Class Note for BIOC 461 with Professor Bourque at UA
Class Note for BIOC 461 with Professor Bourque at UA
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Date Created: 02/06/15
Page1 of 31 Chapter 4 Notes Biochemistrv 461 Fall 2009 CHAPTER 41 Part 1 LECTURE TOPICS DNA and RNA MOLECULES OF HEREDITY 1 DNARNA structures nomenclature shorthand conventions 2 DNA and RNA as enetic material 3 General properties of DNA Double Helix 4 Basic mechanism of DNA replication 5 Important physicalchemical properties of DNA Reminder from Chapter 25 Lectures Nucleic acids DNA RNA are polymers consisting of pentose sugars phosphate and bases H Base BaseH Base 5 CH 7v rev 7 HO O OH 4 I H H Sugar Sugar H H Phosphate Phosphate Phosphate Phosphate Phosphate 2 HO OH Ribose H PURINES 5 EH H JM 0 HO O OH 1 a IN 7H N amp N r H 4 H H I 2 a a J H x s H J H N NH HKN N M N NH 3 2 H H Purine Adenine Guanine HO H Deuxyribose PVRMDNES NH1 0 0 2 CH3 u Mt NW 1154 N Kr H DAN 0 DANM A n n Pyrimidine cytosine Uracil Thymine nm 1 D 390 0 N l l Page 2 of 31 RNA and DNA are chains of ribo or dexyribonucleosides connected by 539 to 339 phosphodiester bonds They are golknucleotides The chains havegolariLk and are always written and read from 539 to 339 left to right as in the examples of DNA and RNA trinucleotides ng 5 3 base DNA base RNA Page 3 of 3 Nucleic Acid Shorthand Notations Trinucleotide shorthand example Fig57 pACG A C 3 see also Powerpoint version 339 339 3 GE Of 0 539 5 5 r o r I d93quot dmidt sagar Page 4 of 31 DNA and RNA as genetic material Proofs 0 Transformation with pure DNA Pneumococcus 1928 1944 o Bacteriophage T2 DNA not Protein 1952 Hz ktyW w no emfms 0quot Maui but lnFerndk P quot C 35 BACTERIOPHAGE VIRUS LIFE CYCLE Scena o attach to cell inject DNA reproduce new DNA and proteins kill cells release progeny new virus infect more cells 397 Progeny 2 1 phage xf W V L 1 Aquot tis IIIIII r gt 5 1 7145351 1394 I j 39upatW a h Iquotquotquot elf RIFJ V T 33 DNAquot Lysed bacterium 39 39 1 Activatiunquotquot39 with released E colt Bacterial Lysogenic T 39 DNA cell PamVar it DNA integrated in E coh genome Page 5 of 31 O TMV RNA as genetic information1955 k iTo bM M M0913 Vivu 5 O Retroviruses RNA to DNA 197039s Fig523 Reverse Reverse Reverse transcriptase transcriptase transcriptase Viral RNA DNARNA DNA transcript Doublehelical hybrid of viral RNA viral DNA Page 6 of 31 PRIDNS 7 Proteins not DNA or RNA are transmissible agents 1970 s to present SLOW BRAIN INFchioNs39 sapuve Rocky mmmfam k a lease Chmnic wasting disease wilh spongifmm snoepha a alh 24 scmmnc Amrucm August 19 1 fg mw giw mp Winn 60m 5amp7 MMG E Page 7 of 31 DNA chromosomes are long as seen by electron microsocopy of E coli DNA Fig58 DNA molecules are doblehelices deduced from xray diffraction patterns of BDNA in 1938 The data showed that there had to be regularly spaced units at 34 Angstroms along the helix Fig510 34 A spacing Page 8 of 31 DNA Structure WatsonCrick Double Helix 19531 0 BDNA was the form upon which Watson and Crick derived their model DNA occurs primarily in this form in vivo The important features ofthis model of DNA are 0 Two helical polynucleotide chains coil around a common axis The chains are antiparallel in polarity 0 The purine and pyrimidine bases are inside the helix whereas the phosphate and deoxyribose units are on the outside 0 The planes ofthe bases are perpendicularto the helix axis 0 The planes ofthe sugars are nearly at right angles to those ofthe bases 0 The helix diameter is 20A 0 Adjacent bases are spaced 34A along the helix axis Adjacent bases are related by a rotation of 36 degrees Hence the helical structure repeats after each ten residues on each chain 360 degrees and at intervals of 34A 0 The two chains are held together by hydrogen bonds between pairs of bases Adenine always pairs with thymine Guanine always pairs with cytosine The speci city of the pairing of bases is the most important aspect of the DNA double helix Watson and Crick deduced while building the model that adenine must pair with thymine and guanine with cytosine because of steric and hydrogenbonding features Chemical analysis of DNA Chargaff 1950 showed that AT and GC as also predicted by the WatsonCrick structure 0 Any sequence of bases may occur along a polynucleotide chain The precise sequence of bases carries the genetic information Page 9 of 31 DNA helix flat version shows polaritv and base airin Figure 4 1 page 75 Figure 42 page 77 539 Stryer arachemsm Fourth Edmon I 1995 by W H Fvesman and Company DNA Helical ladder as In real BDNA Page 10 of 31 Space llinq version of Watson and Crick BDNA model Fig511a A 34A Top View lookin down helical axis Figs51b and 513 Page 11 of 31 AT and 60 base pairs Fig 512 AT base pair u NA H CH3 1735er Mme mm 3 Adm c so It 0 Adenine Thymine d b sex 7 use V Cof deaxmhgse GC base pair H 1 nynslne m