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27.2327.23Pyrimidines and PurinesPyrimidines and Purines
Pyrimidines and PurinesPyrimidines and Purines
In order to understand the structure and In order to understand the structure and properties of DNA and RNA, we need to look at properties of DNA and RNA, we need to look at their structural components.their structural components.
We begin with certain heterocyclic aromatic We begin with certain heterocyclic aromatic compounds called pyrimidines and purines.compounds called pyrimidines and purines.
Pyrimidines and PurinesPyrimidines and Purines
Pyrimidine and purine are the names of the Pyrimidine and purine are the names of the parent compounds of two types of nitrogenparent compounds of two types of nitrogen--containing heterocyclic aromatic compounds.containing heterocyclic aromatic compounds.
NN
NN
NN
NN
NN
NNHH
PyrimidinePyrimidine PurinePurine
Important PyrimidinesImportant Pyrimidines
Pyrimidines that occur in DNA are cytosine and Pyrimidines that occur in DNA are cytosine and thymine. Cytosine and uracil are the thymine. Cytosine and uracil are the pyrimidines in RNA.pyrimidines in RNA.
HHNN
NNHH
OO
OO
UracilUracil
HHNN
NNHH
OO
OO
CHCH33
ThymineThymine
HHNN
NNHH
NNHH22
OO
CytosineCytosine
Important PurinesImportant Purines
Adenine and guanine are the principal purines Adenine and guanine are the principal purines of both DNA and RNA.of both DNA and RNA.
AdenineAdenine
NN
NN
NNHH22
NN
NNHH
GuanineGuanine
OO
HHNN
NNHH
NN
NN
HH22NN
Caffeine and TheobromineCaffeine and Theobromine
Caffeine (coffee) and theobromine (coffee and Caffeine (coffee) and theobromine (coffee and tea) are naturally occurring purines.tea) are naturally occurring purines.
CaffeineCaffeine
NN
NN
OO
NN
NN
HH33CC
OO
CHCH33
CHCH33
TheobromineTheobromine
OO
HHNN
NNNN
NN
CHCH33
CHCH33
OO
27.2427.24NucleosidesNucleosides
NucleosidesNucleosides
The classical structural definition is that a The classical structural definition is that a nucleoside is a pyrimidine or purine Nnucleoside is a pyrimidine or purine N--glycoside glycoside of of DD--ribofuranose or 2ribofuranose or 2--deoxydeoxy--DD--ribofuranose.ribofuranose.
Informal use has extended this definition to Informal use has extended this definition to apply to purine or pyrimidine Napply to purine or pyrimidine N--glycosides of glycosides of almost any carbohydrate.almost any carbohydrate.
The purine or pyrimidine part of a nucleoside is The purine or pyrimidine part of a nucleoside is referred to as a referred to as a purine or pyrimidine basepurine or pyrimidine base..
Uridine and AdenosineUridine and Adenosine
Uridine and adenosine are pyrimidine and purine Uridine and adenosine are pyrimidine and purine nucleosides respectively of nucleosides respectively of DD--ribofuranose.ribofuranose.
UridineUridine(a pyrimidine nucleoside)(a pyrimidine nucleoside)
AdenosineAdenosine(a purine nucleoside)(a purine nucleoside)
OO
NN
HOCHHOCH22
HHNN
OO
OHOHHOHO
OO
NN NN
NN NNHOCHHOCH22 OO
OHOHHOHO
NNHH22
27.2527.25NucleotidesNucleotides
NucleotidesNucleotides
Nucleotides are phosphoric acid esters of Nucleotides are phosphoric acid esters of nucleosides.nucleosides.
Adenosine 5'Adenosine 5'--Monophosphate (AMP)Monophosphate (AMP)
Adenosine 5'Adenosine 5'--monophosphate (AMP) is also called 5'monophosphate (AMP) is also called 5'--adenylic acid.adenylic acid.
NN NN
NN NN
OO
OHOHHOHO
NNHH22
OCHOCH22PPHOHO
OO
HOHO
Adenosine 5'Adenosine 5'--Monophosphate (AMP)Monophosphate (AMP)
Adenosine 5'Adenosine 5'--monophosphate (AMP) is also called 5'monophosphate (AMP) is also called 5'--adenylic acid.adenylic acid.
