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Chapter 8
Nucleotides and Nucleic Acids
• Some basics
•Nucleic acid structure
•Nucleic acid chemistry
•Other functions of nucleotides
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8.1 Some Basics
• Gene–A segment of a DNA molecule that
contains the information required for the
synthesis of a functional biological product.
• RNAs–
1. Ribosomal RNAs –structural components
of ribosomes, the complexes that carry out
the synthesis of proteins.
2. Messenger RNAs– intermediaries,
carrying genetic information from one or a
few genes to a ribosome, where the
corresponding proteins can be synthesized.
3. Transfer RNAs– adapter molecules that
faithfully translate the information in mRNA
into a specific sequence of amino acids.
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8.1 Some Basics
• Two types of nucleic acids：DNA & RNA
– RNA：Ribonucleic acid
– DNA：Deoxyribonucleic acid
（p. 85）
• 二者共同特色：均為polymers
– Monomer unit：
– 5C sugar（ribose）＋N base＋Phosphate
• 二者間差異：
– RNA：ribose
– DNA：2’-deoxyribose
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8.1 Some Basics
1. Nucleotides and Nucleic Acids Have Characteristic
Bases and Pentoses
• Nucleotides – have three characteristic components:
(1) A nitrogenous base:
purine (adenine (A) and guanine (G))
pyrimidine： (cytosine (C), thymine (T) [for DNA]
and uracil (U) [for RNA] )
(2) A pentose
(3) A phosphate
• Nucleoside – A nucleotide without the phosphate
group.
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Purine：N9
Pyrimidine：N1
DNA：－OH
RNA：－H
Structure of nucleotides
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p. 274, Fig. 8-1a
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1. Nucleotides and Nucleic Acids Have
Characteristic Bases and Pentoses
•
•
•
•
P. 276, Fig. 8-5 a&b
較少見的purine and pyrimidine bases
DNA：methylated forms
Viral DNAs：hydroxymethylated or
glucosylated
• 角色：調控或保護遺傳訊息
• 命名原則：替代的官能基所在的環的位置
• P. 276, Fig. 8-6：磷酸化的核苷
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2. Phosphodiester Bonds Link Successive
Nucleotides in Nucleic Acids
• Nucleotides 以phosphodiester linkage 結合形成
核酸 (P. 277, Fig. 8-7)
• The Nature & Significance of Primary Structure
– 方向性：因phosphodiester link之連接方式，nucleic
acids有3’-end，5’-end之分別
– 獨特性：組成核酸分子之nucleotide sequence
• 核酸骨幹由磷酸根與核糖交錯串成，具高度親水
性
• 磷酸之pKa近乎0，生理環境下帶負電荷，藉周圍
帶正電荷之蛋白質、金屬離子、多胺
(polyamines)中和其負電荷
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2. Phosphodiester Bonds Link Successive
Nucleotides in Nucleic Acids
• 5-end與3‘-end之定義
– The 5’ end lacks a nucleotide at the 5’ position
– The 3’ end lacks a nucleotide at the 3’ position.
• RNA is hydrolyzed rapidly under alkaline
conditions, but DNA is not; the 2’-hydroxyl
group in RNA are directly involved in the
process. (RNA在鹼性環境下迅速水解，與2’
－OH有關，p. 277, Fig. 8-8)
• Oligonucleotide：≤ 50 nucleotides
• Polynucleotide：＞ 50 nucleotides
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核酸結構的簡要表達方式
By convention, the structure of a single strand of nucleic
acid is always written with the 5’ end at the left and 3’ end
at the right
pACGTA,
Oct, 2007
pA-C-G-T-AOH, or pApCpGpTpA
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3. The Properties of Nucleotide Bases Affect the
Three-Dimentional Structure of Nucleic Acids
• Free pyrimidines and purines are weakly
basic compounds and thus called bases.
• Resonance among atoms in the ring gives
most of the bonds partial double-bond
character. One result is that pyrimidines
are planar molecules; purines are very
nearly planar, with slight pucker.
• Free pyrimidine and purine bases may
exist in two or more tautomeric forms
depending on the pH.
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Tautomeric forms of uracil. The lactam form predominates
at pH 7.0; the other forms become more prominent as pH
decreases. The other free pyrimidines and the free purines
also have tautomeric forms, but they are more rarely
encountered.
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3. The Properties of Nucleotide Bases Affect the
Three-Dimentional Structure of Nucleic Acids
• The purine and pyrimidine bases are
hydrophobic and relatively insoluble in water at
the near-neutral pH of the cell.
