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1 Copyright © The McGraw-Hill Companies, Inc. Permission required to reproduce or display 6-1 Powerpoint to accompany Genetics: From Genes to Genomes Third Edition Hartwell ● Hood ● Goldberg ● Reynolds ● Silver ● Veres Chapter 6 Prepared by Malcolm D. Schug University of North Carolina Greensboro

2 Copyright © The McGraw-Hill Companies, Inc. Permission required to reproduce or display 6-2 DNA How the Molecule of Heredity Carries, Replicates, and Recombines Information

3 6-3 Copyright © The McGraw-Hill Companies, Inc. Permission required to reproduce or display Outline of Chapter 6 How investigators pinpointed DNA as the genetic material How investigators pinpointed DNA as the genetic material The elegant Watson-Crick model of DNA structure The elegant Watson-Crick model of DNA structure How DNA structure provides for the storage of genetic information How DNA structure provides for the storage of genetic information How DNA structure gives rise to the semiconservative model of molecular replication How DNA structure gives rise to the semiconservative model of molecular replication How DNA structure promotes the recombination of genetic information How DNA structure promotes the recombination of genetic information

4 6-4 Copyright © The McGraw-Hill Companies, Inc. Permission required to reproduce or display Chemical characterization localizes DNA in the chromosomes – Friedrich Meischer extracted a weakly acidic, phosphorous rich material from nuclei of human white blood cells which he named nuclein – Friedrich Meischer extracted a weakly acidic, phosphorous rich material from nuclei of human white blood cells which he named nuclein. DNA – deoxyribonucleic acid DNA – deoxyribonucleic acid Deoxyribose – a sugar; acidic Deoxyribose – a sugar; acidic Four subunits belonging to class of compounds called nucleotides linked together by phosphodiester bonds Four subunits belonging to class of compounds called nucleotides linked together by phosphodiester bonds Chromosomes are composed of DNA. Chromosomes are composed of DNA.

5 6-5 Copyright © The McGraw-Hill Companies, Inc. Permission required to reproduce or display The chemical composition of DNA Fig. 6.2

6 6-6 Copyright © The McGraw-Hill Companies, Inc. Permission required to reproduce or display Are genes composed of DNA or protein? DNA DNA Only four different subunits make up DNA. Only four different subunits make up DNA. Chromosomes contain less DNA than protein by weight. Chromosomes contain less DNA than protein by weight. Protein Protein 20 different subunits – greater potential variety of combinations 20 different subunits – greater potential variety of combinations Chromosomes contain more protein than DNA by weight. Chromosomes contain more protein than DNA by weight.

7 6-7 Copyright © The McGraw-Hill Companies, Inc. Permission required to reproduce or display Bacterial transformation implicates DNA as the substance of genes – Frederick Griffith – experiments with smooth (S), virulent strain Streptococcus pneumoniae, and rough (R), nonvirulent strain 1928 – Frederick Griffith – experiments with smooth (S), virulent strain Streptococcus pneumoniae, and rough (R), nonvirulent strain Bacterial transformation demonstrates transfer of genetic material. Bacterial transformation demonstrates transfer of genetic material – Oswald Avery, Colin MacLeod, and Maclyn McCarty determined that DNA is the transformation material – Oswald Avery, Colin MacLeod, and Maclyn McCarty determined that DNA is the transformation material.

8 6-8 Copyright © The McGraw-Hill Companies, Inc. Permission required to reproduce or display Griffith experiment Fig. 6.3a

9 6-9 Copyright © The McGraw-Hill Companies, Inc. Permission required to reproduce or display Griffith experiment Fig. 6.3 b

10 6-10 Copyright © The McGraw-Hill Companies, Inc. Permission required to reproduce or display Avery, MacLeod, McCarty Experiment Fig. 6.4 a

