Chapter 2 Structure and Function of
Nucleic Acids
• Introduction
• Life depends on the genetic instructions. This hereditary
information is passed on from a cell to its daughter cells
at division, and from one generation of an organism to
the next through the organisms’reproductive cells.
Genes, the information-containing elements that
determine the characteristics of a species as a whole and
of the individuals within it.
1 Chemistry of nucleic acids
• Nucleotides are the subunits of DNA and RNA.
• A nucleotide consists of a base, a five-carbon sugar,
and one or more phosphate groups.
•Purines and pyrimidines are nitrogen-containing
heterocyclic compounds.
•Their principal derivatives are nucleosides and nucleotides.
Cytosine (C), thymine (T), and uracil (U) are called
pyrimidine compounds; guaninie (G) and adenine (A) are
purine compounds. Each nucleotide is named by reference to
the unique base that it contains.
Purine and Pyrimidine
Nomenclature
Diverse physiologic functions of Nucleotides
• Specific nucleotides participate in reactions that fulfill
physiologic functions as diverse as protein synthesis,
nucleic acid synthesis, regulatory cascades, and intraand intercellular signal transduction pathways.
• A. Adenosine derivatives: AMP, ADP, ATP, and cAMP.
ATP are the major biologic transducer of free energy.
• B. Guanosine derivatives: cGMP serve as the principal
second messenger in some cells.
• C. Many coenzyme are nucleotide derives: NAD+,
NADP+, FAD, etc.
Other functions of nucleotides
2 Deoxyribonucleic acid (DNA)
The two strands of the double-helical molecule,
each of which possesses a polarity, are antiparallel;
ie, one strand runs in the 5’to 3’ direction and the
other in the 3’ to 5’direction. The two strands, in
which opposing bases are held together by
hydrogen bonds, wind around a central axis in the
form of a double helix. The genetic information
resides in the sequence of nucleotides on one
strand, the template strand. This is the strand of
DNA that is copied during nucleic acid synthesis.
• A always pairs with T, and G with C. This
complementary base-paring enables the base pairs
to be packed in the energetically most favorable
arrangement in the interior of the double helix.
• Each turn of DNA is made up of 10.4 nucleotide
pairs and the center-to center distance between
adjacent nucleotide pairs is 3.4 nm. The coiling of
the two strands around each other creates two
grooves in the double helix, major groove and
minor groove.
• B-DNA, A-DNA, and Z-DNA.
large groove
small
groove
ove
small groove
Three kinds of DNA double-helix
large
groove
Formation of nucleic acids from nucleotides
5' P
P
P
P
P
P
P
P
5' pApCpTpGpCpTpApApC-OH 3'
5' ACTGCTAAC 3'
C
A
A
T
C
G
T
C
A
P
OH 3'
Nucleotides absorb ultraviolet light
• The conjugated double bonds of the
enterocyclic bases of purines an pyrimidines,
and polynucleotides absorbe ultraviolet light.
Their spectra are pH-dependent. However, at
pH 7.0 all the common nucleotides absorb light
at a wavelength close to 260 nm.
DNA supercoiling
• Packaging large DNA molecules to fit into
cells requires DNA supercoiling.
• Nucleosome formation
• Chromatin and chromosome.
Circled DNA
Supercoiled DNA
Denaturation and Renaturation of DNA
• Denaturation (melting) and Renaturation
of DNA
• PCR (Polymerase Chain Reaction)
• cDNA (complementary DNA)
• Southern blotting (DNA/cDNA)
• Northern blotting (DNA/RNA).
• Western Blotting
Figure 4-8. The denaturation and renaturation of double-stranded DNA molecules.
Curve of DNA melting
Transfer of information from DNA to
protein
Ribonucleic acid (RNA)
RNA is a polymer of purine and pyrimidine
ribonucleotides linked together by 3’, 5’phosphodiester bridges analogous to those in DNA.
Although sharing many features with DNA, RNA
possesses several specific differences.
• (1) Bases are attached to ribose rather than 2’deoxyribose.
• (2) U, not T.
• (3) Single strand. however, capable of folding
back on itself like a hairpin.
• (4) Others
• Those cytoplasmic RNA molecules that serve as
templates for protein synthesis are designated
messenger RNAs, or mRNA. Many other
cytoplasmic RNA molecules (ribosomal RNAs,
or rRNA) have structural roles wherein they
contribute to the formation of ribosomes ( the
organellar machinery for protein synthesis) or
serve as adapter molecules (transfer RNAs;
tRNAs) for the translation of RNA information
into specific sequences of polymerized amino
acids.
