Chapter 16 The Molecular Basis of Inheritance Points

Chapter 16: The Molecular Basis of Inheritance Points of Emphasis Know: 1. all the bold-faced terms 2. Know the researchers and what experiments they did and what their experiments demonstrated (proved/revealed) 3. Know the process of DNA replication including all the enzymes. 4. Be sure to understand the difference between the terms, leading and lagging strand. 1

Figure 16. 0 Watson and Crick 2

Figure 16. 1 Transformation of bacteria Griffith’s work with transforming bacteria His work showed that “molecules” from the dead cells had converted or transformed the R or nonpathogenic bacteria into S (pathogenic) bacteria 3

Figure 16. 2 a The Hershey-Chase experiment: phages 4

Figure 16. 2 ax Phages Cell infected by phages (viruses that infect bacteria) H & C labeled one group of phage’s proteins with radioactive S, another group with radioactive P of their DNA. 5

Figure 16. 2 b The Hershey-Chase experiment 6

Figure 16. 3 The structure of a DNA stand Chargaff: it was already known of what DNA was composed and when Chargaff analyzed DNA for its base composition he found that no matter what organism the %A’s = %T’s and %C’s = %G’s. These percentages were different in different organisms however. 7

Figure 16. 4 Rosalind Franklin and her X-ray diffraction photo of DNA It was the pattern that RF discovered that indicated to Watson that DNA was helical and some of its dimensions, indicating that DNA was a double helix. 8

Figure 16. 5 The double helix The uniform diameter of RF’s X-ray indicated to Watson that A did not bind with A 9 because they both were 2 -ringed structures and C and T were 3 -ringed so the diameter would not be uniform.

Unnumbered Figure (page 292) Purine and pyridimine 10

Figure 16. 6 Base pairing in DNA 11

Figure 16. 7 A model for DNA replication: the basic concept (Layer 1) 12

Figure 16. 7 A model for DNA replication: the basic concept (Layer 2) 13

Figure 16. 7 A model for DNA replication: the basic concept (Layer 3) 14

Figure 16. 7 A model for DNA replication: the basic concept (Layer 4) 15

Figure 16. 8 Three alternative models of DNA replication 16

Figure 16. 9 The Meselson-Stahl experiment tested three models of DNA replication (Layer 4) 17

Figure 16. 10 Origins of replication in eukaryotes 18

Figure 16. 11 Incorporation of a nucleotide into a DNA strand DNA Polymerase 19

Figure 16. 12 The two strands of DNA are antiparallel 20

Figure 16. 13 Synthesis of leading and lagging strands during DNA replication The addition of the new nucleotides starts with the construction or presence of an RNA primer. This RNA primer is made by primase. DNA polymerase later removes the RNA primer and replaces it with nucleotides. Topoisomerase 21

Figure 16. 14 Priming DNA synthesis with RNA 22

Figure 16. 15 The main proteins of DNA replication and their functions 23

Figure 16. 16 A summary of DNA replication 24

Figure 16. 17 Nucleotide excision repair of DNA damage 25

Figure 16. 18 The end-replication problem 26

Figure 16. 19 a Telomeres and telomerase: Telomeres of mouse chromosomes 27

Figure 16. 19 b Telomeres and telomerase Telomerase has some RNA along with its enzyme action; this serves as a template Telomerase is not present in most cells and the ends of our somatic cell’s chromosomes do shorten. In gametes, telomerase produces long telomeres. 28

Quick Comments About DNA Replication 1. DNA polymerase will only add bases to a template strand, therefore the template strand controls which of the four deoxyribonucleotides (A, C, G or T) will be added. 2. The addition of the new bases is due to a large favorable free energy change caused by the release of pyrophosphate and its hydrolysis to two free inorganic phosphate groups. 3. At the replication fork, DNA of both new daughter strands is synthesized by a multienzyme complex that contains the DNA polymerase. 29

4. No 3’ – 5’ DNA polymerase has ever been found. 5. The Okazaki fragments are 1000 – 2000 nucleotides long in bacteria and 100 – 200 nucleotides in length in eukaryotes. 6. The synthesis of the leading strand slightly proceeds the lagging strand. 7. The synthesis of the lagging strand is delayed because it must wait for the leading strand to expose the template strand on which each Okazaki fragment is synthesized. 8. 1 mistake is made for every 1 billion nucleotides copied. 9. It is possible for a mismatch to occur where A bonds to C instead of G without affecting the helix geometry. 30

10. In the first step of proofreading by DNA polymerase, the moving DNA polymerase has a higher affinity for the correct nucleotide than an incorrect one because only the correct one can base pair with the template. 11. After nucleotide binding, but before the nucleotide is covalently bonded to the chain, the enzyme undergoes a conformational change and incorrectly bound nucleotide is more likely to dissociate during this step than a correct one. 12. When an incorrect nucleotide is located, a different part of the DNA polymerase will clip it off. 13. An RNA primer is preferred to a DNA primer because the DNA polymerase makes an error about 1 x 105. (There are other processes where errors can occur totaling the earlier mentioned 1 out of 1 billion). This would allow for errors in about 5% of the total genome and this mutation rate would be enormous. 31

14. There really are two DNA helicases, one working on the leading strand one on the lagging strand. 15. DNA polymerase will synthesize only a short string of nucleotides before falling off of the DNA. This allows quick recycling for synthesizing the Okazaki fragments. 16. This rapid falling off is not productive on the leading strand there is a molecular “clamp” that keeps the polymerase firming on the DNA when it is moving but releases as soon as the polymerase encounters a double-stranded region of DNA ahead. 17. On the leading strand, the moving DNA polymerase is tightly bound to the clamp; on the lagging strand, each time the polymerase reaches a 5’end of the preceding Okazaki fragment, the polymerase is released. 32

18. There is also a strand-directed mismatch repair system. This detects distortions in the DNA helix due to the misfit between noncomplementary bases. This makes errors about 1 out of 100 times. This system can identify the mismatch on the newly synthesized strand. In bacteria, the parent strand is methylated and the new bases or unmethylated and can be recognized. In eukaryotic cells, newly synthesized strands are nicked or have single-stranded breaks that is a signal for the proofreading system. 19. A mismatch repair gene can be defective and has been associated with a type of colon cancer, hereditary nonpolyposis colon cancer. 20. There really are two topoisomerases; one nicks one of the two DNA strands, another cuts both strands. 33

21. Prokaryotes have a single origin of replication. Their circular piece of DNA is much smaller than eukaryotes (E. coli is 4. 6 x 106 base pairs); replicates at about 500 – 1000 nucleotides per second. 22. Eukaryotic chromosomes are much larger; new bases are added on at a rate of about 50 nucleotides per second and with an average human chromosome containing about 150 million nucleotide pairs, it would take about 800 hours if a different strategy did not evolve. Hence the presence of multiple replication forks. 23. In eukaryotes, replication origins are activated in clusters called replication units (20 -80 origins). Within a unit the individual origins are spaced at intervals of 30, 000 to 300, 000 nucleotide pairs from one another. 24. That’s enough isn’t it? ? ? 34