chapter 2 structure and function of nucleic acid

Chapter 2 Structure and function of nucleic acid

Contents

1. Composition of nucleic acids

2. Structure and function of DNA

3. Structures and functions of RNA

4. Properties of nucleic acid

Nucleic acid

Deoxyribonucleic acid, DNA

Ribonucleic acid, RNA

Section 1 Composition of nucleic acids

Nucleic acids( 核酸）

Nucleosides （核苷） phosphate （磷酸 )

Nucleotides （核苷酸）

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）

2. Ribose (in RNA) and deoxyribose (in DNA)

• 核糖与脱氧核糖

• 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

5. Nucleoside diphosphates and triphosphates

• 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 f

or DNA biosynthesis DNA 合成原材料 . • ATP, GTP, CTP, GTP (1) raw materials for RNA biosynthesis RNA 合

成原材料 (2) energy donor 能量供应者 (3) Important co-enzymes 重要辅酶 • Cycling nucleotides—cAMP, cGMP –second

ary 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

• Section 2 Structure and function of DNA

1. Primary structure The base sequence （碱基序列） in polydeoxynu

cleotide 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

James D. Watson

Francis H.C. Crick

• Key points on DNA double helic structure (1) DNA is composed of two strand wound round eac

h 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’.

(2) The bases on the inside and the sugar-phosphate backbones （骨架） on the outside.

(3) 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).

The DNA interwinds and wraps about itsself

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 t

ranscription.

Gene （基因） : the minimum functional unit in DNA

Genome （基因组） : the total genes in a living cell or living beings.

Section 3 Structures and functions of RNA

1. Types : • mRNA: messenger RNA, the carrier of genetic i

nformation from DNA to translate into protein • tRNA: transfer RNA , to transport amino acid t

o ribosomes to synthesize protein • rRNA: ribosome RNA, the components of ribo

somes • hnRNA: Heterogeneous nuclear RNA ( 核内不均一 RN

A) • snRNA: small nuclear RNA （核内小 RNA ） • Ribozyme （核酶）

RNA structure

• 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

(1) 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)

真核生物 mRNA 的结构

5' 3'

m7Gppp AAA¡ ¡ An

3'·Ç· ÒëÇø5'·Ç· ÒëÇø

±àÂëÇø

AUG UAA

Ribosome RNA (rRNA)

• A component of ribosomes. • Ribosomes are cytoplasmic structures that synthe

size 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)

• Primary Structure :

Average length: 75 bases

Modified bases: pseudouridine

methylguanosine

dihydrouridine

The sequence CCA at the 3’ terminus

Function: Transport amino acids to ribosomes for assembly into proteins.

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

A general diagram for the structure of tRNA

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

1. General physical and chemical properties: (1) Amphiphilic 两性 molecules; normally a

cidic because of phosphate. (2) Solid DNA white fiber; RNA white powde

r. Insoluble in organic solvents, can be precipitate by ethanol.

(3) 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

The UV absorption spectra of the common ribonucleotides

3. Denaturation 变性• Concept: • the course of hydrogen bonds broken, 3-D

structure was destroyed, the double helix changed into single strand irregular coid

• Results:

(1) the value of 260nm absorption is increased

(2) Viscous 黏度 is decreased

(3) biological functions are lost

• Heat denaturation and Tm

When DNA were heated to certain temperature, the absorption value at 260nm would increased sharply ， which indicates that the double strand helix DNA was separated into single strand. When the absorption value increases to 40%, the value change would low down, which indicates the double strands had been completely separated.

DNA denaturation and Tm

• Tm: melting temperature of DNA

• The temperature of UV absorption increase to an half of maximum value in DNA denaturation.

• Factors affect Tm:

G-C content: there are three hydrogen bonds between G-C pair. The more G-C content, the higher Tm value.

• (G+C)% = (Tm-69.3) × 2.44

Higher G+C

Less G+C

Temperature

Tm of two DNA molecules with different G+C content

4. Renaturation of DNA

• When slowly cooling down the denatured DNA solution, the single strand DNA can reform a double strands helix to recover its biological functions.

5. Molecule hybridization 分子杂交• During the course of lowing down denatu

ring temperature, between different resource DNAs or single stand DNA and mRNA with complementary bases will repair into a double strands to form a hybrid DNA or DNA-RNA . This course is called molecule hybridization.