1. NOTES: CH 16 (part 2) – DNA Replication and Repair

2. ● During DNA replication, base-pairing enables existing (“parental”) DNA strands to serve as templates for new (“daughter”) complementary strands

3. ● Watson and Crick proposed that during DNA replication: 1) the 2 DNA strands separate; 2) each strand is a template for assembling a complementary strand; 3) nucleotides line up singly along the template strand (A-T, G-C); 4) ENZYMES link the nucleotides together at their sugar-phosphate groups.

4. ● Watson and Crick’s proposed model is a SEMICONSERVATIVE model (each of the 2 daughter molecules will have 1 old or CONSERVED strand from the parent molecule and 1 newly created strand)

6. ● DNA replication begins at special sites called ORIGINS OF REPLICATION. -DNA double helix opens at the origin & replication “forks” spread in both directions away from the central initiation site creating a REPLICATION BUBBLE. -100’s to 1000’s of replication origins form in eukaryotic chromosomes, which eventually fuse forming 2 continuous DNA molecules

9. “Unzipping” the parent DNA strands: ● 2 types of proteins involved with separation of parental DNA strands: *HELICASES: enzymes that catalyze the unwinding of parental DNA double helix to expose template *single-strand binding proteins: keep the separated strands apart & stabilize unwound DNA until new strands can be made

12. Elongating the new DNA strands: -new nucleotides align themselves along templates of old DNA strands according to base-pairing rules (A-T, G-C)

13. DNA polymerases catalyze synthesis of new DNA strand: -DNA polymerases link the nucleotides to growing strand. -new strands grow in the 5’ to 3’ direction; new nucleotides are added only to the 3’ end of the growing strand

15. ● Nucleoside triphosphates (nucleotides with 3 phosphate groups linked to the 5’ carbon of the sugar) provides energy for DNA synthesis: -nucleoside triphosphate loses 2 phosphates -exergonic hydrolysis of these phosphate bonds drives the endergonic synthesis of DNA; it provides the energy to form new covalent linkages between nucleotides What is the source of energy that drives the synthesis of the new DNA strands?

18. Now, back to… DNA polymerase can only add on the 3' end!

19. *RECALL: DNA strands run in opposite directions; DNA polymerase can elongate strands only in the 5’ to 3’ direction

20. ● this problem is solved by continuous synthesis of 1 strand (LEADING STRAND) and…discontinuous synthesis of the complementary strand (LAGGING STRAND)

21. ● the LAGGING STRAND is produced as a series of short fragments (“Okazaki” fragments) which are synthesized in the 5’ to 3’ direction and then linked together by the enzyme DNA ligase.

25. ● Before new DNA strands can form, there must be small pre-existing PRIMERS to start the addition of new nucleotides -a primer is a short RNA segment that is complementary to a DNA segment -primers are polymerized by primase enzyme

27. *only 1 primer is necessary for replication of the leading strand, but many primers are necessary to replicate the lagging strand *an RNA primer must initiate the synthesis of each Okazaki fragment! *DNA polymerase removes the RNA primer and replaces it with DNA nucleotides

28. Hydrogen Bonds Breaking!

30. Enzymes proofread DNA during its replication and repair damage to existing DNA

31.  MISMATCH REPAIR: corrects mistakes (mismatched bases) that occur when DNA is being copied *one form of colon cancer is due to a defect in one of the proteins involved in this type of DNA repair

32.  NUCLEOTIDE EXCISION REPAIR: corrects accidental changes that occur in existing DNA -an enzyme (nuclease) cuts out damaged segment of DNA -the enzymes DNA polymerase and ligase fill in the resulting gaps *xeroderma pigmentosum is caused by an inherited defect in an excision-repair enzyme

33. What about the 5’ ends of long DNA molecules?  DNA polymerase can only add nucleotides to the 3’ end of a preexisting polynucleotide…  The usual replication machinery provides no way to complete the 5’ ends of daughter DNA strands;  As a result, repeated rounds of replication produce shorter and shorter DNA molecules

34. Solutions to the problem:  Prokaryotes avoid this problem by having circular DNA molecules…but what about eukaryotes?  The answer is…TELOMERES!

35. TELOMERES:  special nucleotide sequences at the end of eukaryotic chromosomal DNA molecules;  do not contain genes;  contain multiple repetitions of one short nucleotide sequence  example: in humans, TTAGGG.  # of repeats varies between 100 and 1,000.

37. TELOMERES:  expendable, noncoding sequences;  they protect an organism’s genes from being eroded through successive rounds of DNA replication.  a special enzyme, TELOMERASE, catalyzes the lengthening of telomeres

39. Things that make you go hmmmm…  telomerase is NOT present in most cells of multicellular organisms (like ourselves!)…this means  the DNA of dividing somatic cells tends to be shorter in older individuals (older tissues / cells);  thus, telomeres may be a limiting factor in the life span of certain tissues and even the organism as a whole…  telomerase has been found, however, in somatic cells that are cancerous!

41. A note about chromatin packing…