CHAPTER 8

Nucleotides and Nucleic Acids

Key topics:
– Biological function of nucleotides and nucleic acids
– Structures of common nucleotides
– Structure of double-stranded DNA
– Structures of ribonucleic acids
– Denaturation and annealing of DNA
– Chemistry of nucleic acids; mutagenesis
 Functions of
Nucleotides and Nucleic Acids
• Nucleotide Functions:
– Energy for metabolism (ATP)
– Enzyme cofactors (NAD+)
– Signal transduction (cAMP)

• Nucleic Acid Functions:

– Storage of genetic info (DNA)
– Transmission of genetic info (mRNA)
– Processing of genetic information (ribozymes)
– Protein synthesis (tRNA and rRNA)
 Nucleotides and Nucleosides
• Nucleotide =
– Nitrogeneous base
– Pentose
– Phosphate

• Nucleoside =
– Nitrogeneous base
– Pentose

• Nucleobase =
– Nitrogeneous base
 Phosphate Group

• Negatively charged at neutral pH

• Typically attached to 5’ position
– Nucleic acids are built using 5’-triphosphates
• ATP, GTP, TTP, CTP
– Nucleic acids contain one phosphate moiety
per nucleotide
• May be attached to other positions
 Other Nucleotides:
Monophosphate Group in Different Positions
 Pentose in Nucleotides
• -D-ribofuranose in RNA
• -2’-deoxy-D-ribofuranose in DNA

• Different puckered conformations of the sugar ring

are possible
 Nucleobases

• Derivatives of pyrimidine or purine

• Nitrogen-containing heteroaromatic molecules
• Planar or almost planar structures
• Absorb UV light around 250–270 nm
 Pyrimidine Bases

• Cytosine is found in both DNA and RNA

• Thymine is found only in DNA
• Uracil is found only in RNA
• All are good H-bond donors and acceptors
• Cytosine pKa at N3 is 4.5
• Thymine pKa at N3 is 9.5
• Neutral molecules at pH 7
 Purine Bases

• Adenine and guanine are found in both RNA

and DNA
• Also good H-bond donors and acceptors
• Adenine pKa at N1 is 3.8
• Guanine pKa at N7 is 2.4
• Neutral molecules at pH 7
 b-N-Glycosidic Bond
• In nucleotides the pentose ring is attached to the nucleobase via
N-glycosidic bond
• The bond is formed to the anomeric carbon of the sugar in b
configuration
• The bond is formed:
– to position N1 in pyrimidines
– to position N9 in purines
• This bond is quite stable toward hydrolysis, especially in
pyrimidines
• Bond cleavage is catalyzed by acid
 Conformation around N-Glycosidic Bond

• Relatively free rotation can occur around the N-glycosidic bond

in free nucleotides
• The torsion angle about the N-glycosidic bond (N-C1') is
denoted by the symbol c
• The sequence of atoms chosen to define this angle is O4'-C1'-
N9-C4 for purine, and O4'-C1'-N1-C2 for pyrimidine derivatives
• Angle near 0 corresponds to syn conformation
• Angle near 180 corresponds to anti conformation
• Anti conformation is found in normal B-DNA
 UV Absorption of Nucleobases
• Absorption of UV light at 250–270 nm is due to  
* electronic transitions
• Excited states of common nucleobases decay rapidly
via radiationless transitions
– Effective photoprotection of genetic material
– No fluorescence from nucleic acids
Nomenclature
 Nomenclature: Deoxyribonucleotides
You need to know structures, names, and symbols (both
two-letter (dA) and four-letter (dAMP) codes)
 Nomenclature: Ribonucleotides
You need to know structures, names, and symbols (both
one-letter and three-letter codes)
 Minor Nucleosides in DNA
• Modification is done after DNA
synthesis
• 5-Methylcytosine is common in
eukaryotes, also found in bacteria
• N6-Methyladenosine is common in
bacteria, not found in eukaryotes
• Epigenetic marker
• Way to mark own DNA so that cells can degrade foreign DNA
(prokaryotes)
• Way to mark which genes should be active (eukaryotes)
• Could the environment turn genes on and off in an
inheritable manner?
 Epigenetic mechanisms:
metilasi DNA, modifikasi histon, dan perubahan bentuk kromatin
Epigenetika (
bahasa Inggris:
epigenetics), di dalam
biologi, adalah studi
tentang perubahan fenotipe
atau ekspresi genetika yang
disebabkan oleh
mekanisme selain
perubahan sekuens DNA
dasar. Epigenetika berasal
dari bahasa Yunani, epi-
yang berarti "di atas" atau
"menutupi", dan -genetika.
Tidak ada perubahan pada
sekuens DNA dasar,
melainkan faktor non
genetika yang
menyebabkan ekspresi gen
organisme berubah
 Minor Nucleosides in RNA
• Inosine sometimes found in the “wobble position” of the
anticodon in tRNA
– Made by de-aminating adenosine
– Provides richer genetic code