• Some RNA molecules have intrinsic catalytic
activity. The activity of these ribozymes often
involves the cleavage of a nucleic acid. An
example is the role of RNA in catalyzing the
processing of the primary transcript of a gene into
mature messenger RNA.
• In human cells, there are small nuclear RNA
(snRNA) species that are not directly involved in
protein synthesis but that may have roles in RNA
processing and the cellular architecture. These
relatively small molecules vary in size from 90 to
about 300 nucleotides.
mRNA
• This class is the most heterogeneous in size and stability.
mRNAs, particularly in eukaryotes, have some unique chemical
characteristics. The 5’terminal of mRNA is “capped”by a
7-methylguanosine triphosphate that is linked to an adjacent
2’-0 –methyl rebonucleotide at its 5’-hydroxyl through the
three phosphates. The other end of most mRNA molecules, the
3’-hydroxyl terminal, has attached a polymer of adenylate
residues 20-250 nucleotides in length.
• The mRNA molecules present in the cytoplasm are not the
RNA products immediately synthesized from the DNA
template but must be formed by processing from a
precursor molecule before entering the cytoplasm. Thus, in
mammalian nuclei, the immediate products of gene
transcription constitute a fourth class of RNA molecules.
These nuclear RNA molecules are very heterogeneous in
size and are quite large. The heterogeneous nuclear RNA
(hnRNA) molecules may have a molecular weight in
excess of 107, whereas the molecule weight of mRNA
molecules is generally less than 2×106.
mRNA Structure of Eucaryotes
5'
m7Gppp
Coding
region
±àÂëÇø
AUG
5'·Ç·- ÒëÇø region
5‘-untranslation
UAA
3'
AAA¡- ¡- An
3'·Ç·- ÒëÇøregion
3‘-untranslation
Cap structure
OH OH
H
H
NH2
N
N
O
O
H 5'
O5'
O CH2 O P O P O P O CH2
N
N
N
O
O
O
O
H 2'H
3'
N
H
H
CH3
OCH3
O
H
H2N
N
HN
O
(Only on some caps)
7-methylguanosine triphosphate cap
Figure 4-18.
Structure of
the 5′
methylated
cap of
eukaryotic
mRNA.
Figure 4-19. Overview of RNA
processing in eukaryotes using β-globin
gene as an example. The β-globin gene
contains three protein-coding exons (red)
and two intervening noncoding introns
(blue). The introns interrupt the proteincoding sequence between the codons for
amino acids 31 and 32 and 105 and 106.
Transcription of this and many other
genes starts slightly upstream of the 5′
exon and extends downstream of the 3′
exon, resulting in noncoding regions
(gray) at the ends of the primary transcript.
These regions, referred to as untranslated
regions (UTRs), are retained during
processing. The 5′ 7-methylguanylate cap
(m7Gppp; green dot) is added during
formation of the primary RNA transcript,
which extends beyond the poly(A) site.
After cleavage at the poly(A) site and
addition of multiple A residues to the 3′
end, splicing removes the introns and
joins the exons. The small numbers refer
to positions in the 147-aa sequence of βglobin.
Figure 4-30.
Recognition of a
tRNA by
aminoacyl
synthetases.
Aspartyl-tRNA
synthetase
(AspRS) is a
class II enzyme,
and arginyltRNA
synthetase
(ArgRS) is a
class I enzyme.
tRNA
• tRNA molecules vary in length from 74-95
nucleotides. There are at least 20 species of
tRNA molecules in every cell, at least one
(and often several) corresponding to each of
the 20 amino acids required for protein
synthesis.
CCA end
Tψ arm
Anticodon arm
Anticodon
tRNA structure
D arm
Figure 4-26. Structure of tRNAs.
Figure 6-11. Amino acid activation. The two-step process in which an amino acid (with its side chain
denoted by R) is activated for protein synthesis by an aminoacyl-tRNA synthetase enzyme is shown. As
indicated, the energy of ATP hydrolysis is used to attach each amino acid to its tRNA molecule in a highenergy linkage. The amino acid is first activated through the linkage of its carboxyl group directly to an
AMP moiety, forming an adenylated amino acid;the linkage of the AMP, normally an unfavorable reaction,
is driven by the hydrolysis of the ATP molecule that donates the AMP. Without leaving the synthetase
enzyme, the AMP-linked carboxyl group on the amino acid is then transferred to a hydroxyl group on the
sugar at the 3' end of the tRNA molecule. This transfer joins the amino acid by an activated ester linkage to
the tRNA and forms the final aminoacyl-tRNA molecule. The synthetase enzyme is not shown in these
diagrams.