• At acidic or alkaline pH the bases become
charged and their solubility in water increases.
• Hydrophobic stacking interactions in which two
or more bases are positioned with the planes
of their rings parallel are one of two important
modes of interaction between bases in nucleic
acids.
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3. The Properties of Nucleotide Bases Affect the
Three-Dimentional Structure of Nucleic Acids
• The stacking also involved a
combination of van der Waals and
dipole-dipole interactions between
bases.
• Base stacking helps to minimize contact
of the bases with water, and basestacking interactions are very important
in stabilizing the three-dimensional
structure of nucleic acids.
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3. The Properties of Nucleotide Bases Affect the
Three-Dimentional Structure of Nucleic Acids
• Purine & pyrimidine最重要的官能基：
– Ring N、carbonyl groups、exocyclic
animo groups
• H bonds btwn bases:
– 2nd important mold of interaction btwn
bases
– Permit complementary association of 2
strands of nucleic acids
– Base pairs：A＝T(U) ；C≡G (p. 279, Fig. 8-11)
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8.2 Nucleic Acid Structure
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＊
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DNA stores genetic information–The
Avery-MacLeod-McCarty experiment.
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The Hershey-Chase experiment
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2. DNA Molecules Have Distinctive Base
Compositions
• The base composition of DNA generally varies
from one species to another.
• DNA specimens isolated from different tissues
of the same species have the same base
composition.
• The base composition of DNA in a given
species does not change with an organism’s
age, nutritional state, or changing enviroment.
• A =T, and G =C. Thus, A + G = T + C.
(Chargaff’s rules)
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3. DNA Is a Double Helix
• Watson & Crick model (1953)說明DNA之二級結構
(Nobel Prize, 1962)
• Franklin & Wilkins提供X-ray diffraction證據 (p.282,
Fig 8-14)
–
–
–
–
–
–
–
–
螺旋體結構，2 DNA strands
2 DNA strands上的鹼基以氫鍵結合
鹼基配對（base pairing）：A＝T；C≡G
10 pairs/turn （base pairs間彼此相錯36o；距離3.4A）
Height：3.4 nm/turn (34 A/turn)
Antiparallel（反向性質）(p. 283, Fig. 8-16)
2 DNA strands間之互補（complementary）關係
Self-replication：Chargaff’s rules：A＋G＝C＋T
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4. DNA Can Occur in Different ThreeDimentional Forms
(1) Structural variation generally do
not affect the key properties of DNA
defined by Watson and Crick:
strand complementarity, antiparallel
strands, and requirement for A=T
and G≡C base pairs.
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4. DNA Can Occur in Different ThreeDimentional Forms
• (2) DNA不同的結構反映3個狀況
– Deoxyribose可能有不同的conformations
– 核酸骨幹構成鍵結可轉動 (p.284, Fig. 8-18a)
– Ribose之C1’與nitrogen base結合的鍵結可轉
動 (p.284, Fig. 8-18b)
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4. DNA Can Occur in Different ThreeDimentional Forms
• Alternative nucleic acid structures: B, A, Z helices
– B form
• 存在於高溼度狀態
• Helix rise per base pair: 3.4 A
• Base pairs與中心軸較近 (DNA strands橫切面
直徑較小)
• DNA strands表面有大小不同的溝隙 (major &
minor grooves)
• 右旋結構
• 1 turn中含10.5 bp (p. 284, Fig. 8-19, Table )
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4. DNA Can Occur in Different ThreeDimentional Forms
– A form
• 存在於低濕度狀態(脫水、結晶)
例：double-strand RNA、DNA-RNA hybrid
• Base pairs離中心軸較遠 (double helix橫切面直徑較B
form大)
• Base pairs與中心軸非垂直(傾斜角度大, 約20o)
• Helix rise per base pair: 2.6A
• Double helix表面溝紋均勻
• 缺水狀況下穩定
• 右旋結構
• 1 turn含11 bp [p. 284, Fig. 8-19]
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4. DNA Can Occur in Different ThreeDimentional Forms
• Z form
– 左旋
– 12 bp/turn, slender, more elongated
– Zigzag backbone
– Purine-pyrimidine序列特色:
• Alternating C, G
• Alternating 5-methyl C, G
• Alternating syn-purine, anti-pyrimidine
– 可能具有調控特定基因表現的功能
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5. Certain DNA sequences adopt
unusual structures
• Bends occur in the DNA helix whenever four
or more adenosine residues appear
sequentially in one strand. The bending
sequences of DNA provide the sites for the
binding by the special proteins. (-AAAA-)
• Hairpins–Palindromic DNA sequences in the
same strand. (p. 285, Fig. 8-20, 迴文)
• Cruciforms–Palindromic DNA sequences in
both strands of a duplex DNA. (p. 285, Fig. 821, 迴文可能形成hairpins or cruciforms)
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Triplex DNAs
Base-pairing patterns in one wellcharacterized form of triplex DNA. The
Hoogsteen pair in each case is shown in red.