11 6-11 Copyright © The McGraw-Hill Companies, Inc. Permission required to reproduce or display Hershey and Chase experiments 1952 – Alfred Hershey and Martha Chase provide convincing evidence that DNA is genetic material – Alfred Hershey and Martha Chase provide convincing evidence that DNA is genetic material. Waring blender experiment using T2 bacteriophage and bacteria Waring blender experiment using T2 bacteriophage and bacteria Radioactive labels 32 P for DNA and 35 S for protein Radioactive labels 32 P for DNA and 35 S for protein

12 6-12 Copyright © The McGraw-Hill Companies, Inc. Permission required to reproduce or display Avery, MacLeod, McCarty experiment Fig. 6.4 c

13 6-13 Copyright © The McGraw-Hill Companies, Inc. Permission required to reproduce or display Hershey and Chase Waring blender experiment Fig. 6.5 a,b

14 6-14 Copyright © The McGraw-Hill Companies, Inc. Permission required to reproduce or display Hershey and Chase Waring blender experiment Fig. 6.5 c

15 6-15 Copyright © The McGraw-Hill Companies, Inc. Permission required to reproduce or display The Watson-Crick Model: DNA is a double helix – James Watson learns about x-ray diffraction pattern projected by DNA 1951 – James Watson learns about x-ray diffraction pattern projected by DNA Knowledge of the chemical structure of nucleotides (deoxyribose sugar, phosphate, and nitrogenous base) Knowledge of the chemical structure of nucleotides (deoxyribose sugar, phosphate, and nitrogenous base) Erwin Chargaff’s experiments demonstrate that ratios of A and T are 1:1, and G and C are 1:1. Erwin Chargaff’s experiments demonstrate that ratios of A and T are 1:1, and G and C are 1: – James Watson and Francis Crick propose their double helix model of DNA structure – James Watson and Francis Crick propose their double helix model of DNA structure.

16 6-16 Copyright © The McGraw-Hill Companies, Inc. Permission required to reproduce or display X-ray diffraction patterns produced by DNA fibers – Rosalind Franklin and Maurice Wilkins Fig. 6.6

17 6-17 Copyright © The McGraw-Hill Companies, Inc. Permission required to reproduce or display DNA’s chemical constituents 1. Deoxyribose sugar. 3. Four nitrogenous bases Purines Fig. 6.7a

18 6-18 Copyright © The McGraw-Hill Companies, Inc. Permission required to reproduce or display DNA’s chemical constituents Assembly into a nucleotide Fig. 6.7b

19 6-19 Copyright © The McGraw-Hill Companies, Inc. Permission required to reproduce or display DNA’s chemical constituents Fig. 6.7c

20 6-20 Copyright © The McGraw-Hill Companies, Inc. Permission required to reproduce or display Chargaff’s ratios

21 6-21 Copyright © The McGraw-Hill Companies, Inc. Permission required to reproduce or display Complementary base pairing by formation of hydrogen bonds explain Chargaff’s ratios. Fig. 6.8

22 6-22 Copyright © The McGraw-Hill Companies, Inc. Permission required to reproduce or display DNA is double helix DNA is double helix Strands are antiparallel with a sugar-phosphate backbone on outside and pairs of bases in the middle. Strands are antiparallel with a sugar-phosphate backbone on outside and pairs of bases in the middle. Two strands wrap around each other every 30 Angstroms, once every 10 base pairs. Two strands wrap around each other every 30 Angstroms, once every 10 base pairs. Two chains are held together by hydrogen bonds between A-T and G- C base pairs. Two chains are held together by hydrogen bonds between A-T and G- C base pairs. Fig. 6.9

23 6-23 Copyright © The McGraw-Hill Companies, Inc. Permission required to reproduce or display Structurally, purines (A and G) pair best with pyrimadines (T and C). Structurally, purines (A and G) pair best with pyrimadines (T and C). Thus, A pairs with T and G pairs with C, also explaining Chargaff’s ratios. Thus, A pairs with T and G pairs with C, also explaining Chargaff’s ratios. Fig. 6.9 d

24 6-24 Copyright © The McGraw-Hill Companies, Inc. Permission required to reproduce or display Double helix may assume alternative forms. Fig. 6.10

