Nucleic acids are biopolymers made of nucleotides. There are two types: DNA contains the genetic information and RNA plays a role in protein expression. Nucleotides consist of a phosphate, a sugar (ribose in RNA and deoxyribose in DNA), and a nitrogenous base. DNA exists as a double helix with bases on each strand complementary to each other. DNA is replicated semi-conservatively prior to cell division. RNA is single stranded and comes in three main types: mRNA, tRNA, and rRNA. mRNA carries the genetic code from DNA in the nucleus to the cytoplasm. tRNA pairs bases with mRNA during protein synthesis on the ribosome.

1. 174
340
Chapter 28: Nucleosides, Nucleotides, and Nucleic Acids.
Nucleic acids are the third class of biopolymers (polysaccharides
and proteins being the others)
Two major classes of nucleic acids
deoxyribonucleic acid (DNA): carrier of genetic information
ribonucleic acid (RNA): an intermediate in the expression
of genetic information and other diverse roles
The Central Dogma (F. Crick):
DNA mRNA Protein
(genome) (transcriptome) (proteome)
The monomeric units for nucleic acids are nucleotides
Nucleotides are made up of three structural subunits
1. Sugar: ribose in RNA, 2-deoxyribose in DNA
2. Heterocyclic base
3. Phosphate
341
sugar base
sugar base
phosphate
sugar base
phosphate
sugar base
phosphate
sugar base
phosphate
nucleoside nucleotides
nucleic acids
Nucleoside, nucleotides and nucleic acids
The chemical linkage between monomer units in nucleic acids
is a phosphodiester

2. 175
342
28.1: Pyrimidines and Purines. The heterocyclic base; there
are five common bases for nucleic acids (Table 28.1, p. 1166).
Note that G, T and U exist in the keto form (and not the enol
form found in phenols)
N
N
H
N
N
N
N
purine
pyrimidine
N
N
H
N
N
N
N
H
N
NH
NH2 O
NH2
N
H
N
O
NH2
N
H
NH
O
O
N
H
NH
O
O
H3C
adenine (A)
DNA/RNA
guanine (G)
DNA/RNA
cytosine (C)
DNA/RNA
thymine (T)
DNA
uracil (U)
RNA
1
2
3
4
5
6
7
8
9
1
2
3
4
5
6
28.2: Nucleosides. N-Glycosides of a purine or pyrimidine
heterocyclic base and a carbohydrate. The C-N bond involves
the anomeric carbon of the carbohydrate. The carbohydrates for
nucleic acids are D-ribose and 2-deoxy-D-ribose
343
Nucleosides = carbohydrate + base (Table 28.2, p. 1168)
ribonucleosides or 2’-deoxyribonucleosides
O
HO N
HO
N
N
N
X
NH2
O
HO N
HO
N
N
NH
X
O
NH2
RNA: X= OH, adenosine (A)
DNA: X= H, 2'-deoxyadenosine (dA)
RNA: X= OH, guanosine (G)
DNA: X= H, 2'-deoxyguanosine (dG)
O
HO
HO X
N
N
O
NH2
O
HO
HO
N
NH
O
O
H3C
RNA: X= OH, cytidine (C)
DNA: X= H, 2'-deoxycytidine (dC)
DNA: thymidine (T)
O
HO
HO
N
NH
O
O
RNA: R= H, uridine (U)
1
2
3
4
5
6
7
8
9
1'
2'
3'
4'
5'
OH
1'
2'
3'
4'
5' 2
1
3
4
5
6
To differentiate the atoms of the carbohydrate from the base, the
position number of the carbohydrate is followed by a ´ (prime).
The stereochemistry of the glycosidic bond found in nucleic acids
is β.

