2. Nucleic acids An overview of structure These slides provides an introduction to the structure and function of nucleic acids (DNA and RNA) in relation to organisms, genes, gene expression and protein synthesis. Dr. Momna Hejmadi, University of Bath N.B. Some images used in these slides are from the textbooks listed and are not covered under the Creative Commons license as yet DNA basics resources created by Dr. Momna Hejmadi, University of Bath, 2010, is licensed under the Creative Commons Attribution-Non-Commercial-Share Alike 2.0 UK: England & Wales License. To view a copy of this license, visit http://creativecommons.org/licenses/by-nc-sa/2.0/uk/ or send a letter to Creative Commons, 171 Second Street, Suite 300, San Francisco, California 94105, USA.http://creativecommons.org/licenses/by-nc-sa/2.0/uk/

3. Books: Biochemistry (3e) by D Voet & J Voet Molecular biology of the cell (4 th ed) by Alberts et al Essential Cell Biology by Alberts et al Life: The Science of Biology by Sadava et al (8th ed ) Key websites http://www.dnaftb.org/dnaftb/ http://www.dnai.org/lesson/go/2166/1994 http://www.thelifewire.com History, structure and forms of DNA http://www.dnai.org/lesson/go/2166 See document: ‘References: DNA Structure and Function

4. Learning objectives Understand the timeline of discoveries leading to elucidation of DNA structure Describe / draw the structure of nucleotides Understand the alternative DNA conformations Understand RNA structure and diversity

5. Timeline 1869 F Miescher - nucleic acids 1928 F. Griffith - Transforming principle http://www.dnai.org/lesson/go/2166http://www.dnai.org/lesson/go/2166/1994

6. Discovery of transforming principle 1928 – Frederick Griffith – experiments with Streptococcus pneumoniae Smooth (S) virulent strain (polysaccharide coat protects it from immune system) Rough (R) nonvirulent strain (lacks the polysaccharide coat)

7. Griffith experiment showing that strains can be transformed by ‘transforming principle’

8. What is this transforming principle? Bacterial transformation demonstrates transfer of genetic material

9. Timeline 1800’s F Miescher - nucleic acids 1928 F. Griffith - Transforming principle Avery, McCleod & McCarty- Transforming principle is DNA 1944 http://www.dnai.org/lesson/go/2166http://www.dnai.org/lesson/go/2166/1994

10. Avery, MacLeod, McCarty Experiment

11. Transforming principle is DNA

12. Timeline 1800’s F Miescher - nucleic acids 1928 F. Griffith - Transforming principle 1949 Avery, McCleod & McCarty- Transforming principle is DNA 1944 Erwin Chargaff – base ratios http://www.dnai.org/lesson/go/2166http://www.dnai.org/lesson/go/2166/1994

13. E. Chargaff’s ratios A = T C = G A + G = C + T % GC constant for given species regardless of age, nutrition or tissue type

14. Timeline 1800’s F Miescher - nucleic acids 1928 F. Griffith - Transforming principle 1952 Avery, McCleod & McCarty- Transforming principle is DNA 1944 Hershey-Chase ‘blender’ experiment http://www.dnai.org/lesson/go/2166http://www.dnai.org/lesson/go/2166/1994 1949 Erwin Chargaff – base ratios

15. Timeline 1800’s F Miescher - nucleic acids 1928 F. Griffith - Transforming principle 1949 Avery, McCleod & McCarty- Transforming principle is DNA 1944 Hershey-Chase ‘blender’ experiment 1952 Erwin Chargaff – base ratios 1952 R Franklin & M Wilkins–DNA diffraction pattern http://www.dnai.org/lesson/go/2166http://www.dnai.org/lesson/go/2166/1994

16. X-ray diffraction patterns produced by DNA fibers Rosalind Franklin and Maurice Wilkins

17. Timeline 1800’s F Miescher - nucleic acids 1928 F. Griffith - Transforming principle 1952 Avery, McCleod & McCarty- Transforming principle is DNA 1944 Hershey-Chase ‘blender’ experiment 1952 Erwin Chargaff – base ratios 1952 R Franklin & M Wilkins–DNA diffraction pattern 1953 J Watson and F Crick – DNA structure solved http://www.dnai.org/lesson/go/2166http://www.dnai.org/lesson/go/2166/1994

18. The Watson-Crick Model: DNA is a double helix In 1951 Watson learns about x-ray diffraction pattern projected by DNA Erwin Chargaff’s experiments demonstrate that ratio of A and T are 1:1, and G and C are 1:1 Chemical structure of nucleotides were known (deoxyribose sugar, phosphate, and nitrogenous base) Putting this together…… Watson and Crick, 1953, Nature, 171 ….in 1953 James Watson and Francis Crick propose their double helix model of DNA structure