25 6-25 Copyright © The McGraw-Hill Companies, Inc. Permission required to reproduce or display Some DNA molecules are circular instead of linear. Some DNA molecules are circular instead of linear. 1. Prokaryotes 1. Prokaryotes 2. Mitochondria 2. Mitochondria 3. Chloroplasts 3. Chloroplasts 4. Viruses 4. Viruses Some viruses carry single-stranded DNA. 1. bacteriophages Some viruses carry RNA. 1. e.g., AIDS

26 6-26 Copyright © The McGraw-Hill Companies, Inc. Permission required to reproduce or display Four requirements for DNA to be genetic material Must carry information Must carry information Cracking the genetic code Cracking the genetic code Must replicate Must replicate DNA replication DNA replication Must allow for information to change Must allow for information to change Mutation Mutation Must govern the expression of the phenotype Must govern the expression of the phenotype Gene function Gene function

27 6-27 Copyright © The McGraw-Hill Companies, Inc. Permission required to reproduce or display Much of DNA’s sequence-specific information is accessible only when the double helix is unwound. Proteins read the DNA sequence of nucleotides as the DNA helix unwinds. Proteins can either bind to a DNA sequence, or initiate the copying of it. Human genome is believed to be 250 million nucleotides long. Four possible nucleotides. Thus 4 250,000,000 possible sequences in the human genome. An average single coding gene sequence might be about 10,000 bases long. Thus, 4 10,000 possibilities for an average gene. Some genetic information is accessible even in intact, double-stranded DNA molecules. Some proteins recognize the base sequence of DNA without unwinding it. One example is a restriction enzyme. DNA stores information in the sequence of its bases.

28 6-28 Copyright © The McGraw-Hill Companies, Inc. Permission required to reproduce or display Some viruses use RNA as the repository of genetic information. Fig. 6.13

29 6-29 Copyright © The McGraw-Hill Companies, Inc. Permission required to reproduce or display DNA replication: Copying genetic information for transmission to the next generation Complementary base pairing produces semiconservative replication. Complementary base pairing produces semiconservative replication. Double helix unwinds Double helix unwinds Each strand acts as template Each strand acts as template Complementary base pairing ensures that T signals addition of A on new strand, and G signals addition of C. Complementary base pairing ensures that T signals addition of A on new strand, and G signals addition of C. Two daughter helices produced after replication Two daughter helices produced after replication

30 6-30 Copyright © The McGraw-Hill Companies, Inc. Permission required to reproduce or display Fig. 6.14

31 6-31 Copyright © The McGraw-Hill Companies, Inc. Permission required to reproduce or display Experimental proof of semiconservative replication – three possible models Semiconservative replication – Watson and Crick model Semiconservative replication – Watson and Crick model Conservative replication: The parental double helix remains intact; both strands of the daughter double helix are newly synthesized. Conservative replication: The parental double helix remains intact; both strands of the daughter double helix are newly synthesized. Dispersive replication: At completion, both strands of both double helices contain both original and newly synthesized material. Dispersive replication: At completion, both strands of both double helices contain both original and newly synthesized material.

32 6-32 Copyright © The McGraw-Hill Companies, Inc. Permission required to reproduce or display Fig. 6.15

33 6-33 Copyright © The McGraw-Hill Companies, Inc. Permission required to reproduce or display Meselson-Stahl experiments confirm semiconservative replication. Fig. 6.16

34 6-34 Copyright © The McGraw-Hill Companies, Inc. Permission required to reproduce or display The mechanism of DNA replication Arthur Kornbuerg, a nobel prize winner and other biochemists deduced steps of replication. Arthur Kornbuerg, a nobel prize winner and other biochemists deduced steps of replication. Initiation Initiation Proteins bind to DNA and open up double helix. Proteins bind to DNA and open up double helix. Prepare DNA for complementary base pairing Prepare DNA for complementary base pairing Elongation Elongation Proteins connect the correct sequences of nucleotides into a continuous new strand of DNA. Proteins connect the correct sequences of nucleotides into a continuous new strand of DNA.