結構不尋常, 可能是DNA代謝啟動或調控處
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Hoogsteen Pairing
• A cytidine residue (if protonated) can pair
with the guanosine residue of a G≡C
nucleotide pair, and a thymidine can pair
with the adenosine of an A=T pair.
• Hoogsteen pairing allows the formation of
triplex DNAs that are stable at the low pH,
because the G≡C•C+ triplet requires a
protonated cytosine. In the triplex, the pKa
of this cytosine is > 7.5, altered from its
normal value of 4.2.
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G Tetraplex
• Four DNA strands can also pair to form
a tetraplex (also called quadruplex), but
this occurs readily only for DNA
sequences with a very high proportion
of guanosine residues.
• The orientation of strands in the
tetraplex can be parallel or antiparallel.
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H-DNA: 出現在可辨識特定序列的DNA-Bining
Proteins的結合處, 與基因調控有關
A sequence of alternating T and C
residues can be considered a mirror
repeat centered about a central T or C.
The purine strand (alternating A and G
residues) is left unpaired. This structure
produces a sharp bend in the DNA.
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These sequences from an unusual structure in which the
strands in one half of the mirror repeat are separated and the
pyrimidine-containing strand (alternating T and C residues)
folds back on the other half of the repeat to form a triplex helix.
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5. Certain DNA sequences adopt
unusual structures
• In the DNA of living cells, sites recognized by
many sequence-specific DNA-binding proteins
are arranged as palindromes, and
polypyrimidine or polypurine sequences that
can form triplex helices or even H-DNA are
found within regions involved in the regulation
of expression of some eukaryotic genes.
• Synthetic DNA strands designed to pair with
the regulatory sequences of DNA to form
triplex DNA could could disrupt gene
expression.
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6. Messenger RNAs code for polypeptide
chains
• RNA acts as an intermediary by using the
information encoded in DNA to specify the
amino acid sequence of a function protein.
• In prokaryotes a single mRNA molecule may
code for one or several polypeptide chains.
• If it carries the code for only polypeptide, the
mRNA is monocistronic; if it codes for two or
more different polypeptides, the mRNA is
polycistronic. (p. 288, Fig. 8-24)
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7. Many RNAs have more complex
three-dimensional structures
• RNA can base-pair with complementary
regions of either RNA or DNA.
• Base pairing matches the pattern for
DNA: G pairs with C and A pairs with U.
One difference is that base pairing
between G and U residues–unusual in
DNA–is fairly common in RNA.
• The paired strands in RNA or RNA-DNA
duplexes are antiparallel, as in DNA.
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7. Many RNAs have more complex threedimensional structures
• When complementary sequences are present,
the predominant double-stranded structure is
an A-form right-handed double helix. Z-form
helices have been made in the laboratory. The
B form of RNA has not been observed.
• Breaks in the regular A-form helix caused by
mismatched or unmatched bases in one or
both strands are common and result in bulges
or internal loops.
• Specific short base sequences (e.g. UUCG)
are often found at the ends of RNA hairpins
and are known to form particular tight and
stable loops.
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1. Double-helical DNA and RNA can be denatured
• The close interaction between stacked bases in a
nucleic acid has the effect of decreasing its
absorption of UV light relative to that of a solution
with the same concentration of free nucleotides.
• The absorption is decreased further when two
complementary nucleic acids are paired. This is
called the hypochromic effect.
• Denaturation of a double-stranded nucleic acid
produces the opposite result, an increase in
absorption called the hyperchromic effect.
• The transition from double-stranded DNA to the
single-stranded,denatured form can thus be
detected by monitoring the absorption of UV light.
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Heat denaturation of DNA. The denaturation of melting
curves of two DNA specimens. The temperature at the
midpoint of the transition (tm) is the melting point. It
depends on pH and ionic strength and on the size and
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base composition of the DNA.
