BIO 311C Study Guide 1 Notes Compilation
BIO 311C Study Guide 1 Notes Compilation Bio 311C
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This 33 page Study Guide was uploaded by Sena Sarikaya on Thursday September 22, 2016. The Study Guide belongs to Bio 311C at University of Texas at Austin taught by Dr. Buskirk in Fall 2016. Since its upload, it has received 9 views. For similar materials see Introductory Biology I in Biology at University of Texas at Austin.
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Textbook Notes for Handout 1 Ch. 2 2.3 The Formation & Function of Molecules Depend on Chemical Bonding btwn Atoms A. Covalent Bonds covalent bond: sharing of a pair of valence e by 2 atoms molecule: 2 or more atoms held together by cov. bond ex. molecular formula H 2 Lewis Dot structure H:H ex. structural formula HH single bond: 1 pair of shared e, represented w/ “” double bond: 2 pair of shared e ex. O=O valence: bonding capacity; usually # of unpaired e ex. for oxygen its 2; hydrogen its 1; nitrogen its 3; carbon its 4 phosphorus can have 3 or 5 H 2 and O 2 are pure elements NOT compounds compounds are 2 or more dif. elements ex. H O 2 electronegativity: attraction of a particular atom for the e of a covalent bond nonpolar covalent bond: 2 atoms w/ same electronegativity; e shared equally polar covalent bond: e not shared equally; one atom ore electronegative B. Ionic Bonds ions: charged atoms cations: (+) anions: () ionic bond: 2 ions of opp. charge bond ionic compounds or salts: compounds formed by ionic bonds ion can also be a charged molecule ex. +¿ ¿ NH 4 ionic bonds strong when dry but diss. in H 2 arrange in 3D lattice not molecules; formula for ionic comp. is a ratio C. Weak Chemical Bonds a. Hydrogen Bonds hydrogen bonds: attraction btwn H & electronegative atom b. Van der Waals Interactions vdwi: ever changing regions of (+) and () charge enabling atoms & mol. to stick to one & another individually weak but occurring simultaneously > powerful D. Molecular Shape & Function determines how biological molecules organize & respond to one another w/ specificity match btwn structure & funct. Concept Check 2.3 1. Why does HC=CH fail chemically? C needs 8 e in valence shell so missing 2 e per C 2. What holds atoms together in MgCl 2 ? Ionic bonds 3. Why would you want to learn the 3D shapes of naturally occurring signal molecules? Clue to receptor shapes; synthesize molecules that mimic the shapes to treat individuals who can’t produce their own 2.4 Chemical Reactions Make & Break Chemical Bonds chemical reaction: making & breaking of chemical bonds leading ot changes chemical equilibrium: the point @ which rxns offset on another exactly dynamic equil. b/c rxn still going on but no net effect on conc. of react. / prod. Ch. 3 3.1 Polar Covalent Bonds in Water Molecules Result in Hydrogen Bonding polar molecule: unequal sharing of e ex. H O 2 Concept Check 3.1 1. What is electronegativity; how does it affect interactions between water molecules? Electronegativity= how much an e is attracted to the e of a covalent bond. Electronegativity affects interactions in water molecules by causing a polar molecule that forms hydrogen bonds. 2. Why is this unlikely? H H / \ O O \ / H H Because H is partially () so H’s will repel and be attracted to the O’s forming hydrogen bonds between molecules. 3. What would the effect on properties of the water if O and H had equal electronegativity? Hydrogen bonds could not form if the molecule was nonpolar. 3.2 Four Emergent Properties of Water Contribute to Earth’s Suitability for life A. Cohesion of Water Molecules cohesion: H bonds holding the subst. together transport of water & dissolved nutrients against gravity of plants adhesion: clinging of one substance to another surface tension: how difficult it is to break the surface of a liquid related to cohesion B. Moderation of Temperature by Water a. Temperature & Heat kinetic energy: the energy of motion thermal energy: K.E. associated w/ random movement of atoms temperature: measurement of nrg of avg K.E. of molecules in matter doesn’t depend on volume like thermal nrg thermal nrg passes from hotter to cooler object heat: thermal nrg in transfer from one body of matter to another calorie (cal): unit of heat; the amount of heat it takes to raise the temp. of 1g of water 1C kilocalorie (kcal) : 1,000 cal; the amount of heat it takes to raise 1 kg of water 1C joule (J) : energy unit; 1 J = 0.239 cal b. Water’s High Specific Heat specific heat: amount of heat absorbed or lost for 1g of substance to change temp. by 1C water’s specific heat is 1cal/g * C high compared to other sub. ex. ethyl alcohol = 0.6 cal/g * C resist in changing temp. when absorbing or losing heat b/c of hydrogen bonding benefits: @ winter cooling water will warm air @ coastal areas it moderates temp. large body of