Macromolecules: Nucleic Acids

1. T G A C T A C A G G A T C

2. Macromolecules: Nucleic Acids • Examples: • RNA (ribonucleic acid) • single helix • DNA (deoxyribonucleic acid) • double helix • Structure: • monomers = nucleotides DNA RNA

3. Nucleotides • 3 parts • nitrogen base (C-N ring) • pentose sugar (5C) • ribose in RNA • deoxyribose in DNA • phosphate(PO4)group Nitrogen baseI’m the A,T,C,G or Upart! Are nucleic acidscharged molecules?

4. Types of nucleotides Purine = AG Pure silver! • 2 types of nucleotides • different nitrogen bases • purines • double ring N base • adenine (A) • guanine (G) • pyrimidines • single ring N base • cytosine (C) • thymine (T) • uracil (U)

5. Nucleic polymer • Backbone • sugar to PO4 bond • phosphodiester bond • new base added to sugar of previous base • polymer grows in one direction • N bases hang off the sugar-phosphate backbone Dangling bases?Why is this important?

6. Pairing of nucleotides • Nucleotides bond between DNA strands • H bonds • purine :: pyrimidine • A :: T • 2 H bonds • G :: C • 3 H bonds Matching bases?Why is this important?

7. DNA molecule • Double helix • H bonds between bases join the 2 strands • A :: T • C :: G H bonds?Why is this important?

8. Copying DNA • Replication • 2 strands of DNA helix are complementary • have one, can build other • have one, can rebuild the whole

9. When does a cell copy DNA? • When in the life of a cell does DNA have to be copied? • cell reproduction • mitosis • gamete production • meiosis

10. But how is DNA copied? • Replication of DNA • base pairing suggests that it will allow each side to serve as a template for a new strand

11. 1958 Models of DNA ReplicationSemiconservative replication • Meselson & Stahl • label “parent” nucleotides in DNA strands with heavy nitrogen =15N • label new nucleotides with lighter isotope = 14N parent replication 15N/15N 15N parent strands

12. 1958 Semiconservative replication • Make predictions… • 15Nstrands replicated in 14N medium • 1st round of replication? • 2nd round? where should the bands be?

13. DNA Replication • Origin(s) of replication • specific sequence of nucleotides recognized by replication enzymes • Prokaryotes – • Single sequence • Bidirectional Synthesis • Replication proceeds in both directions • Eukaryotes– • hundreds/thousands of origin sites per chromosome • Replication forks • Bubbles elongate as DNA is replicated and eventually fuse

14. Bidirectional Synthesis • In prokaryotes, the circular DNA is opened up, and synthesis occurs in both directions

15. Replication forks • In eukaryotes, the linear DNA has many replication forks

17. DNA Replication Issues 1. DNA strands must be unwound during replication • DNA helicase • unwinds the strands • Single stranded binding proteins (SSB) • prevent immediate reformation of the double helix • Topoisomerases • “untying” the knots that form

18. Replication Issues 2. A new DNA strand can onlyelongate in the 5’  3’ direction • RNA primers initiates DNA polymerase • DNA polymerase can add only at the 3’ end (sliding clamp holds DNA polymerase on DNA strand) • Replication is continuous on one strand • Leading Strand • discontinuous on the other • Lagging strand • Okazaki fragments

19. Okazaki fragments • Synthesis of the leading strand is continuous • The lagging strand (discontinuous) is synthesized in pieces called Okazaki fragments

21. Replication Issues 3. DNA polymerase cannot initiate synthesis because it can only add nucleotides to end of an existing chain • Requires a “primer” to get the chain started • RNA Primase • can start an RNA chain from a single template strand by synthesizing RNA primers • DNA polymerase can begin its chain after a few RNA nucleotides have been added

23. Summary • At the replication fork, the leading strand is copied continuously into the fork from a single primer • Lagging strand is copied away from the fork in short okazaki fragments, each requiring a new primer

25. Learning Check • What is the purpose of DNA replication? • How is the new strand ensured to be identical to the original strand? • How is replication on one side of the strand different from the other side?

26. Replication Issues 4. Presence of RNA primer on the 5’ ends of daughter DNA leading strand leaves a gap of uncopied DNA • Repeated rounds of replication produce shorter and shorter DNA molecules • Telomeres • protect genes from being eroded through multiple rounds of DNA replication

27. Telomeres • Ends of eukaryotic chromosomes, the telomeres, have special nucleotide sequences • Humans - this sequence is typically TTAGGG, repeated 100 - 1,000 times • Telomeraseadds a short molecule of RNA as a template to extend the 3’ end • Room for primase & DNA pol to extend 5’ end

28. Summary • Explain how the cell overcomes each of the following issues in DNA replication • DNA strands must be unwound during replication • A new DNA strand can onlyelongate in the 5’  3’ direction • DNA polymerase cannot initiate synthesis and can only add nucleotides to end of an existing chain • Presence of RNA primer on the 5’ ends of daughter DNA leading strand leaves a gap of uncopied DNA