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Cells and Molecules

by: Helen Blick Sr.

Cells and Molecules BS 111

Helen Blick Sr.
GPA 3.59

Will Kopachik

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Will Kopachik
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This 61 page Class Notes was uploaded by Helen Blick Sr. on Saturday September 19, 2015. The Class Notes belongs to BS 111 at Michigan State University taught by Will Kopachik in Fall. Since its upload, it has received 24 views. For similar materials see /class/207332/bs-111-michigan-state-university in Biological Sciences at Michigan State University.

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Date Created: 09/19/15
BS 111 Cytoskeleton Reading pgs 112118 0 Cytoskeleton is a network of fibers extending throughout the cytoplasm 0 Plays a major role in organizing the structures and activities of the cell I Three types of structures 0 Microtubules o Microfilaments 0 Intermediate filaments o Roles of cytoskeleton I Support motility regulation I Give mechanical support to the cell and maintain its shape 0 Especially in animal cells for lack of cell walls 0 Skeleton is stabilized by a balance between opposing forces exerted by its elements I Provides anchorage for many organelles and even cytosolic enzyme molecules I More dynamic than an animal skeleton Cell motility I Encompasses changes in cell location and more limited movements of parts of the cell I Requires the interaction of the cytoskeleton with motor proteins I Cytoskeletal elements and motor proteins work together with plasma membrane molecules to allow whole cells to move along fibers outside the cell 0 Bend the cilia and agella by gripping microtubules within these organelles an sliding them against each other I Vesicles travel along quotmonorailsquot provided by cytoskeleton o Involved in regulating biochemical activities in the cell in response to mechanical stimulation I Helps regulate and coordinate cell s response 0 Components of the Cytoskeleton o Microtubules are thickest I Wall ofhollow tube is constructed from tubulin 0 Each tubulin protein is a dimer 0 Molecules made up of two subunits 0 Two types ofpolypeptide alpha tubulin and beta tubulin I Microtubules grow in length by adding dimers 0 Can also be disassembled and use tubulin to build microtubules in another spot in the cell I Two ends are slightly different 0 One end can accumulate or release tubulin dimers at a much higher rate than the other 0 o Grows and shrinks significantly in cellular activities 0 quotPlus end Serve as tracks along which organelles with motor proteins can move In animal cells microtubules grow out ofa centrosome 0 Region that is often located near the nucleus and is considered a quotmicrotubuleorganizing center 0 Function as compressionresisting girders of the cytoskeleton 0 Pair of centrioles inside centrosome 0 Each composed of 9 sets of triplet microtubules arranged in a ring 0 Centrioles replicate before the animal cell divides 0 Yeast and plant cells lack centrosomes with centrioles but have wellorganized microtubules Specialized 9 of microtubules is responsible for the beating of agella and cilia Microtubules containing extensions that project from some cells Act as locomotor appendages for unicellular eukaryotes Sperm of animals algae and some plants have agella When used as part ofa tissue layer they can move uid over the surface of the tissue Most cilia occur in large numbers on cells surface 0 Flagella are about same diameter as cilia but longer I Usually limited to one or few per cell Beating patterns 0 Flagella has undulating motions I Generates force in same direction as the agellum s axis 0 Cilia have alternating power and recovery strokes generating force in a direction perpendicular to the cilium s aXis I Like oars on a boat I Cilia can act as a signal receiving quotantennaquot for cell 0 These are generally nonmotile 0 Only one per cell 0 Membrane proteins on this cilium transmit molecular signals from the cell s environment to interior triggering signaling pathways that may lead to changes in the cell s activities 0 This signaling is crucial to rain function and embryonic development 0 Cilia and