Download Pyrimidines and Purines

27.23
Pyrimidines and Purines
Pyrimidines and Purines
In order to understand the structure and
properties of DNA and RNA, we need to look at
their structural components.
We begin with certain heterocyclic aromatic
compounds called pyrimidines and purines.
Pyrimidines and Purines
Pyrimidine and purine are the names of the
parent compounds of two types of nitrogencontaining heterocyclic aromatic compounds.
N
N
N
N
Pyrimidine
N
N
H
Purine
Important Pyrimidines
Pyrimidines that occur in DNA are cytosine and
thymine. Cytosine and uracil are the
pyrimidines in RNA.
O
O
NH2
CH3
HN
HN
HN
O
N
H
Uracil
O
N
H
Thymine
O
N
H
Cytosine
Important Purines
Adenine and guanine are the principal purines
of both DNA and RNA.
NH2
O
N
N
N
N
H
Adenine
N
HN
H2N
N
N
H
Guanine
Caffeine and Theobromine
Caffeine (coffee) and theobromine (coffee and
tea) are naturally occurring purines.
O
H3C
O
N
N
N
O
CH3
N
CH3
Caffeine
N
HN
O
CH3
N
N
CH3
Theobromine
27.24
Nucleosides
Nucleosides
The classical structural definition is that a
nucleoside is a pyrimidine or purine N-glycoside
of D-ribofuranose or 2-deoxy-D-ribofuranose.
Informal use has extended this definition to
apply to purine or pyrimidine N-glycosides of
almost any carbohydrate.
The purine or pyrimidine part of a nucleoside is
referred to as a purine or pyrimidine base.
Uridine and Adenosine
Uridine and adenosine are pyrimidine and purine
nucleosides respectively of D-ribofuranose.
O
NH2
HN
N
O
HOCH2
HO
N
N
HOCH2
O
OH
Uridine
(a pyrimidine nucleoside)
N
N
O
HO
OH
Adenosine
(a purine nucleoside)
27.25
Nucleotides
Nucleotides
Nucleotides are phosphoric acid esters of
nucleosides.
Adenosine 5'-Monophosphate (AMP)
Adenosine 5'-monophosphate (AMP) is also called 5'adenylic acid.
NH2
N
N
O
HO
P
N
N
OCH2
O
HO
HO
OH
Adenosine 5'-Monophosphate (AMP)
Adenosine 5'-monophosphate (AMP) is also called 5'adenylic acid.
NH2
N
N
O
HO
P
HO
N
N
OCH2
5'
4'
3'
HO
O
1'
2'
OH
Adenosine Diphosphate (ADP)
NH2
N
N
O
HO
P
HO
O
O
P
N
N
OCH2
O
HO
HO
OH
Adenosine Triphosphate (ATP)
NH2
N
N
O
HO
P
HO
O
O
P
HO
O
O
P
N
N
OCH2
O
HO
HO
OH
ATP Stores Energy
ATP
ADP
Each step is endothermic.
Energy for each step comes
from carbohydrate metabolism
(glycolysis).
Reverse process is exothermic
and is the source of biological
energy.
AMP
DG° for hydrolysis of ATP to
ADP is –35 kJ/mol
Adenosine 3'-5'-Cyclic Monophosphate
(cAMP)
Cyclic AMP is an important regulator of many
biological processes.
NH2
N
N
N
N
CH2
O
O
HO
O
P
O
OH
27.26
Nucleic Acids
Nucleic Acids
Nucleic acids are polymeric nucleotides
(polynucleotides).
5' Oxygen of one nucleotide is linked to the 3'
oxygen of another.
Fig. 27.22
NH2
N
5'
OCH2
N
O
N
N
3'
A section of a
polynucleotide
chain.
O
OH
O P
O
OCH2
Р
5'
NH2
N
N
O
O
O
3'
O
Р
O
OH
P
NH
OCH2
5'
O
N
O
O
3'
O
Р
O
OH
P
O
O
27.27
Structure and Replication of DNA:
The Double Helix
Composition of DNA
Erwin Chargaff (Columbia Univ.) studied DNAs
from various sources and analyzed the
distribution of purines and pyrimidines in them.
The distribution of the bases adenine (A),
guanine (G), thymine (T), and cytosine (C)
varied among species.
But the total purines (A and G) and the total
pyrimidines (T and C) were always equal.
Moreover: %A = %T, and %G = %C
Composition of Human DNA
For example:
Purine
Pyrimidine
Adenine (A) 30.3%
Thymine (T) 30.3%
Guanine (G) 19.5%
Cytosine (C) 19.9%
Total purines: 49.8%
Total pyrimidines: 50.1%
Base Pairing
Watson and Crick proposed that A and T were
equal because of complementary hydrogen
bonding.
H
N
N
N
N
H
O
H
CH3
N
2-deoxyribose N
N
O
A
T
2-deoxyribose
Base Pairing
Likewise, the amounts of G and C were equal
because of complementary hydrogen bonding.
H
O
N
N
2-deoxyribose
N H
H N
N
N
N
N H
H
G
O
2-deoxyribose
C
The DNA Duplex
Watson and Crick proposed a double-stranded
structure for DNA in which a purine or
pyrimidine base in one chain is hydrogen
bonded to its complement in the other.
O
3'
Fig. 27.24
O
C
5'
O
5'
G
O
Two antiparallel
strands of DNA
are paired by
hydrogen bonds
between purine
and pyrimidine
bases.