water can absorb lots of heat w/o warming up a lot stabilize ocean temp. organisms are made up of a lot of water so better able to resist own temp. change c. Evaporative Cooling liquid to gas = vaporization/ evaporation heat of vaporization: how much heat liquid needs to absorb for 1g of it to go from liq. to gas water has high heat of vaporization b/c of hydrogen bonds effects of high heat of vap. of water… moderate Earth’s climate steam burns evaporative cooling: the surface of liquid that remains, as liquid evaporates, cools down hottest molecules w/ high K.E. leave as gas so cooler mol. left effect of evap. cooling… stabile lake & pond water keeps organisms from overheating B. Floating of Ice on Liquid Water water is less dense as solid than liquid hydrogen bonding C. Water: The Solvent of Life solution: liquid that is homogenous mix of 2 or more substances solvent: the dissolving agent solute: substance that is dissolved aqueous solution: solute is diss. in water; water = solvent water is good solvent b/c hydrogen bonding hydration shell: sphere of water mol. around each dissolved ion a. Hydrophilic & Hydrophobic Substances hydrophilic: substance w/ affinity for water doesn’t always dissolve ex. cellulose hydrophobic: substance that seems to repel water; nonpolar; can’t H bond b. Solute Concentration in Aqueous Solutions molecular mass: sum of masses of all atoms in a mol ex. C 12O 22 11 (sucrose) mol. mass = (12*12)+(22*1)+(11*16)=342 mole (mol): 6.02 x 10^23 or Avogadro’s number molarity: # of moles of solute per liter of solution D. Possible Evolution of Life on Other Planets seasonal streams on mars? b/c of H O rather than water 2 drilling into Mars could be next step if lifeforms are found… evolution gains new perspective Concept Check 3.2 1. Describe how properties of water affect upward movement of water in trees. Cohesion of water molecules cause water to stick to itself and adhesion of water causes water to slowly crawl up the interior side of the tree 2. Explain “It’s not the heat; it’s the humidity.” Humidity has water and water can absorb heat 3. How can freezing water crack boulders? Solid water is denser b/c hydrogen bonds cause water molecules to spread out 4. What is the benefit of water striders’ hydrophobic substance coated legs? What if the substance was hydrophilic? The substance allows the insect to walk on surface w/ water molecules b/c the nonpolar substance repels water; the insect would not be able to walk b/c the substance would interact w/ water and pull the legs and the insect in water 5. Concentration of ghrelin is 1.3 x 10^10M. How many molecules of ghrelin are in 1 L of blood? 1.3 x 10^10 3.3 Acidic & Basic Conditions Affect Living Organisms hydrogen ion (H+): single proton w/ +1 charge hydroxide ion (OH): water molecule w/ lost proton; has charge of 1 H O hydronium ion ( 3 +): water molecule w/ proton bound A. Acids & Bases acid: substance that increase H ion conc. of a sol. ex. HCl base: substance that reduces H ion conc. of sol. ex. NaOH B. The pH Scale pH: negative log (base 10) of H ion conc. pH = log[H+] C. Buffers buffers: substance that minimizes/ resists changes in H+ and OH concent. in sol. D. Acidification: A Threat to Water Quality ocean acidification: when carbon dioxide dissolves in seawater & reacts w/ water to make carbonic acid; pH is lowered in ocean Textbook Notes for Handout 2 Ch. 4 4.1 Organic Chemistry is the Study of Carbon Compounds organic chemistry: study of compounds w/ carbon A. Organic Molecules & the Origin of Life on Earth Stanley Miller brought abiotic synthesis of organic compounds into evol. context complex organic molecules could arise spontaneously under early earth conditions 4.2 Carbon Atoms Can Form Diverse Molecules by Bonding to Four Other Atoms A. The Formation of Bonds with Carbon electron configuration gives covalent capability w/ many dif. elements B. Molecular Diversity Arising from Variation in Carbon Skeleton a. Hydrocarbons hydrocarbons: organic mol. w/ only carbon & hydrogen nonpolar; won’t dissolve in water fats b. Isomers isomers: compounds w/ same # of atoms of same elements but diff. structures & diff. properties structural isomers: differ in covalent arrangement of atoms single or double bond placement cistrans isomers: geometric; differ in spatial arrangement b/c of inflexibility of double bonds single bonds allow free rotation; double doesn’t enantiomers: isomers that are mirror images of each other b/c of asymmetric carbon Concept Check 4.2 1. Can propane ( C H ) form isomers? 3 8 No, because there is only way to form the molecule. There are no double bonds and the hydrogencarbon bonds make the molecule symmetrical. 