agella have a common ultrastructure 0 Core of microtubules sheathed in an extension of the plasma membrane 0 9 doublets of microtubules arranged in a ring I Center of ring is two single microtubules I quot92 pattern 0 Nearly all eukaryotic agella and motile cilia I quot90 pattern 0 Nonmotile primary cilia o Lacks central pair of microtubules o Microtubule assembly of cilium or agellum is anchored in the cell by basal body I Very similar to a centriole o In agella and motile cilia eXible crosslinking proteins evenly spaced along the length of the cilium or agellum connect the outer doublets to each other and to the two central microtubules 0 Outer doublets also have pairs ofproteins spaced along length and reaching toward neighboring doublets I Large motor proteins called dyneins o Composed of several polypeptides o Responsible for bending movement of organelle Have two quotfeetquot to walk along microtubule of adjacent doublet o Microtubule doublets seem to be held in place by the crosslinking proteins 0 Microfilaments actin filaments thinnest Built from molecules ofactin Twisted double chain of actin subunits Seem to be present in all eukaryotic cells Structural role is to bear tension 0 3d network fromed by microfilaments just inside the plasma membrane helps support the cell s shape 0 gives corteX the semisolid consistency ofa gel BS 111 Cells and Molecules Spring 2011 section 001 Coinstructors DrWill Kopachik Dr Ron Patterson Dept of Zoology Dept of Microbiology and Molecular Genetics Dr Will Kopachik coinstructor Office39 Natural Science Building email kopachikmsuedu Phone 35166 Office hours Mondays 130 to 330 without appointment Contact me re other times Weekly questionanswer sessions 300 to 400 Fridays in Natural Science room 128 Special reviews before exams usually the night before Dr Ron Patterson coinstructor Office 4198 BPS Bldg Phone 8845328 Email patter13msuedu Office hours Monday noon to 200 Lecture TA Jameel AIHaddad jameelmsuedufor absenceshep with course content clickers Shirley Reuther Bio Sci Program office 203 N Kedzie 4321316See her for administrative questions drops adds Information on BS 111 class schedule topics text reading assignments examination dates strategies for success are given in the ANGEL website 1 The ANGEL site will be used for posting syllabus announcements Powerpoint slides lecture study guides practice exams 2 The required textbook is by Campbell and Reece Biology 8th ed Benjamin Cummings 3 You will need an iClicker to get credit for in class participation Strategies for doing well Do textbook reading and look at slides before class At lecture add notes Participate in the clicker quizzes Soon after rewrite notes complete study guides For questions see one of us Plan well ahead for the exams Read the syllabus suggestions for improved study habits DATE POINTS Exam 1 W Feb 9 100 2 W March 2 100 3 W April 6 100 Final Exam W May 4 200 Exam Points 500 Clicker Points 30 Total Course Points 530 of Total Possible Points Grade for Course 83 100 40 77 82 35 71 76 30 65 70 25 59 64 20 53 58 15 47 52 10 0 46 00 This room 1281 Anthony and LS A133 will be used for the exams Before the exam you will be told which room to go to BS 111 covers subcellular and cellular biology Topics include Structure function and synthesis of macromolecules Cell structure and function Cellular generation and use of energy Intracellular and extracellular signals Cell reproduction The replication transmission and expression of genetic information in viral prokaryotic and eukaryotic organisms DNA technology and Genomics Applications of this knowledge BS 111 covers the areas in red which form a foundation for biological understanding at all other levels Biological Discipline Population Biology Organismal Biology Physiology Developmental Biology Cell Biology Biochemistry Molecular Biology Level of Analysis Ecosystems Organisms Organs and tissues Embryos Cells and organelles Macromolecules Nucleic acids and genes The hierarchy of bioloqical order from atom to orqanism Organism level Zebra Includes several organ systems Organ system level Circulatory system 0 an level r9 Heart Tissue level E Carcllac muscle 5 tissue Cellular level Cardiac muscle cell