Figure 4-29.
Aminoacylati
on of tRNA.
Amino acids
are covalently
linked to
tRNAs by
aminoacyltRNA
synthetases.
Figure 4-22. Assigning codons using synthetic mRNAs
containing a single ribonucleotide. Addition of such a synthetic
mRNA to a bacterial extract that contained all the components
necessary for protein synthesis except mRNA resulted in synthesis
of polypeptides composed of a single type of amino acid as
indicated.
rRNA
A ribosome is a cytoplasmic nucleoprotein
structure that acts as the machinery for the
synthesis of proteins from the mRNA
templates. On the ribosomes, the mRNA
and tRNA molecules interact to translate
into a specific protein molecule information
transcribed from the gene.
Figure 4-32. The general structure of ribosomes in prokaryotes and eukaryotes.
Figure 4-33. Twodimensional map of the
secondary structure of the
small (16S) rRNA from
bacteria, showing the
location of base-paired
stems and loops. In general,
the length and position of the
stem-loops are very similar in
all species, although the exact
sequence varies from species
to species. The most highly
conserved regions are
represented as red lines, and
the numbered stem-loops
unique to prokaryotes are
preceded by a P. Eukaryotic
small (18S) rRNAs exhibit a
generally similar pattern of
stem-loops, although, as with
prokaryotes, a few are unique.
Figure 4-20. The three roles of RNA in protein synthesis.
Figure 4-25. Translation of nucleic acid sequences in mRNA into amino acid sequences
in proteins requires a two-step decoding process. First, an aminoacyl-tRNA synthetase
couples a specific amino acid to its corresponding tRNA. Second,a three-base sequence in
the tRNA (the anticodon) base-pairs with a codon in the mRNA specifying the attached
amino acid. If an error occurs in either step, the wrong amino acid may be incorporated into
a polypeptide chain.
Figure 6-17. The genetic code. The standard oneletter abbreviation for each amino acid is presented
below its three-letter abbreviation. Codons are
written with the 5'-terminal nucleotide on the left.
Note that most amino acids are represented by more
than one codon and that variation is common at the
third nucleotide (see also Figure 3-16).
Figure 4-35. Two types of methionine tRNA are found in all cells. One,
designated tRNAiMet, is used exclusively to start protein chains, and the
other, designated tRNAMet, delivers methionine to internal sites in a
growing protein chain. In bacteria, a formyl group (CHO) is added to
methionyl-tRNAiMet, forming fMet-tRNAiMet
Small stable RNA
• A large number of discrete, highly conserved, and
small stable RNA species are found in eukaryotic
cells. The majority of these molecules exist as
ribonucleoproteins and are distributed in the
nucleus, in the cytoplasm, or in both. They range
in size from 90 to 300 nucleotides and are present
in 100,000-1,000,000 copies per cell. Small
nuclear RNA (snRNA) are significantly involved
in mRNA processing (intron removal and
processing of hnRNA into mRNA) and gene
regulation.
Nuclease
• Enzymes capable of degrading nucleic acids.
• Deoxyribonucleases (DNAase) and Ribonucleases
(RNAase).
• Exonuclease and Endonuclease.
• Endonuclease: enzymes capable of cleaving internal
phosphodiester bonds to produce either 3’-hydoxyl
and 5’-phosphoryl terminals or 5’-hydroxyl and 3’phosphoryl terminals.
• Some are capable of hydrolyzing both strands of a
double-stranded molecules, whereas others can
only cleave single strands of nucleic acids. Some
nuclease can hydrolyze only unpaired single
strands, while others are capable of hydrolyzing
single strands participating in the formation of
double-stranded molecule.
• There exist classes of endonucleases that
recognize specific sequences in DNA; the majority
of these are the restriction endonucleasee, which
have in recent years become important tools in
molecular genetics and medical sciences.
Restriction endonucleases
•
•
•
•
•
•
•
•
5’----GGATCC----3’ BamHI 5’----G
GATCC----3’
3’----CCTAGG----5’
3’----CCTAG
G----5’
5’----GTTAAC----3’
3’----CAATTG----5’
HpaI
5’----GTT
3’----CAA
AAC----3
TTG----5’
5’----GAATTC----3’
3’----CTTAAG----5’
EcoRI
5’----G
AATTC----3’
3’----CTTAA
G----5’
• Palindromic: The nucleotide sequence is the same if
the helix is turned 180 degrees around the center of
the short region of the helix that is recognized.
