Nucleic Acids
The blueprints
Types of Molecules
• Polymers of nucleotides
• DNA: code for genetic information
• RNA
– mRNA intermediates in protein synthesis
– rRNA carry out protein synthesis
– tRNA translate info on mRNA into a.a.
• Gene
Nucleotide Components
• Bases + sugar + phosphate
• Bases
– purine
• adenine
• guanine
– pyrimidines
• thymine
• cytosine
• uracil
Bases
Purines
Pyrimidines
NH2
N
O
N
N
N
N
Thymine (T) (DNA only)
O
N
NH2
N
N
O
N
Adenine (A)
N
H3C
N
NH2
O
N
Guanine (G)
Cytosine (C)
O
N
N
O
Uracil (U) (RNA only)
Nucleotide Components
• Sugars
– ribose
– Deoxyribose
– Rings numbered using
primes
• PO4
OH
OH
HO
ribose (RNA)
• C1 = 1’ etc
3-
O
HOH2C
O
HOH2C
HO
OH
H
2-deoxyribose (DNA)
Nucleotide Structure
NH2
• Base-sugar-phosphate
• Base attached to C1
of sugar
N
N
N
O
HO
P
O
O
O
O
P
O P
O
O
N
O
OH
O
OH
– Note sugar is β
• Phosphate attached to
C5 of sugar
• Usually nucleotides
are triphosphates, but
can be mono or di
Adenosine Triphosphate (ATP) (a ribonucleotide)
O
H3C
N
O
N
O
HO
P
O
O
O
O
P
O
O P
O
O
H
O
OH
Thymidine Triphosphate (TTP) (a deoxyribonucleotide)
Nucleic Acid, a polymer of
nucleotides
Nucleic Acids
• Polymer of nucleotides
• Phosphodiester linkage
– 3’ of one sugar to 5’ of other
– vectorial
• Sequence read 5’ - 3’
• Previous slide is C-A-A
• Next slide (a cartoon drawing) is A-T-G-C
Phosphodiester Bond
Chain elongation
• 3’ hydroxyl on chain has unshared pair on oxygen
– attacks phosphorus on first phosphate of new nucleotide
– Nucleophilic attack
• Driven by hydrolysis of PPi
O
HO
P
O
O
O
O
P
O
OH
2 O
P
OH
O
pyrophosphate
phosphate
Chain elongation
O
R
O
O
N
P
O
O
H O
chain
N
O
3- OH
N
N
N
NH2
H
N
+
N
N
O
HO
P
O
O
O
O
P
O P
O
O
N
nucleotide
O
H
O
OH
O
R
O
O
O
N
N
P
O
N
O
N
N
NH2
N
H
longer chain
O
O
P
O
N
N
O
N
O
H
OH
O
+
HO
P
O
O
O
P
O
pyrophosphate
OH
Base pairs
– Bases are planar
• sp2 hybridization
• Bases nonpolar
– In Nucleic acids, there is base pairing
– Complementarity
• Purines always base-pair with pyrimidines
– Cytosine hydrogen bonds with guanine
– Thymine hydrogen bonds with adenine or uracil
• Due to distancing and proximity of unshared pairs
and hydrogens
GC base pair
H
N
O -- -- -- H
N
NH -- -- --
N
R
N
N
N
O
N H -- -- --
R
H
Guanine
3 H- bonds
cytosine
AT base Pair
H
N H -- -- -- O
N
N
R
N
-- -- -- -- HN
N
adenine
O
thymine
2 H-bonds
N
R
A-U base Pair (RNA)
H
N H
N
N
R
N
N
O
H
N
N
O
adenine
uracil
2 H bonds
R
Base Pairs (Cartoon drawing)
Complementarity
• One strand is complementary to the other
• If know sequence of one, can deduce that of
the other
– Templates
– Implications in copying
DNA structure
• Double helix
• http://sbchem.sunys
b.edu/msl/dna.gif
DNA structure
• B-DNA is most common
• Antiparallel
• bases inside
– Hydrophobic
– Perpendicular to helix
• stands complementary
– Very important for information transfer
– Each strand a template for the other.
