DNA and DNA Replication

Chapter 5 & 6 DNA & DNA Replication History  DNA Comprised of genes  In non-dividing cell nucleus as chromatin   Protein/DNA complex  Chromosomes form during cell division  Duplicate to yield a full set in daughter cell DNA is Genetic Material From Chapter 2  Nucleic acids are polymers Monomers are called nucleotides  Nucleotides = base + sugar + phosphate   Base   = purine or pyrimidine Purines = adenine, guanine Pyrimidines = thymine, cytosine, uracil  Sugar = deoxyribose or ribose  Phosphate, a single phosphate in DNA  Sugar of nt 1 is linked to the phosphate of nt 2 by a phosphodiester bond Panel 2-6 Chapter 2 – cont’d DNA is a Double Helix     Nucleotides  A, G, T, C Sugar and phosphate form the backbone Bases lie between the backbone Held together by H-bonds between the bases   A-T – 2 H bonds G-C – 3 H bonds H - Bonds  Base-pairing rules   AT only (AU if DNARNA hybrid) GC only   DNA strand has directionality – one end is different from the other end 2 strands are anti-parallel, run in opposite directions   Complementarity results Important to replication Helical Structure Nucleotides as Language  We must start to think of the nucleotides – A, G, C and T as part of a special language – the language of genes that we will see translated to the language of amino acids in proteins Genes as Information Transfer A gene is the sequence of nucleotides within a portion of DNA that codes for a peptide or a functional RNA  Sum of all genes = genome  DNA Replication Semiconservative  Daughter DNA is a double helix with 1 parent strand and 1 new strand  Found that 1 strand serves as the template for new strand  DNA Template   Each strand of the parent DNA is used as a template to make the new daughter strand DNA replication makes 2 new complete double helices each with 1 old and 1 new strand Replication Origin  Site where replication begins   1 in E. coli 1,000s in human  Strands are separated to allow replication machinery contact with the DNA  Many A-T base pairs because easier to break 2 H-bonds that 3 H-bonds  Note anti-parallel chains Replication Fork  Bidirectional movement of the DNA replication machinery DNA Polymerase    An enzyme that catalyzes the addition of a nucleotide to the growing DNA chain Nucleotide enters as a nucleotide tri-PO4 3’–OH of sugar attacks first phosphate of triPO4 bond on the 5’ C of the new nucleotide  releasing pyrophosphate (PPi) + energy DNA Polymerase Bidirectional synthesis of the DNA double helix  Corrects mistaken base pairings  Requires an established polymer (small RNA primer) before addition of more nucleotides  Other proteins and enzymes necessary  How is DNA Synthesized?  Original theory   Begin adding nucleotides at origin Add subsequent bases following pairing rules   Expect both strands to be synthesized simultaneously This is NOT how it is accomplished Correction: Refer to Figure 6-15 on page 205 of your textbook for “corrected” figure. This figure fails to show the two terminal phosphate groups attached on the 5’ end of the nucleotide strand located at the top of this figure. Why DNA Isn’t Synthesized 3’5’ How is DNA Synthesized?  Actually how DNA is synthesized  Simple addition of nucleotides along one strand, as expected the leading strand  DNA polymerase reads 3’  5’ along the leading strand from the RNA primer  Synthesis proceeds 5’  3’ with respect to the new daughter strand  Called  Remember how the nucleotides are added!!!!! 5’  3’ How is DNA Synthesized?  Actually how DNA is synthesized Other daughter strand is also synthesized 5’3’ because that is only way that DNA can be assembled  However the template is also being read 5’3’   Compensate for this by feeding the DNA strand through the polymerase, and primers and make many short segments that are later joined (ligated) together  Called the lagging strand DNA Replication Fork Fig 6-12 Mistakes during Replication  Base pairing rules must be maintained  Mistake = genome mutation, may have consequence on daughter cells   Only correct pairings fit in the polymerase active site If wrong nucleotide is included  Polymerase uses its proofreading ability to cleave the phosphodiester bond of improper nucleotide  Activity 3’  5’  And then adds correct nucleotide and proceeds down the chain again in the 5’  3’ direction Proofreading Starting Synthesis DNA polymerase can only ADD nucleotides to a growing polymer  Another enzyme, primase, synthesizes a short RNA chain called a primer  DNA/RNA hybrid for this short stretch  Base pairing rules followed (BUT A-U)  Later removed, replaced by DNA and the backbone is sealed (ligated)  Primers – cont’d  Simple addition of primer along leading strand  RNA primer synthesized 5’  3’, then polymerization with DNA  Many primers are needed along the lagging strand   1 primer per small fragment of new DNA made along the lagging strand Called Okazaki fragments Removal of Primers  Other enzymes needed to excise (remove) the primers Nuclease – removes the RNA primer nucleotide by nucleotide  Repair polymerase – replaces RNA with DNA  DNA ligase – seals the sugar-phosphate backbone by creating phosphodiester bond   Requires Mg2+ and ATP Other Necessary Proteins    Helicase opens double helix and helps it uncoil Single-strand binding proteins (SSBP) keep strands separated – large amount of this protein required Sliding clamp   Subunit of polymerase Helps polymerase slide along strand  All are coordinated with one another to produce the growing DNA strand (protein machine) Components of the DNA Replication Polymerase & Proteins Coordinated   One polymerase complex apparently synthesizes leading/lagging strands simultaneously Even more complicated in eukaryotes DNA Repair For the rare mutations occurring during replication that isn’t caught by DNA polymerase proofreading  For mutations occurring with daily assault  If no repair  In germ (sex) cells  inherited diseases  In somatic (regular) cells  cancer  Effect of Mutation Uncorrected Replication Errors  Mismatch repair  Enzyme complex recognizes mistake and excises newly-synthesized strand and fills in the correct pairing Mismatch Repair – cont’d  Eukaryotes “label” the daughter strand with nicks to recognize the new strand  Separates new from old Depurination or Deamination   Depurination – removal of a purine base from the DNA strand Deamination is the removal of an amine group on Cytosine to yield Uracil  Could lead to the insertion of Adenine rather than Guanosine on next round Chemical Modifications Thymine Dimers   Caused by exposure to UV light 2 adjacent thymine residues become covalently linked Repair Mechanisms    Different enzymes recognize, excise different mistakes DNA polymerase synthesizes proper strand DNA ligase joins new fragment with the polymer