3. 176
344
28.3: Nucleotides. Phosphoric acid esters of nucleosides.
Nucleotides = nucleoside + phosphate
O
HO X
HO B
ribonucleoside (X=OH)
deoxyribonucleoside (X=H)
ribonucleotide 5'-monophosphate (X=OH, NMP)
deoxyribonucleotide 5'-monophosphate (X=H, dNMP)
O
HO X
O B
P
HO
O
O
O
HO X
O B
P
O
O
O
P
HO
O
O
O
HO X
O B
P
O
O
O
P
O
O
O
P
HO
O
O
ribonucleotide 5'-diphosphate (X=OH, NDP)
deoxyribonucleotide 5'-diphosphate (X=H, dNDP)
ribonucleotide 5'-triphosphate (NTP)
deoxyribonucleotide 5'-triphosphate (X=H, dNTP)
O
O OH
O B
P
O
O
ribonucleotide
3',5'-cyclic phosphosphate (cNMP)
Kinase: enzymes that catalyze the phosphoryl transfer reaction
from ATP to an acceptor substrate. M2+ dependent
O
HO
HO
OH
OH
OH
O N
N
N
N
NH2
HO OH
O
P
O
O
O
P
O
O
O
P
O
O
O
O
HO
HO
OH
OH
OPO3
2-
ATP
O N
N
N
N
NH2
HO OH
O
P
O
O
O
P
O
O
O
ADP
Glucose-6-phosphate
Glucose
345
O N
N
N
N
NH2
HO OH
O
P
O
O
O
P
O
O
O
P
O
O
O
ATP
O N
N
N
N
NH2
HO OH
O
P
O
O
O
AMP
O
O OH
O
P
O
O
N
N
N
N
NH2
-P2O7
adenylyl
cyclase H2O
cAMP
O N
N
N
NH
O
HO OH
O
P
O
O
O
P
O
O
O
P
O
O
O
GTP
O N
N
N
NH
O
HO OH
O
P
O
O
O
GMP
O
O OH
O
P
O
O
N
N
N
NH
O
-P2O7
guanylate
cyclase H2O
cGMP
NH2 NH2 NH2
1971 Nobel Prize in Medicine or Physiology:
Earl Sutherland
28.4: Bioenergetics. (Please read)
28.5: ATP and Bioenergetics. (Please read)
+ HPO4
2-
O N
N
N
N
NH2
HO OH
O
P
O
O
O
P
O
O
O
P
O
O
O
ATP
H2O O N
N
N
N
NH2
HO OH
O
P
O
O
O
P
O
O
O
ADP
+ ~31 KJ/mol
(7.4 Kcal/mol)

4. 177
346
28.6: Phosphodiesters, Oligonucleotides, and
Polynucleotides. The chemical linkage between
nucleotide units in nucleic acids is a phosphodiester,
which connects the 5’-hydroxyl group of one
nucleotide to the 3’-hydroxyl group of
the next nucleotide.
By convention, nucleic acid sequences are written
from left to right, from the 5’-end to the 3’-end.
Nucleic acids are negatively charged
28.7: Nucleic Acids.
1944: Avery, MacLeod & McCarty - Strong evidence that DNA
is genetic material
1950: Chargaff - careful analysis of DNA from a wide variety of
organisms. Content of A,T, C & G varied widely according
to the organism, however: A=T and C=G (Chargaff’ Rule)
1953: Watson & Crick - structure of DNA (1962 Nobel Prize with
M. Wilkens, 1962)
RNA, X= OH
DNA, X=H
O
O
O X
Base
P
O
O
O
O
O X
Base
P
O
O
O
3'
3'
5'
5'
3'
5'
347
28.8: Secondary Structure of DNA: The Double Helix.
Initial “like-with-like”, parallel helix:
Does not fit with with Chargaff’s Rule: A = T G = C
Wrong tautomers !!
Watson, J. D. The Double Helix, 1968
N
N
N
N
N
H
dR
N
N
N
N
N
H
dR
H
N
N
dR
O
H
O
N
N
dR
O
H
O
purine - purine pyrimidine - pyrimidine
N
N
dR
N
H
O
N
N
dR
N
H
O
H
N
N
N
N
O
N
H
dR
N
N
N
N
O
H
dR
H
H
H
N
H
H
H

