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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
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nucleotide
Adenosine
triphosphate (ATP)
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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 only)
(RNA only)
Purine bases
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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
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absorbance
Nucleotides
240
250
260
270
Wavelength (nm)
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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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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
Stable, but
hydrolyzable by acid
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Phosphate group
No phosphate :
One phosphate:
Two phosphates:
Three phosphates:
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Nucleoside triphosphates
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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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Fig.87
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Linear polymers
No branching or cross-links
Directionality
5 end is different from 3 end
We read the sequence from 5 to 3
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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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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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You have or will learn about the discovery of the DNA helix in other courses: Genetics,
Molecular Biology
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Right strand:
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NURSES RUN
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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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DNA1
DNA2
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Helix
Melted
Helix
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Molecular
Mechanisms of DNA
Mutagenesis
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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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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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tRNA anticodon
5 A A G 3
3 U U U 5
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Codon - mRNA
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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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(Vitamin B5)
Nucleotides can
function as coenzymes
(Vitamin B2)
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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