1、Chapter 02: nucleic acids structure and properties,1 Overview,1.1.1 DNA deoxyribonucleic acid; function: The genetic information carrier, responsible for the genetic information storage and transmission； distribution： Eukaryotes: nucleus（98%）,organelle（2%）； prokaryotes: nucleoid、plasmids viruses,1.1
2、 type and distribution of nucleic acid,1.1.2 RNA,ribonucleic acid； Function: mainly participate the expression of genetic information Type: rRNA（ribosomal RNA）mRNA（messenger RNA）tRNA（transfer RNA） distribution: cytoplasm(90%), nucleus(10%)；viruses,mRNA,rRNA,tRNA,1.1.2.1 mRNA,种类最多，比例最低，寿命最短； Each pol
3、ypeptide has corresponding mRNA，the difference among different mRNA is quite big(in length and molecular weight)； Functions: as intermediaries, carrying genetic information from genes to ribosomes, where the corresponding proteins can be synthesized (as templates).,1.1.2.2 tRNA,分子量最小； Functions: as
4、adapter molecules (transport amino acids), that faithfully translate the information in mRNA into a specific sequence of amino acids； 每个Aa至少有一个对应的tRNA（如丙氨酸tRNA、tRNAAla）。 不同tRNA分子的大小很相似，73-78Nts,1.1.2.3 rRNA,比例最大，分子量最大； Functions: structural components of ribosomes, the complexes that carry out the s
5、ynthesis of proteins,已经发现的RNA种类,summary,核酸是生命遗传信息的携带者和传递者（生命的延续、遗传特性的保持、生长发育、细胞分化） The RNA world，the DNA core,nucleic acid,nucleotide,1.2 the components of nucleic acid,means pentose, DNA has deoxyribose, RNA has ribose；,means nitrogenous bases,means phosphate,nucleotide,1.2.1 pentose,ribose （in RNA
6、）,2- deoxyribose （in DNA）,1.2.2 base,DNA,RNA,Modified bases,The chemical modification of bases is widespread, and has a number of specific roles. Such as: the methylation of the N-6 position of A、the 4-amino group and the 5-position of C,1.2.3 nucleoside and nucleotide,2.3.1 nucleoside： DNA: 2-deoxy
7、ribose + A、T、C、G RNA: ribose + A、U、C、G The base is linked to position 1 on a pentose by a glycosidic bond from N1 of pyrimidine or N9 of purine,H2O,H2O,base,phosphoric acid,pentose,glycosidic bond,Phosphate bond,1.2.3.2 nucleotide,2 Nucleic acid structure,2.1 primary structure of nucleic acid defini
8、tion：the nucletide residue sequence of the polynucleotide chain； linkage：3,5-phosphodiester bond； backbone：phosphate + pentose； direction：from the 5 terminus to the 3 terminus ； representation,2.2 secondary structure of DNA,means DNA double helix,Three discoveries (physical chemistry studies and aci
9、d and alkali titrate studies on DNA base、chargaff rules、x-ray photograph of DNA)converged in the construction of the double helix model for DNA by Watson and Crick in 1953,the base composition of DNA varies from one species to another, while DNA specimens isolated from different tissues of the same
10、species have the same base composition； in nature DNA,the number of G units equals the number of C units and the number of A units equals the number of T units ( this strongly hinted towards the base pair makeup of DNA )； The base composition of DNA in a given species does not change with an organis
11、ms age,nutritional state,or changing environment。,Chargaff rules：,Xray photograph of DNA with high quality：DNA specimens from different species have the same results（constant width;3.4nm）； Chargaff rules：the rule of the composition of DNA physical chemistry studies and acid and alkali titrate studie
12、s on DNA base ；,Two polynucleotide chains in a DNA double helix antiparallel（one strand runs in the 53 direction,whlie its partner runs 35） Along the same axis，two chains are wound around each other, resulting in a right-handed double helix forms a major groove and a minor groove,2.2.1 key notes of
13、DNA double helix,The bases lie on the inside，the sugar-phosphate backbone is on the outside The bases are flat structure, lying in pairs perpendicular to the axis,The diameter of the double helix is 2nm There is a complete turn every 3.4nm, with 10bp per turn.,Two chains in the double helix associat
14、e by hydrogen bonding between the bases,G with C and A with T(base pairing , complementary). Three hydrogen bond can form specifically between G and C,but only two can form between A and T;,1. Two chains,antiparallel, right-handed, major groove and minor groove,2. outside(sugar-phosphate backbone),
15、inside(bases), 3,5-phosphodiester bond 3. 2nm in diameter, 10bp per turn, 3.4nm 4. Base pairing,2.2.2 important meanings,Explains for the first time how genetic information is encoded in DNA and passed from one generation to the next； tremendous strides in our understanding of the structure of DNA a