4.3 A Few Chemical Groups Are Key to Molecular Function properties of organic molecules depend on carbon skeleton & attached chem. groups A. The Chemical Groups Most Important in the Processes of Life functional groups: chemical groups directly involved in chemical reactions hydroxyl, carbonyl, carboxyl, amino, sulfhydryl, phosphate, methyl B. ATP: An Important Source of Energy for Cellular Processes adenosine triphosphate (ATP): adenosine attached to three phosphate groups when ATP reacts w/ water inorganic phosphate, ADP, and nrg are the products Ch.5 5.1 Macromolecules Are Polymers, Built from Monomers macromolecules: carbohydrates, proteins, nucleic acids polymer: long molecule w/ similar/identical building blocks lined w/ covalent bonds monomers: building blocks of polymers A. The Synthesis & Breakdown of Polymers enzymes: specialized macromolecules that speed up chemical rxns dehydration reaction: monomers are connected covalently w/ the loss of a water molecule hydrolysis: polymers disassembled to monomers; reverse of dehydration rxn breakage w/ water hydrogen from water attach to one monomer hydroxyl group attach to adjacent monomer ex. digestion B. The Diversity of Polymers 40 to 50 common monomers small molecules > unique macromolecules Concept Check 5.1 1. What are the four main classes of molecules? Which class does not have polymers? Carbohydrates, Lipids, Proteins, Nucleic Acids. Lipids 2. How many molecules of water are needed to hydrolyze a polymer of ten monomers? 9 3. If you eat fish, what must occur for the amino acid monomers to be converted to new proteins? Released by hydrolysis and condensation reaction to synthesize new polypeptide chains 5.2 Carbohydrates serve as fuel & Building Material carbohydrates: sugars & polymers of sugars monosaccharides disaccharides= 2 monosacc. w/ covalent bond polysaccharides = joined w/ dehydration rxns A. Sugars monosaccharide: multiple of unit of C H 2 glucose C 6 O12 6 carbonyl group & mult. hydroxyl group disaccharide: 2 monom. w/ glycosidic link glycosidic linkage: covalent bond formed btwn 2 monos. by dehydration rxn succrose lactose maltose B. Polysaccharides polysaccharides: 1001000s of monosaccharides w/ glycosidic linkage a. Storage Polysaccharides starch: polymer of glucose monomers granules w/in plastids (cellular structures; includes chloroplasts); for plants alpha glucose glycogen: polymer of glucose like amylopectin but more branched; for animals alpha glucose depleted w/in a day unless replenished b. Structural Polysaccharides cellulose: major component of cell walls beta glucose never branched in plants, grouped together into microfibirils “insoluble fibers” chitin: carbohydrate used by arthropods to build exoskeletons Concept Check 5.2 1. Write the formula for a monosaccharide that has 3 carbons. C H 3 8 2. Two glucose molecules synthesize to make maltose. Glucose is C6H O12 6 . What is maltose? C 3 O22 11 5.3 Lipids Are a Diverse Group of Hydrophobic Molecules lipids: no true polymers; not big enough to be macromol.; mix poorly w/ water if at all A. Fats fat: glycerol & fatty acids fatty acid: long carbon skeleton (16 or 18 carbons) w/ carboxyl group @ one end triacylglycerol: 3 fatty acids linked to one glycerol molecule saturated fatty acid: w/ hydrogen unsaturated fatty acid: one or more double bonds w/ fewer H atoms on each double bounded carbon -trans fat: hydrogenated unsaturated fat into saturated fats and unsaturated fats with trans double bonds B. Phospholipids -phospholipid: two fatty acids attached to glycerol (not three like fats); third hydroxyl group is joined to phosphate group which has a (-) charge -usually another small charged mol. is linked -ex. Choline -hydrocarbon tails = hydrophobic -phosphate group & attachment = hydrophilic -assemble into bilayers C. Steroids -steroids: lipids w/ carbon skeleton consisting of four fused rings -Cholesterol: a type of steroid; in animal cell membrane; precursor for other steroids -ex. sex hormones Concept Check 5.3 1. Compare the structure of a fat with a phospholipid. Fat= a glycerol with three fatty acids (hydrocarbon chain); nonpolar; hydrophobic Phospholipid= glycerol attached to fatty acids; polar head, nonpolar tail; hydrophobic and hydrophilic; phosphate group 2. Why are human sex hormones lipids? Hormones are steroids which are hydrophobic lipids Textbook Notes from Handout 3 Ch. 5 5.4 Proteins Include A Diversity of Structures, Resulting in A Wide Range of Functions catalysts: chem. agents that speed chem. rxn w/o being consumed by rxn polypeptides: polymers of amino acids protein: biologically funx. mol. that consists of one or more polypeptides A. Amino Acid Monomers amino acid: organic molecule w/ both amino groups & carboxyl group (& R group) B. Polypeptides peptide bond: 2 amino acids positioned so that carboxyl group of one is adjacent to amino group of another w/ dehydration rxn polypeptide of any length always has N terminus & C terminus C. Protein Structure & Function polypeptide NOT synonymous to protein ex. long