Cells and Molecules
Cells and Molecules BS 111
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Helen Blick Sr.
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This 17 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 Jerry Caldwell in Fall. Since its upload, it has received 22 views. For similar materials see /class/207331/bs-111-michigan-state-university in Biological Sciences at Michigan State University.
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Date Created: 09/19/15
DNA amp The Molecular Basis of Inherita nce Outline By Clay Connolly Discovering DNA is inherited Determining DNA s structure DNA General Properties DNA Replication Synthetic DNA Replication Xhat is the inherited material Morgan found two components in chromosomes Protein DNA 80 which was responsible for the inheritance oftraits 1928 Grif th Experiment 1944 Avery McCarty MacLeod Bacteriophage Background 1952 Herslieinhase Blender Experiment So What is the inherited mate rial Griffith transformation possible Avery et al DNA responsible for transformation Hershey and Chase DNA contained in bacterial cell from radiolabeled phage Thus DNA is the inherited material 1950 Chargoff s Observations DNA composition varies among species However within a single species saw a similarity Named Chargoff s Rule Adenine Thymidine Cytosine Guanine But not yet known how these bases make up the structure of DNA Rosalind Franklin s XARay Crystallography XRay Crystallography Based upon the diffraction of light Franklin s XARay Crystallography Determined Sugar phosphate backbone on the exterior Paired nitrogenous bases in the middle 1953 Watson and Crick Used Franklin s diffraction pattern to deduce the structure of DNA Double helix Width of nitrogenous bases showed Adenine pairs with Thymine Guanine pairs with Cytosine Thus Chargoff s rule was explained Overall DNA Structure Space lling double helix model Right hand twist Overall DNA Structure Pllosphateesugar Backbone l PhosphateSugar Backbone l PhosphateSugar Backbone quot 539 End 1 539 end 3 and T lt 3955 3 N at l on ed 0quot l x eg ivey arg o l in Phosphate group gig 2 o o is R l f antiparallel 04 2 quot26 HCCH0 H E o lp l H H l r D o H I H Q quotQC 3 392 0 I OH H mite 2Douxwibosn quot 39 quot 51nd Complimentary Base Pairing lComplimentary Base Pairing N H r a rquot i Wquot N 3 2 Hydmgen Bonds Suns r N 0 Sum Adenlna A Thymine T N Pyrimidine Purine FuleAs Gum o H N Nm 3Hydmgenaands Sugar N w o Stigar Guanla 6 mama C Nucleotide VS Nucleoside Phosphate Am 2cm C WWquot 39 Nucleotide Nudeosme Phnsphate Present NO Phosphate Present How does DNA Replicate Based upon structure One strand serves as the template for the formation of the other Three competing ideas Firs Second Pamnl can mplicallon mpllcmlon a Conservative model 730939 7000 b Semiconserva ve model c Disparsive 1 AVA I I model A A 7 ll A y39l 39 quotII Eaclerla 7 Eaclerla cultured In transferred to urn lum autumnan mumman N N DNA sample DNA sampla Lass unlriluged eenlrlluged dame am 241 mm 40 mm H d u M a llcallnn ta llmlon 399 no J p I dam Flrsl mplinallnn 53mm replication IEmsarvmlve 1 V 7 vii W70 vi 30110 Smlconsarva uve W modal h f l r l W V A i Dlsparslve u A A A A mntial 13 Meselson and Smhl s Experiment Prokzryotic DNA Replication Step 1 Initiation at the Origin Of Replication ORI I I O 39 in of reglication Parental template strand I aughtar new strand DoubIe Replication fork s randed Replication DNA molecule bubble I Two daugh bar I D NA molecules a Origins of replicaxlon In E coil Step 1 Continued 2 Singlestrand binding Ovarvlaw 39 Pllcallan 1 Helicase Overall directions a replicauon Step 2 New DNA strand synthesis LeadingStrand IIIIIIIIIIIII RNA primer 1 quotSliding clampquot 3 2 DNA I m Parental DNA E W 3 Daughter DNA 5 synthesixed 539 to 339 directlon 4 Islicase continues to nwind DNA Synthesis Mechanism Ell M W Daughter stran Template strand 5 en 339 and M 539 end 339 end n E 9 9 53 OH W Pyrophcsphala 339 and Nuclenside triph nsphata 2G a rldTTP i N A 539 end S39end Step 2 Continued Recall DNA replication occurs on both strands but One template strand is 5 to 3 Leading strand One strand is 3 to 5 Lagging strand Problem DNA polymerase only works in the 5 to 3 direction Solution Okazaki Fragments Okazaki Fragments Gumvim origin at mplina on Landing 3mm 1 Laggan slum Singlestrami hlnding protein Oman ninuliam lt al mglleallnn Dgt DNA OI Ill Lagging strand Okazaki Fragments Helicase here a RNA 5 1 RNA primase pl ll39 er lays down RNA mm 7 5m 2 DNA polymerase synthesizes new 9 DNA strand process on next segment of 3 DNA template DNA I 3 a 5 palymarase 5 539 reaches pre existing RNA 1 339 primer and stops i 7 539 Overall direction of replication 439 Rep at Step 3 Removal of RNA Primers Occurs in both leading and lagging strands 1 DNA pol l removes RNA primer and simultaneously synthesizes new DNA IF free 3 to start from Nick r thasey Oll POAaser baseOP O basez 2 DNA Ligase seals the nick left by DNA poll Sealed Nick DNA Ligase Other DNA Replication Issues Increased Tension When helicase unwinds DNA The downstream DNA twists and forms supercoils like a telephone cord or rubber band Need to relieve tension