DGumm H N N K W N N N quot N N5lt N H I V H CV01 T o 2 deaxynbuse Guanine Cytosine mm a N c W Fair 95 49 and 4m page 51 r Buchamxim rm uiliuu 392 H bowls 95 MW u mam w Curmrw sm Page 12m 31 A three base pair stack of DNA showi g armparaHe pmamy 35 and 53 bases paraHE m Each Either and perpendmu artu hehx ast dexynbuse perpendmu artu bases phusphates un uutswde uf hehx r I u r Sign bases sugm PWWQ mumu mm m mm mm m mm mm NW um WNWmquotW mmmm R Page 13 of 31 REPLICATION OF DNA Watson and Crick deduced that the complementary chains of a double helix are templates for each other in replication The base sequence of each chain determines that of daughter DNA molecules 0 DNA replication is semiconservative Shown by the MeselsonStahl 1958 experiment Figs 413 Fig 14 15 0 DNA strands with 15N and MN containing bases were analyzed through several generations of E coli cell division and DNA replication properties of DNA below of old WEN vs new MMDNA after each generation proved that parent DNA strands 0 Changes in buoyant density see physicochemica A were conserved during replication 1 MN lSN Re liw v an is ssmcowsmmwus lt37 l 4 149 aquarium E M N quot N N Original parm mnlmuln First aluminaquot diunhw mvlnculs A A 5mm numluion mumv Malawian 1 1 Wu WW quotw Page 14 of 31 DNA Replicatian Primer TemEIate relatianshigs Primerfree 3390H DNA quot1 DNA quot2 v 3 r C 3 if 3 5W 5 PW T m 5 W z A 9 3 AL 9 3 i r 4 C G Y C A C G Y C A C G C A z s39 3 y a a I e 539 Template basepaired ta primer DNA ReEIicatian by DNA Ealymerase reguires 0 All four dNTPs dATP dGTP dCTP and dTTP 0 Mg 0 A primer chain with a free 339 OH end 0 A template strand to which the primer is basepaired o Doublestranded DNA that is fully intact and lacking a 39ee 339 OH end will not be replicated ex intact circular DNA WHINT Draw vaur awn TemplatePrimer camplex ta see haw it warksj Page 15 at 31 DNA Replication Phos hodiester bondformationb DNA 0 erase Primer wand e e E E s a 3 5 D M No Summa of the baslc mechanism of DNA re licatlon Repttcatton ts semtcunservettve DNA poiymerase requtres a temptatepnmer compiex dNTPs are the substrates for DNA synthesis Ppt breakdown to 2 moies ot Pt cataiyzed by pyrophosphatase drNes DNA synthesis reactton Page met 31 WWW Reversmxe separatmnrreassumatmn uf DNA strands DenaturErenaturememng temperature Tm prupumuna m quotA670 bp Bunyant densny ana ysws uf DNA shuvvs n s prupumuna m quotADC bp Enurmuus range uf Engths e um m em Engths o Cunfurmatmn uf DNA ean be mean emes upensuperm ed 5mger 55 Dr duub ers tranded D5 Reversible strand se arauon of DNA b heat and other denaturams quot1N el 5W Mt Relative absorbance 260 nm Page 17 of 31 DNA UVlight absorbance by A single and doublestranded DNA Single stranded U E E 5 3 c Double helical 300 220 260 Wavelength nm Denaturation AT vs GC base pairs Aquotv N quot Meltin tem erature of DNA ro ortional to GC base airs IGC 35m 50 85 ll s 13 3 3 12 2 5 making 65 vs 85 11 temperature Tomgumwr he mtquot E Tm 80 60 70 Temperature C Page 18 of 31 Enormous size ranges of DNA molecules in nature O From about 2 microns virus DNA to 21cm Drosophila largest chromosome to 16 82 cm human chromosome 0 Note Useful conversion factors 1 kb DNA 10 3 basepairs 034 x 10quoti meters Most have doublestranded DNA but some viruses X174 have single stranded DNA in the virus These DNA molecules replicate in host cells in a doublestranded replicative form RF Which gives rise to new singlestranded viral DNA that is packaged into new virus particles 0 Some DNAs are circularE coli chromosome mitochondrial DNA Fig518 plasmids some are linear T7 DNA lambda phage DNA 0 Circular DNA molecules can be supercoiled or relaxed Supercoiling is necessary for quotpackagingquot in cells Fig518 B l l A I um Definitions 1 kb kilobase of DNA or RNA 1000 bases long single or doublestranded 1 kb doublestranded DNA 034 pm long 1 kb 1 kb doublestranded DNA 660 kd Page 19 of 31 SUMMARY DNA and RNA Molecules of Heredity 1 DNARNA structures 0 Know nomenclature shorthand conventions 2 DNA and RNA as genetic material Transformation with DNA T2 DNA not Protein TMV RNA RNA to DNA Retroviruses PRIONS Proteins as transmissible agent 3 General properties of WatsonCrick DNA Double Helix Antiparallel strands Righthanded helix 10 bphelix turn 34Angstromsbp bases on inside and parallel bases perpendicular to deoxyriboseP chain Adouble bondT and Gtriple bondC base pairs 4 Basic mechanism of DNA replication 0 Semiconservative 0 DNA polymerase I templateprimer complex 0 PPi gt 2Pi pyrophosphatase drives DNA synthesis 5 Some important physicalchemical properties of DNA 0 Buoyant density proportional to GC Denaturerenature melting T proportional to GC pm to cm lengths linear circles opensupercoiled 88 DS 0 o o 0 RNA molecules usually exist as partially doublestranded structures
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