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DNA Structure/Composition

DNA Structure/Composition. Taryono Faculty of Agriculture Gadjah Mada University. Flow of Genetic Information. DNA. RNA. Protein. RNA Transcription. DNA Replication. Protein Translation. DNA. Discovery of the DNA double helix A. 1950’s

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DNA Structure/Composition

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  1. DNA Structure/Composition Taryono Faculty of Agriculture Gadjah Mada University

  2. Flow of Genetic Information DNA RNA Protein RNA Transcription DNA Replication Protein Translation

  3. DNA • Discovery of the DNA double helix A. 1950’s B. Rosalind Franklin- X-ray photo of DNA. C. Watson and Crick- described the DNA molecule from Franklin’s X-ray.

  4. DNA is the Genetic Material • DNA encodes all the information in the cell • The composition of the DNA is the same in all cells within an organism • Variation among different cells is achieved by reading the DNA differently • DNA contains four bases that encode all the information to make a bacteria or a human • In some viruses the genetic material is RNA

  5. How is Information Encoded in DNA? • DNA Consists of four kinds of bases (A,C,G,T) joined to a sugar phosphate backbone • Bases carry the genetic information while the phosphate backbone is structural • Two complementary strands of bases (C-G) and (A-T)

  6. DNA is a Polymer of Deoxyribonucleotide Units DEOXYRIBONUCLEOTIDE DEOXYRIBONUCLEOTIDE

  7. Deoxyribonucleic Acid (DNA) Nucleotide: 1. Phosphate group 2. 5-carbon sugar 3. Nitrogenous base • ~2 nm wide

  8. Phosphate Group O O=P-O O 5 CH2 O N Nitrogenous base (A, G, C, or T) C1 C4 Sugar (deoxyribose) C3 C2 DNA Nucleotide

  9. “Rungs of ladder” Nitrogenous Base (A,T,G or C) “Legs of ladder” Phosphate & Sugar Backbone DNA Double Helix

  10. 5 O 3 3 O P P 5 5 C O G 1 3 2 4 4 2 1 3 5 O P P T A 3 5 O O 5 P P 3 DNA Double Helix

  11. A or G T or C Nitrogenous Bases • PURINES 1. Adenine (A) 2. Guanine (G) • PYRIMIDINES 3. Thymine (T) 4. Cytosine (C)

  12. 3 H-bonds G C BASE-PAIRINGS Base # of Purines Pyrimidines PairsH-Bonds Adenine (A)Thymine (T) A = T 2 Guanine (G)Cytosine (C) C G 3

  13. H-bonds G C A T BASE-PAIRINGS

  14. C T A G Chargaff’s Rule • Adenine must pair with Thymine • Guanine must pair with Cytosine • Their amounts in a given DNA molecule will be about the same.

  15. Deoxy ribo nucleotide Ribose= Five Carbon Sugar Molecule 5´ 5´ 1´ 1´ 4´ 4´ 2´ 2´ 3´ 3´ Ribose (RNA) Deoxyribose (DNA) Backbone Sugar Molecules

  16. 5´ 1´ 3´ 2´ 5´ 1´ 3´ 2´ 5´ 1´ 3´ 2´ The DNA Backbone is a Deoxyribose Polymer Deoxyribose sugars are linked by Phosphodiester Bonds 5´-p 3´-OH 5´ 3´

  17. 5´ 3´ 3´ 5´ 5´ 5´ 1´ 3´ 2´ 5´ 1´ 3´ 2´ 5´ 1´ 3´ 2´ 3´

  18. Base 5´ 5´ 1´ 1´ 3´ 3´ 2´ 2´ Base 5´ 5´ 1´ 1´ 3´ 3´ 2´ 2´ Base 5´ 5´ 1´ 1´ 3´ 3´ 2´ 2´

  19. DeoxyRibonucleotide Deoxyadenosine 5´-triphosphate (dATP) Deoxyadenosine DeoxyRibonucleoside

  20. 9 9 Two Purines Adenine Guanine Two Pyrimidines 1 1 Thymine Cytosine DNA is Composed of Four Different Ribonucleotides

  21. T C T A 5´ 3´ G A 3´ 5´

  22. Base Pairing Follows: Chargaff’s Rule: • DNA has equal numbers of thiamines and adenines (A=T) and equal numbers of guanines and cytosines (G=C) Note that in each pair there is one purine and one pyrimidine A-T G-C

  23. Base Pairing Occurs Through Hydrogen Bonds G-C A-T

  24. G C = A T

  25. Advantages of Double-Stranded Nature of DNA • Forms a stable structure • Hydrophobic bases stack on top of one another away from solvent • Charged phosphate backbone is on the outside accessible to solvent • Each strand can serve as the template • For a new strand of DNA (replication) • For an RNA molecule (transcription)

  26. Double-stranded DNA Forms a Double Helix

  27. Native DNA Forms a B-DNA Helix • Two strands wind about each other in a right-handed manner • Diameter: ~20Å • Bases per turn: 10 (~34Å) • A major and a minor groove Major Minor 20Å

  28. DNA is Highly Packaged within the Cell • If the DNA from a single human cell were stretched out end to end, it would be ~2 meters in length DNA 2 M Cell Nucleus (magnified lots of times) 5 x 10-8 M

  29. Mechanisms of Packaging • Has to be Organized so that DNA can be Untangled for Replication and Transcription • Supercoiling • Wrapping around Proteins to Create Chromatin • Enzymes that Modulate the Packaging of DNA are called Topoisomerases

  30. Supercoiling • Most native DNA exists in a negatively supercoiled state • This means that it is slightly unwound and it is a bit easier to pull the two strands apart More supercoiling

  31. Topoisomerases Modulate Supercoiling • Topoisomerases act as Molecular Scissors • They can make a cut in the DNA and pass second strand through that break to untangle the DNA

  32. DNA is Coiled Around Histone Proteins • DNA is wrapped around abundant nuclear proteins called Histones • This forms a complex called a Nucleosome • Histones are H1, H2A, H2B, H3, H4

  33. DNA is Further Packaged

  34. Take Home Message • DNA is a double helix composed of a sugar-phosphate backbone and base pairs (a polymer of deoxyribonucleotides) • Composition/Structure • DNA is compacted to fit into the cell through: • Supercoiling • Extensive interactions with proteins • These factors all contribute to how the DNA is Read

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