5. 178
348
Two polynucleotide strands, running in opposite directions
(anti-parallel) and coiled around each other in a double helix.
The strands are held together by complementary hydrogen-
bonding between specific pairs of bases.
O
OR
RO
N
N
N
O
H
H
O
OR
RO
N
N N
N
O
N
H
H
H
Hydrogen Bond
Donor
Hydrogen Bond
Donor
Hydrogen Bond
Acceptor
Hydrogen Bond
Acceptor
3'
5'
Hydrogen Bond
Acceptor
Hydrogen Bond
Donor
5'
O2
N4
O6
3'
Antiparallel C-G Pair
N3 N1
N2
O
OR
RO
N
N
O
O
O
OR
RO
N
N N
N
N
H
H
H
5'
3'
3'
5'
Hydrogen Bond
Donor
N6
Hydrogen Bond
Acceptor
Hydrogen Bond
Acceptor O4
Hydrogen Bond
Donor
Antiparallel T-A Pair
N1
N3
349
DNA double helix
one
helical
turn
34 Å
major
groove
12 Å
minor
groove
6 Å
backbone: deoxyribose and phosphodiester linkage
bases

6. 179
350
28.9: Tertiary Structure of DNA: Supercoils. Each cell contains
about two meters of DNA. DNA is “packaged” by coiling around
a core of proteins known as histones. The DNA-histone
assembly is called a nucleosome. Histones are rich is lysine
and arginine residues.
Pdb code 1kx5
351
28.10: Replication of DNA.
The Central Dogma (F. Crick):
DNA replication DNA transcription mRNA translation Protein
(genome) (transcriptome) (proteome)
Expression and transfer of genetic information:
Replication: process by which DNA is copied with very high
fidelity.
Transcription: process by which the DNA genetic code is read
and transferred to messenger RNA (mRNA). This is an
intermediate step in protein expression
Translation: The process by which the genetic code is converted
to a protein, the end product of gene expression.
The DNA sequence codes for the mRNA sequence, which
codes for the protein sequence
“It has not escaped our attention that the specific pairing we have postulated immediately
suggests a possible copying mechanism for the genetic material.” Watson & Crick

7. 180
352
DNA is replicated by the coordinated efforts of a number of
proteins and enzymes.
For replication, DNA must be unknotted, uncoiled and the
double helix unwound.
Topoisomerase: Enzyme that unknots and uncoils DNA
Helicase: Protein that unwinds the DNA double helix.
DNA polymerase: Enzyme that replicates DNA using each strand
as a template for the newly synthesized strand.
DNA ligase: enzyme that catalyzes the formation of the
phosphodiester bond between pieces of DNA.
DNA replication is semi-conservative: Each new strand of DNA
contains one parental (old, template) strand and one
daughter (newly synthesized) strand
353
Unwinding of DNA by helicases expose the DNA bases
(replication fork) so that replication can take place. Helicase
hydrolyzes ATP in order to break the hydrogen bonds between
DNA strands
DNA replication

8. 181
354
DNA Polymerase: the new strand is replicated from the 5’ → 3’
(start from the 3’-end of the template)
DNA polymerases are Mg2+ ion dependent
The deoxynucleotide 5’-triphosphate (dNTP) is the reagent for
nucleotide incorporation
G
O
O
O
P
O
-O
A
O
O
O
T
O
OH
O P O
O
C
O
OH
O
O-
P
O-
O
O P
O-
O
O-
Mg2+
5'
3'
5'
template
strand
(old)
(new)
3’-hydroxyl group of the growing DNA strand acts as a nucleophile
and attacks the α-phosphorus atom of the dNTP.
dNTP
355
Replication of the leading strand occurs continuously in the
5’ → 3’ direction of the new strand.
Replication of the lagging strand occurs discontinuously. Short
DNA fragments are initially synthesized and then ligated together.
DNA ligase catalyzes the formation of the phosphodiester bond
between pieces of DNA.
animations of DNA processing: http://www.wehi.edu.au/education/wehi-tv/dna/

