A T C G Isn’t this a great illustration!?

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

Nucleotides 3 parts nitrogen base (C-N ring) pentose sugar (5C) ribose in RNA deoxyribose in DNA phosphate (PO4) group Nitrogen base I’m the A,T,C,G or U part! Are nucleic acids charged molecules? DNA & RNA are negatively charged: Don’t cross membranes. Contain DNA within nucleus Need help transporting mRNA across nuclear envelope. Also use this property in gel electrophoresis.

Types of nucleotides 2 types of nucleotides different nitrogen bases 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)

Dangling bases? Why is this important? 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?

Pairing of nucleotides Nucleotides bond between DNA strands H bonds purine :: pyrimidine A :: T 2 H bonds G :: C 3 H bonds The 2 strands are complementary. One becomes the template of the other & each can be a template to recreate the whole molecule. Matching bases? Why is this important?

H bonds? Why is this important? DNA molecule Double helix H bonds between bases join the 2 strands A :: T C :: G H bonds = biology’s weak bond • easy to unzip double helix for replication and then re-zip for storage • easy to unzip to “read” gene and then re-zip for storage H bonds? Why is this important?

Matching halves? Why is this a good system? Copying DNA Replication 2 strands of DNA helix are complementary have one, can build other have one, can rebuild the whole when cells divide, they must duplicate DNA exactly for the new “daughter” cells Why is this a good system? Matching halves? Why is this a good system?

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 when cells divide, they must duplicate DNA exactly for the new “daughter” cells Why is this a good system?

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

Models of DNA Replication Can you design a nifty experiment to verify? Models of DNA Replication Alternative models become experimental predictions conservative semiconservative dispersive P 1 2

Replication forks In eukaryotes, the linear DNA has many replication forks

Learning Check Break the toothpicks at the center of your models and replicate your DNA strand You should end up with 2 complete strands of DNA Keep in mind Chargaff’s rules and Meselson & Stahl’s semi-conservative model Animation

Replication- Create a diagram that shows how the following components interact with each other (15 min) Replication fork RNA primer Leading strand DNA ligase RNA primase Okazaki fragments Lagging strand Helicase DNA polymerase Single stranded binding protein Topoisomerase

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

Replication Issues 2. A new DNA strand can only elongate in the 5’  3’ direction DNA polymerase can add only at the 3’ end Replication is continuous on one strand Leading Strand discontinuous on the other Lagging strand Okazaki fragments

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

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 DNA polymerase can begin its chain after a few RNA nucleotides have been added

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

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?

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

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

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 only elongate 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