Biochemistry I, Spring Term
Lecture 34
April 15, 2013
Lecture 34: Nucleic Acids.
1. Monomeric Units
a) Nucleoside triphosphates are the building blocks of nucleic acids.
b) The base ("sidechain") is connected to the C1' of the sugar ("mainchain") by
an N-linked glycosidic bond.
Base + sugar = nucleoside.
Base + sugar + 1 phosphate=nucleotide
c) The carbon atoms on the sugar are numbered 1' to 5'. The primes distinguish
the atoms on the sugar from those on the base.
d) DNA differs from RNA in the sugar as well in one base.
e) Four different monomers, A, G, C, T in DNA. U replaces T in RNA.
f) Aromatic rings of bases absorb light at ~260 nm.
A
Nitrogenous
Base
Adenine
H
N
N
Nucleoside
Adenosine
H
H
H
N
N
N
N
O
N
Protein
280
260
wavelength
Deoxynucleoside
Triphosphate
dATP
H
HO
N
H
O
O
O
O P O P O P O
O
O
O
N
N
N
O
H
N
N
N
OH OH
G
C
T
U
H
N
N
HO
O
N
Deoxyadenosine (dA)
N
N
N
Deoxynucleoside
Absorbance
Guanine
Cytosine
Thymine
Uracil
Guanosine
Cytidine
5-methyluridine
Uridine
OH H
OH H
Deoxyguanosine (dG)
Deoxycytidine (dC)
Thymidine (dT)
Deoxyuridine (dU)
dGTP
dCTP
dTTP
dUTP
HO
O
2. DNA and RNA are Polynucleotides
a) The phosphodiester backbone is comprised of deoxyribose (DNA) or ribose
(RNA) sugars bridged by phosphates between the 3' and 5' positions of the
sugars.
O
A
O
P
i) The phosphates are always ionized (pKa~1), therefore nucleic acids are
polyanions.
ii) Note that the polarity, i.e. 5'  3', be able to identify the 5’ and 3’ ends.
b) The sequence of nucleotides encodes the information in DNA.
O
O
O
G
O
O
P
O
O
O
Sequence of nucleotide bases is written in the 5'-3' direction.
OH
1
T
Biochemistry I, Spring Term
Lecture 34
3. Chemical Stability.
a) DNA is stable to acids and bases.
b) RNA is hydrolyzed at high pH
(alkaline hydrolysis).
O
P
April 15, 2013
O
O
P
O
O
OO
OO
OO
Base
Base
Base
O
O
O
O
O
P
O
O H
O
O
O P
O
O P O
O
O P O
O
O
HO
4. Double Helical Structures: B-DNA
O
O
P O
O
O
O
O
A
O
O
O P O
O
O
P O
O
O
O
G
O
O
O P O
O
O
P O
O
O
T
O
O
O P O
O
O
a) The helix is right-handed; the chains are antiparallel.
b) Rise 3.4Å/base pair; 10 bp/turn.
c) The spacing between the two phosphate chains in the
direction of the helix is not uniform. There is a wider
groove (major groove) and a narrower groove (minor
groove).
d) The grooves are filled with water and ions (e.g. Na+)
e) The helix interior is filled with stacked base.
f) T pairs with A via two "Watson-Crick H-bonds"
g) C pairs with G via three "Watson-Crick hydrogen
bonds"
5. Hydrogen Bond
major groove
Donors and
Acceptors in
Major and Minor
DNA Grooves:
H
(WC Hbonds shown
O O
N H
P
O
as lines)
O
O
O
N
N
N
H N
O
H N
H
O
O P O
2
O
N
O
P O
O
N
minor groove
Cytosine
major groove
Guanine
H3C
O O
O P
O
N
O
O
O
O
P O
O
OO
P O
O
O
H N
N H
N
H
O
N
N
O
P
O
O
N
O
minor groove
Adenine
Thymine
O
O
P O
Biochemistry I, Spring Term
Lecture 34
April 15, 2013
6. DNA Topology:Taking a linear double stranded segment of DNA and joining the
two ends will make circular DNA. This is referred to as closed circular, relaxed DNA.
Supercoiled DNA is made by:
i) breaking the phosphodiester bonds,
ii) rotate the DNA 360 degrees,
iii) rejoin the broken strands.
This induces stress in the DNA (poor
vdw contacts between bases) that is
relieved by introducing a twist, or
supercoil in the circular DNA,
restoring good vdw between the bases.
360o
AT
GC
AT
GC
GC
GC
TA
TA
TA
CG
CG
CG
GC
GC
GC
AT
GC
AT
GC
AT
GC
GC
GC
TA
TA
CG
CG
GC
GC
7. RNA versus DNA Helical Structure:
i) DNA and double-helical RNA.
Same right-handed anti-parallel
structure.
ii) RNA cannot adopt exactly the
same -form as DNA (the
presence of the 2'-OH
interferes).
a) Spacing of phosphates chains
is more uniform.
b) The depth of the grooves
alternate between shallow and
deep in RNA versus narrow
(minor) and wide (major) in
DNA.
c) Bases are displaced from
helical axis in RNA.
iii) U pairs with A.
8. Other Structural Features
of RNA.
3
RNA
DNA