• Pseudouridine ( ) found widely in tRNA and rRNA

– More common in eukaryotes but found also in eubacteria
– Made from uridine by enzymatic isomerization after RNA
synthesis
– May stabilize the structure of tRNA
– May help in folding of rRNA
 Polynucleotides
• Covalent bonds formed via phosphodiester linkages
– negatively charged backbone
• DNA backbone is fairly stable
– Hydrolysis accelerated by enzymes (DNAse)
• RNA backbone is unstable
– In water, RNA lasts for a few years
– In cells, mRNA is degraded in few hours
• Linear polymers
– No branching or cross-links
• Directionality
– 5’ end is different from 3’ end
– We read the sequence from 5’ to 3’
 Hydrolysis of RNA
• RNA is unstable under alkaline conditions
• Hydrolysis is also catalyzed by enzymes (RNase)
• RNase enzymes are abundant around us:
– S-RNase in plants prevents inbreeding
– RNase P is a ribozyme (enzyme made of RNA) that
processes tRNA precursors
– Dicer is an enzyme that cleaves double-stranded
RNA into oligonucleotides
• protection from viral genomes
• RNA interference technology
 Mechanism of
Base-catalyzed RNA Hydrolysis
 Hydrogen-Bonding Interactions
• Two bases can hydrogen bond to form a base pair
• For monomers, large number of base pairs is possible
• In polynucleotide, only few possibilities exist
• Watson-Crick base pairs predominate in double-
stranded DNA
• A pairs with T
• C pairs with G
• Purine pairs with pyrimidine
AT and GC Base Pairs
 Discovery of DNA Structure
• One of the most important discoveries in biology

• Why is this important?

“This structure has novel features which are of considerable
biological interest”
―Watson and Crick, Nature, 1953

• Good illustration of science in action

– Missteps in the path to a discovery
– Value of knowledge
– Value of collaboration
– Cost of sharing your data too early
 Covalent Structure of DNA (1868–1935)
OH

HO P

O
O
• Friedrich Miescher
Thymine C5H7O isolates “nuclein” from
O cell nuclei
HO P O

Structure of DNA: O

1929 Adenine C5H7O • Hydrolysis of nuclein

(Levene & London) O – phosphate
– pentose
OH
HO P O – and a nucleobase
H O

H H
H H

Thymine CH2O
OH

P O
• Chemical analysis
O
H O – phosphodiester linkages
Structure of DNA:
1935 H
H H H – pentose is ribofuranoside
OH
(Levene & Tipson) Adenine CH2O P O
O O
 Road to the Double Helix
• Watson and Crick • Franklin and Wilkins
– Missing layer means – “Cross” means helix
alternating pattern – “Diamonds” mean
(major & minor groove) that the phosphate-
– Hydrogen bonding: sugar backbone
A pairs with T is outside
– Calculated helical
G pairs with C
parameters
Double helix fits the data!

Watson, Crick, and Wilkins shared

1962 Nobel Prize
Franklin died in 1958
Watson-Crick Model of B-DNA
Other Forms of DNA
 Complementarity of DNA Strands

• Two chains differ in sequence

(sequence is read from 5’ to 3’)
• Two chains are complementary
• Two chains run antiparallel