Download Chapter 2 nucleic acid

Chapter 2 Structure and
function of nucleic acid
Contents
1.
2.
3.
4.
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
Nucleotides（核苷酸）
Nucleic acids(核酸）
Nucleosides （核苷）
Bases （碱基）
purines 嘌呤
pyrimidines 嘧啶
phosphate（磷酸)
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
for 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 –
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
• Section 2 Structure and function
of DNA
1. 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
(1) 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’.
(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.
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.
•
(4)
•
(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
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•
•
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）
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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
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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 a living cell
or living beings.
Section 3 Structures and functions of RNA
1. 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
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hnRNA: Heterogeneous nuclear RNA (核内不均一
RNA)
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'
m7Gppp
5'·Ç·- ÒëÇø
±àÂëÇø
AUG
UAA
3'
AAA¡- ¡- An
3'·Ç·- ÒëÇø
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
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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
acidic because of phosphate.
(2) Solid DNA white fiber; RNA white powder.
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
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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
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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
Less G+C
Higher 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
denaturing 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.