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Cell Bio Module I

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Cell Bio Module I BIOL 541

. Notetaker
GPA 3.8
Cell Biology
Dr. Stella Lee

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Module I, chapters 1-8 excluding chapter 4 which is covered in Module II.
Cell Biology
Dr. Stella Lee
Study Guide
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This 11 page Study Guide was uploaded by . Notetaker on Tuesday August 11, 2015. The Study Guide belongs to BIOL 541 at Kansas State University taught by Dr. Stella Lee in Fall 2014. Since its upload, it has received 76 views. For similar materials see Cell Biology in Biology at Kansas State University.


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Date Created: 08/11/15
Cell Bio 825 A Cell basic structural and functional unit of all known living organisms a 1 um micro meter 10quot3 mm 10quot6 m b lclicker what is untrue of a cell all cells don39t have a nucleus B Cell Theory amp History a Robert Hooke observed compartments in cork amp rst named cells cellula i His observations limited by low magni cation power only had 30x b Leeuwenhoek better lens 300 x magni cation c Microscopes i 1830 compound microscopes invented two lenses structures only 1 micrometer in size could be seen d Robert brown identi ed nucleus in plant cells e Matthias schleiden plant tissues composed of cells Theodor schwann made same conclusion in animal cells f Cell theory i 1 All organisms consist of one or more cells ii Cell is basic unit of structure for all organisms iii Cells arise from preexisting cells g Cytology cell structure emphasizes optical techniques h Biochem cellular function i Genetics information ow and heredity C Microscopes a Light earliest identify organelles membrane bound structures i Resolution how far apart objects must be to appear as distinct smaller the limit of resolution greater resolving power 1 Visible light 400700 nm 2 Limit of resolution 200350 nm 10001500x ii Bright eld passes light directly through specimen iii Fluorescence locations of speci c molecules in cell absorbs UV radiation amp emit visible light tag molecules of interest with dyes or antibodies iv Phase contrast enhances contrast in unstained cells by amplifying variations in refractive index v Differential interference contrast uses optical modi caitons to exaggerate differences in refractive index vi Confocal uses lasers and special optics to focus illuminating beam on single plane within specimen vii GFP green uorescent protein from bioluminescent jelly sh discovered by Roger Tsien b Electron beam of electrons rather than light limit of resolution is 12nm up to 100000x magni cation i Transmission electrons transmitted through the specimen ii Scanning surface of specimen is scanned by detecting electrons de ected from the outer surface D Biochemistry a Friedrich wohler compound urea synthesized in lab b Louis Pasteur easts could ferment sugar into alcohol c Eduard amp hans Buchner yeast extracts could do the same Pasteur i Led to discovery of enzymes Gustav embden amp otto meyehof glycolysis amp krebs cycle e Advances i Radioactive isotopes trace the fate of speci c atoms amp molecules ii Subcellular fractionation such as centrifugation to separateisolate different structures and macromolecules iii Ultracentrifuges capable of very high speeds E Scienti c Method a Facts tenuous amp dynamic b Hypothesis data collected amp interpreted accept or reject hypothesis c Theory a hypothesis that has been extensively tested by many invetigators using different approaches widely accepted d Law theory that has been tested and con rmed over long period of time with virtually no doubt e In the lab i In vitro using puri ed chemicals and cellular components ii In vivo using live cells or organisms iii In silico using computer analysis or large amounts of data 0 Chapter 2 A Carbon a Speci c binding properties of carbon account for the characteristics of carboncontaining compounds i Valence of 4 can form 4 chemical bonds with other atoms ii Form covalent bonds with O H N S iii Extremely stable especially with double and triple bonds iv If covalent bonds was lower energy visible light would break covalent bonds spontaneously 1 UV more hazardous breaks bonds v Hydrocarbon chains or rings 1 Economically important petroleum gasoline natural gas 2 Not soluble in water vi Bio compounds C H O N P S usually part of functional groups 1 Carboxyl amp phosphate negatively charged 2 Amino positively charged 3 Hydroxyl sulfhydroxyl carbonyl aldehyde uncharged but polar Bond polarity electrons not shared equally 1 High electrognegativity af nity for electrons 2 High water solubility compared to CC CH b Stereoisomers i Tetrahedral structure nonsuperimposable con gurations are mirror images ii Asymmetric carbon four different substituents two stereoisomers are possible for each asymmetric carbon atom v39 