O
O P O
3' O
3'
Р
O P O
O
T
5'
A
O
O P O
O
T
5'
A
O
O P O
O
O
G
5'
O
3'
O
O
O P O
3' O
3'
Р
Р
O
5'
O
O
O P O
3' O
3'
Р
Р
O
5'
O
O
C
5'
O
Р
Fig. 27.25
Helical structure of
DNA. The purine
and pyrimidine
bases are on the
inside, sugars and
phosphates on the
outside.
Fig. 27.26 DNA Replication
C
T
As the double helix
unwinds, each strand acts
as a template upon which
its complement is
constructed.
A
G
Fig. 27.26 DNA Replication
A'
C
T
G'
C'
A
G
T'
27.28
DNA-Directed Protein Biosynthesis
DNA and Protein Biosynthesis
According to Crick, the "central dogma" of
molecular biology is:
"DNA makes RNA makes protein."
Three kinds of RNA are involved.
messenger RNA (mRNA)
transfer RNA (tRNA)
ribosomal RNA (rRNA)
There are two main stages.
transcription
translation
Transcription
Transcription is the formation of a strand of
mRNA using one of the DNA strands as a
template.
The nucleotide sequence of the mRNA is
complementary to the nucleotide sequence of
the DNA template.
Transcription begins at the 5' end of DNA and is
catalyzed by the enzyme RNA polymerase.
Transcription
A G G T C A C T G
T C C A G T G A C
T
A
G
C
A
T
A
G C
T C
As double-stranded DNA
unwinds, a complementary
strand of mRNA forms at the 5'
end.
A T
G T
C
A G
G
C
A
T
T A
C 5'
G 3'
Transcription
A G G T C A C T G
T C C A G T G A C
T
A
G
C
A
T
A
G C
T C
Uracil is incorporated in RNA
instead of thymine.
A T
A
G T
C
G
A G
G
C
C
A
U
T
A
T A
C 5'
G
G 3'
Translation
The nucleotide sequence of mRNA codes for
the different amino acids found in proteins.
There are three nucleotides per codon.
There are 64 possible combinations of A, U, G,
and C.
The genetic code is redundant. Some proteins
are coded for by more than one codon.
Table 27.4: mRNA Codons
Alanine
Arginine
Asparagine
Aspartic Acid
Cysteine
GCU GCA
GCC GCG
CGU CGA
AGA CGC
CGG AGG
AAU
AAC
GAU
GAC
UGU
UGC
Glutamic acid
GAA
GAG
Glutamine
CAA
CAG
Glycine
GGU GGA
GGC GGG
Histidine
CAU
CAC
Isoleucine
AUU AUA
AUC
Leucine
UUA CUU
CUA UUG
CUC CUG
Lysine
AAA
AAG
Methionine
AUG
Phenylalanine Proline
UUU
CCU CCA
UUC
CCC CG
Serine
UCU UCA
AGU UCC
UCG AGC
Threonine
ACU ACA
ACC ACG
Tryptophan
UGG
Tyrosine
UAU
UAC
Valine
GUU GUA
GUC GUG
Transfer tRNA
There are 20 different tRNAs, one for each
amino acid.
Each tRNA is single stranded with a CCA triplet
at its 3' end.
A particular amino acid is attached to the tRNA
by an ester linkage involving the carboxyl group
of the amino acid and the 3' oxygen of the
tRNA.
Phenylalanine tRNA
O
OCCHCH2C6H5
Phenylalanine tRNA
G A
G
G
This AAA triplet is
complementary to a
UUU triplet
of mRNA; it is an
anticodon.
C UC
GA
+
A NH3
C
C
A
C
G
C
U
U
A
CU
A
AC A C
C
G
G
A
U
U
AU
UGUG
CU
GA G C
C
C
A
G
A
GA G
G
U
A
U
A AA
G
C
27.29
DNA Sequencing
DNA Sequencing
Restriction enzymes cleave the polynucleotide
to smaller fragments.
These smaller fragments (100-200 base pairs)
are sequenced.
The two strands are separated.
DNA Sequencing
Single stranded DNA divided in four portions.
Each tube contains adenosine, thymidine,
guanosine, and cytidine plus the triphosphates
of their 2'-deoxy analogs.
OH
OH
OH
HO
P
O
O
P
O
O
base
POCH2
O
O
HO
H
DNA Sequencing
The first tube also contains the 2,'3'-dideoxy analog of
adenosine triphosphate (ddATP); the second tube the
2,'3'-dideoxy analog of thymidine triphosphate (ddTTP),
the third contains ddGTP, and the fourth ddCTP.
OH
OH
HO
P
O
O
P
O
OH
O
base
POCH2
O
O
H
H
DNA Sequencing
Each tube also contains a "primer," a short
section of the complementary DNA strand,
labeled with radioactive phosphorus (32P).
DNA synthesis takes place, producing a
complementary strand of the DNA strand used
as a template.
DNA synthesis stops when a dideoxynucleotide
is incorporated into the growing chain.
DNA Sequencing
The contents of each tube are separated by
electrophoresis and analyzed by
autoradiography.
There are four lanes on the electrophoresis gel.
Each DNA fragment will be one nucleotide
longer than the previous one.
Figure 27.29
ddA
ddT
ddG
ddC
Sequence of
fragment
T
TG
TGA
TGAC
TGACA
TGACAT
TGACATA
TGACATAC
TGACATACG
TGACATACGT
Figure 27.29
ddA
ddT
ddG
ddC
Sequence of
fragment
Sequence of
original DNA
T
A
TG
AC
TGA
ACT
TGAC
ACTG
TGACA
ACTGT
TGACAT
ACTGTA
TGACATA
ACTGTAT
TGACATAC
ACTGTATG
TGACATACG
ACTGTATGC
TGACATACGT
ACTGTATGCA