NN NN
NN NN
OO
OHOHHOHO
NNHH22
OCHOCH22PPHOHO
OO
HOHO1'1'
2'2'3'3'
4'4'5'5'
Adenosine Diphosphate (ADP)Adenosine Diphosphate (ADP)
NN NN
NN NN
OO
OHOHHOHO
NNHH22
OCHOCH22PPOO
OO
HOHO
PP
OO
HOHO
HOHO
Adenosine Triphosphate (ATP)Adenosine Triphosphate (ATP)
NN NN
NN NN
OO
OHOHHOHO
NNHH22
OCHOCH22PPOO
OO
HOHO
PP
OO
HOHO
OOPP
OO
HOHO
HOHO
ATP Stores EnergyATP Stores Energy
AMPAMP
ADPADP
ATPATP Each step is endothermic.Each step is endothermic.
Energy for each step comes Energy for each step comes from carbohydrate metabolism from carbohydrate metabolism (glycolysis).(glycolysis).
Reverse process is exothermic Reverse process is exothermic and is the source of biological and is the source of biological energy.energy.
∆∆G° for hydrolysis of ATP to G° for hydrolysis of ATP to ADP is ADP is ––35 kJ/mol35 kJ/mol
Adenosine 3'Adenosine 3'--5'5'--Cyclic Cyclic Monophosphate (cAMP)Monophosphate (cAMP)
Cyclic AMP is an important regulator of many Cyclic AMP is an important regulator of many biological processes.biological processes.
NN NN
NN NN
OO
OHOHOO
NNHH22
CHCH22
PPOO
HOHO
OO
27.2627.26Nucleic AcidsNucleic Acids
Nucleic AcidsNucleic Acids
Nucleic acids are polymeric nucleotides Nucleic acids are polymeric nucleotides ((polynucleotides).polynucleotides).
5' Oxygen of one nucleotide is linked to the 3' 5' Oxygen of one nucleotide is linked to the 3' oxygen of another.oxygen of another.
Fig. 27.22Fig. 27.22
O
NH2N
N NN
OHO
OCH2
P OCH2GO
O O
NH2
NN
O OH
O
P OCH2
OGO
O OH
O NNH
O
O
PGOO
O
3'
3'
3'
5'
5'
5'
A section of a A section of a polynucleotide polynucleotide chain.chain.
27.2727.27Structure and Replication of DNA:Structure and Replication of DNA:
The Double HelixThe Double Helix
Composition of DNAComposition of DNA
Erwin Chargaff (Columbia Univ.) studied DNAs Erwin Chargaff (Columbia Univ.) studied DNAs from various sources and analyzed the from various sources and analyzed the distribution of purines and pyrimidines in them.distribution of purines and pyrimidines in them.
The distribution of the bases adenine (A), The distribution of the bases adenine (A), guanine (G), thymine (T), and cytosine (C) guanine (G), thymine (T), and cytosine (C) varied among species.varied among species.
But the total purines (A and G) and the total But the total purines (A and G) and the total pyrimidines (T and C) were always equal.pyrimidines (T and C) were always equal.
Moreover: %A = %T, and %G = %CMoreover: %A = %T, and %G = %C
Composition of Human DNAComposition of Human DNA
Adenine (A) 30.3%Adenine (A) 30.3% Thymine (T) 30.3%Thymine (T) 30.3%
Guanine (G) 19.5%Guanine (G) 19.5% Cytosine (C) 19.9%Cytosine (C) 19.9%
Total purines: 49.8%Total purines: 49.8% Total pyrimidines: 50.1%Total pyrimidines: 50.1%
For example:For example:
PurinePurine PyrimidinePyrimidine
Base PairingBase Pairing
Watson and Crick proposed that A and T were Watson and Crick proposed that A and T were equal because of complementary hydrogen equal because of complementary hydrogen bonding.bonding.
22--deoxyribosedeoxyribose
NNN
N N
H
H
NN
O CH3
O
H
22--deoxyribosedeoxyriboseAA TT
Base PairingBase Pairing
Likewise, the amounts of G and C were equal Likewise, the amounts of G and C were equal because of complementary hydrogen bonding.because of complementary hydrogen bonding.
NNN
N O
NH
H
HN
N
N
O
HH
22--deoxyribosedeoxyribose
22--deoxyribosedeoxyribose
GG CC
The DNA DuplexThe DNA Duplex
Watson and Crick proposed a doubleWatson and Crick proposed a double--stranded stranded structure for DNA in which a purine or structure for DNA in which a purine or pyrimidine base in one chain is hydrogen pyrimidine base in one chain is hydrogen bonded to its complement in the other.bonded to its complement in the other.
O
O
GO
GO
GO
O
O
O
O
OP
O
O
P O
OO
P O
OO
O
O
OG
OG
OG
O
O
O
O
O P
O
OPO
OO
PO
OO
C G
AT
AT
CG
3'
5'
5'
5'
5' 5'
5'
5'
5'
3'
3'3'
3'3'
3'
3'
Fig. 27.24Fig. 27.24
Two antiparallel Two antiparallel strands of DNA strands of DNA are paired by are paired by hydrogen bonds hydrogen bonds between purine between purine and pyrimidine and pyrimidine bases.bases.
