Chapter 3 Nucleic Acids
Section 1 Nucleotides and Nucleic Acids
Outline
11.1 Nitrogenous Bases
11.2 The Pentoses of Nucleotides and NA
11.3 Nucleosides are Formed by Joining a
Nitrogenous Base to a Sugar
11.4 Nucleotides - Nucleoside Phosphates
11.5 Nucleic Acids are Polynucleotides
11.6 Classes of Nucleic Acids
11.7 Hydrolysis of Nucleic Acids
Concept
nucleic acids:
– Polynucleotides,The nucleotide
residues are linked in a specific
sequence by phosphodiester bonds;
– DNA and RNA
1869 F,Miescher (nuclein)
1889 R,Altman (nucleic acid)
11.1 Nitrogenous Bases含氮碱
Know the basic structures
Pyrimidines (嘧啶）
– Cytosine 胞 ~ (DNA,RNA)
– Uracil 尿 ~ (RNA)
– Thymine 胸 ~ (DNA)
Purines （ 嘌呤）
– Adenine 腺 ~ (DNA,RNA)
– Guanine 鸟 ~ (DNA,RNA)
尿酸黄嘌呤次黄嘌呤
Properties of Pyrimidines and
Purines
Keto-enol tautomerism （ 酮 -烯醇互变异构）
Acid/base dissociations （ 酸碱解离）
Strong absorbance of UV light （ 紫外吸收）
内酰胺 内酰亚胺
G (Keto) G (Enol) A
99.99% 0.01%
Base Tautomerization
(碱基 互变异构）
5
11.2 Pentoses戊糖 of Nucleotides
Know these structures too
D-ribose 核糖 (in RNA)
2-deoxy-D-ribose (in DNA)
The difference - 2'-OH vs 2'-H
This difference affects secondary
structure and stability
11.3 Nucleosides核苷
Linkage of a base to a sugar
Base is linked via a glycosidic bond （ 糖苷键）
The carbon of the glycosidic bond is anomeric 异头物
Named by adding -idine to the root name of a
pyrimidine or -osine to the root name of a purine
Conformation can be syn（ 顺） or anti （ 反）
Sugars make nucleosides more water-soluble than
free bases
11.4 Nucleotides
Nucleoside phosphates
Know the nomenclature
"Nucleotide phosphate" is redundant多余的 !
Most nucleotides are ribonucleotides核糖核苷酸
Nucleotides are polyprotic acids 多质子酸
Nomenclature
Purines
adenine adenosine
guanine +ribose guanosine
Pyrimidines
thymine thymidine
cytosine +ribose cytidine
uracil uridine
Nucleoside Nucleotide
Base +deoxyribose +phosphate
Functions of Nucleotides
Nucleoside 5'-triphosphates are carriers of
energy
Bases serve as recognition units
Cyclic nucleotides are signal molecules and
regulators of cellular metabolism and
reproduction
ATP is central to energy metabolism
GTP drives protein synthesis
CTP drives lipid synthesis
UTP drives carbohydrate metabolism
11.5 Nucleic Acids - Polynucleotides
Polymers linked 3' to 5' by phosphodiester
bridges
Ribonucleic acid and deoxyribonucleic acid
Know the shorthand notations
Sequence is always read 5' to 3'
In terms of genetic information,this
corresponds to "N to C" in proteins
11.6 Classes of Nucleic Acids
DNA - one type,one purpose
RNA - 3 (or 4) types,3 (or 4) purposes
– ribosomal RNA - the basis of structure and
function of ribosomes
– messenger RNA - carries the message
– transfer RNA - carries the amino acids
The DNA Double Helix
Stabilized by base stacking force & hydrogen bonds !
"Base pairs" arise from hydrogen bonds
Erwin Chargaff had the pairing data,but didn't
understand its implications
Rosalind Franklin's X-ray fiber diffraction data
was crucial
Francis Crick knew it was a helix
James Watson figured out the H-bonds
R,Franklin &
M,Wilkins的 x-
射线衍射图
电位滴定
物化数据
3.4nm
（ ~1.2nm,~0.85 nm）
（ ~0.6nm,~0.75 nm）
Double helix
Right-handed
10 base pairs/turn
3.4 nm /turn
Diameter,ca,2.0 nm
The Structure of DNA
An antiparallel double helix
Diameter of 2 nm
Length of 1.6 million nm (E,coli)
Compact and folded (E,coli cell is only
2000 nm long)
Eukaryotic DNA wrapped around histone
proteins to form nucleosomes
Base pairs,A-T,G-C
Messenger RNA
Transcription转录 product of DNA
In prokaryotes原核生物,a single mRNA
contains the information for synthesis of
many proteins
In eukaryotes 真核生物,a single mRNA
codes for just one protein,but structure
is composed of introns内含子 and exons外显子
Eukaryotic mRNA
DNA is transcribed to produce heterogeneous
nuclear RNA （ hnRNA核内不均一 RNA）
– mixed introns and exons with poly A
– intron - intervening sequence
– exon - coding sequence
– poly A tail - stability?