19. 1962 Nobel Prize in Physiology or Medicine for their discoveries concerning the molecular structure of nucleic acids and its significance for information transfer in living material" James WatsonFrancis CrickMaurice Wilkins

20. Nucleotides DNARNA Originally elucidated by Phoebus Levine and Alexander Todd in early 1950’s 2’-deoxy-D-ribose 2’-D-ribose Made of 3 components 1) 5 carbon sugar (pentose) 2) nitrogenous base 3) phosphate group 1) SUGARS

21. 2) NITROGENOUS BASES planar, aromatic, heterocyclic derivatives of purines/pyrimidines adenine uracil thymine cytosine guanine pyrimidines purines Note: Base carbons denoted as 1 etc Sugar carbons denoted as 1’ etc

22. Nucleotide monomer nucleotide = phosphate ester monomer of pentose dinucleotide - Dimer Oligonucleotide – short polymer (<10) Polynucleotide – long polymer (>10) Nucleoside = monomer of sugar + base

23. 1) Phosphodiester bonds 5’ and 3’ links to pentose sugar 2) N-glycosidic bonds Links nitrogenous base to C1’ pentose in beta configuration 5’ – 3’ polynucleotide linkages

24. 3’ end 5’ end 5’ – 3’ polarity

25. Structurally, purines (A and G) pair best with pyrimidines (T and C) Thus, A pairs with T and G pairs with C, also explaining Chargaff’s ratios

26. Essential features of B-DNA Right twisting Double stranded helix Anti-parallel Bases on the inside (Perpendicular to axis) Uniform diameter (~20A) Major and minor groove Complementary base pairing

27. A- DNA B-DNAZ-DNA Helix Right-handed Left-handed WidthWidestIntermediateNarrowest Planes of bases planes of the base pairs inclined to the helix axis planes of the base pairs nearly perpendicular to the helix axis Central axis 6A hole along helix axis tiny central axisno internal spaces Major groove Narrow and deepWide and deepNo major groove Minor groove Wide and shallowNarrow and deep DNA conformations

28. Right-handed helix intermediate planes of the base pairs nearly perpendicular to the helix axis tiny central axis wide + deep major groove narrow + deep minor groove B-DNA

29. DNA conformations Right-handed helix Widest planes of the base pairs inclined to the helix axis 6A hole along helix axis narrow + deep major groove Wide + shallow minor groove A- DNA

30. Left-handed helix Narrowest planes of the base pairs nearly perpendicular to the helix axis no internal spaces no major groove narrow + deep minor groove Z-DNA DNA conformations

31. AB Z

32. The tertiary structure is similar to DNA, but with several important differences: Single stranded but usually forms intra-molecular base pairs major and minor grooves are less pronounced Uracil instead of thymine Structural, adaptor and transfer roles of RNA are all involved in decoding the information carried by DNA RNA Structure

33. Types of RNA in the human genome

34. Class of RNA Example typesFunction Ribosomal RNA16,23,18,28SRibosomal subunits Transfer RNA22 mitochondrial 49 cytoplasmic mRNA binding Small nuclear RNA(snRNA) U1,U2,U4,U5 etcRNA splicing Small nucleolar RNA (snoRNA) U3,U8 etcrRNA modification and processing microRNA (miRNA)>200 typesRegulatory RNA XIST RNAInactivation of X chromosome Imprinting associated RNA H19 RNAGenomic imprinting Antisense RNA>1500 typesSuppression of gene expression Telomerase RNATelomere formation

35. What you need to remember from this lecture Classic experiments that lead to the elucidation of DNA structure Watson-Crick B-DNA structure (linkages, 5’-3’ polarity) Other DNA conformations Types of RNA

36. 1. Try the problem from this link: http://www.dnaftb.org/dnaftb/19/concept/index.html http://www.dnaftb.org/dnaftb/19/concept/index.html Self-test 2. Use the questions on the following slides

37. What sugar is used in in a DNA monomer? A) 3'-deoxyribose B) 5'-deoxyribose C) 2'-deoxyribose D) Glucose

38. What is the base found in RNA but not DNA? A) Cytosine B) Uracil C) Thymine D) Adenine E) Guanine

39. What covalent bonds link nucleic acid monomers? A) Carbon-Carbon double bonds B) Oxygen-Nitrogen Bonds C) Carbon-Nitrogen bonds D) Hydrogen bonds E) Phosphodiester bonds

40. Each deoxyribonucleotide is composed of A) 2'-deoxyribose sugar, Nitrogenous base, 5'- hydroxyl B) 3'-deoxyribose sugar, Nitrogenous base, 5'- hydroxyl C) 3'-deoxyribose sugar, Nitrogenous base, 5'- Phosphate D) Ribose sugar, Nitrogenous base, 5'-hydroxyl E) 2'-deoxyribose sugar, Nitrogenous base, 5'- phosphate