B Water a Universal solvent most abundant component of cells and organisms 80 cell b Polar i Bent rather than linear ii 0 highly electronegative iii Partial charge on Oxygen amp partial charge on hydrogen atoms c Cohesive molecules attractd to each other i High surface tension boiling point speci c heat heat of vapo za on ii Speci c heat amount of heat a substance must absorb to raise temp to 1C iii Heat of vaporization amound of energy required to convert one gram of liquid into vapor d Solvent i Solutes have af nity for water and dissolve init easily are called hyrophilic ii Molecules cannot dissolve hydrophobic C Membranes selectively permeable lipid bilayer a Polar head hydrophilic nonpolar tails hydrophobic i Head phosphate group neg charged always polar ii Tail hydrocarbon chains iii Consists of phospholipids glycolipids and membrane proteins enzmes receptors transporters 1 Most contain sterols cholesterol animals ergosterols fungi phytosterols plants b Permeability i Readily permeable to nonpolar molecules impermeable to polar molecules and ions 1 Very small molecules that diffuse 02 C02 H20 D Polymerization a Macromolecules proteins nucleic acids polysaccharides i Stepwise polymerization 1 Monomers activated by coupling to carrier molecule using ATP 2 Monomer condensation condensation of two activated monomers release of one carrier molecule 3 Polymerization addition of next activated monomer to polymer that already consists of n monomeric units ii Self assembly info needed to specify the folding of macromolecules and their interactions to form complex structures is inherent in polymers themselves 1 Occurs spontaneously once macromolecules made in cell iii Molecular chaperones needed in some proteins 1 Assisted selfassembly requires speci c molecules to help but these molecules are not in the completed structure and convey no information 2 Example proteasome 66 polypeptides 11 molecular iv Noncovalent bonds amp covalent bonds involved 1 Non hydrogen ionic van der waals hydrophobic a Ionic electrostatic interaction between two oppositely charged ions b Van der was weak attractions between two atoms that only occur if atoms are close to one another and oriented appropriately c Hydrophobic tendency of nonpoar groups to bond with other and minimize their contact with water Chapter 3 a Proteins a Enzymes increasing rates of chemical reactions i Transferase transfers functional groups from one molecule to the next b Structural physical support amp shape i Cytoskeleton c Receptor enabe cells to respons to chemical stimuli from environment insulin receptor d Amino acids i 20 amino acids everyone has carboxyl group amino group R group ii Poar charged acidic or basic iii AA linked together by linear polyer by dehydration 1 Three atoms comprising the water are removed a covalent cn bond peptide bond is formed 2 Polypeptide immediate product of amino acid polymerization 3 Protein stably folded biologically active polypeptides iv Directionality end with amino group is called N terminus v End with carboxyl group is called Cterminus vi Single polypeptide monomeric proteins multimeric two or more polypeptides e Folding amp stability i Covalent amp noncovaent needed for proteins to fold 1 Covalent disulfide between sulfur atoms of two cysteine residues a Form through removal of two hydrogen ions oxidation and can be broken by addition of hydrogens ii Hydrogen H bonded with OSNF iii Ionic between two charged R groups changes in PH can disrupt ionic bonds iv Van der waals nonpoar covalent bonds may have transient positively and negatively charged regions v Hydrophobic tendency of hydrophobic to be excluded from interatctions with water 1 Hydrophobic side chains vi Structure 1 Primary amino acid sequence a Covalent peptide b First protein to sequence insulin c Genertically important because sequence is speci ed by order 2 Secondary local folding of polypeptide a Hydrogen b Alpha helix telephone cord i 36 amino acids per turn of helix ii H bonds between two turns iii H bonds between CO amp NH iv Leucine methionine glutamate c Beta sheets i R groups on alternating sides of sheet ii lnvolve different polypeptides or different regions of single polypeptide iii Parallel or antiparallel iv H bonds between CO and NH v lsoleucine valine phenylalanine 3 Tertiary threedimensional conformation a Disul de bonds hydrogen ionic vander waals hydrophobic b Results on the sum of hydrophobic hydrophilic repulsion of similar charged residues attraction of oppositely charged residues c Native conformation most stable possible three dimensional structure of particular polypeptide i Fibrous 1 Highly ordered repetitive structure 2 Keratin collagen elastin ii Globular 1 Folded into compact structures each has own unique tertiary structure 2 Mainly helical mainly B or mix 3 Domainlocally folded unit or tertiary structure speci c function 50350 amino acids regions of a amp B sheets packed together