Splicing produces final mRNA without introns
Ribosomal RNA
Ribosomes are about 2/3 RNA,1/3 protein
rRNA serves as a scaffold 脚手架 for
ribosomal proteins
23S rRNA in E,coli is the peptidyl
transferase!
Transfer RNA
Small polynucleotide chains - 73 to 94
residues each
Several bases usually
methylatedmethylated 甲基化
Each a.a,has at least one unique tRNA
which carries the a.a,to the ribosome
3'-terminal sequence is always CCA-a.a,
Aminoacyl tRNA 氨酰 tRNA molecules are the
substrates of protein synthesis
假尿嘧啶核苷 二氢尿嘧啶核苷胸腺嘧啶核糖核苷
4-硫尿核苷 次黄嘌呤核苷 1-甲基鸟苷 N-6-异戊烷腺苷
DNA & RNA Differences?
Why does DNA contain thymine?
Cytosine spontaneously 自发地 deaminates 脱氨
to form uracil
Repair enzymes recognize these "mutations"
and replace these Us with Cs
But how would the repair enzymes
distinguish natural U from mutant U?
Nature solves this dilemma by using thymine
(5-methyl-U) in place of uracil
DNA & RNA Differences?
Why is DNA 2'-deoxy and RNA is not?
Vicinal 邻近的 -OH groups (2' and 3') in RNA
make it more susceptible易受影响 to
hydrolysis
DNA,lacking 2'-OH is more stable
This makes sense - the genetic material
must be more stable
RNA is designed to be used and then
broken down
Hydrolysis of Nucleic Acids
RNA is resistant to dilute acid 稀酸
DNA is depurinated 脱嘌呤 by dilute acid
DNA is not susceptible 敏感 to base
RNA is hydrolyzed by dilute base
Restriction Enzymes
Bacteria have learned to "restrict" the
possibility of attack from foreign DNA by
means of "restriction enzymes"
Type II and III restriction enzymes cleave
DNA chains at selected sites
Enzymes may recognize 4,6 or more bases
in selecting sites for cleavage
An enzyme that recognizes a 6-base
sequence is a "six-cutter"
Section 1 Nucleotides and Nucleic Acids
Outline
11.1 Nitrogenous Bases
11.2 The Pentoses of Nucleotides and NA
11.3 Nucleosides are Formed by Joining a
Nitrogenous Base to a Sugar
11.4 Nucleotides - Nucleoside Phosphates
11.5 Nucleic Acids are Polynucleotides
11.6 Classes of Nucleic Acids
11.7 Hydrolysis of Nucleic Acids
Concept
nucleic acids:
– Polynucleotides,The nucleotide
residues are linked in a specific
sequence by phosphodiester bonds;
– DNA and RNA
1869 F,Miescher (nuclein)
1889 R,Altman (nucleic acid)
11.1 Nitrogenous Bases含氮碱
Know the basic structures
Pyrimidines (嘧啶）
– Cytosine 胞 ~ (DNA,RNA)
– Uracil 尿 ~ (RNA)
– Thymine 胸 ~ (DNA)
Purines （ 嘌呤）
– Adenine 腺 ~ (DNA,RNA)
– Guanine 鸟 ~ (DNA,RNA)
尿酸黄嘌呤次黄嘌呤
Properties of Pyrimidines and
Purines
Keto-enol tautomerism （ 酮 -烯醇互变异构）
Acid/base dissociations （ 酸碱解离）
Strong absorbance of UV light （ 紫外吸收）
内酰胺 内酰亚胺
G (Keto) G (Enol) A
99.99% 0.01%
Base Tautomerization
(碱基 互变异构）
5
11.2 Pentoses戊糖 of Nucleotides
Know these structures too
D-ribose 核糖 (in RNA)
2-deoxy-D-ribose (in DNA)
The difference - 2'-OH vs 2'-H
This difference affects secondary
structure and stability
11.3 Nucleosides核苷
Linkage of a base to a sugar
Base is linked via a glycosidic bond （ 糖苷键）
The carbon of the glycosidic bond is anomeric 异头物
Named by adding -idine to the root name of a
pyrimidine or -osine to the root name of a purine
Conformation can be syn（ 顺） or anti （ 反）
Sugars make nucleosides more water-soluble than
free bases
11.4 Nucleotides
Nucleoside phosphates
Know the nomenclature
"Nucleotide phosphate" is redundant多余的 !
