Chapter 15- DNA and the Gene: Synthesis and Repair

15.1 What Are Genes Made Of?

• During the infection, the exterior protein coat, or capsid, of the virus is left behind on the exterior of the host cell 
• ==Each deoxyribonucleotide consists of a deoxyribose sugar, a phosphate group, and a nitrogenous base==
• Deoxyribonucleotides link together into a polymer when a hydroxyl group on the 3' carbon of one deoxyribose and the phosphate group attached to the 5’ carbon of another deoxyribose are joined by a covalent bond called a phosphodiester linkage, or phosphodiester bond
• Watson and Crick realized that these antiparallel strands will twist around each other into a double-stranded spiral-or double helix-and that only certain bases fit together snugly in pairs within the helix by complementary base pairing.
• The double-helical DNA molecule is stabilized in two ways: 
  • complementary base pairing
  • interactions between the stacked base pairs inside the helix.

15.2 Testing Early Hypotheses about DNA Synthesis

• Alternative hypotheses about DNA replication include: 
  • Semiconservative replication: If the parental strands of DNA separated, each one could then be used as a template for the synthesis of a new daughter strand. 
  • Conservative replication: If the bases of both strands temporarily turned out from the helix, they could serve as a template for the synthesis of an entirely new double helix all at once. 
  • Dispersive replication This proposed that the parental double helix was fragmented into small pieces before replication and then each piece was replicated by either a conservative or semi conservative mechanism.
• Like all organisms, bacterial cells copy their entire complement of DNA，their genome, before every cell division. 

15.3 A Model for DNA Synthesis 

• The initial breakthrough on DNA replication came with discovery of an enzyme called DNA polymerase.
• The potential energy of the deoxyribonucleotide monomers is first raised by reactions that add two phosphate groups to form deoxyribonucleoside triphosphates (dNTPs). 
• Initially, the replication bubble forms at a specific sequence of bases called the origin of replication
• A replication fork is the Y-shaped region where the parental DNA double helix is separated into single strands and copied.
• Single-strand DNA-binding proteins (SSBPs) attach to the separated strands to prevent them from snapping back into a double helix 
• A topoisomerase is an enzyme that cuts DNA, allows it to unwind, and rejoins it. 
• A short strand of RNA called a primer that is base-paired to 1e DNA template
• The other strand, appropriately called the lagging strand, or discontinuous strand, must be synthesized in a direction αwαy from the moving replication fork.
• These short DNAs, which were attached to RNA primers came to be known as Okazaki fragments 
• Once the RNA primer is removed and replaced by DNA, an enzyme called DNA ligase catalyzes the formation of a phosphodiester bond between the 3’ and 5’ ends of adjacent Okazaki fragments, closing up the backbone
• The proteins and enzymes work together in a large macromolecular machine called the replisome

15.4 Replicating the Ends of Linear Chromosomes

• The region at the end of a eukaryotic chromosome is called a telomere
• An enzyme called telomerase replicates telomeric DNA. ==Telomerase catalyzes the synthesis of DNA using an RNA template that is an integral part of the enzyme.==
• Any cell not involved in gamete formation is a somatic cell. 

15.5 Repairing Mistakes and DNA Damage

• The ability of DNA polymerase to recognize and remove an incorrect deoxyribonucleotide is called proofreading. 
• Mismatch repair is a form of error correction that cleans up errors introduced during DNA synthesis
• ==Mismatch repair is the final layer of error detection and correction for errors introduced during DNA synthesis.==
• Xeroderma pigmentosum (XP) is a rare autosomal recessive disease in humans.

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