yarn NOT synonymous to sweater many proteins are spherical (globular proteins) other proteins are long fibers (fibrous proteins) a. Four Levels of Protein Structure primary structure: sequence of amino acids secondary structure: the coils and folds as result of H bond btwn polypeptide backbone (NOT amino acid side chains) th alpha helix: coil w/ H bond btwn every 4 amino acid beta pleated sheet: two or more polypeptide chain lying side by side connected by H bonds btwn two parallel segments of polypeptide backbone tertiary structure: overall shape of polypeptide from side chains (R groups) hydrophobic interactions: as polypeptide folds to funx. shape, amino acids w/ hydrophobic side chains w/ clusters @ core of protein no contact with water disulfide bridge: covalent bond enforcing shape of protein b/c of cysteine monomers w/ sulfhydryl groups are brought together quaternary structure: overall protein structure from aggregation of polypeptide subunits b. SickleCell Disease: A Change in Primary Structure sickle cell disease: inherited blood disease b/c substitution of one amino acid (valine) for normal (glutamic acid) at the primary structure of hemoglobin hemoglobin carries oxygen in red blood cells simple change in structure has devastating effect on funx c. What Determines Protein Structure? arrangement of polypeptide chain physical & chemical conditions of protein’s environment pH, salt, temp., etc. denaturation: protein unravels & loses native shape; protein becomes biologically inactive d. Protein Folding in the Cell chaperonins: protein mol. that assist in proper folding of other proteins do not specify final structure of polypeptide keeps new polypeptide separate from disruptive chemical cond. in cytoplasm while it folds spontaneously Xray crystallography: diffraction of Xray beams by atoms of crystallized mol. build 3D model of every possible atom in protein first worked out for myoglobin Concept Check 5.4 1. What parts of a polypeptide participates in bonds that hold secondary structure? Tertiary structure? Secondary = hydrogen bonds Tertiary = interaction of side chain 3. Where would you expect a polypeptide region rich in amino acids valine, leucine, and isoleucine to be located in a folded polypeptide? Explain. Nonpolar and hydrophobic so it is protected from the polar inside of the cell. 5.5 Nucleic Acids Store, Transmit, and Help Express Hereditary Information gene: amino acid sequence of a polypep. programed by discrete unit of inheritance nucleic acids: polymers of monomers called nucleotides A. Roles of Nucleic Acids deoxyribonucleic acid (DNA): nucleic acid genetic material; directs RNA synthesis; directions for own replication ribonucleic acid (RNA): nucleic acid; controls protein synthesis gene expression: DNA and RNA processes B. The Components of Nucleic Acids polynucleotides: nucleic acid macromolecules that exist as polymers nucleotide: fivecarbon sugar (a pentose), a nitrogencontaining base (nitrogenous base), one or more phosphate groups pyrimidine: 6membered ring of carbon and nitrogen atoms cytosine (C), thymine (T), uracil (U) purine: sixmembered ring fuses to a fivemembered ring adenine (A), guanine (G) C. Nucleotide Polymers nucleotide into polynucleotide requires dehydration rxn sugarphosphate backbone nitrogenous base NOT part of backbone 5’ to 3’ carbon D. The Structures of DNA & RNA Molecules double helix: two polynucleotides that wind around an imaginary axis backbones run opposite 5’ to 3’ from each other antiparallel: opposite 5’ to 3’ direction arrangement double helix strands are complimentary A always pairs with T T always pairs with C RNA molecules are single strands complimentary base pairing can occur btwn two RNA mol. or btwn two stretches of nucleotides in same RNA molec. b/c T not present in RNA… A pairs with U more versatile > genetics of earlier life 5.6 Genomics & Proteomics Have Transformed Biological Inquiry and Applications bioinformatics: use of comp. software to handle & analyze large data sets (genomes) genomics: solving problems by analyzing large sets of genes or whole genomes of diff. species proteomics: analysis of large sets of proteins & their sequences determined by using biochem techniques or translating DNA that code for them A. DNA & Proteins as Tape Measures of Evolution molecular genealogy closely related on anatomical & fossil evidence > share proportion of DNA human genome 9598% identical to chimp Textbook Notes from Handout 4 Ch. 25 25.1 Conditions on Early Life made the Origin of Life Possible how did living cells appear? observations & experiments propose one scenario chem. & physical processes could have produced simple cells through 4 stages 1. abiotic synthesis of organ. molecules 2. synthesis of small organ. mol. to macromolecules 3. packaging of molecules in protocells protocells: droplets w/ membranes & internal chem. diff. from surrounding 4. origin of selfreplication molecules > inheritance A. Synthesis of Organic Compounds on Early Earth no water but lots of water vapor hot little oxygen compounds released by volcanic eruptions as earth cooled > water vapor condensed to bodies of water & H into space A.I. Oparin & J.B.S. Haladane independently hypothesized early earth atmosphere = reducing environ organ compounds form from simpler mol. lightning & UV radiation = nrg for synthesis Stanley Miller & Harold Urey lab conditions like early earth yielded amino acids & organ. comp. another hypothesis that organ. comp. produced in deepsea hydrothermal vents hydrothermal vents: areas on seafloor w/ heated water & minerals that come from earth’s interior into the ocean some “black smokers” release hot water that make comp. unstable alkaline vents: release high pH warm water (more suitable for origin of life) pH 911 temp. 4090C another source for organic mol. = meteorites ex. Murchison meteorite contains amino acids not from earth b/c contains D & L isomers organism only make & use L isomers B. Abiotic Synthesis of Macromolecules abiotic synthesis of RNA can occur spont. from precursor mol. amino acid or RNA drips on hot sand, clay, rock produces polymers spontaneous no enzymes or ribosomes C. Protocells all organisms must reproduce & process nrg (metabolism) necessary conditions may be met in vesicles ex. vesicles form spontaneously w/ lipids in water adding montmorillonite (soft mineral from volcanic ash) incr. rate of vesicle selfassembly surface for organ. mol. conc. inc. likelihood of mol. rxns & forming vesicles abiotically produces vesicles can “reproduce” on their own & grow/ inc. size w/o diluting contents vesicles can absorb montmorillonite particles RNA & organ. mol. attached some vesicles have selectively permeable bilayer & do metabolic rxns w/ external reagents D. SelfReplicating DNA first RNA not DNA ribozymes: RNA catalysts make short RNA complementary copies w/ supplied nucleotides RNA mol. w/ certain nuc. seq. replicates faster & w/ fewer errors than other seq. RNA = template for DNA DNA more chem. stable for genetic info & replicated more accurately 25.3 Key Events in Life’s History Include the Origins of Unicellular & Multicellular Organisms & The Colonization of Land geologic record: standard time scale diving earth’s history into 4 eons 1 eon = Hadean 2 eon = Archaean 3 eon = Proterozoic th 4 eon = Phanerozoic Paleozoic Mesozoic Cenozoic A. The First SingleCelled Organisms stromatolites: layered rocks that form when certain prokaryotes bind sediments earlies direct evidence of life (3.5 billion y.a.) currently found in few shallow marine bays a. Photosynthesis and the Oxygen Revolution most atmospheric oxygen = water splitting from photosynthesis at first w/ photosynthesis the free oxygen dissolved in surrounding water @ high enough conc. it would react w/ elements dissolved in water ex. iron > iron oxide > sediments once all dissolved iron precipitates, more oxygen dissolves oceans etc. saturated w/ oxygen now then oxygen “gasses out” from water to atmosphere cyanobacteria = oxygenreleasing photosynthetic bact originates 2.7 billion y.a. oxygen had huge impact on life attacks chem. bonds inhibits enzymes damages cells doomed prokaryotes some survived in anaerobic conditions some adapt w/ cellular resp. b. The First Eukaryotes endosymbiont theory: mitochondria & plastids (things like chloroplasts) were small prokaryotes that started living w/ larger cells developed mutually beneficial relationship serial endosymbiosis: mitochondria evolved before plastids b/c of endosymbiotic events all eukaryotes of mitochondria like remains not all have plastids evidence for endosymbiotic origin of mitochondria & chloroplast… inner membranes have transport systems like prokaryotes replicate by splitting process like prokaryotes circular DNA like bacteria; no large histones cellular machinery like ribosomes ribosomes more like prokaryotes than eukaryotes B. Origin of Multicellularity a. Early Multicellular Eukaryotes oldest fossils of mut. euk. from 1.2 billion y.a. from microbial world to evolutionary change b. The Cambrian Explosion Cambrian explosion: present day animal phyla suddenly appearing C. Colonization of Land milestone in history of life End of Chapter 25 Qs 1. Fossilized stromatolites A. formed around deepsea vents B. resemble structures formed by bacterial communities that are found today in some shallow marine bays C. provide evidence that plants moved onto land in the company of fungi around 500 million years D. contain the first undisputed fossils of eukaryotes and date from 1.8 billion years ago 2. The oxygen revolution changed Earth’s environment dramatically. Which of the following took advantage of the presence of free oxygen in the oceans and atmosphere? A. the