BS 1 1 1 Drgacnelle level all nucleus topics Molecular level DNA Atomic level Oxygen atom Copyrighl iil Pearson Education Inn publishing as Beniamin Cummings WARNING The many new terms with specific meanings used in each lecture will add up quickly Think of this as a vocabulary course where you will have to learn these terms as you encounter them Try making 1SrgncyamdssrThese will be used a lot eg DNA RNA NADH For new terms I will briefly use the full term eg Adenosine triphosphate but then for convenience I will use ATP OverviewChemical Bonds Ch 3 pp46475056 tRNA is the one molecule that adapts the u nucleic acid and amino acid languages The most Important hypothesis in all of biology is that everything that animals do atoms do In other words there is nothing that living things do that cannot be understood from the point of view that they are made of atoms acting according to the laws of physics Richard P Feynman Nobel Prize in Physics 1965 Transfer RNA Structure I A Big Picture View of seven unifying principles in all cellular life 1 The rules of physics and chemistry govern life 2 All cells use the same set of core hydrocarbonbased molecules in an aqueous solution 1000 molecules When available only one enantimor optical isomer is used eg Only lefthanded not righthanded amino acids are used LevoL L isomer Dextr0D D isomer c Enantiomers optical isomers Water is the universal solvent for life on earth A ms N NH3 is a good solvent but not for us A mmom n A mmom39a Macromolecules are constructed of polymer linear molecules made by linking simpler molecules eg proteins are amino acid polymers Shown is one way the beads on a string model to depict a protein 3 A core of multistep biochemical pathways of synthesis anab01ism use and breakdown catabolism of molecules is similar in all gusack points H A represent key W n I I biochemicals and 39 ram ma the green arrows 1 1 3553 I show reaction I 39 5N3 n gt l j 1amp5 5ng quot interconnecting was 39 5 them in a yeast cell The catabolism of various food molecules ll Amino Sugars Glyrol Fa acids U acids awaitsth alums Main point The core metabolic functions are interconnected by reaction pathways massi You do not have to memorize this figure U ELECTRON TRANSPORT CHAlN AND Glycgr dehydaw Mum OXIDA39I WE PHDSPHUHYLHTION Copyright I13 Pearson Education Inc pmlishing as Beniamin Cummings 4 All cells are bordered a liposomes Artificial membranebound vesicles phospholipid 39 membrane making possible a compartment of those core molecules of life a mu Pusan Pmn m Hall Int 4 ContinuedOnly two cell types exist prokaryotic cell two border membranes no nucleus limited internal membranes eukaryoticcell single outer membrane but extensive internal membranebordered organelles with a nucleus Comparison of chemiosmosis in mitochondria and chloroplasts Mitochondrion Chloroplast Mitochondrion K and chloroplas are exampe of organelle compartments INTERMEMBRANE THYLAKOID SPACE 7 SPACE MEMBRANE 39 Mitochondrion Chloroplast structure structure MATRIX STROMA Low Hquot W concentration Gopy gtil m Pearson Education Inc pubrishing aa Benjamin Cummings Which is a potential question topic on an important point for the first exam A Recalling verbatim Feynman s opening quote about physics and chemistry B That BS 111 covers cells macromolecules and genes C All biological macromolecules are polymers D A high concentration of H ions across the thylakoid to stroma space is used to make ATP What is the value of a membrane bounded compartment to an animal cell This will be the second clicker question A W90 5 Adenosine triphosphate ATP is universally used as energy currency ATP consists of three phosphate groups ribose and adenine o o o or Ilv o Ir o Ir o CHZ Phosphate groups OH OH Ribose e 9Za Biological Science 2 2005 Pearson Prentice Halnc You do not have to know the ATP structure at this time 6 All cells and viruses use polymers of nucleic acids for inheritable genetic information The central dogma of information flow occBrNiAall cells l RNA l Protein 7 All cells must arise from a preexisting cell Both daughter cells get the necessary genetic and para gene cspa aL organizational information plus a high energy State to Figure maintain life