Fig. 27.25Fig. 27.25
Helical structure of Helical structure of DNA. The purine DNA. The purine and pyrimidine and pyrimidine bases are on the bases are on the inside, sugars and inside, sugars and phosphates on the phosphates on the outside.outside.
Fig. 27.26 DNA Replication
C
G
T
AAs the double helix unwinds, each strand acts as a template upon which its complement is constructed.
Fig. 27.26 DNA Replication
A
C
G
T
T'
A'
G'
C'
27.2827.28DNADNA--Directed Protein BiosynthesisDirected Protein Biosynthesis
DNA and Protein BiosynthesisDNA and Protein Biosynthesis
According to Crick, the "central dogma" of According to Crick, the "central dogma" of molecular biology is:molecular biology is:
"DNA makes RNA makes protein.""DNA makes RNA makes protein."
Three kinds of RNA are involved.Three kinds of RNA are involved.messenger RNA (mRNA)messenger RNA (mRNA)transfer RNA (tRNA)transfer RNA (tRNA)ribosomal RNA (rRNA)ribosomal RNA (rRNA)
There are two main stages.There are two main stages.transcriptiontranscriptiontranslationtranslation
TranscriptionTranscription
Transcription is the formation of a strand of Transcription is the formation of a strand of mRNA using one of the DNA strands as a mRNA using one of the DNA strands as a template.template.
The nucleotide sequence of the mRNA is The nucleotide sequence of the mRNA is complementary to the nucleotide sequence of complementary to the nucleotide sequence of the DNA template.the DNA template.
Transcription begins at the 5' end of DNA and is Transcription begins at the 5' end of DNA and is catalyzed by the enzyme catalyzed by the enzyme RNA polymeraseRNA polymerase..
TranscriptionTranscription
A G G T C A C T G
T C C A G T G A CA
TG
C TT
T
T
T
TC
C
C
C
C
A
A
AA
A
G
G
A
G
G
G
As doubleAs double--stranded DNA stranded DNA unwinds, a complementary unwinds, a complementary strand of mRNA forms at the 5' strand of mRNA forms at the 5' end.end.
5'5'
3'3'
TranscriptionTranscription
A G G T C A C T G
T C C A G T G A CA
TG
C TT
T
T
T
TC
C
C
C
C
A
A
AA
A
G
G
A
G
G
G
A
AG
GU
C
5'5'
3'3'
Uracil is incorporated in RNA Uracil is incorporated in RNA instead of thymine.instead of thymine.
TranslationTranslation
The nucleotide sequence of mRNA codes for The nucleotide sequence of mRNA codes for the different amino acids found in proteins.the different amino acids found in proteins.
There are three nucleotides per codon.There are three nucleotides per codon.
There are 64 possible combinations of A, U, G, There are 64 possible combinations of A, U, G, and C.and C.
The genetic code is redundant. Some proteins The genetic code is redundant. Some proteins are coded for by more than one codon.are coded for by more than one codon.
Table 27.4: mRNA CodonsTable 27.4: mRNA Codons
AlanineAlanine ArginineArginine AsparagineAsparagine Aspartic AcidAspartic Acid CysteineCysteine
GCUGCU GCAGCA CGUCGU CGA CGA AAUAAU GAU GAU UGUUGUGCCGCC GCGGCG AGAAGA CGC CGC AACAAC GACGAC UGC UGC
CGGCGG AGG AGG
Glutamic acidGlutamic acid GlutamineGlutamine GlycineGlycine HistidineHistidine IsoleucineIsoleucineGAAGAA CAACAA GGUGGU GGAGGA CAUCAU AUUAUU AUAAUAGAGGAG CAGCAG GGCGGC GGGGGG CACCAC AUCAUC
LeucineLeucine LysineLysine MethionineMethionine PhenylalaninePhenylalanine ProlineProlineUUAUUA CUUCUU AAAAAA AUGAUG UUUUUU CCUCCU CCA CCA CUACUA UUGUUG AAGAAG UUCUUC CCC CCC CGCGCUCCUC CUGCUG
SerineSerine ThreonineThreonine TryptophanTryptophan TyrosineTyrosine ValineValineUCUUCU UCA UCA ACUACU ACAACA UGGUGG UAUUAU GUUGUU GUAGUAAGUAGU UCC UCC ACCACC ACGACG UACUAC GUC GUC GUGGUGUCGUCG AGC AGC
Transfer tRNATransfer tRNA
There are 20 different tRNAs, one for each There are 20 different tRNAs, one for each amino acid.amino acid.