35 6-35 Copyright © The McGraw-Hill Companies, Inc. Permission required to reproduce or display Fig. 6.18a

36 6-36 Copyright © The McGraw-Hill Companies, Inc. Permission required to reproduce or display Fig. 6.18b

37 6-37 Copyright © The McGraw-Hill Companies, Inc. Permission required to reproduce or display Enzymes involved in replication Pol III – produces new stands of complementary DNA Pol III – produces new stands of complementary DNA Pol I – fills in gaps between newly synthesized Okazaki segments Pol I – fills in gaps between newly synthesized Okazaki segments DNA helicase – unwinds double helix DNA helicase – unwinds double helix Single-stranded binding proteins – keep helix open Single-stranded binding proteins – keep helix open Primase – creates RNA primers to initiate synthesis Primase – creates RNA primers to initiate synthesis Ligase – welds together Okazaki fragments Ligase – welds together Okazaki fragments

38 6-38 Copyright © The McGraw-Hill Companies, Inc. Permission required to reproduce or display Replication is bidirectional. Replication forks move in opposite directions. Replication forks move in opposite directions. In linear chromosomes, telomeres ensure the maintenance and accurate replication of chromosome ends In linear chromosomes, telomeres ensure the maintenance and accurate replication of chromosome ends In circular chromosomes, such as E. coli, there is only one origin of replication. In circular chromosomes, such as E. coli, there is only one origin of replication. In circular chromosomes, unwinding and replication causes supercoiling, which may impede replication. In circular chromosomes, unwinding and replication causes supercoiling, which may impede replication. Topoisomerase – enzyme that relaxes supercoils by nicking strands Topoisomerase – enzyme that relaxes supercoils by nicking strands

39 6-39 Copyright © The McGraw-Hill Companies, Inc. Permission required to reproduce or display The bidirectional replication of a circular chromosome Fig. 6.19a-b

40 6-40 Copyright © The McGraw-Hill Companies, Inc. Permission required to reproduce or display Fig. 6.19c-f

41 6-41 Copyright © The McGraw-Hill Companies, Inc. Permission required to reproduce or display Cells must ensure accuracy of genetic information. Redunancy Redunancy Basis for repair of errors that occur during replication or during storage Basis for repair of errors that occur during replication or during storage Enzymes repair chemical damage to DNA. Enzymes repair chemical damage to DNA. Errors during replication are rare. Errors during replication are rare.

42 6-42 Copyright © The McGraw-Hill Companies, Inc. Permission required to reproduce or display Recombination reshuffles the information content of DNA. During recombination, DNA molecules break and rejoin. During recombination, DNA molecules break and rejoin. Meselson and Weigle - Experimental evidence from viral DNA and radioactive isotopes Meselson and Weigle - Experimental evidence from viral DNA and radioactive isotopes Coinfected E. coli with light and heavy strains of virus after allowing time for recombination Coinfected E. coli with light and heavy strains of virus after allowing time for recombination Separated on a CsCl density gradient Separated on a CsCl density gradient

43 6-43 Copyright © The McGraw-Hill Companies, Inc. Permission required to reproduce or display Meselson and Weigle demonstrate recombination occurs by breakage and rejoining of DNA. Fig. 6.20

44 6-44 Copyright © The McGraw-Hill Companies, Inc. Permission required to reproduce or display Heteroduplexes mark the spot of recombination. Products of recombination are always in exact register; not a single base pair is lost or gained. Products of recombination are always in exact register; not a single base pair is lost or gained. Two strands do not break and rejoin at the same location; often they are hundreds of base pairs apart. Two strands do not break and rejoin at the same location; often they are hundreds of base pairs apart. Region between break points is called heteroduplex. Region between break points is called heteroduplex.

