Chem 109 C
Fall 2014
Armen Zakarian
Office: Chemistry Bldn 2217
OVERVIEW
DNA, RNA, etc.
Structure and Classification
•  DNA: Deoxyribonucleic acid
encodes hereditary information
controls cell division and growth
•  RNA: Ribonucleic acid
transcription and translation
stores genetic information in viruses
DNA, RNA, etc.
Structure and Classification
O P O-
O P Obase
O
O
O
5'
5'
2'
2'
O
base
O
O
OH
O P O-
O P Obase
O
base
O
O
O
O
O
O P O-
O P O-
base
O
OH
base
O
O
O
O
DNA
O
OH
RNA
DNA, RNA, etc.
Structure and Classification
DNA and RNA
RNA
only
DNA
only
DNA, RNA, etc.
Structure and Classification
DNA and RNA
RNA
only
DNA
only
DNA, RNA, etc.
Structure and Classification
DNA and RNA
RNA
only
DNA
only
DNA, RNA, etc.
Structure and Classification
DNA and RNA
RNA
only
DNA
only
DNA, RNA, etc.
Structure and Classification
DNA and RNA
RNA
only
DNA
only
DNA, RNA, etc.
Structure and Classification
DNA and RNA
RNA
only
DNA
only
DNA, RNA, etc.
Structure and Classification
nucleosides = base + sugar
NH2
NH2
N
N
N
N
N
O
HO
N
N
N
O
HO
HO
2'-deoxyadenosine
HO
OH
adenosine
PRACTICE PROBLEM Draw the structures and provide names for all other
nucleosides
DNA, RNA, etc.
Structure and Classification
nucleotides = base + sugar + phosphate
N
HN
H2N
-O
O
P
O-
O
O
O
N
N
N
HN
H2N
N
N
-O
HO
O
HO
2'-deoxyguanosine
5'-monophsphate
a deoxynucleotise
H2N
O
O
O
OH
N
HN
O
P
O-
N
N
O
O
O
O P O-
O P O-
O-
O-
guanosine
3'-monophosphate
a ribonucleotide
OH
DNA, RNA, etc.
Structure and Classification
nucleotides = nucleoside phosphates
NH2
NH2
dAMP
2’-deoxy
Adenosine
Mono
Phosphate
N
N
O
O
O
P
N
O
O-
-O
O
HO
O
P
O-
O
O
P
O-
O
O
O
P
N
O
O-
O
HO
OH
OH
cytidine
5'-triphosphate
cytidine
5'-monophosphate
CMP
CTP
NH2
NH2
N
PRACTICE PROBLEM 2 Draw
the structures for:
dCMP, UDP, dTTP
O
O
P
O-
O
N
N
O
-O
O
HO
O
P
O-
O
O
P
O-
O
N
O
O
HO
2'-deoxycytidine
5'-monophosphate
2'-deoxycytidine
5'-diphosphate
dCMP
dCDP
DNA, RNA, etc.
Structure and Classification
dinucleotides
2 nucleotides
oligonucleotides
3-10 nucleotides
polynucleotides
many (human DNA - 3,100,000,000 bp)
NH2
N
-O
O
P
O-
O
O
P
O-
O
O
P
O-
O
NH2
N
O
O
+
HO
dCTP
-O
N
N
O
P
O-
O
O
P
O-
O
O
P
O-
N
O
HO
dATP
N
O
DNA, RNA, etc.
NH2
N
-O
O
P
O-
O
O
P
O-
O
O
P
O-
O
N
O
O
+
O
O P O- N
O
N
O
NH2
-O
O
P
O-
O
O
P
O-
O-
N
N
HO
CAGTAACCTGAGAACCAATCGGAA…
Synthesis: nucleotide triphosphates, 5’
3’
DNA, RNA, etc.
Facts about DNA
!  double helix
!  two anti-parallel strands
A pairs with T, G pairs with C
pairing through hydrogen bonds
stacking interactions
DNA, RNA, etc.
Facts about DNA
double helix
two anti-parallel strands
!  A pairs with T, G pairs with C
pairing through hydrogen bonds
stacking interactions
DNA, RNA, etc.
Facts about DNA
double helix
two anti-parallel strands
A pairs with T, G pairs with C
!  pairing through hydrogen bonds
stacking interactions
DNA, RNA, etc.
Facts about DNA
double helix
two anti-parallel strands
A pairs with T, G pairs with C
pairing through hydrogen bonds
!  stacking interactions
DNA, RNA, etc.
PRACTICE PROBLEM 4 and 5 Indicate which functional group of the five
heterocyclic bases can function as a hydrogen bond donor (D), a hydrogen
bond acceptor (A), or both (D/A)
How would the base pairing be affected if the bases existed in the “enol”
form?
DNA, RNA, etc.
PRACTICE PROBLEM 7 If one of the strands of DNA has the following
sequence of bases running in the 5’ → 3’ direction,
GGACAATCTGC
a. what is the sequence of bases in the complementary strand?
b. what base is closest to the 5’-end in the complementary strand?
DNA, RNA, etc.
DNA is stable, RNA is not
O P O-
O P Obase
O
base
O
O
OH
O
-O
O P O-
O
O
P OO
O
B
O
OH
RNA
O-
2',3'-phosphodiester
H
+
O
O
P
base
O
base
O
O
:B
2'
O
base
O
O
5'
O P O-
O
OH
base
OH
O
O
OH
DNA, RNA, etc.
DNA is stable, RNA is not
O P O-
O P Obase
O
base
O
O
OH
O
-O
O P O-
O
O
P OO
O
B
O
OH
RNA
O-
2',3'-phosphodiester
H
+
O
O
P
base
O
base
O
O
:B
2'
O
base
O
O
5'
O P O-
O
OH
base
OH
O
O
OH
DNA, RNA, etc.
DNA (bio)synthesis
!  is called replication
strand separation, replication fork
!  done by DNA polymerase
again, always in 5’ → 3’ direction
using nucleotide triphosphates
DNA, RNA, etc.
DNA (bio)synthesis
is called replication
!  strand separation, replication fork
done by DNA polymerase
!  again, always in 5’ → 3’ direction
using nucleotide triphosphates