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Nucleotides

and Nucleic
Acids

Lehninger
Chapter 8

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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 BCH261
nucleic
W 2015acids; mutagenesis
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So far..
Monomer
Amino Acids
Monosaccharides

Nucleotides

Oligomer
Peptides

Polymer
Polypeptides
(proteins)

Oligosaccharides

Polysaccharides
(glycans)

Oligonucleotides

Polynucleotides
(nucleic acids)
Macromolecules
in cells

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Functions of
nucleotides and nucleic Acids
Energy for metabolism (ATP)

Nucleotide Functions

Enzyme cofactors (NAD+)


Signal transduction (cAMP)
Storage of genetic info (DNA)

Nucleic Acid Functions

Transmission of genetic info


(mRNA)
Protein synthesis (tRNA and
rRNA)
Processing of genetic
information (ribozymes)

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Two major functions of


nucleotides and nucleic Acids
nucleic acids

nucleotide
Adenosine
triphosphate (ATP)

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Deoxyribonucleic acid (DNA)


Ribonucleic acid (RNA)

The anatomy of a nucleotide


Phosphate

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Nucleobases
Derivatives of pyrimidine or purine
Pyrimidine is single-ringed
Purine is double-ringed
Nitrogen-containing heteroaromatic
molecules
Planar ring structures
Absorb UV light around 250-270 nm
fig81b

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Pyrimidine bases

(DNA and RNA)

(DNA only)

(RNA only)

All are good H-bond donors and acceptors


Neutral at neutral pH
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Purine bases

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Both found in DNA


and RNA
Also good H-bond
donors and acceptors
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Neutral at neutral pH

UV absorption of nucleobases
Absorption of UV light at 250-270 nm
This is due to ____________________
Excited states of common nucleobases
decay rapidly via radiation-less transitions
Effective photoprotection of genetic
material
No fluorescence from nucleic acids

Used to measure nucleic acid concentration

Fig. 8-10, Lab 8

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Absorbance of nucleotides is slightly


different that that of aromatic amino acids
Aromatic
amino
acids

absorbance

Nucleotides

240

250

260

270

Wavelength (nm)

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280

290
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Pentose in nucleotides
-D-ribofuranose in RNA
-2-deoxy-D-ribofuranose in DNA

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Conformation of Ribose

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Ribose rings are not planar:


different puckered conformations
of the sugar ring are possible

C-2 or C-3 are the carbons that undergo bendin


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Joining the base to the


pentose
The N-Glycosidic Bond

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N-Glycosidic bond
The pentose ring is attached to the nucleobase via a N-glycosidic bond
The anomeric carbon of the sugar is in configuration
It forms a bond with position
N1 in pyrimides and
position N9 in purines

Free rotation in free


nucleotides

Stable, but
hydrolyzable by acid
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Joining the phosphate to the


pentose
The phosphoester bond

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Phosphate group

No phosphate :
One phosphate:
Two phosphates:
Three phosphates:
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Nucleoside triphosphates

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Nucleotides and phosphate number

NMP = NUCLEOSIDE MONOPHOSPHATE


NDP = NUCLEOSIDE DIPHOSPHATE
NTP = NUCLEOSIDE TRIPHOSPHATE

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Nomenclature

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Nomenclature:
Ribonucleotides
Recognize general
structure, and the specific names and
symbols (both one-letter (A) and three-letter (AMP) codes)

Nomenclature:
Deoxyribonucleotides
Recognize
general structure, and the specific names and
symbols (both one-letter (dA) and three-letter (dAMP) codes)

Joining nucleotides
together: the
phosphodiester bond

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Nucleic Acids
Nucleic acids are made by covalently
bridging nucleosides with a
phosphodiester bond
Phosphate links the 3 end of one
nucleoside to the 5 end of another
Phosphodiester bonds are not fully
extended with respect to bases and
sugars

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Nucleic Acid Synthesis


The monomers used for
nucleic acids are
(d)NTPs!
Formation of Phosphodiester bond
is directional!
A nucleotide is added to the 3
end of an existing chain
Formation of phosphodiester
bonds results in release of
pyrophosphate
No branching
Polynucleotide chain is
directional: exposed 5 and
3 ends
Always read and write
sequence from 5 to 3
end
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Two types of nucleic acids

Fig.87

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Some properties of RNA and DNA


Covalent bonds formed via phosphodiester linkages
negatively charged backbone

Linear polymers
No branching or cross-links

Directionality
5 end is different from 3 end
We read the sequence from 5 to 3

DNA backbone is fairly stable


DNA from mammoths?
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
Degraded by Alkali conditions

DNA is a helix and RNA


is typically not
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Watson-Crick model of B-DNA

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rall DNA structure with GC and AT base p

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What drives DNA HELIX formation?