45 6-45 Copyright © The McGraw-Hill Companies, Inc. Permission required to reproduce or display Heteroduplex region Fig.6.21a-b

46 6-46 Copyright © The McGraw-Hill Companies, Inc. Permission required to reproduce or display In heterozygotes, mismatches within heteroduplexes must be repaired. Gene conversion – a deviation from expected 2:2 segregation of alleles due to mismatch repair. Gene conversion – a deviation from expected 2:2 segregation of alleles due to mismatch repair. Studied most extensively in yeast where tetrad analysis makes possible to follow products of meiosis Studied most extensively in yeast where tetrad analysis makes possible to follow products of meiosis

47 6-47 Copyright © The McGraw-Hill Companies, Inc. Permission required to reproduce or display Gene conversion in yeast Mismatch leads to 3:1 ratio of a:A. Ratio of B:b and C:c which lie outside of heteroduplex are both 2:2, as expected. Fig c Insert figure 6.21c Redrawn here

48 6-48 Copyright © The McGraw-Hill Companies, Inc. Permission required to reproduce or display Double stranded break model of meiotic recombination Homologs physically break, exchange parts, and rejoin. Homologs physically break, exchange parts, and rejoin. Breakage and repair create reciprocal products of recombination. Breakage and repair create reciprocal products of recombination. Recombination events can occur anywhere along the DNA molecule. Recombination events can occur anywhere along the DNA molecule. Precision in the exchange prevents mutations from occurring during the process. Precision in the exchange prevents mutations from occurring during the process. Gene conversion can give rise to unequal yield of two different alleles. 50% of gene conversions are associated with crossing over of adjacent chromosomal regions, and 50% of gene conversions are not associated with crossing over. Gene conversion can give rise to unequal yield of two different alleles. 50% of gene conversions are associated with crossing over of adjacent chromosomal regions, and 50% of gene conversions are not associated with crossing over.

49 6-49 Copyright © The McGraw-Hill Companies, Inc. Permission required to reproduce or display Double stranded break formation Spo11 protein breaks one chromatid on both strands. Fig step 1

50 6-50 Copyright © The McGraw-Hill Companies, Inc. Permission required to reproduce or display Resection 5’ ends on each side of break are degraded to produce two 3’ single stranded tails. Fig step 2

51 6-51 Copyright © The McGraw-Hill Companies, Inc. Permission required to reproduce or display First strand invasion RecA binds 3’ tail and double helix allowing invasion and migration. Fig step 3

52 6-52 Copyright © The McGraw-Hill Companies, Inc. Permission required to reproduce or display Formation of Holliday junctions New DNA synthesis forms two X structures called Holliday junctions. Fig step 4

53 6-53 Copyright © The McGraw-Hill Companies, Inc. Permission required to reproduce or display Branch migration Both invading strands zip up and migrate while newly created heteroduplex molecules rewind behind. Fig step 5

54 6-54 Copyright © The McGraw-Hill Companies, Inc. Permission required to reproduce or display The Holliday intermediate Interlocked nonsister chromatids disengage. Two resolutions are possible. Fig step 6

55 6-55 Copyright © The McGraw-Hill Companies, Inc. Permission required to reproduce or display Alternative resolutions Endonuclease cuts Holliday intermediate Fig step 7

56 6-56 Copyright © The McGraw-Hill Companies, Inc. Permission required to reproduce or display Probability of crossover occurring Resolution of Holliday junction in same plan results in noncrossover chromatids. Resolution in different planes results in crossover. Fig step 8 Insert figure 6.23 Step 8 Redrawn here

57 6-57 Copyright © The McGraw-Hill Companies, Inc. Permission required to reproduce or display Essential Concepts DNA is the nearly universal genetic material. DNA is the nearly universal genetic material. The Watson-Crick model shows that DNA is a double helix composed of two antiparallel strands of nucleotides: each nucleotide consists of one of four nitrogenous bases (A,T,C, or G), a deoxyribose sugar, and a phosphate. An A pairs with a T and a G pairs with a C. The Watson-Crick model shows that DNA is a double helix composed of two antiparallel strands of nucleotides: each nucleotide consists of one of four nitrogenous bases (A,T,C, or G), a deoxyribose sugar, and a phosphate. An A pairs with a T and a G pairs with a C. DNA carries information in the sequence of its bases, which may follow one another in any order. DNA carries information in the sequence of its bases, which may follow one another in any order.


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