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Relationship between tm and the GC
content of a DNA. (DNA分子的熔點)
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1. Double-helical DNA and RNA can be denatured
• Notably, RNA duplexes are more stable
than DNA duplexes. At neutral pH,
denaturation of a double-helical RNA
often requires temperatures 20°C or
more higher than those required for
denaturation of a DNA molecule with a
comparable sequence.(在中性pH, 雙股
RNA較雙股DNA穩定，熔點較高)
• The stability of an RNA-DNA hybrid is
generally intermediate between that of
RNA and that of DNA.
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2. Nucleic Acids from Different Species Can Form
Hybrids
p.293, Fig. 8-32 DNA hybridization
Two DNA samples to be
compared are completely
denatured by heating. When the
two solutions are mixed and
slowly cooled, DNA strands of
each sample associated with
their normal complementary
partner and anneal to form
duplexes. If the two DNAs have
significant sequence similarity,
they also tend to form partial
duplexes or hybrids with each
other: the greater the sequence
similarity of hybrids formed.
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3. Nucleotides and nucleic acids undergo
nonenzymatic transformations
• Deamination reactions: deamination of cytosine (in
DNA) to uracil occurs in about one every 107
cytidine residues in 24 hours. Deamination of
adenine and guanine is about 100 times slower.
Cytosine deamination would gradually lead to a
decrease in GC base pairs and an increase in
A=U base pairs in the DNA of all cells.
• Depurination: As many as one in 105 purines are
lost from DNA every 24 hours under typical cellular
conditions. Incubation of DNA at pH 3 causes
selective removal of the purine bases, resulting in
a derivative called apurinic acid.
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3. Nucleotides and nucleic acids undergo
nonenzymatic transformations
• Formation of pyrimidine dimers induced by UV
light. UV light induces the condensation of two
ethylene groups to for a cyclobutane ring or form a
6-4 photoproduct.
• Both x rays and gamma rays can cause ring
opening and fragmentation of bases as well as
breaks in the covalent backbone of nucleic acids.
• Chemical reagents that cause DNA damage.
• Oxidative damages: Excited-oxygen species such
as hydrogen peroxide, hydroxyl radicals, and
superoxide radicals arise during irradiation or as a
byproduct of aerobic metabolism.
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4. Some Bases of DNA Are Methylated
• DNA特定區域或序列的特定鹼基會被甲基化；
A、C較G、T頻繁
• All DNA methylase用S-adenosylmethionine
為methyl group donor
• Methylation之功能？
• E. coli有二甲基化系統
– 辨識本身（甲基化）與外來（未甲基化）DNA
(restriction-modification system)
– Dam (DNA adenine methylation) methylase將
(5’)GATC(3’)之A為6‘-methyladenosine：修復
mismatched BP
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4. Some Bases of DNA Are Methylated
• Eukryotic cells：DNA約5%之C被甲基化
為5-methylcytidine
• 主要將DNA雙股之CpG甲基化，產生對
稱結構
• CpG甲基化程度因DNA之區域而異
• 甲基化可抑制DNA 之migration of
segments (transposons)
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亞硝酸鹽
硝酸鹽
p. 296, Fig. 8-35a
Chemical agents that cause DNA
damage. Precursors of nitrous
acid, which promotes
deamination reaction.
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4. The DNA Sequences of Long DNA Strands Can Be
Determined: DNA sequencing by the Sanger method
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Chemical synthesis of DNA
DMT: an acid-labile
dimethoxytrityl group
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Nucleotides carry chemical energy in
cells
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The phosphate ester and
phosphoanhydride bonds of ATP
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The UV absorption spectra of NAD+ and NADH.
Reduction of the nicotinamide ring produces a
new, broad absorption band with a maximum at
340 nm.
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四﹑From Gene to Protein
• The Genetic Code:（p.147, Fig. 5.16）
– Start signal: AUG
• Prokaryotes: N-formylmethionine
• Eukaryotes: methionine at N-terminus
– Stop signals: UAA, UAG, UGA
• Translation:（p.147, Fig. 5.18）
–
–
–
–
aminoacyl-tRNA:（p.148, Fig. 5.19）
AA at 3’ end of tRNA
anticodon loop
Procedures: p.149, Fig. 5.20
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四﹑From Gene to Protein
• Posttranslational Processing of Proteins
–[以insulin為例 (p.149, Fig. 5.21)]
–在 Protein 生成後，所進行之進一步的結
構修飾作用，以形成在生物細胞中具有完整
結構與功能的protein之過程，稱之
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