Themes for understanding cellular life 1 Energy Name and Elemn 395 Dot 8 ace Molecular distribution Structure and lling Formula Structural Moda Formula 2 Matter s 1 nos aux ns quot Ribosomas Upoprotein an pulvaoln39d hy marognnbonalng l LlprolysacCharlde mRNA 3 Phospholipid RNA DNA W Peptidoglycan u X r 1 Protein aw orm k um a 0 Short review of the chemical context of life If you need a longer review of background inorganic chemistry see Ch 2 optional reading Here we will focus on A Elements Molecular Weight Molarity B Bonds Five important types C Water Special properties D Carbon Uniqueness for life s molecules From CEM 141 I will assume you understand these terms Element isotope atomic number atomic weight dalton electron orbital Van der Waals forces ionic bonds covalent bonds hydrogen bonds polar bond nonpolar bond electronegative molecular weight molarity anion cation hydrophilic hydrophobic pH I will briefly give biological examples of their use to refresh your memory AElements in biology 96 are COHN rest mainly PSClCaK plus 16 trace elements 25 in total 99 Mg magnesium a trace element is required for all DNA polymerases hich copy DNA l iodine is required for thyroxin a hormone made the thyroid gland CEM 141 topics continued Atomic number protons 11Na Atomic weight mass protons and neutrons 23Na Oxygen has 8 protons 8 neutrons 16 daltons Radioisotopes in blue used in biomedical research HYDROGEN 1 proton H mass of1 Dalton TRITIUM 1 proton 2 neutrons a Bemitter 3H CARBON12 6 protons 6 neutrons CARBON14 6 protons 8 neutrons a Bemitter decays to 14N PHOSPHORUS32 and SULPHUR35 are also used These and other low energy beta emitters are used for tracing labeled molecules An example radioisotopelabeled reactants were used to show where the C H and 0 go in photosynthesis Reactants 6 CO2 12 H20 Wv Products CGH1 206 6 H20 6 O2 cuayugmmooa Pearson Educaimn Inc publishing as Pearson Ben amin Cummings You do not have to memorize this figure at this time But you will later in the topic of photosynthesis Can you determine the molecular weight of glucose CBH1206 Atomic weights are C 12 H 1 0 16 The MW of an average size protein that has catabolic reaction with glucose is 50000 daltons mes u bstrate Enzy complex Sometimes proteins are identified simply by their MW eg P53 is a protein of 53000 daltons CEM 141 MOLECULAR WEIGHT AND MOLARITY M9804 7H20 molecular weight 24679 1 mole 24679 1 mole in total of1 L H2O 1 Molar solution abbrev 1 M 1 mole in total of 10L H20 01M solution 24679 in 100ml of H20 1M solution 1mmole mM solution use 2467 m9 024679 in 1 L NaCl molecular weight 58449 to make a 1mM NaCl solution 0001M with a total volume of 100 ml 5844m9L or 5844m9 NaCl100ml The concentration of sodium chloride MW 584 gmole is 150 millimolar mM in blood How would you make a 100 ml solution at that molarity B Biochemical bonds The number and distribution of electrons in the outer shell determines chemical properties of the elements Name and Electron Lewis Dot Space Molecular distribution Structure and filling Formula Diagram Structural Model Formula b Oxygen 02 Covalent bonds result from sharing valence electrons The atoms get a lower therefore more stable energy state Also covalent bonds can have variable degrees of polarity as in water 6 Figure 213 6 8 Polarity creates the opportunity for H bonds which are very important for structure Water H20 Hydrogen bond Ammonia NH3 Five Types of Biochemical Bonds Type Strength Interaction Locationl Van der Waals 061 kcalmole complementary nonpolar electrostatic areas H bond 153 H attraction to mainly hydro electronegative atom philic areas Ionic bond 37 electrostatic same Covalent bond 60 100 sharing valence everywhere electrons Double covalent 150 same same You need to know this table and where the bonds are in a protein next slide A type of covalent bond peptide bond links amino acids of a protein here shown as a green ribbon model Interactions that determine the tertiary structure of proteins Hydrogen bond be tween side chain and carboxyl oxygen van der Waals interaction hydrophobic H region Hydrogen bond between quot 5quot hams Disulfide bond Figure 3153 Biological Science2le 2005 Pearson Prentice Hall Inc Many H bonds on