Chapter 15 DNA and the Gene Synthesis and Repair 15 1 What Are Genes Made Of Chromosomes are a complex of protein and DNA The Hershey Chase Experiment Secondary structure consists of antiparallel strands that twist into a double helix because of the hydrogen bonding that occurs between nitrogenous bases T2 infections start when genes are injected into the cell wall of E coli The exterior protein coat caspid of the virus is left outside of the cell T2 is made up almost entirely of protein and DNA Hershey and Chase s experiment was based on the fact that only protein contains sulfur and only DNA contains Phosphorus A population with radioactive protein was made A population with radioactive DNA was made All radioactive protein was found in the capsids and outside of the cell All radioactive DNA was found in the cell and is therefore the hereditary material The Secondary Structure of DNA DNA is made of a deoxyribose sugar a nitrogenous base and a phosphate group cid 127 Monomers of DNA are linked by phosphodiester bonds and built in the 5 carbon to 3 carbon direction Primary structure consists of A backbone of sugars and phosphates Nitrogenous bases that project from the backbone Complementary base pairing 15 2 Testing Early Hypotheses about DNA Synthesis Complementary base pairing allows new strands to be synthesized by the old strands of DNA Three Alternative Hypotheses parent DNA strand The Meselon Stahl Experiment Dispersive replication cuts the parental double helix to create a mixture of new and old strands All organisms copy their entire genome before every cell division Cells were grown in different isotopes of nitrogen in order to have varied densities The parental and daughter strands would have different densities This is called density gradient centrifugation and separates molecules based on their density 15 3 A Model for DNA Synthesis DNA polymerase polymerizes deoxyribonucleotides into DNA it catalyzes DNA synthesis Semiconservative replication means parent strands are separated and each is used as a template for a new daughter strand Conservative replication temporarily separates the strands and puts them back together once a new strands have been synthesized resulting in a whole These can only work in one direction so monomers are only added to the 3 carbon and DNA polymerase synthesizes in the 5 3 direction DNA synthesis is exergonic because monomers of DNA have three closely spaces phosphate groups and two must be severed in order to synthesize DNA How Does Replication Get Started A replication bubble begins at a sequence called the origin of replication on a DNA strand DNA synthesis is bidirectional it occurs in both directions at the same time the bubble grows in both directions Synthesis takes place in replication forks formed by the replication bubble as it moves down the helix How is the Helix Opened and Stabilized DNA helicase breaks hydrogen bonds between base pairs Single stranded DNA binding proteins SSBPs attach to the separated strands to prevent them from coming back together Topoisomerase cuts DNA and allows it to unwind so tension does not built up from the opening of the replication bubble A Primer is a few nucleotides long and provides DNA polymerase with a hydroxyl group that it can use to create a phosphodiester bond with a new strand of How is the Leading Strand Synthesized DNA Primase synthesizes RNA before DNA is synthesized Primase is an RNA polymerase that does not require a primer to begin synthesis DNA polymerase holds onto the strand as it moves down and is followed by a donut structure called a sliding clamp that holds DNA polymerase in place The leading strand heads towards the replication fork and is synthesized continuously cid 127 cid 127 cid 127 cid 127 cid 127 cid 127 cid 127 cid 127 cid 127 cid 127 cid 127 cid 127 cid 127 cid 127 cid 127 cid 127 cid 127 cid 127 cid 127 cid 127 cid 127 cid 127 cid 127 cid 127 cid 127 cid 127 cid 127 cid 127 cid 127 cid 127 cid 127 cid 127 cid 127 cid 127 cid 127 cid 127 cid 127 How is the Lagging Strand Synthesized cid 127 Only the leading strand can be synthesized in the same direction that the replication fork is going The lagging strand is synthesized in the direction leading away from the fork The replication fork moves and exposes sections of single stranded DNA The Discontinuous Replication Hypothesis Primase synthesizes RNA primers for the lagging strand as the replication fork exposes sections DNA polymerase uses the primers to synthesize short fragments that are eventually linked together The Discovery of Okazaki Fragments Short strands were called Okazaki fragments Short strands of about 1000 base pairs were present after the pulse and later became larger during the chase as they were synthesized into longer pieces Specialized DNA polymerase hooks onto 3 end of an Okazaki fragment and moves along to remove RNA primer and add DNA nucleotides DNA ligase comes after the polymerase and catalyzes the appearance of a phosphodiester bond between fragments All of these enzymes are joined into one large macromolecular machine called the replisome 15 4 Replication the Ends of Linear Chromosomes The End Replication Problem A telomere is the region at the end of an eukaryotic chromosome DNA polymerase synthesizes the leading strand all the way to the end of the parent DNA strand The lagging strand primase adds an RNA primer close to the end of the template strand DNA polymerase cannot add DNA to the end of the strand because there is no primase for it to hook on to The single stranded DNA at the end of the strand will eventually degrade but this would result in the shortening of DNA strands Telomerase Solves the End Replication Problem Telomeres are short DNA bases repeated over and over they do not contain any genes Telomerase carries its own template and is involved in replicating telomeres It catalyzes the synthesis of DNA from RNA and adds DNA onto the end of a chromosome to prevent it from getting shorter Telomerase binds to overhanging DNA and begins synthesis The template for this is a portion of the RNA held within telomerase Telomerase catalyzes the additions of short repeated DNA strands to the end of a growing single strand and the lagging strand becomes slightly longer than it was originally Telomerase Regulation 15 5 Repairing Mistakes and DNA Damage Correcting Mistakes in DNA Synthesis Telomerase is not active in all cells it is usually found in gametes It is not usually present in
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