DNA: The Genetic Material. Chapter 14

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1 DNA: The Genetic Material hapter 14 1

2 Frederick Griffith 1928 Studied Streptococcus pneumoniae, a pathogenic bacterium causing pneumonia 2 strains of Streptococcus S strain is virulent R strain is nonvirulent Griffith infected mice with these strains hoping to understand the difference between the strains 2

3 Griffith s results Live S strain cells killed the mice Live R strain cells did not kill the mice Heat-killed S strain cells did not kill the mice Heat-killed S strain + live R strain cells killed the mice 3

4 opyright The McGraw-Hill ompanies, Inc. Permission required for reproduction or display. Live Virulent Strain of S. pneumoniae Live Nonvirulent Strain of S. pneumoniae Polysaccharide coat Mice die Mice live a. b. 4

5 opyright The McGraw-Hill ompanies, Inc. Permission required for reproduction or display. Heat-killed Virulent Strain of S. pneumoniae Mixture of Heat-killed Virulent and Live Nonvirulent Strains of S. pneumoniae + c. Mice live d. Mice die Their lungs contain live pathogenic strain of S. pneumoniae 5

6 Transformation Information specifying virulence passed from the dead S strain cells into the live R strain cells ur modern interpretation is that genetic material was actually transferred between the cells 6

7 Avery, MacLeod, & Mcarty 1944 Repeated Griffith s experiment using purified cell extracts Removal of all protein from the transforming material did not destroy its ability to transform R strain cells DNA-digesting enzymes destroyed all transforming ability Supported DNA as the genetic material 7

8 Hershey & hase 1952 Investigated bacteriophages Viruses that infect bacteria Bacteriophage was composed of only DNA and protein Wanted to determine which of these molecules is the genetic material that is injected into the bacteria 8

9 Bacteriophage DNA was labeled with radioactive phosphorus ( 32 P) Bacteriophage protein was labeled with radioactive sulfur ( 35 S) Radioactive molecules were tracked nly the bacteriophage DNA (as indicated by the 32 P) entered the bacteria and was used to produce more bacteriophage onclusion: DNA is the genetic material 9

10 opyright The McGraw-Hill ompanies, Inc. Permission required for reproduction or display. 35 S-Labeled Bacteriophages + Phage grown in radioactive 35 S, which is incorporated into phage coat Virus infect bacteria Blender separates phage coat from bacteria entrifuge forms bacterial pellet 35 S in supernatant 32 P-Labeled Bacteriophages + Phage grown in radioactive 32 P. which is incorporated into phage DNA Virus infect bacteria Blender separates phage coat from bacteria entrifuge forms bacterial pellet 32 P in bacteria pellet 10

11 DNA Structure DNA is a nucleic acid omposed of nucleotides 5-carbon sugar called deoxyribose Phosphate group (P 4 ) Attached to 5 carbon of sugar Nitrogenous base Adenine, thymine, cytosine, guanine Free hydroxyl group ( H) Attached at the 3 carbon of sugar 11

12 Pyrimidines Purines opyright The McGraw-Hill ompanies, Inc. Permission required for reproduction or display. Phosphate group P 5 H 2 8 Nitrogenous base N N 4 NH 2 N H NH 2 N N N N H Adenine H Nitrogenous Base N N H N N H Guanine H NH 2 NH H N H 3 N H H N H 3 2 H Sugar H in RNA H in DNA H N H ytosine (both DNA and RNA) H N H Thymine (DNA only) H N H Uracil (RNA only) 12

13 Phosphodiester bond Bond between adjacent nucleotides Formed between the phosphate group of one nucleotide and the 3 H of the next nucleotide The chain of nucleotides has a 5 - to-3 orientation opyright The McGraw-Hill ompanies, Inc. Permission required for reproduction or display. Phosphodiester bond P 4 H 2 5 P H 2 Base Base H 3 13

14 hargaff s Rules Erwin hargaff determined that Amount of adenine = amount of thymine Amount of cytosine = amount of guanine Always an equal proportion of purines (A and G) and pyrimidines ( and T) 14