caused by supercoiling Solution topoisomerase corrects overwinding ahead of replication forks by breaking swiveling and Eukaryotic DNA Replication Steps 1 3 and topoisomerase are the same Multiple ORI sites Different naming system than prokaryotes RNA primase function done by DNA pol o DNA polymerase III and function performed by DNA pol a and 6 RNA primer removed by nuclease Eukaryotic ORI Origin of rleplicatioliDoublestranded DNA molecule l Parental ltternplate strand Dau liter new strand Two daughter DNA molecules FLEET WE VE iquot eukam e Issues in Eukzryotic DNA Replication Chromosome Structure Issues in Eukaryotic DNA Replication l in Chromosome Structure is will in Louis 555de jaomnm 39 39her V 4 gt 445 r Replicaned39 DNA the doul chrnmosume 1400 rim aonm ber Lnuped domains Metaphase 300mm ber chromosome Issues in Eukzryotic DNA Replication Chromosome Structure Heterochromatin Compact dense DNA regions Includes centromere Inaccessible to cell machinery Solution Chromosome modi cation Move histones Euchromatin Loosely packed Easily accessible Does not pose a problem issues in Eukaryotic DNA Replication The End Replication Problem Solution Telomere and Telomerase Telomere Stretch of repeated sequence at the end of each chromosome Shortening might protect cells from cancerous growth by limiting the number of cell Telomerase Enzyme that adds repetitive sequence Evidence of telomerase activity in cancer cells which may allow cancer cells to persist DNA Damage Errors during replication DNA polymerase average error rate is 1 in 105 without proofreading reduced to 1 in 109 with proofreading Environmental damage Chemical damage DNA Damage Solutions DNA polymerase exonuclease activity Mismatch repair Nucleotide excision repair I DNA DNA polymerase n ase g 1 Nucleotide Excision Repair divisio Synthetic DNA Replication Polymerase Chain Reaction PCR Invented by Kary Mullis Mimics a cell s normal DNA replication scheme Performed in vitro or outside of the cell Amplifies a small amount of targeted template DNA to millions of identical copies Three step process that repeatedly cycles Typically 30 to 40 cycles Step 1 Denature Mimics unwinding by DNA helicase Heat reaction to 95 C Break hydrogen bonds Create single stranded DNA Step 2 Anneal Mimics RNA primase Cool the reaction down to the optimum primer binding temperature Allows primers to bind to the single stranded DNA Speci es what region of DNA to amplify Important for DNA polymerase function Step 3 Extension DNA polymerase Taq binds at the 3 end ofthe primer 2811 BS 111002 SS11 EXAM 1 STUDY GUIDE In preparation for exam 1 students should be wellversed on the following items and topics 0 Students should the conditions of Earth s early atmosphere and the evolution of photosynthetic proka ryotes 0 Students should know the significance of the MillerUrey experiment to understanding how life possibly evolved on Earth 0 Know the 3 tenets of the cell theory 0 Know the fundamental properties of life 0 Know the 3 domains of life 0 Know and be able to explain the central dogma of biology 0 Know the steps and process of the scientific method 0 Know what emergent properties are 0 Know atomic structure and symbolism 0 Know what isotopes are 0 Know the relationship and differences between elements molecules and compounds 0 Know how atoms are arrange in the periodic table and how to predict the reactivity ie the tendency of an atom to either gain or lose an electron base on its location group and period in the table only to the extent that this topic was discussed in class 0 Know the different types of chemical bonding and how is effected by an atom s electronegativity 0 Know the what polarity and nonpolarity as they relate to electronegativity and chemical bonding 0 Know why water is a polar molecule and the resultant special properties of water 0 Know the different types of isomers and if given example molecules be able to identify what type of isomers they are 0 Be able to define pH potential of Hydrogen 0 Know what biological buffers are 0 Know the formula and structure of the functional groups their chemical characteristics and the types of molecules that contain them 0 Know the 4 biomacromolecules know if they are a polymeric molecule and their subunit building blocks and the specific name of the covalent bond that hold the subunits together for a particular biomolecule 0 Know the biological significance of each of the 4 biomacromolecules 0 Be able to identify alpha and beta glycosidic bonds 0 Based on its side chain be able to identify which of the three categories an amino acid belongs 0 Know the characteristics of the 4 levels of protein structure including which atoms are involved in hydrogen bonds 0 Know the structure and bonding patterns of nucleic acids DNA and RNA including the 5 nucleotides and their bonding pattern 0 Know the significance of 5 a3 and antiparallelism o Distinguish between saturated and unsaturated fats and between cis and trans fat molecules 0 Distinguish between the following pairs pyrimidine and purine nucleotide and nucleoside ribose and deoxyribose the 539 end and 339 end ofa nucleotide 0 Know the significance of the ratio