the protein surfacenot shown greatly stabilize protein structure and make it soluble Other important points from the previous slide ionic bonds would be most sensitive ie broken by changes in the water solution The bonds are additive in contributing to maintaining the structure of the molecule YUP W1C Cl Enzymesubstrate complex C The special chemistry of water As mentioned water is a polar molecule Therefore it s a good solvent for hydrophilic molecules H bonding is abundant between water and dissolved molecules and between and among polymeric molecules like proteins Cells are 70 water and therefore the solution of 30 hydrocarbon molecules in a cell is very concentrated see next slide You do not have to know their arrangement 0 ote density of molecules and relative sizes of lecules From Dobson C Nature Dec Chemical Space in Biology Rlbasomas W Phospholipid DNA Lipopolysaccharide MM 0 2 0 Protein Lipoprmein RNA Peptidnglycan 004 The H bonds make it easy for sa sto L nquot Q5 quot7 9 f a c a aw Salt dissolved in water amp Aquot Figure 226 Biological Science2 Salt in absence of water quot9 2005 Pearson Prentice Hall Inc Water makes a hydration shell around dissolved proteins and other hydrophilic molecules a 31 b Lysozyme molecule purple in an aqueous c Ionic and polar regions environment on the protein s surface attract water molecules sowrignm 2005 Pearson Enucanm m publlshlng as Pearson Ben anyln Cummmgs Fig 38 Nonpolar molecules with nonpolar C H bonds eg greases and oils are hydrophobic cannot form many H bonds and water separates from them Certain types phospholipids can form thin layers the membranes QBESWQE ignite Qtlbg quot y39 9 i 390 39 Fatty acid palmitic acid u g azxybftssgpn quot41 1 glycerol I315 a A Sibbmsth M gu a Dehydration reaction in the synthesis of a fat Figure 514 But water dissociates at a low rate to hydrogen H and OH hydroxide ions Hydronium Hydroxide ion H30 ion OH H20 is in equilibrium with H OH which dissociate from it CEM 141 The pH scale pH is negative log of H concentration pH Iog H Neutral soln H is 10397 M at 250 pH of 70 0000000 2 times higher pH of 67 00000002N 5 times higher pH of 63 00000005N 10 times higher pH of 60 0000001 1000000 times higher pH of 10 01M pH is on a log scale You do not have to memorize this scale Acidic solution OH39OH H39 H OH39 OH OH39W H H4 Neutral solution a 011 CH Hr ow solution Neutral W OH39 lncreasingly Basic 14 lt OH l pH Scale 7 0 2 73 V 7 1 Battery acid Gastric juice lemon juice Vinegar beer wine cola Tomato juice 5 Black coffee Rainwater Urine Saliva Pure water Human blood tears Seawater Milk of magnesia Household ammonia Household bleach Oven cleaner Copylighl a 2003 Pearson E unallon inc publishing as Pearson Benjamin Cummings The pH of soil near the polar cap region of Mars was determined to be 83 How much more basic is this versus pH 7 A 13 times more basic B 83 times more basic C 13 times more basic D Almost 20 times more basic CEM 141 Acids bases and Stron gag HCL dissociates almost completely into H and CI39 in water HCI gt H Cl Weaker acids are in equilibrium and not fully dissociated as in the example for gt CH3COO H 4 Buffer like carbonic acid reversibly releases and accepts H ions HZCO3 H donor acid gt H003 H h Blood pH is 74 and maintained in a narrow range Just 04 pH lower or higher is lethal because the bonds of proteins are disrupted and they lose shape What bonds in a protein would be least broken by increasing or decreasing pH 04 unit Suggestion for use of the study guides Make a definition of the term and then use the term in a sentence to make what you consider to be the most important point or points which include the term If in doubt ask me or Jameel in the review session or compare your answers to those of fellow students Study guide 1 terms to know enantiomer optical isomer macromolecule polymer anabolism catabolism compartment prokaryotic cell eukaryotic cell adenosine triphosphate Central Dogma Atomic weight mass radioisotope Molecular weight molarity Valence electrons covalent bonds polar covalent bond nonpolar covalent bond ionic bonds hydrogen bonds Van der Waals interaction bond hydration shell


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