energy (nonspontaneous) The Structure and Hydrolysis of ATP ATP is a nucleotide Remember hydrolysis is when H 2 is used to break down a molecule ATP + H O ADP + Phosphate 2 This reaction has a really large ΔG between reactants and products o All phosphates are negatively charged naturally repulse each other, meaning they are unstable. APT Regeneration ATP is regenerated by adding a phosphate to ADP o Phosphorylation energy comes from catabolic reactions (Endergonic reactions that require an input of energy). Enzymes An enzyme is a type of catalyst They speed up reactions without being used up As well, they allow reactions to get over the Activation Barrier that requires an input of energy. Activation Energy Barrier Even if the reaction is favorable (spontaneous, exergonic, - ΔG, with no need of energy put in), reactions often require some activation energyA(E ) How NOT to lower the E BaArier In a controlled setting, we suppAy E as heat o However…. Most cells don’t have enough heat to do this Heat denatures proteins so they cannot perform the proper function ALL reactions will speed up, not just the one that was desired. How Enzymes Lower the E BarrAer When a chemical reaction involves two or more reactants, the enzyme provides a site where the reactants are positioned very close to each other and in an orientation that facilitates the formation of new covalent bonds. o Does not change the ΔG o Hastens already exergonic reactions o And is very specific Affecting Enzyme Activity An enzymes activity can be affected by: o Substrate concentration As substrate increases, enzyme activity increases Levels off (saturated!) o Environment (temperature and pH) Enzymes have an optimal temperature and pH Greater reaction rate as temperature increases Too hot, too acidic/basic causes the enzyme to denature. o Chemicals Cofactors: non-protein enzyme helpers Cofactors may be ions, coenzymes Enzyme Inhibitors Two types of inhibitors: o Competitive inhibitors Things that bind to the enzyme’s active site to keep the substrate from linking. o Noncompetitive inhibitors Bind to another part of the enzyme and makes the enzyme change its active site shape so the substrate cannot link. Many toxins, poisons, pesticides, and antibiotics are irreversible enzyme inhibitors o Sarin (nerve gas—chemical weapon) o DDT (pesticide) o Penicillin (antibiotic) Enzymes and Metabolisms Metabolic pathways need tight regulation of enzymes This is done in two ways: o Turning an enzyme on or off to manage the amount of enzymes working and present o Regulate enzyme activity Changing the abundance of reactants, products, inhibitors, and altering properties like temperature and pH. **THIS IS ALL THE INFO FOR EXAM II**
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