9. 182
356
DNA replication occurs with very high fidelity:
Most DNA polymerases have high intrinsic fidelity
Many DNA polymerases have “proof-reading”
(exonuclease) activity
Mismatch repair proteins seek out and repair base-pair
mismatches due to unfaithful replication
28.11 Ribonucleic Acid
RNA contains ribose rather than 2-deoxyribose and uracil rather
than thymine. RNA usually exist as a single strand.
There are three major kinds of RNA
messenger RNA (mRNA):
ribosomal RNA (rRNA)
transfer RNA (tRNA)
DNA is found in the cell nucleus and mitochondria; RNA is more
disperse in the cell.
357
Transcription: only one of the DNA strands is copied (coding
or antisense strand). An RNA polymerase replicates the DNA
sequence into a complementary sequence of mRNA (template
or sense strand). mRNAs are transported from the nucleus to
the cytoplasm, where they acts as the template for protein
biosynthesis (translation). A three base segment of mRNA
(codon) codes for an amino acid.The reading frame of the
codons is defined by the start and stop codons.

10. 183
358
5'-cap 5'-UTR start stop 3'-UTR
Coding sequence
The mRNA is positioned in the ribosome through complementary
pairing of the 5’-untranslated region of mRNA with a rRNA.
Transfer RNA (tRNA): t-RNAs carries an amino acid on the
3’-terminal hydroxyl (A) (aminoacyl t-RNA) and the ribosome
catalyzes amide bond formation.
Ribosome: large assembly of proteins and rRNAs that catalyzes
protein and peptide biosynthesis using specific, complementary,
anti-parallel pairing interactions between mRNA and the
anti-codon loop of specific tRNA’s.
359
Although single-stranded, there are complementary sequences
within tRNA that give it a defined conformation.
The three base codon sequence of mRNA are complementary
to the “anti-codon” loops of the appropriate tRNA. The base-
pairing between the mRNA and the tRNA positions the tRNAs
for amino acid transfer to the growing peptide chain.
aminoacyl t-RNA
TψC loop
D loop
variable loop

11. 184
360
28.12: Protein Biosynthesis. Ribosomal protein synthesis
P site
U G U A
A U C U C
G U U
3'
5'
A site
A C
U
O
O
H
N
SCH3
OHC
U G U A
A U C U C
G U U
3'
5'
A C
U
O
O
H
N
SCH3
OHC
U A
A
O
O
H2N
OH
U G U A
A U C U C
G U U
3'
5'
U A
A
O
O
HN
OH
O
N
H
CH3S
A C
U
OH
OHC
U G U A
A U C U C
G U U
3'
5'
U A
A
O
O
HN
OH
O
N
H
CH3S
A C
U
OH
OHC
U G U A
A U C U C
G U U
3'
5'
U A
A
O
O
HN
OH
O
N
H
CH3S
A C
U
OH
OHC
E site
E site
U G U A
A U C U C
G U U
3'
5'
U A
A
O
O
HN
OH
O
N
H
CH3S
OHC
G A
C
O O
CH3
H2N
U G U A
A U C U C
G U U
3'
5'
O
HN
OH
O
HN
G A
C
O O
CH3
HN
SCH3
U A
A
OH
OJHC
U G U A
A U C U C
G U U
3'
5'
O
HN
OH
O
HN
G A
C
O O
CH3
HN
SCH3
U A
A
OH
OHC
U G U A
A U C U C
G U U
3'
5'
O
HN
OH
O
HN
G A
C
O O
CH3
HN
SCH3
U A
A
OH
OHC
361
28.13: AIDS. (please read)
28.14: DNA Sequencing.
Maxam-Gilbert: relys on reagents that react with a specific DNA
base that can subsequent give rise to a sequence
specific cleavage of DNA
Sanger: Enzymatic replication of the DNA fragment to be
sequenced with a DNA polymerase, Mg+2, and
dideoxynucleotides triphosphate (ddNTP) that truncates
DNA replication
Restriction endonucleases: Bacterial enzymes that cleave
DNA at specific sequences
5’-d(G-A-A-T-T-C)-3’
3’-d(C-T-T-A-A-G)-5’
5’-d(G-G-A-T-C-C)-3’
3’-d(C-C-T-A-G-G)-5’
EcoR I
BAM HI
5'
3'
3'
5'
5'
3'
3'
5'
OH 2-O3PO
2-O3PO OH
restriction
enzyme

