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BIOCHEMISTRY

BIOCHEMISTRY. NEUCLEIC ACIDS. CONTENTS. 4.1 Two Nucleic Acids: DNA and RNA 4.2 Propertie of nucleotides 核苷酸 4.3 Primary Structure of Nucleic Acids 核酸的一级结构 4.4 Secondary Structure and tertiary Structure of Nucleic Acids 核酸的二级结构和三级结构

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BIOCHEMISTRY

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  1. BIOCHEMISTRY NEUCLEIC ACIDS

  2. CONTENTS • 4.1 Two Nucleic Acids: DNA and RNA • 4.2 Propertie of nucleotides 核苷酸 • 4.3 Primary Structure of Nucleic Acids 核酸的一级结构 • 4.4 Secondary Structure and tertiary Structure of Nucleic Acids 核酸的二级结构和三级结构 • 4.5 Stability of Secondary and Tertiary Structure核酸的二级结构和三级结构的稳定性

  3. 4.2 Nucleotides Nucleotides = Base + Sugar + Phosphate Nucleoside= Sugar + Base (no phosphate) P R base P dR Ribose or deoxyribose(核糖 或脱氧核糖） base

  4. Purine bases Pyrimidine Bases adenine（腺嘌呤） guanine（鸟嘌呤） urecil（尿嘧啶） cytosine（胞嘧啶） thymine（胸腺嘧啶）

  5. Standard Nucleotides： • 5’- adenosine monophosphate 5’-AMP（ 5’-腺苷酸） • 5’- guanosine monophosphate 5’-GMP（ 5’-鸟苷酸） • 5’- cytidine monophosphate 5’-CMP（ 5’-胞苷酸） • 5’- uridine monophosphate 5’-UMP （ 5’-脲苷酸） • 5’- deoxyadenosine monophosphate 5’-dAMP • （ 5’ -脱氧腺苷酸） • 5’- deoxyguanosine monophosphate 5’-dGMP • （5’-脱氧鸟苷酸） • 5’- deoxycytidine monophosphate 5’-dCMP（5’-脱氧胞苷酸） • 5’-deoxythymidine monophosphate） 5’-dTMP • （5’-脱氧胸腺苷酸

  6. Minor Bases or Modified bases(稀有碱基或修饰碱基)

  7. Nucleotide polyphosphate多磷酸核苷 • 8 NDPs（ 5’-nucleotide diphosphate 5’-核苷二磷酸） • 8 NTPs（ 5’-nucleotide triphosphate 5’-核苷三磷酸） ATP

  8. Cyclic Nucleotides

  9. CoA、NAD +（P）and FAD • Co-enzyme A（CoA） • Nicotinamide adenine dinucleotide（NAD+）烟酰胺腺嘌呤二核苷酸、 • Flavin Adenine Dinucleotide（FAD）黄素腺嘌呤二核苷酸

  10. NAD

  11. NADP

  12. FAD

  13. Nucleotide propertics • 1. Dissociation in water • The phosphate group of a nucleotide acts as a strong acid (pKa 1), • The amine groups of the purine and pyrimidine bases can be protonated.

  14. 2.Tautomerization of the bases • The bases can tautomerize(互变异构）; that is, the bases can redistribute positions of hydrogens and double bonds

  15. Unusual base pair 见于酵母苯丙氨酰tRNA

  16. 1-methyladenine =T

  17. Nucleotide propertics 3. Spectrum • Nucleotides absorb light strongly in the near-ultraviolet region of the spectrum.

  18. 260（X104） AMP 1.54 GMP 1.17 CMP 0.75 dTMP 0.92 UMP 0.99.

  19. Biological functions of nucleotides • 1、The monomeric units of nucleic acids • 2、Energy carrier：ATP、GTP、CTP、UTP • 3、signals ：cAMP、cGMP • 4、coenzymes：FAD、NAD、CoA

  20. 4.3 Primary Structure of Nucleic Acids • The primary structure is the sequence of nucleoside monophosphates • Directionality ：5’3’ • Individuality pGGTA——, pGpGpTpA——, GGTA—— pGGTA（OH）

  21. Significance of Primary Structure • Genetic information stored in nucleotide sequence of DNA • Gene is a particular DNA sequence

  22. DNA is genetic substance. Avery, MacLeod, McCarty

  23. Hershey and Chase - Bacteriophage T2 transfers DNA to bacteria

  24. 4.4 Secondary structure of DNA • The secondary structure refers to the shape a nucleic acid assumes as a result of the primary structure. • B-DNA : predominant form in the aqueous environment of the cell • A-DNA • Z-DNA : purine/pyrimidine tracts

  25. 12/ 0.38nm Minor groove 10/ 0.34nm Secondary structure of DNA 11/ 0.23nm Major groove

  26. Structure of B-DNA — The two chains in the double helix are antiparallel — Phosphate groups link together the sugar backbone via phosphodiester bonds. — The bases on the two chains pair in a complementary fashion. A=T，G=C — Hydrogen bonds between bases hold the double helix together. (A=T，GC) —B-DNA:d= 2 nm，pitch = 3.4 nm , 10 bp / turn of the helix

  27. DNA base pair

  28. DNA base pair

  29. DNA base pair Prictice: Write the sequence .

  30. The discovery of DNA double helix • Chargaff's Rule (A=T, G=C in DNA) • Franklin, Wilkins: X-ray DiffractionRefined Structure

  31. Watson, Crick

  32. Significance of DNA double helix semi-conservative model of DNA replication

  33. Meselson and Stahl experiment • 1958

  34. Molecule hybridization Application of Complementarity DNA半保留复制 核酸分子杂交实验

  35. Unusual Secondary Structures of DNA • Palindromes(回文结构）Cruciform formation in palindrome sequencesGGCGCGCCCCGCGCGG

  36. H-DNA • purines/pyrimidines on one strand

  37. 4.5 Tertiary structure of DNA • Tertiary structure refers to large-scale folding in a linear polymer that is at a higher order than secondary structure. The tertiary structure is the specific three-dimensional shape into which an entire chain is folded.

  38. Tertiary structure of DNA

  39. Circular DNA and Supercoiling • Circular DNAs • Supercoiling : • Positive(+)----additional twists added beyond the normal amount for linear DNA • negative (-)----reduced numbers of twists compared to linear DNA.

  40. Supercoiling • Twists(T, 缠绕数): The total number of times the two strands of the helix cross over each other, excluding writhing. Twist is a measure of how tightly the helix is wound. • Writhes (W,扭曲数): The number of times the helix as a whole crosses over itself - that is, the number of superhelical turns that are present • Linking number (L ,连接数): The total number of times two strands of a DNA helix cross each other by means of either twist or writhe L = T + W • The superhelical density : L/L0, where L0 is the linking number of the DNA in its unstrained (relaxed state).

  41. Besides writhing, unwinding DNA, cruciform formation (via palindromes), triple helix formation (H-DNA), and Z-DNA formation, can all reduce superhelical tension, too.

  42. Ethidium bromide(溴乙锭)change DNA supercoil

  43. problem set • 1. 计算一个260bps的环状DNA在松弛态和w=-2的L和超螺旋密度。 松弛态：L= T=260/10=26 超螺旋：T=26；L=T+W=26+（-2）=24； =-2/24=-0.08 2. (已知自然界存在大多数DNA分子的superhelical density（超螺旋密度）是-0.06，一个10000bpDNA分子，假定是B型构像，将形成多少圈超螺旋？ • 3 .为什么DNA倾向形成负超螺旋而不是正超螺旋？

  44. RNA

  45. tRNA

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