evolution of cellular respiration, which used oxygen to help harvest energy from organic molecules B. the persistence of some animal groups in anaerobic habitats C. the evolution of photosynthetic pigments that protected early algae from the corrosive effects of oxygen D. the evolution of chloroplasts after early protists incorporated photosynthetic cyanobacteria 1. Which of the following steps has not yet been accomplished by scientists studying the origin of life? A. Synthesis of small RNA polymers by ribozymes B. Formation of molecular aggregates with selectively permeable membranes C. Formation of protocells that use DNA to direct the polymerization of amino acids D. Abiotic synthesis of organic molecules Textbook Notes Based on Handout 5 Ch. 6 6.1 Biologists Use Microscopes and the Tools of Biochemistry to Study Cells A. Microscopy light microscope (LM): visible light passes through specimen then through glass lenses first used by Renaissance scientists & used in labs lenses refract light so that image of specimen is magnified as it’s projected to eye 3 important parameters in microscopy magnification = ratio of object’s image size to real size LM mag. to 1,000x actual size resolution = measure of clarity of image LM cannot resolve more than 0.3 micrometers regardless of mag. contrast = difference in brightness between light and dark areas staining & labeling cell components enhance contrast organelles: membraneenclosed structures in eukaryotic cells until recently LM resolution barrier prevented studying electron microscope (EM): focuses beam of elections through specimen or onto its surface resolution inversely related to wavelength of light shorter wavelengths than vis. light theoretically can resolve about 0.002 nanometers in practice can only resolve about 2 nanometers scanning electron microscope (SEM): electron beam scans surface o sample usually coated w/ film of gold; beam excited surface e and secondary e are detected by device that translate pattern of e into electronic signal sent to video screen useful for detailed topography 3D look uses electromagnets as lenses not glass transmission electron microscope (TEM): aims electron beam through thin section of specimen; specimen stained w/ atoms of heavy metals which attaches to cell struct.; some parts of cell’s e density are enhanced image displays pattern of transmitted e study internal structure of cells uses electromagnets as lenses not glass advantage of EM… subcellular struc. revealed disadvantage of EM… methods for prep kill specimen cytology = study of cell struc. A. Cell Fractionation cell fractionation: takes cells apart & separates organelles & subcellular struc. from one another centrifuge used 6.2 Eukaryotic Cells Have Internal Membranes that Compartmentalizes Their Functions Bacteria & Archaea = prokaryotic protists (unicellular eukaryotes), fungi, animals, plants = eukaryotic A. Comparing Prokaryotic & Eukaryotic Cells cytosol: semifluid, jellylike substance where subcellular components suspend eukaryotic cell: most of DNA is in the nucleus bounded by a double membrane prokaryotic cell: DNA is concentrated in nucleoid; not membrane enclosed eukaryotic = true nucleus cytoplasm: interior of a cell in eukaryotes = btwn nucleus & plasma mem. in prokaryotes = prokaryotes don’t have membranebound struct. organized in diff. regions eukaryotic cells larger plasma membrane: selective barrier that allows passage of oxygen, nutrients, wastes ratio to volume is critical when cell grows, surface area grows less than volume utilize microvilli or folds larger organisms DO NOT have larger cells, they have more cells B. A Panoramic View of the Eukaryotic Cell 6.3 The Eukaryotic Cell’s Genetic Instructions Are Housed in The Nucleus And Carried Out By the Ribosomes A. The Nucleus: Information Central nucleus: contains genes in eukaryotic cell nuclear envelope: encloses the nucleus; separates from cytoplasm double membrane lipid bilayer pore complex = intricate protein structure regulating entry & exit of proteins & RNAs & macromol. nuclear lamina: netlike protein filament array giving nucleus the shape w/ mechanical support not @ pores nuclear matrix = framework of protein fibers through nuclear interior chromosomes: in nucleus how DNA is organized into discrete units each has one long DNA mol. w/ associated proteins chromatin: complex of DNA & protein making up chromosomes chromosomes can’t be distinguished nucleolus: dense granules & fibers joining chromatin where rRNA (ribosomal RNA) is synthesized proteins imported from cytoplasm are assembled w/ rRNA into large & small ribosome subunits nucleus directs protein synthesis synthesizes mRNA (messenger RNA) according to DNA mRNA transported to cytoplasm by nuclear pores ribosomes translate mRNA genetic message into primary structure B. Ribosomes: Protein Factories ribosomes: