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Types of Molecules
• 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 O
N H3C
N N
N N N O
Adenine (A) Thymine (T) (DNA only)
O
NH2
N
N
N
N N NH2
N O
Guanine (G)
Cytosine (C)
O
N
N O
Uracil (U) (RNA only)
Nucleotide Components
• Sugars HOH2C O OH
– ribose
HO OH
– Deoxyribose
– Rings numbered using ribose (RNA)
primes
• C1 = 1’ etc
HOH2C O OH
• PO43-
HO H
2-deoxyribose (DNA)
Nucleotide Structure
NH2
N
• Base-sugar-phosphate N
N N
• Base attached to C1 O O O O
HO P O P O P O OH
of sugar O O O OH
• Phosphate attached to Adenosine Triphosphate (ATP) (a ribonucleotide)
C5 of sugar O
H3C
• Usually nucleotides N
N O
are triphosphates, but O O O O
can be mono or di HO P O P O P O H
O O 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 O
O
HO P O P OH 2 O P OH
O O
O
pyrophosphate
phosphate
Chain elongation
O
R O
O N
P N
O O chain
O N N N
NH2
3- OH H O H
N
+ N
N N
O O nucleotide
O O
HO P O P O P O H
O O O OH
O
R O
O N
N
P
O O N
O N N
O O
NH2
N + HO P O P OH
H N O O
longer chain O O N N pyrophosphate
P O
O
O H
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
N
NH -- -- -- N
N
R N R
O
N H -- -- --
H
Guanine cytosine
3 H- bonds
AT base Pair
H
N N H -- -- -- O
N N -- -- -- -- HN N
R N R
O
adenine thymine
2 H-bonds
A-U base Pair (RNA)
H
N N H O
N N N N
H R
R
N
O
adenine uracil
2 H bonds
Base Pairs (Cartoon drawing)
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 CH2 A
O P O N
N
O
OH O
O O
U
O P N
O CH2
O
N O
O
O OH
O N
N
G
O P N N NH 2
O CH2
O
NH 2
O O OH
N
O P C
O CH 2 N O
O
OH 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
