Review: Chapter 14 - DNA and the Gene: Synthesis and Repair DNA, not protein, is the hereditary material.I. The primary and the secondary structures of DNA 1. DNA’s primary structure: a long, linear polymer made up of nucleotides. Each nucleotide consists of a deoxyribose sugar, a negative phosphate, and a nitrogenous base. Nucleotides are linked together with phosphodiester bonds.  A sugar-phosphate backbone written from 5’  3’2. DNA’s secondary structure: two antiparallel strands H-bound together at the nitrogenous bases. The two strands twist around each other to form a double helix. The secondary structure is stabilized by hydrogen bonds between complementary base pairs. Adenine always pairs with thymine. Guanine always pairs with cytosine. %T=%A %G=%C Purines and pyrimidines?II. Testing Early Hypotheses about DNA Synthesis: The Meselson −Stahl Experiment Semiconservative replication model The two original DNA strands separate, each serving as a template for a new strand.  Correct model. Each new daughter DNA molecule consist of one parent and one new strand. [Experiments showed that both, Conservative replication model and Dispersive replication model  not correct]III. A Comprehensive Model for DNA Synthesis (Table 14.1) A. The enzyme, DNA polymerase III catalyzes DNA synthesis. It is a template dependent enzyme. Requires a primer? DNA polymerases add dNTPs only to the 3' end of a growing DNA strand. DNA synthesis always proceeds in the 5' → 3' direction. B. How does replication get started? Electron micrographs show that DNA replication is bidirectional. a. Replication is initiated at an origin of replication, forming areplication bubble. - Bacterial chromosomes have a single origin of replication. - Eukaryotic chromosomes have multiple origins. b. Replication proceeds in both directions at the same time. Each side of the bubble forms a Y-shaped replication fork (Two replication forks per origin). C. How is the helix opened and stabilized? 1. Helicases open the replication fork by breaking hydrogen bonds between DNA strands, thus producing single strands. 2. Single-stranded binding proteins stabilize single strands. 3. Topoisomerases relieve tension (unwinding) in the DNA molecule. Topoisomerases nick the DNA downstream and allow it to untwist. D. How is the leading strand synthesized? 1. Primase, an RNA polymerase, builds a short RNA primer that is complementary to the parent strand. 2. DNA polymerase III adds dNTPs to the 3' end of the primer, moving into the replication fork that is unzipping ahead of it.1- DNA polymerase can add dNTPs only to an existing −OH group. - The primer provides an −OH group to which DNA polymerase can add the first dNTP. 3. Behind DNA polymerase III, a doughnut-shaped structure called the sliding clamp holds the newly synthesized strand in place. 4. This process occurs continuously (without interruption) on the leading strand. You should be able to list the enzymes involved and, for each one, predict the consequences if it were defective………E. How is the lagging strand synthesized?i. The other parent strand is antiparallel to the leading strand, so afterprimase adds a primer, DNA polymerase III must work away from the replication fork on this strand, called the lagging strand. ii. When helicase expands the replication fork, a new segment of parent strand is exposed.- A new primer must be made to initiate replication in this section.- This results in discontinuous replication on the lagging strand. iii. Okazaki tested this hypothesis in a pulse-chase experiment. Conclusion: The lagging strand is synthesized in short, discontinuous fragments (“Okazaki fragments”). iv. Removing the primers and joining the fragments a. DNA polymerase I removes the primers at the start of each fragment. b. DNA ligase catalyzes the formation of a phosphodiester bond between the 3'–OH of one fragment and the 5'–P of the next fragment  “seal” the gap v. The enzymes required for DNA synthesis are organized into the replisome. Can you label the components in a repliosome? IV. Replicating the Ends of Linear Chromosomes – Telomeres?A. The telomere is the region at the end of a linear eukaryotic chromosome. B. Telomere replication problem (Fig. 14.12) 1. Replication of the leading strand can proceed to the end of the chromosome. 2. Replication of the lagging strand cannot proceed to the end of the chromosome. WHY?C. How do eukaryotic cells protect the integrity of their chromosomes? Telomerase enzymes can replicate telomeres. Telomerase is an enzyme that carries an RNA template. This allows the normal replication machinery to come in and replicate the lengthened telomere. -Telomeres in somatic cells actually do degrade over successive replications. Telomere shortening may eventually cause cells to stop dividing altogether. Cancer cells may have functioning telomerases or some other way to maintain telomere length. V. Repairing Mistakes and Damage  Proofreading, Mismatch repair, and Nucleotide excision repair.A. Correcting mistakes in DNA synthesis. DNA replication must be extremely accurate because mistakes would accumulate during development and could be passed on to the next generation. Mutations? DNA polymerase can proofread. Polymerase III checks nucleotides after they are added to the new strand (during replication).  Polymerase III has a proofreading function. 2B. Mismatch repair  Soon after DNA replication is completed, other DNA repair systems correct most remaining mismatches within several minutes. Mismatch repair enzymes were discovered in E. coli mutants. The enzyme functions like a copy editor who corrects typos. C. Even after replication, DNA bases can become damaged by chemicals and environmental elements (mutagens) Induced mutations. Cells fix damaged nucleotides by cutting them out and replacing them with undamaged nucleotides; the system is called nucleotide excision repair. Enzymes find damaged nucleotides by identifying irregularities in DNA’s secondary structure. Enzymes remove single-stranded DNA around the damage. DNA synthesis machinery replaces the excised nucleotides. T=T dimmers? Genetic disease: Xeroderma pigmentosum?If the overall mutation rate in a cell is elevated because of defects in DNA repair genes, then the mutations that trigger cancer become more