Each tRNA is single stranded with a CCA triplet Each tRNA is single stranded with a CCA triplet at its 3' end.at its 3' end.
A particular amino acid is attached to the tRNA A particular amino acid is attached to the tRNA by an ester linkage involving the carboxyl group by an ester linkage involving the carboxyl group of the amino acid and the 3' oxygen of the of the amino acid and the 3' oxygen of the tRNA.tRNA.
Phenylalanine tRNAPhenylalanine tRNA
Phenylalanine tRNAPhenylalanine tRNA OCCHCHOCCHCH22CC66HH55
NHNH33++
OO
A
CC
A A A
A
A
AA
A
AA
AA
A
A
A
A
AC CC
C
CC
CC
C C
CC
U
U
U U
U
UU
UU
UU
GG
G
G GG
GG
G
GG
G
UG G
G
GC
This AAA triplet is This AAA triplet is complementary to a complementary to a UUU tripletUUU tripletof mRNA; it is an of mRNA; it is an anticodonanticodon..
27.2927.29DNA SequencingDNA Sequencing
DNA SequencingDNA Sequencing
Restriction enzymes cleave the polynucleotide Restriction enzymes cleave the polynucleotide to smaller fragments.to smaller fragments.
These smaller fragments (100These smaller fragments (100--200 base pairs) 200 base pairs) are sequenced.are sequenced.
The two strands are separated.The two strands are separated.
DNA SequencingDNA Sequencing
Single stranded DNA divided in four portions.Single stranded DNA divided in four portions.
Each tube contains adenosine, thymidine, Each tube contains adenosine, thymidine, guanosine, and cytidine plus the triphosphates guanosine, and cytidine plus the triphosphates of their 2'of their 2'--deoxy analogs.deoxy analogs.
POCHPOCH22
OHOH
OOOO
OO
OHOH
PP
OO
OHOH
PP
OO
HOHO basebase
HHHHOO
OO
DNA SequencingDNA Sequencing
The first tube also contains the 2,'3'The first tube also contains the 2,'3'--dideoxy analog of dideoxy analog of adenosine triphosphate (ddATP); the second tube the adenosine triphosphate (ddATP); the second tube the 2,'3'2,'3'--dideoxy analog of thymidine triphosphate (ddTTP), dideoxy analog of thymidine triphosphate (ddTTP), the third contains ddGTP, and the fourth ddCTP.the third contains ddGTP, and the fourth ddCTP.
POCHPOCH22
OHOH
OOOO
OO
OHOH
PP
OO
OHOH
PP
OO
HOHO basebase
HHHH
OO
DNA SequencingDNA Sequencing
Each tube also contains a "primer," a short Each tube also contains a "primer," a short section of the complementary DNA strand, section of the complementary DNA strand, labeled with radioactive phosphorus (labeled with radioactive phosphorus (3232P).P).
DNA synthesis takes place, producing a DNA synthesis takes place, producing a complementary strand of the DNA strand used complementary strand of the DNA strand used as a template.as a template.
DNA synthesis stops when a dideoxynucleotide DNA synthesis stops when a dideoxynucleotide is incorporated into the growing chain.is incorporated into the growing chain.
DNA SequencingDNA Sequencing
The contents of each tube are separated by The contents of each tube are separated by electrophoresis and analyzed by electrophoresis and analyzed by autoradiography.autoradiography.
There are four lanes on the electrophoresis gel.There are four lanes on the electrophoresis gel.
Each DNA fragment will be one nucleotide Each DNA fragment will be one nucleotide longer than the previous one.longer than the previous one.
Figure 27.29Figure 27.29
TT
TTGG
TTGGAA
TTGGAACC
TTGGAACCAA
TTGGAACCAATT
TTGGAACCAATTAA
TTGGAACCAATTAACC
TTGGAACCAATTAACCGG
TTGGAACCAATTAACCGGTT
ddAddA ddTddT ddGddG ddCddCSequence of Sequence of fragmentfragment
Figure 27.29Figure 27.29
TT
TTGG
TTGGAA
TTGGAACC
TTGGAACCAA
TTGGAACCAATT
TTGGAACCAATTAA
TTGGAACCAATTAACC
TTGGAACCAATTAACCGG
TTGGAACCAATTAACCGGTT
ddAddA ddTddT ddGddG ddCddC
AA
AACC
AACCTT
AACCTTGG
AACCTTGGTT
AACCTTGGTTAA
AACCTTGGTTAATT
AACCTTGGTTAATTGG
AACCTTGGTTAATTGGCC
AACCTTGGTTAATTGGCCAA
Sequence of Sequence of fragmentfragment
Sequence of Sequence of original DNAoriginal DNA