of the cells surface area and volume Chapter12 The Cell Cycle Mitosis 4511 Ga 0F INTERPHASE PROPHASE PROMETAPHASE Centrosomes Chromatin Early mitotic Aster Fragments Kinemchure with centriole pairs duplicated Spindle cemmmere of nulclear Nonkins ochom enve ope r gtmicrotubules Nucleolus Nuclear Plasma Chromosome consisting Kinelochore envelope membrane of two sister chromatlds microtubule METAPHASE ANAPHASE TELOPHASE AND CYTOKINESIS Metaphase Cleavage Nucleoius plate furrow v forming Nuclear Centrosome at Daughter envelope spind39e one spindle pole chromosomes forming Key Concepts The ability of organisms to reproduce best distinguishes living things from nonliving matter The continuity of life is based on the reproduction of cells or CELL DIVISION Cell division results in genetically identical daughter cells The mitotic phase alternates with interphase in the cell cycle The eukaryotic cell cycle is regulated by a molecular control system In unicellular organisms division of one cell reproduces the entire organimsm Multicellular organisms depend on cell division for Development from a fertilized cell Growth Repair Cell division is an integral part ofthe cell cycle the life of a cell from formation to its own division Concept Cell division in genetically identical daughter cells Most cell division results in daughter cells with identical genetic information DNA mitosis A special type ofdivision meiosis produces nonidentical daughter cells gametes or sperm and egg cells Cellular Organization of the Genetic Material All the DNA in a cell constitutes the cell s genome A genome can consist of a single DNA molecule common in prokaryotic cells or a number of DNA molecules common in eukaryotic cells DNA molecules in a cell are packaged in chromosomes Every eukaryotic species has a characteristic number of chromosomes in each cell nucleus Somatic Cells nonreproductive cells have two sets of chromosomes DlPLOlD Gametes reproductive cells have half as many chromosomes as somatic cells HAPLOID Sperm and egg form a ZYGOTE diploid Eukaryotic chromosomes consists of chromatin a complex of DNA and proteins that condenses during cell division Distribution of Chromosomes During Eukaryotic Cell Division In preparation for cell division DNA is replicated and the chromosomes condense Each duplicated chromosome has two sister chromatids while separate during cell division The centromere is the narrow waist ofthe duplicated chromosome where the two chromatids are most closely attached 8 Chromosome i In pllcmiun Sister H chromatids l 739quot L Chromosome dlslrlbullon W m daughter calls 39 Eukaryotic Cell Division Eukaryotic cell division consists of Mitosis the division ofthe nucleus Gam etes are produced by a variation of cell division call meiosis Meiosis produces two nonidentical daughter cells Concept The mitotic phase alternates with interphase in the cell cycle Phase ofthe cell C le o M phase mitosis and cytokinesis 39 h 39 ceu div on90 ofthe cell cycle Subphase s 61 phase first gapquot most of growth 1st keycheckpoint S phase chromosomes copied synthesis39 62 phase more growth second gapquot 2nd key checkpoint 57R l l muquot terph 31 753p 1 2 call gruvst Gap 2 luau Prepares ta39dwidal M rMItDSlS Calls that cell mm ceasedivision Mitosis is ve phases Pro hase Telophase Cytokinesis has started by late telophase canlmsams A mm cnnlnnll plirs at Chroma n dupncma V Nucllulus Nuclear Plasma cmomosommonsxsnng Spindle Km uacnm envelope mmhrane allwaslshrcmummld pale micmmbula Wammmm n mmwNunmmwnw Arcmus yuanus Ann cvvamnzsls Meuphue Cleavlge Nuclwlul rum durum larmhg Dagmar 5mm hramnsnmls Wwwmmm WuhMMMM The Muouc Spmd e BS 111002 5511 3162011 EXAM STUDY GUIDE MIDTERM EXAM 2 March 24 2011 Chapter 7 Membrane Structure 8 Function 1 2 Pquot 9 Be able to define the following terms amphipathic molecules aquaporins diffusion Be able to explain how membrane fluidity is influenced by temperature and membrane composition Be able to distinguish between the following pairs or sets ofterms peripheral and integral membrane proteins channel and carrier proteins osmosis facilitated diffusion and active transport hypertonic hypotonic and isotonic solutions Explain how transport proteins facilitate diffusion Explain how an electrogenic pump creates voltage across a membrane and name two electrogenic pumps Explain how large molecules are transported across a cell membrane ie endocytosis and exocytosis Chapter 8 Energy Enzymes and MetabolismRegulation 7 Distinguish between the following pairs of terms catabolic and anabolic pathways kinetic and potential energy open and closed systems exergonic and endergonic reactions In your own words explain the second law of thermodynamics and explain why it is not violated by living organisms Explain in general terms how cells obtain the energy to do cellular work Explain how ATP performs cellular work Explain why an investment of activation energy is necessary to initiate a spontaneous reaction Describe the mechanisms by which enzymes lower activation energy Describe how allosteric regulators may inhibit or stimulate the activity of an enzyme
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