• right handed
• major and minor groove
Other forms of DNA
• Z - DNA left handed; structure not fully
understood
• A- DNA; tighter helix
DNA Types
B- DNA (most common)
•
http://images.google.com/imgres?imgurl=http://gibk26.bse.kyutech.ac.jp/jouhou/image/nucleic/dna/dna_st.small.gif&
imgrefurl=http://gibk26.bse.kyutech.ac.jp/jouhou/image/nucleic/dna/dna.html&h=306&w=375&sz=32&hl=en&start=
32&tbnid=muC9F_v90eYO7M:&tbnh=100&tbnw=122&prev=/images%3Fq%3DA%2BDNA%26start%3D20%26nd
sp%3D20%26svnum%3D10%26hl%3Den%26lr%3D%26sa%3DN
A-DNA (supercoiled)
•
http://images.google.com/imgres?imgurl=http://gibk26.bse.kyutech.ac.jp/jouhou/image/nucleic/dna/dna_st.small.gif&imgrefurl=http://gibk26.
bse.kyutech.ac.jp/jouhou/image/nucleic/dna/dna.html&h=306&w=375&sz=32&hl=en&start=32&tbnid=muC9F_v90eYO7M:&tbnh=100&tb
nw=122&prev=/images%3Fq%3DA%2BDNA%26start%3D20%26ndsp%3D20%26svnum%3D10%26hl%3Den%26lr%3D%26sa%3DN
Z-DNA
•
http://images.google.com/imgres?imgurl=http://gibk26.bse.kyutech.ac.jp/jouhou/image/nucleic/dna/dna_st.small.gif&imgrefurl=http://gibk26.
bse.kyutech.ac.jp/jouhou/image/nucleic/dna/dna.html&h=306&w=375&sz=32&hl=en&start=32&tbnid=muC9F_v90eYO7M:&tbnh=100&tb
nw=122&prev=/images%3Fq%3DA%2BDNA%26start%3D20%26ndsp%3D20%26svnum%3D10%26hl%3Den%26lr%3D%26sa%3DN
Look down Axis
• http://www.accelrys.com/reference/gallery/life/dna.gif
Sequence dependent structures
•
•
•
•
palindromes
hairpins
inverted repeats
mirror repeats
RNA
•
•
•
•
•
codes for protein
no consistent secondary structure
single stranded
Ribose instead of deoxyribose
Thymine (T) replaced by Uracil
RNA
NH2
5' end
N
N
O
O
P
O
CH2
A
N
O
N
O
OH
O
O O
O
O
U
N
P
CH2
O
N
O
O
O
OH
O
N
O P
N
N
G
O
CH2
NH2
N
O
NH2
O
O
OH
N
O P
C
O
CH2
OH
N
O
O
OH
3 ' end
Transfer RNA
• http://www.mie.utoronto.ca/labs/lcdlab/biopic/fig/12.07.jpg
Instability of RNA
• RNA unstable due to reactivity of 2’
hydroxyl on ribose
• Very labile
• DNA extremely stable
Nucleic Acid Chemistry
• Denaturation
– unzip by heating
– reannealing
– CoT curves: more GC=higher temp
• Uses of DNA to find sequences
– probes
– forensic
DNA probes
• Take DNA from crime scene
• DNA from suspect, random other person etc
• See what matches
Nucleic Acid Chemistry
• Mutations
– changes in
sequence/structure
– nonenzymatic changes
• thymine dimers
• deamination
• oxidative damage
Nucleic Acid Chemistry
• http://www.dnalc.org/resources/BiologyAni
mationLibrary.htm
• Sequencing
• PCR
• Southern Blotting
• Probes
DNA sequencing, Sanger dideoxy
method
• 4 samples
• Each gets template and nucleotides
– One dideoxy nucleotide
– Has no 3’ OH so chain can’t elongate
• Sample 1
– ddTTP…stops at T
• Sample 2
– ddATP…stops at A
• Sample 3
– ddCTP…stops at C
• Sample 4
– ddGTP…stops at G
• Run on Gel
– Read from bottom up
Sample Sanger Gel
Human Genome Project
• http://www.ornl.gov/sci/techresources/Hum
an_Genome/home.shtml