complexes made of rRNA & protein; carry out protein synthesis NOT an organelle b/c not membrane bound free ribosomes = suspended in cytosol proteins made by them funx in cytosol ex. enzymes bound ribosomes = attached to endoplasmic reticulum proteins made by them are inserted into membrane or packaged into lysosome or secreted can alternate btwn free & bound 6.4 The Endomembrane System Regulates Protein Traffic & Performs Metabolic Functions in the Cell endomembrane system: nuclear envelope, endoplasmic reticulum, Golgi apparatus, lysosomes, vesicles, vacuoles, plasma membrane tasks… protein synthesis, protein transport into membranes & organelles & out, metabolism, lipid movement, poison detox vesicles: sacs of membrane A. The Endoplasmic Reticulum: Biosynthetic Factor endoplasmic reticulum (ER): extensive network of membranes; more than half of total membrane in eukaryotic cells ER lumen = cavity/ cisternal space separate from cytosol by ER mem. smooth ER: no bound ribosomes rough ER: bound ribosomes a. Functions of Smooth ER lipid synthesis, carbohydrate metabolism, poison detox, calcium ion storage steroids, sex hormones secreted adding hydroxyl to drug mol. more soluble > easy to flush out b. Functions of Rough ER secreted protein production glycoproteins: proteins w/ carbohydrates covalently bonded built into ER membrane transport vesicles: vesicles in transit from one part of cell to others membrane factory for cell makes membrane phospholipids from cytosol precursors B. Golgi Apparatus: Shipping & Receiving Center Golgi apparatus: warehouse for receiving, sorting, shipping, & some manufact. products of ER are modified & stored & sent to other destination flattened membranous sacs = cisternae structural directionality cis face = where vesicles from ER can add membrane to Golgi trans face = where vesicles pinch off & travel to other sites manufactures some macromolecules pectin, non cellulose polysaccharides cisternal maturation model = cisternae of Golgi progress forward from cis to trans face carrying modified cargo during move molecular identification tags added like mailing labels ex. phosphate groups transport vesicles from Golgi have external mol. on membrane that recog. “docking sites” on specific organelle surfaces or plasma mem. correct targeting of vesicles C. Lysosomes: Digestive Compartments lysosome: membranous sac of hydrolytic enzymes for digesting macromol. too many lysosome leakages can destroy cell by selfdigestion hydrolytic enzymes & membrane made by rough ER then transferred to Golgi for processing 3D shapes of proteins protect vulnerable bonds from own enzymatic attack phagocytosis: eating by engulfing smaller organisms/ food ex. amoebas & unicellular eukaryotes, some human cells (macrophages) autophagy = recycle cell’s own organic material TaySachs disease caused by accumulation of lipids b/c lipiddigesting enzyme is missing/ inactive brain is impaired D. Vacuoles: Diverse Maintenance Compartments vacuoles: large vesicles from endoplasmic reticulum & Golgi apparatus food vacuoles: formed by phagocytosis contractile vacuoles: pumps excess water out of cell in unicellular eukaryotes in fresh water maintain suitable conc. of ions & molec. certain vac. in plants & fungi have enzymatic hydrolysis carried out plants have small vac. to reserve organ. compounds help protect plants against herbivores b/c have poisonous compounds stored some have pigments to attract pollination central vacuole: coalescence of smaller vacuoles in mature plant cells cell sap made inside E. The Endomembrane System: A Review Concept Check 6.4 1. Describe functional and structural distinctions between rough and smooth ER. The rough ER has ribosomes; both make phospholipids 2. Describe how transport vesicles integrate the endomembrane system. Substances are enclosed between endomembrane components. 3. Describe the proteins path through the cell staring with the mRNA molecule that specifies the protein if a protein function in the ER but requires modification in the Golgi apparatus before achieving that function. mRNA is synthesized in the nucleus and then to nuclear pore and then to bound ribosome on the rough ER where protein is synthesized and transport vesicle takes the protein to the Golgi apparatus and then back the ER. 6.5 Mitochondria & Chloroplasts Change Energy From One Form to Another mitochondria: site of cellular respiration; oxygen to ATP by extracting nrg from sugars chloroplasts: sites of photosynthesis A. The Evolutionary Origins of Mitochondria and Chloroplasts endosymbiont theory: early ancestry of eukaryotic cells engulfs oxygenusing nonphotosynthetic prokaryotic cell B. Mitochondria: Chemical Energy Conversion double phospholipid bilayer outer membrane is smooth cristae: membrane inner foldings creates larger surface area mitochondrial matrix: enclosed by inner membrane