a Multiple functions separate domains d Predictions not able to exactly guess how a protein will fold especially for larger proteins 4 Quaternary interactions between monomeric proteins to form multimeric unit a Same as tertiary b Difference multimeric proteins vii Motifs combos of a helices amp b sheets 1 BaB the hairpin loop and helixturnhelix motifs b Nucleic acids a b c d e DNA amp RNA d deoxyribose vs ribose i AT 2 H GC 3 H Monomers are nucleoties ATGC Nomenclature AMP one phosphate group ADP 2 phosphate groups ATP 3 phosphate groups Polymers are DNA and RNA linkage between two adjacent nucleotides 339 539 phosphodiester bridge RNA i Normally single stranded AU c Polysaccharides long chain polymers of sugars that are not informational molecules a b c d e Alto or keto sugar LOT 339 j Mono nutrient energy building block glucose fructose Di nutrient sucrose lactose maltose Oligo attach to proteins and lipids Poly storage amp structures starch glycogen cellulose i Aldo is aldehyde ii Keto ketone Trioses 3 C Glucose i Dglucose exists in dynamic equilibrium between the linear and ring form Disaccharides two mono units covalently bonded Storage i Starch in plants and glycogen in amimal and bacteria 1 Both sonsist of aDglucose unitls linked by aglycosidic bonds involving carbons 1 and 4 2 Glycogen a A 14 once every 810 glucose Chitin polymers of Nacetylgucosamine B bonds i Found in insect exoskeletons crustacean shells fungal cell walls k Glycosidic bonds i Rigid linear B linkages no branches cellulose chitin ii Loose helices a linkages branched starch and glycogen d Lipids formed by same type of linear polmeraization as proteins nucleic acids polysaccharides a Macromolecules because of high molecular weight and importance b Fatty acids long amphipathic unbranched hydrocarbon chain with C d carboxyl group head at one end i Structure unsaturated fatty acids one or more double bonds less tight packing ii Saturated no double bonds Trans fats unsaturated fatty acid with particular type of double bond that causes less of a bend rare in nature Triaclyglycerols i Storage lipids glycerol molecule with three fatty acids 1 Glycerol is 3 carbon alcohol with hydroxyl groups on each carbon Chapter 5 2 Fatt acids linked to glycerol ii Function energy storage 1 Fats saturated 2 Vegetable oil unsaturated fatty acids are liquid at room temp Phospholipids amphipathic nature i Phosphoglycerides glycerol backbone has phosphate amp R group 1 Small hydrophilic alcohol linked to phosphate by an ester bond ii Sphingolipids back bone is called sphingosineunsaturated bonds close to end 1 Hydrocarbon chain form amide bond to longchain fatty acid resulting in molecules called ceramide Glycolipids contain carb group onstead of phosphate group occur largely on outer monolyer of plasma membrane Steroids gourringed hydrocarbon nonpolar hydrophobic most common is cholesterol i Insoluble and found in plasma membrane ii Plant stigmasterol amp sitosterol and fungal cells ergosterol Terpenes synthesized from vecarbon compound isoprene i Vitamin A dolichols coenzyme Q A Bioenergetics law of thermodynamics first energy is conserved second thermodynamic spontaneity a b h Synthetic work process of photosynthesis Mechanical contraction musclesxsomes move along spindle in mitosis organelles and vesicle transport ribosomes move along RNA Concentration work accumulation of molecules in cells Electrical work membrane potential of mitochondrion i Production of atp possible proton pump ii Neurotransmission Heat production shivering in the cold producing heat is major use in all homeotherms regulate body pemp Bioluminescence re ies jelly sh Flow of matter I Phototrophs producers use sunlight energy to produce reduced cellular compounds thru photosynthesis ii Chemotrophs consumers take in reduced compounds and oxidize them to release their stored energy iii Autotrophs depending on their source of carbon iv Oxidation removal of electrons from substanceand addition of 02 v Reduction addition of electrons to substance loss of oxygen vi Open capable of uptake amp release of energy vii Closed no energy in or out B Biological systems a Heatwork exhance of energy between system and surroundings i Work use of energy to drive a process other than heat b 1St law thermodynamics conservation of energy i H E PV ii deltaH if negative reaction is exothermic iii deltaH if positive reaction is endothermic c 2nCI law of thermodynamics law of spontaneity measure of whether or not a reaction process can occur i Have directionality can only proceed spontaneously in one direction ii detaS change in entropy iii detaG change in free energy iv detaG deltaH TdetaS v spon reactions entropy can increase decrease or stay the same 1 spon has decrease in free energy of system detaG 2 detaG lt0 reaction can occur exergonic 3 delta G gt0 do not occur spontaneously endergonic vi equalibirum constant ratio of product to reactant concentrations at