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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 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 • 4.5 Stability of Secondary and Tertiary Structure核酸的二级结构和三级结构的稳定性
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
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)
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
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
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
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.
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
Unusual base pair 见于酵母苯丙氨酰tRNA
Nucleotide propertics 3. Spectrum • Nucleotides absorb light strongly in the near-ultraviolet region of the spectrum.
260(X104) AMP 1.54 GMP 1.17 CMP 0.75 dTMP 0.92 UMP 0.99.
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
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)
Significance of Primary Structure • Genetic information stored in nucleotide sequence of DNA • Gene is a particular DNA sequence
DNA is genetic substance. Avery, MacLeod, McCarty
Hershey and Chase - Bacteriophage T2 transfers DNA to bacteria
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
12/ 0.38nm Minor groove 10/ 0.34nm Secondary structure of DNA 11/ 0.23nm Major groove
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,GC) —B-DNA:d= 2 nm,pitch = 3.4 nm , 10 bp / turn of the helix
DNA base pair Prictice: Write the sequence .
The discovery of DNA double helix • Chargaff's Rule (A=T, G=C in DNA) • Franklin, Wilkins: X-ray DiffractionRefined Structure
Significance of DNA double helix semi-conservative model of DNA replication
Molecule hybridization Application of Complementarity DNA半保留复制 核酸分子杂交实验
Unusual Secondary Structures of DNA • Palindromes(回文结构)Cruciform formation in palindrome sequencesGGCGCGCCCCGCGCGG
H-DNA • purines/pyrimidines on one strand
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.
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.
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).
Besides writhing, unwinding DNA, cruciform formation (via palindromes), triple helix formation (H-DNA), and Z-DNA formation, can all reduce superhelical tension, too.
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?