Chapter 2 Structure and function of nucleic acid. Contents. Composition of nucleic acids Structure and function of DNA Structures and functions of RNA Properties of nucleic acid. Deoxyribonucleic acid, DNA. Nucleic acid. Ribonucleic acid, RNA. Section 1 Composition of nucleic acids.
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Contents • Composition of nucleic acids • Structure and function of DNA • Structures and functions of RNA • Properties of nucleic acid
Deoxyribonucleic acid, DNA Nucleic acid Ribonucleic acid, RNA
Section 1 Composition of nucleic acids Nucleic acids(核酸） Nucleotides（核苷酸） Nucleosides （核苷） phosphate（磷酸) Bases （碱基） purines 嘌呤 pyrimidines 嘧啶 ribose（核糖） ribose 核糖 deoxyribose D-2-脱氧核糖
1. Bases 碱基 • Purines and pyrimidines • Purines （嘌呤）: • adenine (腺嘌呤), guanine （鸟嘌呤） • Pyrimidines （嘧啶）: cytosine （胞嘧啶）, thymine （胸腺嘧啶）
3. Ribonucleosides核苷 • Ribonucleoside = ribose/deoxyribose + bases
The common ribonucleosides-cytidine, uridine, adenosine and guanosine. Also inosine drawn in anti conformation.
4. Nucleotides 核苷酸 • Nucleotide = nucleoside + phosphate
6. Polynucleic acid chain 多核苷酸链 Polynucleic acid chain = connected nucleotides binding by 3’5’phosphodiester bonds （3’5’磷酸二酯键）
3’,5’phosphodiester bridges link nucleotides together to form polynucleotide chains
7. Some important nucleotides • dATP, dGTP, dCTP, dUTP—raw materials for DNA biosynthesis DNA合成原材料. • ATP, GTP, CTP, GTP • raw materials for RNA biosynthesis RNA合成原材料 • energy donor 能量供应者 • Important co-enzymes 重要辅酶 • Cycling nucleotides—cAMP, cGMP –secondary messengers in hormones action. 某些激素作用的第二信使
cAMP 环腺苷酸 and cGMP环鸟苷酸
Primary structure • The base sequence（碱基序列） in polydeoxynucleotide chain. • The smallest DNA in nature is virus(病毒) DNA. The length of φX174 virus DNA is 5,386 bases (a single chain). The DNA length of human genome is 3,000,000,000 pair bases.
2. Secondary structure DNA double helix structure
Francis H.C. Crick James D. Watson
Key points on DNA double helic structure • DNA is composed of two strand wound round each other to form a double helix. The two DNA stands are organized in an antiparallel arrangement: the two strands run in opposite directions, one strand is oriented 5’→3’ and the other is oriented 3’ →5’. • The bases on the inside and the sugar-phosphate backbones （骨架）on the outside. • The diameter of the double helix is 2 nm, the distance between two base is 0.34 nm, each turn of the helix involves 10 bases pairs, 34 nm.
(4) The bases of two strands form hydrogen bonds to each other, A pairs with T, G pairs with C. this is called complementary base pairing互补碱基配对. • (5) stable configuration稳定构象 can be maintained by hydrogen bond and base stacking force碱基堆积力
The antiparallel nature of the DNA double helix
Conformational variation in double-helical structure • B-DNA • A-DNA • Z-DNA
3. Tertiary structure:Supercoils Supercoils: double-stranded circular DNA form supercoils if the strands are underwound (negatively supercoiled) or overwound (positively supercoiled).
Supercoils in long, linear DNA arranged into loops whose ends are restrained-model for chromosomal DNA
The DNA in a prokaryotic cell is a supercoil. • The DNA in eukaryotic cell is packaged into chromosomes.
Eukaryotic chromosomes（真核染色体） • Nucleosome（核小体） • ↓ • 30nm fiber（纤丝） • ↓ • Radial loops（突环） • ↓ • Rosette（玫瑰花结） • ↓ • Coid（螺旋圈） • ↓ • Chromatid（染色单体） • ↓ • Chromosome（染色体）
Nucleosome • Histones interact ionically with • the anionic phosphate groups in • the DNA backbone to form • nucleosomes, structures in • which the DNA double helix is • wound around a protein “core” • composed of pairs of four • different histone polypeptides.
Functions of DNA • The carrier of genetic information. • The template strand involved in replication and transcription. • Gene（基因）: the minimum functional unit in DNA • Genome（基因组）: the total genes in aliving cell or living beings.
Section 3 Structures and functions of RNA • Types : • mRNA: messenger RNA, the carrier of genetic information from DNA to translate into protein • tRNA: transfer RNA , to transport amino acid to ribosomes to synthesize protein • rRNA: ribosome RNA, the components of ribosomes • hnRNA: Heterogeneous nuclear RNA (核内不均一RNA) • snRNA: small nuclear RNA （核内小RNA） • Ribozyme（核酶）
RNAstructure • RNA molecules are largely single-stranded but there are double-stranded regions.
Massager RNA( mRNA) • The carrier of genetic information from DNA for the synthesis of protein. Composition: vary considerably in size (500-6000bases in E. coli)
Eukaryotic mRNA Structure • Capping: linkage of 7-methylguanosine 7’-甲基鸟嘌呤to the 5’ terminal residue. (2) Tailing: attachment of an adennylate polymer (poly A 多聚A)
Ribosome RNA (rRNA) • A component of ribosomes. • Ribosomes are cytoplasmic structures that synthesize protein, composed of both proteins and rRNA. • The ribosomes of prokaryotes and eukaryotes are similar in shape and function. The difference between them is the size and chemical composition.
The organization and composition of prokaryotic and eukaryotic ribosomes
The proposed secondary structure for E. coli 16S rRNA
Transfer RNA (tRNA) Function: Transport amino acids to ribosomes for assembly into proteins. • Primary Structure : Average length: 75 bases Modified bases: pseudouridine methylguanosine dihydrouridine The sequence CCA at the 3’ terminus
Secondary structure: warped cloverleaf 三叶草 • Four loops and four arms四环四臂 • Amino acid arm氨基酸臂(7bp): to bide amino acid • D loop(8-14bp) D-环and D arm(3-4bp): • Anticode loop(5bp) 反密码环and arm(7bp): to recognize amino acid • TψC loop（7bp） TψC 环and arm(5bp) • Variable loop(4-5bpor 13-21bp)可变环
The complete nucleotid sequence and cloverleaf structure of yeast Alanine tRNA
(a)the three-dimensional structure of yeast phenylalanine Trna as deduced from X-ray diffraction studies of its crystal. (b)a space-filling model of the molecule.
Section 4 Properties of nucleic acid • General physical and chemical properties: • Amphiphilic 两性 molecules; normally acidic because of phosphate. • Solid DNA white fiber; RNA white powder. Insoluble in organic solvents, can be precipitate by ethanol. • Can be hydrolyzed by acid/alkaline/enzymes
2. UV Absorption紫外吸收 • Specific absorption at 260nm. • This can be used to identify nucleic acid