composed of enzymes C. Chloroplasts: Capture of Light Energy double membrane thylakoids: another membranous system of flattened interconnects sacs granum: thylakoid stacks stroma: fluid outside the thylakoids; contains chloroplast DNA plastids: chloroplasts a member of this specialized family ex. amyloplasts = colorless organelle that stores starch (amylose) ex. chromoplast = gives yellow/orange color to fruits & flowers D. Peroxisomes: Oxidation peroxisome: specialized metabolic compartment bound by single membrane enzymes remove hydrogen atoms from substrates & transfer to oxygen produces hydrogen peroxide ex. glyoxysomes = fat storing tissues of plants have these to converse fatty acid to sugar Concept Check 6.5 1. Describe two common characteristics of chloroplasts and mitochondria. Function = energy Membrane structure = folding or thylakoid membrane for larger surface area 2. Do plant cells have mitochondria? Explain. Yes; mitochondria make energy from sugars 3. Argue against why mitochondria and chloroplasts should be classified in the endomembrane system. Neither are synthesized by the ER and are not bound to a single membrane. 6.6 The Cytoskeleton is a Network of Fibers that Organizes Structures & Activities in the Cell cytoskeleton: network of fibers extending throughout cytoplasm A. Roles of the Cytoskeleton: Support & Motility obvious function = mechanical support & maintain shape especially important for animal cells b/c no cell walls some cell motility motor proteins: interacts w/ cytoskeleton to move ex. how vesicles w/ neurotransmitter mol. migrate to axon tips manipulates plasma membrane bending to form food vacuoles/ phagocytic vesicles B. Components of the Cytoskeleton a. Microtubules microtubules: hollow rods constructed from globular protein (tubulin) each protein is a dimer = mol. of 2 subunits alphatubulin & betatubulin grows by adding dimers one end can accumulate or release tubulin dimers @ higher rate plus end guides vesicles from ER to Golgi apparatus to plasma membrane i. Centrosomes & Centrioles centrosome: where microtubules grow out of near nucleus centrioles: within centrosome; composed of 9 sets of triplet microtubules in a ring shape ii. Cilia & Flagella flagella & cilia: microtubulecontaining extensions that project from some cells flagella undulate like a fish tail cilia work like oars w/ alt. power & recovery strokes cilia can be signalreceiving “antenna” motile will have nine doublets of microtubules in a ring shape w/ 2 single microtubules in center “9+2” nonmotile will have “9+0” basal body: what cilia/flagella are anchored by; struct. similar to centriole “9+0” like a centriole sperm flagellum becomes centriole when entering the egg dyeins: large motor proteins that bend the flagella & motile cilia attached along outer microtubule doublet 2 “feet” that “walk” along microtubule of adjacent doublet using ATP b. Microfilaments (Actin Filaments) microfilaments: thin solid rods built by actin actin: globular protein twisted double chai of actin subunits like microtubules, present in all eukaryotic cells NOT compressionresisting like microtubule but tension bearing cortical microfilaments = support cell shape cortex: outer cytoplasmic layer of cell shaped by cortical microfila. to be semisolid consistency of gel myosin: protein that makes up actin filaments & thicker filaments interaction causes contraction of muscle cells pseudopodia: extending cellular extensions that allow cell to crawl along a surface cytoplasmic streaming: circular flow of cytoplasm within cells actinmyosin interactions contribute c. Intermediate Filaments intermediate filaments: named for diameter; only found in cells of some animals (ex. vertebrates) specialized for bearing tension each constructed from family of proteins who include keratins more permanent than microfilaments & microtubules persist even after cell death especially sturdy for reinforcing shape of a cell & position of organelles ex. nucleus sits in cage of intermediate filaments End of Chapter 6 Qs 1. Which structure is not part of the endomembrane system? A. Nuclear envelope C. Golgi apparatus B. Chloroplast D. Plasma membrane 2. Which structure is common to plant and animal cells? A. Chloroplast C. Mitochondrion B. Central vacuole D. Centriole 3. Which of the following is present in a prokaryotic cell? A. Mitochondrion C. Nuclear envelope B. Ribosome Chloroplasts 6. What is the most likely pathway taken by a newly synthesized protein that will be secreted by a cell? A. Golgi→ ER → Lysosome B. Nucleus→ ER → Golgi C. ER → Golgi → vesicles that fuse with plasma membrane D. ER → Lysossome → vessicels that fuse with plasma membrane 7. Which cell would be best for studying lysosomes? A. Muscle Cell B. Nerve Cell C. Phagocytic White Blood Cell D. Bacterial Cell
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