15 opyright The McGraw-Hill ompanies, Inc. Permission required for reproduction or display. Rosalind Franklin Performed X-ray diffraction studies to identify the 3-D structure Discovered that DNA is helical Using Maurice Wilkins DNA fibers, discovered that the molecule has a diameter of 2 nm and makes a complete turn of the helix every 3.4 nm a. b. ourtesy of old Spring Harbor Laboratory Archives 15

16 James Watson and Francis rick 1953 Deduced the structure of DNA using evidence from hargaff, Franklin, and others Did not perform a single experiment themselves related to DNA Proposed a double helix structure 16

17 Double helix opyright The McGraw-Hill ompanies, Inc. Permission required for reproduction or display. 5 P Phosphate group Phosphodiester bond 3 2 P strands are polymers of nucleotides Phosphodiester backbone repeating sugar and phosphate units joined by phosphodiester bonds P carbon sugar Nitrogenous base Wrap around 1 axis Antiparallel P H

18 opyright The McGraw-Hill ompanies, Inc. Permission required for reproduction or display. 2nm 5 3 T A G 3.4nm Minor groove T G A T 0.34nm G Major groove G A T G Major groove Minor groove

19 omplementarity of bases A forms 2 hydrogen bonds with T G forms 3 hydrogen bonds with Gives consistent diameter opyright The McGraw-Hill ompanies, Inc. Permission required for reproduction or display. H Sugar H Sugar N N N G N A N H N N H H Hydrogen bond N H N H N N N H H H N Hydrogen bond H T N Sugar H 3 N H H H Sugar 19

20 DNA Replication 3 possible models 1. onservative model 2. Semiconservative model 3. Dispersive model 20

21 opyright The McGraw-Hill ompanies, Inc. Permission required for reproduction or display. onservative 21

22 opyright The McGraw-Hill ompanies, Inc. Permission required for reproduction or display. onservative Semiconservative 22

23 opyright The McGraw-Hill ompanies, Inc. Permission required for reproduction or display. onservative Semiconservative Dispersive 23

24 Meselson and Stahl 1958 Bacterial cells were grown in a heavy isotope of nitrogen, 15 N All the DNA incorporated 15 N ells were switched to media containing lighter 14 N DNA was extracted from the cells at various time intervals 24

25 Meselson and Stahl s Results onservative model = rejected 2 densities were not observed after round 1 Semiconservative model = supported onsistent with all observations 1 band after round 1 2 bands after round 2 Dispersive model = rejected 1 st round results consistent 2 nd round did not observe 1 band 25

26 opyright The McGraw-Hill ompanies, Inc. Permission required for reproduction or display. DNA E. coli 15 N medium E. coli cells grown in 15 N medium 14 N medium ells shifted to 14 N medium and allowed to grow 0 min 0 rounds 20 min 1 round Samples taken at three time points and suspended in cesium chloride solution 40 min 2 rounds Samples are centrifuged 0 rounds 1 round 2 rounds Top Bottom Rounds of replication From M. Meselson and F.W. Stahl/PNAS 44(1958):671 26

27 DNA Replication Requires 3 things Something to copy Parental DNA molecule Something to do the copying Enzymes Building blocks to make copy Nucleotide triphosphates 27

28 DNA replication includes Initiation replication begins Elongation new strands of DNA are synthesized by DNA polymerase Termination replication is terminated 28

29 opyright The McGraw-Hill ompanies, Inc. Permission required for reproduction or display. Template Strand New Strand Template Strand New Strand H 3 5 H 3 5 Sugar phosphate backbone P T A G P P P T A G P P P P P A T P DNA polymerase III P A T P P G P P G P P P 5 A A T 3 H H P P P P P 5 A A T 3 P H P P Pyrophosphate 29

30 5 opyright The McGraw-Hill ompanies, Inc. Permission required for reproduction or display RNA polymerase makes primer DNA polymerase extends primer DNA polymerase Matches existing DNA bases with complementary nucleotides and links them All have several common features Add new bases to 3 end of existing strands Synthesize in 5 -to-3 direction Require a primer of RNA 30

