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Nucleic Acids

Nucleic Acids

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Nucleic Acids

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  1. Nucleic Acids The blueprints

  2. Types of Molecules • Polymers of nucleotides • DNA: code for genetic information • RNA • mRNA intermediates in protein synthesis • rRNA carry out protein synthesis • tRNA translate info on mRNA into a.a. • Gene

  3. Nucleotide Components • Bases + sugar + phosphate • Bases • purine • adenine • guanine • pyrimidines • thymine • cytosine • uracil

  4. Bases

  5. Nucleotide Components • Sugars • ribose • Deoxyribose • Rings numbered using primes • C1 = 1’ etc • PO43-

  6. Nucleotide Structure • Base-sugar-phosphate • Base attached to C1 of sugar • Note sugar is β • Phosphate attached to C5 of sugar • Usually nucleotides are triphosphates, but can be mono or di

  7. Nucleic Acid, a polymer of nucleotides

  8. Nucleic Acids • Polymer of nucleotides • Phosphodiester linkage • 3’ of one sugar to 5’ of other • vectorial • Sequence read 5’ - 3’ • Previous slide is C-A-A • Next slide (a cartoon drawing) is A-T-G-C

  9. Phosphodiester Bond

  10. Chain elongation • 3’ hydroxyl on chain has unshared pair on oxygen • attacks phosphorus on first phosphate of new nucleotide • Nucleophilic attack • Driven by hydrolysis of PPi

  11. Chain elongation

  12. Base pairs • Bases are planar • sp2 hybridization • Bases nonpolar • In Nucleic acids, there is base pairing • Complementarity • Purines always base-pair with pyrimidines • Cytosine hydrogen bonds with guanine • Thymine hydrogen bonds with adenine or uracil • Due to distancing and proximity of unshared pairs and hydrogens

  13. GC base pair

  14. AT base Pair

  15. A-U base Pair (RNA)

  16. Base Pairs (Cartoon drawing)

  17. Complementarity • One strand is complementary to the other • If know sequence of one, can deduce that of the other • Templates • Implications in copying

  18. DNA structure • Double helix • http://sbchem.sunysb.edu/msl/dna.gif

  19. DNA structure • B-DNA is most common • Antiparallel • bases inside • Hydrophobic • Perpendicular to helix • stands complementary • Very important for information transfer • Each strand a template for the other. • right handed • major and minor groove

  20. Other forms of DNA • Z - DNA left handed; structure not fully understood • A- DNA; tighter helix

  21. DNA TypesB- DNA (most common) • http://images.google.com/imgres?imgurl=http://gibk26.bse.kyutech.ac.jp/jouhou/image/nucleic/dna/dna_st.small.gif&imgrefurl=http://gibk26.bse.kyutech.ac.jp/jouhou/image/nucleic/dna/dna.html&h=306&w=375&sz=32&hl=en&start=32&tbnid=muC9F_v90eYO7M:&tbnh=100&tbnw=122&prev=/images%3Fq%3DA%2BDNA%26start%3D20%26ndsp%3D20%26svnum%3D10%26hl%3Den%26lr%3D%26sa%3DN

  22. A-DNA (supercoiled) • http://images.google.com/imgres?imgurl=http://gibk26.bse.kyutech.ac.jp/jouhou/image/nucleic/dna/dna_st.small.gif&imgrefurl=http://gibk26.bse.kyutech.ac.jp/jouhou/image/nucleic/dna/dna.html&h=306&w=375&sz=32&hl=en&start=32&tbnid=muC9F_v90eYO7M:&tbnh=100&tbnw=122&prev=/images%3Fq%3DA%2BDNA%26start%3D20%26ndsp%3D20%26svnum%3D10%26hl%3Den%26lr%3D%26sa%3DN

  23. Z-DNA • http://images.google.com/imgres?imgurl=http://gibk26.bse.kyutech.ac.jp/jouhou/image/nucleic/dna/dna_st.small.gif&imgrefurl=http://gibk26.bse.kyutech.ac.jp/jouhou/image/nucleic/dna/dna.html&h=306&w=375&sz=32&hl=en&start=32&tbnid=muC9F_v90eYO7M:&tbnh=100&tbnw=122&prev=/images%3Fq%3DA%2BDNA%26start%3D20%26ndsp%3D20%26svnum%3D10%26hl%3Den%26lr%3D%26sa%3DN

  24. Look down Axis • http://www.accelrys.com/reference/gallery/life/dna.gif

  25. Sequence dependent structures • palindromes • hairpins • inverted repeats • mirror repeats

  26. RNA • codes for protein • no consistent secondary structure • single stranded • Ribose instead of deoxyribose • Thymine (T) replaced by Uracil

  27. RNA

  28. Transfer RNA • http://www.mie.utoronto.ca/labs/lcdlab/biopic/fig/12.07.jpg

  29. Instability of RNA • RNA unstable due to reactivity of 2’ hydroxyl on ribose • Very labile • DNA extremely stable

  30. Nucleic Acid Chemistry • Denaturation • unzip by heating • reannealing • CoT curves: more GC=higher temp • Uses of DNA to find sequences • probes • forensic

  31. DNA probes • Take DNA from crime scene • DNA from suspect, random other person etc • See what matches

  32. Nucleic Acid Chemistry • Mutations • changes in sequence/structure • nonenzymatic changes • thymine dimers • deamination • oxidative damage

  33. Nucleic Acid Chemistry • http://www.dnalc.org/resources/BiologyAnimationLibrary.htm • Sequencing • PCR • Southern Blotting • Probes

  34. DNA sequencing, Sanger dideoxy method • 4 samples • Each gets template and nucleotides • One dideoxy nucleotide • Has no 3’ OH so chain can’t elongate • Sample 1 • ddTTP…stops at T • Sample 2 • ddATP…stops at A • Sample 3 • ddCTP…stops at C • Sample 4 • ddGTP…stops at G • Run on Gel • Read from bottom up

  35. Sample Sanger Gel

  36. Human Genome Project • http://www.ornl.gov/sci/techresources/Human_Genome/home.shtml