12. 185
362
Sanger Sequencing:
key reagent: dideoxynucleotides triphosphates (ddNTP)
N
N
N
N
NH2
O
O
P
O
O-
O
P
O
O-
O
P
O
-O
O-
NH
N
N
N
O
O
O
P
O
O-
O
P
O
O-
O
P
O
-O
O-
ddATP
NH2
ddGTP
O
O
P
O
O-
O
P
O
O-
O
P
O
-O
O-
O
O
P
O
O-
O
P
O
O-
O
P
O
-O
O-
ddTTP ddCTP
N
NH
O
O
N
N
NH2
O
When a ddNTP
is incorporated
elongation of
the primer is
terminated
The ddNTP is
specifically
incorporated
opposite its
complementary
nucleotide base
DNA polymerase
3'
5'-32P
3'
5'
primer
Template
unknown sequence
Mg2+, dNTP's
+ one ddATP
O
N3
HO N
NH
O
O
O
HO N
N
N
NH
O
S
O OH
N
N
H2N
O
O
HO N
N
NH2
O
ddI
AZT
(-)-3TC
Anti-Viral Nucleosides
d4C
363
Sanger Sequencing
Larger
fragments
Smaller
fragments
G
T
A
A
C
G
T
A
A
T
C
A
C
A
G
ddA ddG ddC ddT
C
A
T
T
G
C
A
T
T
A
G
T
G
T
C
5'
32
P
3'
5'
3'
32
P-5' 3'
primer template

13. 186
364
28.15: The Human Genome Project. (please read)
28.16: DNA Profiling and Polymerase Chain Reaction (PCR).
method for amplifying DNA using a DNA polymerase, dNTPs and
cycling the temperature.
Heat stable DNA Polymerases (from archaea):
Taq: thermophilic bacteria (hot springs)- no proof reading
Pfu: geothermic vent bacteria- proof reading
Mg 2+
two Primer DNA strands (synthetic, large excess)
one sense primer and one antisense primer
one Template DNA strand (double strand)
dNTP’s
1 x 2 = 2 x 2 = 4 x 2 = 8 x 2 = 16 x 2 = 32 x 2 = 64 x 2 = 128 x 2 = 256 x 2 = 512 x 2
= 1,024 x 2 = 2,048 x 2 = 4,096 x 2 = 8,192 x 2 = 16,384 x 2 = 32,768 x 2 = 65,536 x 2
= 131,072 x 2 = 262,144 x 2 = 524,288 x 2 = 1,048,576
In principle, over one million copies per original, can be obtained after just twenty cycles
KARY B. MULLIS, 1993 Nobel Prize in Chemistry for his invention of the
polymerase chain reaction (PCR) method.
365
Polymerase Chain Reaction
For a PCR animation go to: http://www.blc.arizona.edu/INTERACTIVE/recombinant3.dna/pcr.html
http://users.ugent.be/~avierstr/principles/pcrani.html
5'
3'
3'
5'
95 °C
denaturation
5' 3'
3' 5'
anneal
(+) and (-) primers
55 - 68 °C
5' 3'
3' 5'
3'
3'
72 °C
Taq, Mg 2+, dNTPs
extension
5'
3'
3'
5'
5'
3'
3'
5'
95 °C
denaturation
2nd cycle
5'
3'
3'
5'
5'
3'
3'
5'
amplification of DNA
2 copies of DNA
repeat temperature cycles