31 Prokaryotic Replication E. coli model Single circular molecule of DNA Replication begins at one origin of replication Proceeds in both directions around the chromosome Replicon DNA controlled by an origin 31

32 opyright The McGraw-Hill ompanies, Inc. Permission required for reproduction or display. rigin Termination Termination Replisome Replisome rigin Termination Termination rigin Termination rigin rigin 32

33 E. coli has 3 DNA polymerases DNA polymerase I (pol I) Acts on lagging strand to remove primers and replace them with DNA DNA polymerase II (pol II) Involved in DNA repair processes DNA polymerase III (pol III) Main replication enzyme All 3 have 3 -to-5 exonuclease activity proofreading DNA pol I has 5 -to-3 exonuclase activity 33

34 opyright The McGraw-Hill ompanies, Inc. Permission required for reproduction or display. Replisomes Supercoiling Replisomes No Supercoiling DNA gyrase Unwinding DNA causes torsional strain Helicases use energy from ATP to unwind DNA Single-strand-binding proteins (SSBs) coat strands to keep them apart Topoisomerase prevent supercoiling DNA gyrase is used in replication 34

35 Semidiscontinous DNA polymerase can synthesize only in 1 direction Leading strand synthesized continuously from an initial primer Lagging strand synthesized discontinuously with multiple priming events kazaki fragments 35

36 opyright The McGraw-Hill ompanies, Inc. Permission required for reproduction or display First RNA primer Lagging strand (discontinuous) pen helix and replicate 3 pen helix and replicate further Second RNA primer RNA primer 5 3 Leading strand (continuous) RNA primer

37 Partial opening of helix forms replication fork DNA primase RNA polymerase that makes RNA primer RNA will be removed and replaced with DNA 37

38 Leading-strand synthesis Single priming event Strand extended by DNA pol III Processivity subunit forms sliding clamp to keep it attached opyright The McGraw-Hill ompanies, Inc. Permission required for reproduction or display. a. b. a-b: From Biochemistry by Stryer. 1975, 1981, 1988, 1995 by Lupert Stryer. Used with permission of W.H. Freeman and ompany 38

39 Lagging-strand synthesis Discontinuous synthesis DNA pol III RNA primer made by primase for each kazaki fragment All RNA primers removed and replaced by DNA DNA pol I Backbone sealed DNA ligase Termination occurs at specific site DNA gyrase unlinks 2 copies 39

40 5 opyright The McGraw-Hill ompanies, Inc. Permission required for reproduction or display. DNA ligase Lagging strand (discontinuous) RNA primer DNA polymerase I kazaki fragment made by DNA polymerase III Leading strand (continuous) Primase 3 40

41 Replisome Enzymes involved in DNA replication form a macromolecular assembly 2 main components Primosome Primase, helicase, accessory proteins omplex of 2 DNA pol III ne for each strand 41

42 Replication fork opyright The McGraw-Hill ompanies, Inc. Permission required for reproduction or display. New bases β clamp (sliding clamp) Leading strand Single-strand binding proteins (SSB) DNA gyrase lamp loader pen β clamp Parent DNA Helicase Primase DNA polymerase III Lagging strand kazaki fragment New bases DNA polymerase I 3 5 DNA ligase RNA primer 42

43 opyright The McGraw-Hill ompanies, Inc. Permission required for reproduction or display. 5 3 Helicase DNA gyrase RNA primer DNA polymerase III lamp loader Leading strand RNA primer First kazaki fragment 5 3 Primase Single-strand binding proteins (SSB) β clamp Lagging strand RNA primer 5 3 Loop grows Second kazaki fragment nears completion A DNA polymerase III enzyme is active on each strand. Primase synthesizes new primers for the lagging strand. 2. The loop in the lagging-strand template allows replication to occur 5 -to- 3 on both strands, with the complex moving to the left DNA polymerase III DNA polymerase I Lagging strand releases 5 3 β clamp releases 3. When the polymerase III on the lagging strand hits the previously synthesized fragment, it releases the β clamp and the template strand. DNA polymerase I attaches to remove the primer. 43