• Cohesive ends: Some restriction nucleases produce
staggered cuts, which leave short single-stranded tails
at the two ends of each fragment. Ends of this type ar
known as chohesive ends, as each tail can form
complementary base pairs with the tail at any other
end by the same enzyme. The cohesive ends generated
by restriction enzymes allow any two DNA fragments
to be easily joined together, as long as the fragments
were generated with the same restriction enzymes (or
with another nuclease that produces the same cohesive
ends).
选择题练习
核酸化学
1. The element that could be used in
nucleic acid quantitation is ( )
A. C
B. O
C. N
D. H
E. P
2. The basic unit composition of nucleic acid is (
A. Ribose and deoxyribose
B. phosphoric acid and pentaglucose
C. Pentaglucose and basic group
D. mononucleotide
E. phosphoric acid，pentose and basic group
)
3．脱氧核糖核苷酸彻底水解，生成的
产物的产物是(
)
A 核糖和磷酸
B 脱氧核糖和碱基
C 脱氧核糖和磷酸
D 磷酸，核糖和碱基
E 脱氧核糖，磷酸和碱基
4．在核酸分子中核苷酸之间的连接方式是(
A. 3’,3’－磷酸二酯键
B. 糖苷键
C. 2’,5’ －磷酸二酯键
D. 肽键
E. 3’,5’－磷酸二酯键
)
5. The ultraviolet absorption maximum of
nucleic acid is about ( )
A. 220nm
B. 240nm
C. 260nm
D. 280nm
E. 300nm
6.
含有稀有碱基比例较多的核酸是(
A. mRNA
B. DNA
C. tRNA
D. rRNA
E. hnRNA
)
7.
核酸分子中储存、传递遗传信息的关键部分是(
A. 核苷
B. 戊糖
C. 磷酸
D. 碱基序列
E. 戊糖磷酸骨架
)
8．DNA分子碱基含量关系哪种是错误的？
A. A+T=C+G
B. A+G=C+T
C. G=C
D. A=T
E. A/T=G/C
9.
ATP的生理功能不包括(
A. 为生物反应供能
B. 合成RNA
C. 贮存化学能
D. 合成DNA
E. 转变为cAMP
)
10.
型?
下列哪种核酸的二级结构具有”三叶草”
A. mRNA
B. 质粒DNA
C. tRNA
D. 线粒体DNA
E. rRNA
11.
关于mRNA的论述不正确的是(
)
A. mRNA分子中含有生物遗传信息
B. mRNA在生物细胞内种类最多
C. 各种mRNA3’末端和5’末端都有相同的结构
D. mRNA的碱基序列可以指导多肽链的合成
E. mRNA的所有碱基都有编码氨基酸的作用
12. The protein not in nucleosome core particle is (
A. H1
B. H2A
C. H2B
D. H3
E. H4
)
13.
DNA变性是指(
)
A. 多核苷酸链解聚
B. DNA分子由超螺旋变为双螺旋
C. 分子中磷酸二酯键断裂
D. 碱基间氢键断裂
E. 核酸分子的完全水解
14.
DNA Tm值较高是由于下列哪组核苷酸含量
较高所致?
A. G+A
B. C+G
C. A+T
D. C+T
E. A+C
15. Where does DNA reside in?
A. Golgi's body
B. rough endoplasmic reticulum
C. mitochondrium
D. chromosome
E. lysosome
16.
含有腺苷酸的辅酶有(
A.NAD
B.NADP
C.FAD
D.FMN
E.CoA-SH
)
17.
关于tRNA的论述不正确的是(
A. 分子中含有稀有碱基
B. 分子中含有密码环
C. 是细胞中含量最多的是RNA
D. 主要存在于胞液
E. 其二级结构为倒L型
)
18.
维持DNA双螺旋结构的稳定因素包括(
A. 分子中的磷酸二酯键
B. 碱基对之间的氢键
C. 碱基平面间的堆积力
D. 磷酸戊糖骨架的支撑力
E. 骨架上磷酸之间的负电排斥力
)
19.
DNA变性的实质是(
)
A. 多核苷酸链解聚
B. 碱基的甲基化
C. 磷酸二酯键断裂
D. 加热使碱基对间氢键断裂
E. 使DNA双螺旋结构松散,变成单链
20. What does the Tm refer to about DNA?
A. optimum temperature
B. hydrolytic temperature
C. Renaturation temperature
D. melting temperature
E. denaturation temperature
Thank you!