1.Phosphate and pentose are
hydrophillic
- exposed to water
- forms a hydration shell

2. Hydrogen bonding between


bases
- between bases on opposite strands

3. Base stacking
- bases are hydrophobic rings
- bases are planar
- adjacent bases in the same
strand are able to stack very closely
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Hydrogen bonding interactions (1)


Two bases can hydrogen bond to form a base
pair
In double-stranded DNA, Watson-Crick base
pairs predominate
A pairs with T
C pairs with G

Purine pairs with pyrimidine

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Stick model of a GC base pair showing H-bond

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Stick model of a AT base pair showing H-bonds

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Base stacking interactions

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Chemistry reminder: stacking interaction


between aromatic rings

Pi stacking (also called stacking) refers to attractive,


noncovalent interactions between aromatic rings.
These interactions are important in nucleobase stacking
within DNA and RNA molecules, protein folding, and
molecular recognition
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DNA can be visualized with


fluorescent dyes: this takes
advantage of the ring stacking
interactions in DNA.
Base 1

Base 1

Base 2

Base 2

Ethidium bromide
Excited by UV, and fluorescent only when bound to DNA
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Complementarity
of DNA strands
Two chains run ________
Two chains are __________ together
Two chains are _______ in sequence
(sequence is read from 5 to 3)

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Discovery of DNA structure

You have or will learn about the discovery of the DNA helix in other courses: Genetics,
Molecular Biology

Elucidated by Watson and Crick

They used X-ray data obtained by Franklin and Wilkins

One of the most important discoveries in biology. Why?

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Replication of Genetic Code


Strand separation occurs
first
Each strand serves as a
template for the synthesis
of a new strand
Synthesis is catalyzed
by enzymes known as
DNA polymerases
Newly made DNA
molecule has one
daughter strand and one
parent strand.
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NA can assume different conformatio

The B-form of DNA is the most common


form,
However Z-DNA is also very important.
Z-DNA is found in regions of DNA that
are actively being transcribed, and we
have proteins that specifically
recognize Z-DNA in order to facilitate
transcription.

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What causes DNA to assume


different conformations?
1. Rotation about the
Phosphate and
Phosphodiester bonds in the
backbone
2. Rotation of the C-1-Nglycosyl bond
3. Conformation of deoxyribose
(pucker of the 2 or 3
position)

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cal characteristics of different DNA f

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Describing DNA sequences


Always write sequence in 5 - > 3
direction:
Left strand:

Right strand:

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Unusual DNA sequences


Stretches of six adenosines can bend DNA 18
Palindrome sequences
Palindromes: words or phrases that are
the same when read backward or
forward:
ROTATOR

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NURSES RUN

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Self-complementary within same strand

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Palindrome DNA can form hairpins and


cruciform conformations

May regulate gene


regulation or
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DNA Denaturation
Covalent bonds remain intact
Genetic code remains intact
Hydrogen bonds are broken
Two strands separate
Base stacking is lost
Denaturation can be induced by high temperature,
or change in pH
Tm = melting temperature at which half of DNA
molecules are denatured
Denaturation may be reversible: __________
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Body temperature

Body temperature

Decrease
temperatu
re
further

Increase
temperat
ure

Increase
temperatur
e
further

Decrease
temperatu
re

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DNAs with different sequence composition


differ in melting temperature

DNA1
DNA2

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Factors Affecting DNA


Denaturation
The midpoint of melting (Tm) depends on base
composition
high CG increases Tm

Tm depends on DNA length


Longer DNA has higher Tm
Important for short DNA

Tm depends on pH and ionic strength


High salt increases Tm
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Higher GC content increases Tm of


DNA helix

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Denaturation of VERY Large DNA Molecules is not


