Nucleic Acids The blueprints. Types of Molecules Polymers of nucleotides DNA: code for genetic...
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Transcript of Nucleic Acids The blueprints. Types of Molecules Polymers of nucleotides DNA: code for genetic...
![Page 1: Nucleic Acids The blueprints. Types of Molecules Polymers of nucleotides DNA: code for genetic information RNA –mRNA intermediates in protein synthesis.](https://reader035.fdocuments.us/reader035/viewer/2022062314/56649e915503460f94b973d9/html5/thumbnails/1.jpg)
Nucleic Acids
The blueprints
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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
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Nucleotide Components
• Bases + sugar + phosphate• Bases
– purine• adenine
• guanine
– pyrimidines• thymine
• cytosine
• uracil
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Bases
N N
NN
NH2
N N
NN
O
NH2
N
N
O
O
CH3
N
N
O
NH2
N
N
O
O
Adenine (A)
Guanine (G)
Purines Pyrimidines
Thymine (T) (DNA only)
Cytosine (C)
Uracil (U) (RNA only)
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Nucleotide Components
• Sugars– ribose
– Deoxyribose
– Rings numbered using primes
• C1 = 1’ etc
• PO43-
OH
OHOH
OHOH2C
OH
HOH
OHOH2C
ribose (RNA)
2-deoxyribose (DNA)
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Nucleotide Structure
• Base-sugar-phosphate
• Base attached to C1 of sugar– Note sugar is β
• Phosphate attached to C5 of sugar
• Usually nucleotides are triphosphates, but can be mono or di
OH P O
O
O
P OO
O
P O
O
O
N
O
N
N
OH
OH
N
NH2
OH P O
O
O
P OO
O
P O
O
O OH
OH
N
N
O
O
CH3
Adenosine Triphosphate (ATP) (a ribonucleotide)
Thymidine Triphosphate (TTP) (a deoxyribonucleotide)
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Nucleic Acid, a polymer of nucleotides
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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
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Phosphodiester Bond
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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
OH P O
O
O
P OHO
O
O P OH
O
O
pyrophosphate
2
phosphate
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Chain elongation
H
OO
N N
NN
O
N
P
O
O
OR
OH
OH P O
O
O
P OO
O
P O
O
O
N
O
N
N
H
OH
N
NH2
H
OO N N
NN
O
N
P
O
O
OR
O
PO
O
O N
ON
N
H
OH
N
NH2OH P O
O
O
P OHO
O
+
chain
nucleotide
3- OH
+
longer chainpyrophosphate
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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
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GC base pair
NN
N
NH
O
N HR
H
Guanine
NN
O
N
H
H
R
-- -- --
-- -- --
-- -- --
cytosine
3 H- bonds
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AT base Pair
N
N
N
N
N H
H
R
adenine
NNH
O
O
R
-- -- --
-- -- -- --
thymine
2 H-bonds
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A-U base Pair (RNA)
N
N
N
N
N H
RNN
O
O
H R
H
adenine uracil
2 H bonds
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Base Pairs (Cartoon drawing)
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Complementarity
• One strand is complementary to the other
• If know sequence of one, can deduce that of the other– Templates– Implications in copying
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DNA structure
• Double helix• http://
sbchem.sunysb.edu/msl/dna.gif
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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
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Other forms of DNA
• Z - DNA left handed; structure not fully understood
• A- DNA; tighter helix
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DNA TypesB- 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%26ndsp%3D20%26svnum%3D10%26hl%3Den%26lr%3D%26sa%3DN
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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&tbnw=122&prev=/images%3Fq%3DA%2BDNA%26start%3D20%26ndsp%3D20%26svnum%3D10%26hl%3Den%26lr%3D%26sa%3DN
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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&tbnw=122&prev=/images%3Fq%3DA%2BDNA%26start%3D20%26ndsp%3D20%26svnum%3D10%26hl%3Den%26lr%3D%26sa%3DN
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Look down Axis
• http://www.accelrys.com/reference/gallery/life/dna.gif
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Sequence dependent structures
• palindromes
• hairpins
• inverted repeats
• mirror repeats
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RNA
• codes for protein
• no consistent secondary structure
• single stranded
• Ribose instead of deoxyribose
• Thymine (T) replaced by Uracil
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RNA
O
OHOH
CH2OO P
OO
O
N
OH
CH2O
O P
OO
ON
OH
CH2OO P
OO
O P O
O
O
O N
OH
N
NN
NH2
CH2
N
O
O
N
NN
O
NH2
N
N
O
NH2
5' end
A
U
G
C
3 ' end
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Transfer RNA
• http://www.mie.utoronto.ca/labs/lcdlab/biopic/fig/12.07.jpg
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Instability of RNA
• RNA unstable due to reactivity of 2’ hydroxyl on ribose
• Very labile
• DNA extremely stable
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Nucleic Acid Chemistry
• Denaturation– unzip by heating– reannealing– CoT curves: more GC=higher temp
• Uses of DNA to find sequences– probes– forensic
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DNA probes
• Take DNA from crime scene
• DNA from suspect, random other person etc
• See what matches
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Nucleic Acid Chemistry
• Mutations– changes in
sequence/structure
– nonenzymatic changes• thymine dimers
• deamination
• oxidative damage
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Nucleic Acid Chemistry
• http://www.dnalc.org/resources/BiologyAnimationLibrary.htm
• Sequencing
• PCR
• Southern Blotting
• Probes
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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
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Sample Sanger Gel
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Human Genome Project
• http://www.ornl.gov/sci/techresources/Human_Genome/home.shtml