44 opyright The McGraw-Hill ompanies, Inc. Permission required for reproduction or display lamp loader DNA polymerase I detaches after removing RNA primer DNA ligase patches nick 4. The clamp loader attaches the β clamp and transfers this to polymerase III, creating a new loop in the lagging-strand template. DNA ligase joins the fragments after DNA polymerase I removes the primers Loop grows New bases Leading strand replicates continuously 5. After the β clamp is loaded, the DNA polymerase III on the lagging strand adds bases to the next kazaki fragment

45 45

46 Eukaryotic Replication omplicated by Larger amount of DNA in multiple chromosomes Linear structure Basic enzymology is similar Requires new enzymatic activity for dealing with ends only 46

47 Multiple replicons multiple origins of replications for each chromosome Not sequence specific; can be adjusted Initiation phase of replication requires more factors to assemble both helicase and primase complexes onto the template, then load the polymerase with its sliding clamp unit Primase includes both DNA and RNA polymerase Main replication polymerase is a complex of DNA polymerase epsilon (pol ε) and DNA polymerase delta (pol δ) 47

48 Telomeres Specialized structures found on the ends of eukaryotic chromosomes Protect ends of chromosomes from nucleases and maintain the integrity of linear chromosomes Gradual shortening of chromosomes with each round of cell division Unable to replicate last section of lagging strand 48

49 Replication first round opyright The McGraw-Hill ompanies, Inc. Permission required for reproduction or display. Leading strand (no problem) Lagging strand (problem at the end) Last primer rigin Leading strand Lagging strand Primer removal Replication second round Removed primer cannot be replaced Shortened template 5 49

50 Telomeres composed of short repeated sequences of DNA Telomerase enzyme makes telomere section of lagging strand using an internal RNA template (not the DNA itself) Leading strand can be replicated to the end Telomerase developmentally regulated Relationship between senescence and telomere length ancer cells generally show activation of telomerase 50

51 opyright The McGraw-Hill ompanies, Inc. Permission required for reproduction or display. 5 T T G 3 Synthesis by telomerase Telomerase 5 3 T A T A G G G G A A Telomere extended by telomerase Template RNA is part of enzyme Telomerase moves and continues to extend telomere 5 T T G G G G T T G 3 Now ready to synthesize next repeat A A A A 51

52 DNA Repair Errors due to replication DNA polymerases have proofreading ability Mutagens any agent that increases the number of mutations above background level Radiation and chemicals Importance of DNA repair is indicated by the multiplicity of repair systems that have been discovered 52

53 DNA Repair Falls into 2 general categories 1. Specific repair Targets a single kind of lesion in DNA and repairs only that damage 2. Nonspecific Use a single mechanism to repair multiple kinds of lesions in DNA 53

54 Photorepair Specific repair mechanism For one particular form of damage caused by UV light Thymine dimers ovalent link of adjacent thymine bases in DNA Photolyase Absorbs light in visible range Uses this energy to cleave thymine dimer 54

55 opyright The McGraw-Hill ompanies, Inc. Permission required for reproduction or display. DNA with adjacent thymines T A T A UV light Helix distorted by thymine dimer Thymine dimer A A Photolyase binds to damaged DNA Photolyase A A Visible light Thymine dimer cleaved T A T A 55

56 Excision repair Nonspecific repair Damaged region is removed and replaced by DNA synthesis 3 steps 1. Recognition of damage 2. Removal of the damaged region 3. Resynthesis using the information on the undamaged strand as a template 56

57 opyright The McGraw-Hill ompanies, Inc. Permission required for reproduction or display. Damaged or incorrect base Excision repair enzymes recognize damaged DNA Uvr A,B, complex binds damaged DNA Excision of damaged strand Resynthesis by DNA polymerase DNA polymerase 57

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