16、nd, as a result our ability to work with and manipulate the information-rich DNA molecule base pairing DNA semi-conservative replication mechanism,2.2.3 stable factors of the double helix,In physiological conditions,the DNA double helix is very stable. stable factors： H bonding between complementary
17、 base pairs； Base-stacking interaction（hydrophobic effect, the major factor）； electrovalent bond（between the negative charges carried on the phosphate groups and the positive charges carried on the proteins or metal ions）,2.2.4 DNA can occur in different three-dimendional forms,Base Obliquity,helix
18、rise per base pair,bp number per turn,Helical sense,diameter （nm）,B-form,Z-form,0-1 19-20 9,0.34 nm 0.23 nm 0.38 nm,10 11 12,R handed R handed L handed,2.0-2.37 2.55 1.8-1.84,A-form,B-form：relative humidity is 92% A-form：relative devoid of water (under 75%) Z-form：left handed helix H-form：triple hel
19、ix,H-forms,2.3 structure of RNA,Pentose is ribose，T is replaced by U； 大多数RNA分子是单链，不遵守碱基的数量比例关系 局部的碱基互补配对+不能配对的部分hairpin or internal loop or bulge； RNA分子是含短的不完全的螺旋区的多核苷酸链。,Primary structure of mRNA,Prokaryote mRNA ：polycistron/,Eukaryote mRNA ：monocistroncap in 5 terminus polyA in 3 terminus,cistron：
20、mRNA上能够翻译出一条多肽链的核苷酸功能片段。 polyA：指20250个多聚腺苷酸。 cap：甲基化（ 碱基）的鸟苷酸，通过焦磷酸与另一个发生了甲基化（核糖）的核苷酸以5, 5-三磷酸相连。,“帽子”结构：,G甲基化,焦磷酸,OCH3,甲基化,H,任意碱基,1,2,3,Four stems,Modified bases,cloverleaf,Secondary structure of tRNA,4,Four loops,Aa acceptor arm 包含有3-端和5-端 3-端是CCA 功能：携带活化Aa Anticodon arm 环正中的3个核苷酸残基称为anticodon 功能：
21、通过反密码子与mRNA上密码子的配对，来决定Aa的正确位置,D arm 环：8-12个核苷酸 臂：3-4bp 功能：氨酰-tRNA合成酶结合位点 TC arm 此环中基本含有TC 功能：结合核糖体 Variable loop 变化较大，是不同tRNA的区别之处,Tertiary structure of tRNA,在二级结构的基础上，突环上未配对的碱基通过整个分子的扭曲而配成对 已知tRNA的三级结构均为倒L形。,3 Properties of nucleic acid,3.1 chemical and physical properties of nucleic acid 颜色形状：DNA为
22、白色纤维，RNA为白色粉末； 溶解度：微溶于水，钠盐的溶解度较高。不溶于有机溶剂（用乙醇从溶液中沉淀核酸）；DNA核蛋白 RNA核蛋白0.14mol/L NaCl - +1-2mol/L NaCl + -,viscosity：DNA solutions have a high viscosity, while RNA decreases sharply颜色反应：DNA（2-deoxyribose）+二苯胺在酸性条件下形成兰紫色化合物； RNA（ribose）+苔黑酚在浓盐酸和加热条件下形成绿色化合物。,3.2 nucleic acid enzymolysis,according to subs
23、trates：DNases、RNases according to function methods：exonucleases、endonucleases exonucleases：catalyze the hydrolysis of single nucleotides from the end of a DNA or RNA chain； endonucleases：catalyze the hydrolysis of bonds between nucleic acids in the interior of DNA or RNA sequence. Restricition endon
24、uclease recognizes specific DNA sequences and cut the DNA backbone at a specific site within that sequence,Palindromis sequence,Restriction enzymes may give products with 5- or 3- tails or blunt ends,Sticky ends,3.3 UV absorption properties,The conjugated aromatic of basesnucleic acid absorb UV max=
25、260nm The UV absorption properties of nucleic acids can be used for detection,quantitation and assessment of purity,RNA： OD260 / OD280=2.0 DNA ：OD260 / OD280=1.8The value greater than 1.8,suggests RNA contaminationless proteinOD260 = 1.0 = 50g/mL dsDNA= 40g/mL ssDNA/RNA= 20g/mL (d)NTP,3.4 denaturati
26、on,renaturation and hybridization,3.4.1 denaturation 3.4.1.1 definition: a number of physical and chemical factors can lead to the destruction of double-stranded hydrogen-bonded regions of DNA and RNA,the double-stranded nucleic acids are converted to single strands.,3.4.1.2 characters of denatural
27、DNA： biological activity changed(even lost)； The UV absorption value increased (hyperchromicity),viscosity decreased，solubility decreased,buoyant density increased； The structure became loose,easy to be hydrolyzed； Molecular weight remained unchanged,3.4.1.3 thermal denaturation and Tm,Increased tem
28、perature can bring about DNA denaturation; 将DNA的变性达到50%时的温度称为DNA的解链温度（melting temperature, Tm）, 也称熔解温度或DNA的熔点。 Tm是DNA的特征常数。,影响Tm值的因素：,G+C content： G和C的含量高，Tm值高。通过测定Tm值，可反映DNA分子中GC含量：（G+C）%=（Tm-69.3）2.44 DNA的均一性：均一性较好，则Tm值范围较小； 介质的离子强度：DNA应保存在含盐的缓冲液中,3.4.2 renaturation,3.4.2.1 definition：热变性DNA在温度逐渐降
29、低时，在一定浓度的盐溶液中，两条分开的单链可以重新恢复双螺旋结构，又称为退火（annealing） 。 3.4.2.2 characters of renaturation biological activity resumed hypochromicity viscosity increased, solubility increased, buoyant density decreased,3.4.2.3 factors that influence renaturation,temperature：缓慢比快速好 DNA concentration：越高越快 Size of DNA seg
30、ments：片段越大，越不容易 DNA complexity：重复片段(repetitive segment)越多复性速度越快，单重复片段复性速度最慢,3.4.3 hybridization,定义：the renaturation of regions of complementarity between different nucleic acid strands(DNA or RNA) 特点：灵敏度高、专一性强,学 习 要 求,掌握核酸的种类、分布及功能； 掌握核酸的分子组成，连接方式，表示符号； 掌握DNA二级结构的内容（双螺旋要点，意义，稳定因素，碱基配对原则等）； 掌握tRNA二级结构的内容； 熟悉核酸的颜色反应； 掌握核酸的紫外吸收，变性、复性，分子杂交；,