equilibrium 1 ratio less than K means that the rreaction will generate more product 2 ratio more than K means the reaction will proceed to the left reactants vii limitations on detaG tells us nothing about rate or mechanisms of reaction viii Standard state DeltaG 1 Ph 7 temp 25 pressure1 atm 1M ix Linear relationships between standard detaG amp K 1 DeltaG stand can be calculated directly from K provided K was determined under same standard conditions 2 If K is greater than 1 detaG standard will be negative and reaction will proceed towards proucts 3 If k is less than 1 then detaG stand will be positive and reation will tend toward reactants 4 detaG thermodynamically feasible work can be done by reaction 5 detaG reaction not feasible energy must be supplied Chapter 6 A enzymes presence of one can determine whether a reaction will occur or not a metastable state result of activation barrier b activation energy amount of energy required before collisions between the reactants will give rise to products i reactants need to reach intermediate stage called transistion state 1 higher free energy than tht of initial reactions ii how to overcome 1 increase energy content of molecules raise temp 2 lower activation energy enzymes a enzymes bring activation energy down towards the left side c biological catalysts form transient reversible complexes with substrate molecules i they change the rate at which equilibrium is achieved not the position d active site cluster of amino acids i results from 3D folding of protein ii where substrates bind amp catalysis takes place iii usually a groove or pocked that accommodates the intended substrates with high af nity iv only cys his ser asp glu and lys can only serve as active sites e cofactors prosthetic groups i these are nonprotein part of enzymes needed for catalytic activity 1 either metal ions or coenzymes small organic molecules derivative of vitamins 2 located at the active site and are indispensable for enzyme activity f specificity due to shape amp chemistry of active site i some enzymes will accept a number of closely related substrates group specificity seen in enzymes involved in synthesis of degradation of polymers ii sensitive to ionic strength of environment g substrate binding i involves H ionic or both ii reversible iii inducedfit substrate binding at the active site induces a conformational change in shape of enzyme 1 brings needed amino acid side chains into active site iv activation 1 mechanisms a bond distortion making it more susceptible to catalytic attack b proton transfer increases reactivit of substrate c electron transfer temp covalent bonds between enzyme and substrate 2 catalytic event a random collision substrate molecules with actie site results in it binding there b substrate binding induces conformational change that tightens fit facilitating the conversion of substrate into products i then release from active site h kinetics quan aspects of enzyme catalysis i michaelismenten Km S l2 vmax ii v vmax SKm S 1 v initial reaction velocity depends on substrate concentration j 2 low S doubling S will double v but as S increases each additional increase in S results in smaller increase in v 3 more 5 eventually get a vmax called saturation cannot increase anymore unless you add more enzyme 4 S ltlt km initial velocity of reaction is roughly proportional to S 5 S gtgt km initial velocity of reaction is independent of variation in S and vmax is velocity at saturating substrate concentrations 6 S km shows that km is the speci c substrate concentration at which the reaction proceeds at one half its max velocity 7 Why are these important a Lower km value of enzyme higher the af nity enzyme has for substrate b Vmax measure of potential max rate of reaction c Knowing both vivo substrate concentration estimate likely rate of reaction under cellular conditions iii lineweaver burk doublereciprocal plot linearize kinetic data inversion 1 slope kmvmax 2 xinercept 1km 3 yintercept 1vmax inhibitors i irreversible bind enzyme covalently cuase permanent loss of catalytic activity ii reversible bind enzymes noncovalently and can dissociate from enzme iii competitive occupy same site on active site on enzme iv noncompetite inhibitor and substate bind to different sites v aspirin irreversible inhibitor blocks substrate substrate level regulation depends on interactions of substrates and products with enzyme i allosteric regulation single most important rates of enzymatic reactions are adjusted to meet the cells needs feeback inhibition 1 allosteric effector binds to site called allosteric site distinct fromactive site ii covalent modification phosphorylationdephosphorylation proteolytic 1 phos transfer of phosphate group from aTP SEr Thr Tyr OH 2 proteolytic cleavage one time irreversible removal of part of polypeptide chain enzmes of pancreas trypsin chymotrypsin iH bozy


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