Nucleic Acids and Bases In 1869 Swiss chemist Friedrich Miescher discovered a white substance from the nuclei that was slightly acidic so he called it nucleic acid DNA contains 3 main parts 1 A 5 carbon sugar 2 A phosphate group 3 A nitrogenous nitrogen containing base The base can be a large purine A G or a small pyrimidine T C C and T form two hydrogen bonds and are therefore easier to melt G and A form three and are therefore harder to melt We refer to the five carbons on a 5 carbon sugar with the prime symbol In DNA the phosphate connects to the 5 carbon atom and the base connects to the 1 A free hydroxyl OH is connected to the 3 carbon atom The phosphodiester bond links the hydroxyl of the 3 atom to the phosphate of the 5 atom It is called that because the phosphate is now linked by way of ester bonds This forms long acid polymers Erwin Chargaff discovered that DNA isn t constant It s complex and it varies a lot but it always has the same amount of A and T and it always has the same amount of C and G So even though one species might have more C than the other there will always be G to match it Using x ray diffraction where crystals of a molecule are bombarded with X rays we proved that DNA is a helix shape The different structural forms of bases called tautomers are due to whether they have keto C O versus enol C OH and whether they have amino NH2 versus imino C NH The two strands of the helix are made of repeating sugar and phosphate units which we call the phosphodiester backbone A single phosphodiester strand has inherent polarity because the 3 side ends with OH and the 5 side ends with PO4 Thus they are referred to as having 3 to 5 polarity or 5 to 3 polarity Strands are antiparallel meaning one side runs 3 to 5 and another runs 5 to 3 DNA Replication Models There are three main models of DNA replication but they all begin with a two strand parent and they all end in a pair of two strand daughters four strands total 1 A conservative model where the original strand is preserved alongside the copy 2 A semiconservative model is where each daughter has one strand of the copy and one 3 A dispersive model is where bits and pieces of the original and copy are dispersed in strand of the original each of the four strands The Meselson Stahl experiment supported the semiconservative model They took a batch of bacteria replicated it and replicated it again Here s the thing after the first replication a strand of the bacteria 15N turns into a strand of the much lighter 14N So basically after the first replication their two strand heavy 15N helix now had a copy that was one heavy strand and one light strand When they replicated it again during the second round the heavy strand once again became a light strand and a heavy strand and the light strand became two light strands DNA replication requires something to copy DNA something to do the copying enzymes and building blocks to make the copy nucleoside triphosphates The three stages are 1 Initiation 2 Elongation 3 Termination process begins majority of building blocks are added process ends Prokaryotic Replication Prokaryotic replication starts at a single origin this origin a chromosome the replicon This is not only the origin of replication but where the replication is controlled The textbook uses E Coli as an example and its origin is called oriC Prokaryotes have one replicon eukaryotes have multiple DNA polymerase are a class of enzymes that use DNA template to assemble a new complimentary strand but they only assemble in the 5 to 3 direction and they require a primer Other times polymerases can act as a nuclease and cleave the nucleotide chain into smaller acids Either they are an endonuclease and can do it from inside or an exonuclease which can only do it at the end on the outside The textbook covers three main DNA polymerases DNA POL III is the main replication enzyme DNA POL I removes primers and replaces them with DNA DNA POL II is involved in repair A helicase is an enzyme that unwinds the DNA to replicate it When unwound the helix undergoes a form of strain called torsional strain and it supercoils Topology studies how forms twist and coil so this supercoiled state of DNA is called the Topological State Topoisomerases are enzymes that relieve the torsional strain and prevent supercoiling DNA gyrase is the topoisomerase involved in DNA replication Because they are antiparallel DNA strands must be synthesized in opposite directions One strand the leading strand is synthesized continuously from a single primer and the other strand the lagging strand is synthesized discontinuously in short bursts from lots of primers Each fragment of the lagging strand is called an Okazaki fragment The Okazaki fragments are then joined by a DNA ligase DNA having to be opened up slightly to be replicated creates a shape called replication fork The enzyme DNA primase synthesizes primers which attracts DNA polymerases which creates a new strand to go with one of the split off template strands All of these many enzymes involved in DNA replication come together as a macromolecule called the replisome Eukaryotic Replication Eukaryotic replication is complicated by linear chromosomes and large amounts of DNA The process and the replisome is different for a few reasons There are multiple origins and multiple replicons but each origin can only be used once per cycle The replication fork is more complex The Okazaki fragments are shorter The ends of eukaryotic chromosomes have special structures called telomeres Eukaryotic replications proteins are rooted in evolution There is a gradual shortening of chromosomes with each round of cell division Telomeres are made by an enzyme called telomerase This activity is high but it goes down during old age causing the ends of chromosomes to get shorter
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