Most nucleotides are ribonucleotides核糖核苷酸
Nucleotides are polyprotic acids 多质子酸
Nomenclature
Purines
adenine adenosine
guanine +ribose guanosine
Pyrimidines
thymine thymidine
cytosine +ribose cytidine
uracil uridine
Nucleoside Nucleotide
Base +deoxyribose +phosphate
Functions of Nucleotides
Nucleoside 5'-triphosphates are carriers of
energy
Bases serve as recognition units
Cyclic nucleotides are signal molecules and
regulators of cellular metabolism and
reproduction
ATP is central to energy metabolism
GTP drives protein synthesis
CTP drives lipid synthesis
UTP drives carbohydrate metabolism
11.5 Nucleic Acids - Polynucleotides
Polymers linked 3' to 5' by phosphodiester
bridges
Ribonucleic acid and deoxyribonucleic acid
Know the shorthand notations
Sequence is always read 5' to 3'
In terms of genetic information,this
corresponds to "N to C" in proteins
11.6 Classes of Nucleic Acids
DNA - one type,one purpose
RNA - 3 (or 4) types,3 (or 4) purposes
– ribosomal RNA - the basis of structure and
function of ribosomes
– messenger RNA - carries the message
– transfer RNA - carries the amino acids
The DNA Double Helix
Stabilized by base stacking force & hydrogen bonds !
"Base pairs" arise from hydrogen bonds
Erwin Chargaff had the pairing data,but didn't
understand its implications
Rosalind Franklin's X-ray fiber diffraction data
was crucial
Francis Crick knew it was a helix
James Watson figured out the H-bonds
R,Franklin &
M,Wilkins的 x-
射线衍射图
电位滴定
物化数据
3.4nm
（ ~1.2nm,~0.85 nm）
（ ~0.6nm,~0.75 nm）
Double helix
Right-handed
10 base pairs/turn
3.4 nm /turn
Diameter,ca,2.0 nm
The Structure of DNA
An antiparallel double helix
Diameter of 2 nm
Length of 1.6 million nm (E,coli)
Compact and folded (E,coli cell is only
2000 nm long)
Eukaryotic DNA wrapped around histone
proteins to form nucleosomes
Base pairs,A-T,G-C
Messenger RNA
Transcription转录 product of DNA
In prokaryotes原核生物,a single mRNA
contains the information for synthesis of
many proteins
In eukaryotes 真核生物,a single mRNA
codes for just one protein,but structure
is composed of introns内含子 and exons外显子
Eukaryotic mRNA
DNA is transcribed to produce heterogeneous
nuclear RNA （ hnRNA核内不均一 RNA）
– mixed introns and exons with poly A
– intron - intervening sequence
– exon - coding sequence
– poly A tail - stability?
Splicing produces final mRNA without introns
Ribosomal RNA
Ribosomes are about 2/3 RNA,1/3 protein
rRNA serves as a scaffold 脚手架 for
ribosomal proteins
23S rRNA in E,coli is the peptidyl
transferase!
Transfer RNA
Small polynucleotide chains - 73 to 94
residues each
Several bases usually
methylatedmethylated 甲基化
Each a.a,has at least one unique tRNA
which carries the a.a,to the ribosome
3'-terminal sequence is always CCA-a.a,
Aminoacyl tRNA 氨酰 tRNA molecules are the
substrates of protein synthesis
假尿嘧啶核苷 二氢尿嘧啶核苷胸腺嘧啶核糖核苷
4-硫尿核苷 次黄嘌呤核苷 1-甲基鸟苷 N-6-异戊烷腺苷
DNA & RNA Differences?
Why does DNA contain thymine?
Cytosine spontaneously 自发地 deaminates 脱氨
to form uracil
Repair enzymes recognize these "mutations"
and replace these Us with Cs
But how would the repair enzymes
distinguish natural U from mutant U?
Nature solves this dilemma by using thymine
(5-methyl-U) in place of uracil
DNA & RNA Differences?
Why is DNA 2'-deoxy and RNA is not?
Vicinal 邻近的 -OH groups (2' and 3') in RNA
make it more susceptible易受影响 to
hydrolysis
DNA,lacking 2'-OH is more stable
This makes sense - the genetic material
must be more stable
RNA is designed to be used and then
broken down
Hydrolysis of Nucleic Acids
RNA is resistant to dilute acid 稀酸
DNA is depurinated 脱嘌呤 by dilute acid
DNA is not susceptible 敏感 to base
RNA is hydrolyzed by dilute base
Restriction Enzymes
Bacteria have learned to "restrict" the
possibility of attack from foreign DNA by
means of "restriction enzymes"
Type II and III restriction enzymes cleave
DNA chains at selected sites
Enzymes may recognize 4,6 or more bases
in selecting sites for cleavage
An enzyme that recognizes a 6-base
sequence is a "six-cutter"