Uniform
AT rich regions melt at a lower temperature than GC-rich
regions

Helix

Melted
Helix

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Molecular
Mechanisms of DNA
Mutagenesis

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Molecular mechanisms of mutagenesis


Spontaneous mutagenesis
Deamination (enhanced by certain chemicals)
Depurination (enhanced by certain chemicals)

Chemical alkylation
Methylation of guanine

Oxidative damage
Hydroxylation of guanine
Mitochondrial DNA is most susceptible

Radiation damage
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Deamination

Deamination
Very slow reactions
Large number of residues
The net effect is significant:
100 C U events /day in a
mammalian cell

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Depurination

Depurination
N-glycosidic bond is hydrolyzed
Significant for purines:
10,000 purines lost/day in a
mammalian cell

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Radiation-Induced Mutagenesis
UV light induces dimerization of
pyrimidines, this may be the main
mechanism for skin cancers
Ionizing radiation (X-rays and -rays)
causes ring opening and strand breaking.
Cells can repair some of these
modifications, but others cause mutations.
Accumulation of mutations is linked to
aging and carcinogenesis
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RNA
Is synthesized using DNA template
Contains ribose instead of deoxyribose
Contains uracil instead of thymine
Can contain modified nucleosides
Can form DNA/RNA hybrids
Can form RNA double helices (viruses)
Can form complex tertiary structures
Several types of RNA
Can have unusual base pairs (eg. G-U)
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Conformations that RNA can adopt

Messenger RNA:
code carrier for the sequence of proteins
Is synthesized using DNA
template:
TRANSCRIPTION
mRNAs encode for proteins
TRANSLATION
Stabilized by base stacking
instead of H-bonding but can
form base pairs
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Transfer RNA: matching amino


acids with the mRNA Code
tRNA molecules have quite complex structures
Where the amino acid goes

Where the anti-codon is interacts with mRNA codon


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RNA and mRNA interaction is driven by base pa

tRNA anticodon

5 A A G 3
3 U U U 5
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Codon - mRNA

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Other structural and enzymatic RNAs


Ribosomal RNAs (rRNAs) molecules have quite
complex structures. Part of the protein synthesis
machinery
Micro RNAs (miRNAs) molecules are involved in
gene regulation
Small nuclear RNAs (snRNAs) molecules are
involved in catalysis, intron splicing
Enzymatic RNAs are called ribozymes
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Ribosomal RNAs (rRNAs) molecules have


quite complex structures. Part of the protein
synthesis machinery

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subunit_of_the_ribosome_3CC2.png

Nucleotide functions
1. Energy carriers

2. Co-enzymes

3. Signaling molecules

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ATP is the main energy carrier in cells


used to drive endergonic reactions

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Nucleotides are used as energy carriers in cells:


ATP is predominant, but GTP, UTP and CTP are also
used in some reactions
Phosphoanhydride bonds are high energy: 30
kJ/mol/anhydride
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Coupled to synthetic reactions to drive endergonic

Nucleotides can function as co-enzymes


NAD+ used by many enzymes in redox reactions
(Vitamin B3/ Niacin)

e.g. Alcohol dehydrogenase

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Nucleotides can function as co-enzymes

(Vitamin B5)

It is a coenzyme, notable for its role in the synthesis and oxidation of


fatty acids, and the oxidation of pyruvate in the citric acid cycle

Nucleotides can
function as coenzymes
(Vitamin B2)

FAD is a redox cofactor, more


specifically a prosthetic group,
involved in several important
reactions in metabolism.
Very important in the process
known as oxidative
phosphorylation
(a topic for BCH361).

Nucleotides can function as


signaling molecules
hormone

cAMP is derived from ATP


It is a second messenger signaling molecule

ATP

Adenyla
te
cyclase

cAMP
Fig. 8-39

Hormon
e
actions
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Chapter 8: Summary
Function of nucleotides and nucleic acids
Names and structures of common
nucleotides
Structural basis of DNA function
Reversible denaturation of nucleic acids
RNA structures and functions
Aspects of mutagenesisQuestions, 6e
Questions in blue
would be good
exam questions.
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1, 2, 3, 5, 8 10, 12
Questions 5e
1, 2, 3, 5, 7, 8,10
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