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Review of Ester Bonds
What is a phosphoanhydride bond?
High-energy bond between two phosphate groups
γ β α γ β α γ β α γ β α
March 3 rd and 5 th , 2010 Biochemistry Recitation MBioS 303 - - PDF document
March 3 rd and 5 th , 2010 Biochemistry Recitation MBioS 303 - - PDF document
3/8/2010 March 3 rd and 5 th , 2010 Biochemistry Recitation MBioS 303 Spring 2010 Review of Ester Bonds What is an ester bond? O R C O R Phosphodiester bond? Two ester linkages to same phosphate group 1 3/8/2010 Review of
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Outline
DNA Base Pairing and Tm Structural Features (palindromes, hairpins, etc.) DNA Damage DNA Supercoiling DNA Sequencing Higher Order DNA Structure (Chromatin)
DNA Base Pairing and Tm
Biochemistry, 5th Ed.
What DNA bases typically pair with each other?
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DNA Base Pairing and Tm
Molecular Cell Biology, W.H. Freeman & Co., 1999
How would you define Tm?
DNA/RNA Structural Features
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DNA Structural Forms
A-DNA: More compact than B; found in dessicated forms B-DNA: Structure typically found in cells. KNOW the above characteristics! Z-DNA: More stretched than B; the only left-handed form.
DNA Structural Forms
Which pictures represent A, B and Z DNA?
A B C A B C
Genomes, 2nd Ed.
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DNA Structural Forms: Palindromes
Both strands have the same sequence, in antiparallel
- rientation
Examples: GAATTC ACCTAGGT CTTAAG TGGATCCA GACTCCXXXXXXGGAGTC CTGAGGXXXXXXCCTCAG
http://en.wikipedia.org/wiki/Image:Stem-loop.svg Landes Bioscience, Eurekah.com
See example
- n board
Mirror Repeats
The same sequence is present on one strand, as a
mirror image
Can’t form hairpins
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Mirror Repeats
The same sequence is present on one strand, as a
mirror image
Can’t form hairpins CAN form DNA triple helices Functional importance: produces sharp bend in DNA
Landes Bioscience, Eurekah.com
DNA Damage
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Who Cares?
Damaged RNA and proteins can be easily replaced by
reading from the DNA sequence
There is no way to replace the DNA molecules! Unrepaired DNA mutations linked to disease, including
cancer
Unrepaired mutations may be passed to offspring if
- ccur in gametes
Cells have a number of DNA repair systems to fix such
mutations
Sources of Damage
Endogenous cellular sources
Reactive Oxygen Species (ex. from electron transport
chain)
Base hydrolysis (ex. deamination, depuriniation, etc.) Base mismatch (from errors in DNA replication)
Exogenous sources of damage
UV light Ionizing radiation Chemical sources (may cause many types of DNA
damage)
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Depurination
Hydrolysis of N-glycosidic bond linking sugar and purine
base
Occurs spontaneously in the cell
Up to 10,000 purines lost from DNA every 24 hours in a mammalian
cell
The Cell: A Molecular Approach, 2nd Ed.
What kind of problem could this cause in a cell? Why?
Deamination
Loss of exocyclic amino
groups
Occurs spontaneously in
the cell
About 100 deaminations
- ccur in a mammalian
cell every day
May explain why DNA
contains T rather than U
The Cell: A Molecular Approach, 2nd Ed.
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UV Induced DNA Damage: CPDs
UV light
Cross-linking between C5 and C6 on adjacent pyrimidine
bases (usually thymine) forming a ring structure = cyclobutane pyrimidine dimer (CPD)
Molecular Cell Biology, W.H. Freeman & Co., 1999
UV Induced DNA Damage: CPDs
Causes “kink” in DNA Dimer can’t fit
normally into double helix, blocking replication and gene expression until removed
http://home.twcny.rr.com/geomanagement/ensmingr/menagerie.html
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UV Induced DNA Damage: 6-4 PP
Cross-linking between C6 on one
pyrimidine to C4 on an adjacent pyrimidine = 6-4 photoproduct
Occur less frequently than CPDs,
but are more damaging
Cause bigger “kink” in DNA,
which tends to be lethal rather than mutagenic
Modern Genetic Analysis
DNA Damage: Summary
Deamination Depurination Cyclobutyl pyrimidine dimers 6-4 photo- products
Cause Spontaneous Spontaneous UV light UV light Result Loss of exocyclic amine group Loss of purine base Formation of cyclobutyl ring structure; can block replication and gene expression Formation of 6- 4 crosslink that causes significant kink in DNA backbone; can block replication/ gene expression
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DNA Supercoiling Supercoiling
Coiling a coil Intrinsic property of
DNA
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Linking Number
Lk = number of times
- ne strand passes
through the “plane” created by the other strand
Change in Linking Number
For B-DNA, Linking
number (Lk) = (# base pairs)/10.5
More base pairs per
turn (ex. 12 instead of 10.5) = -Lk
Fewer base pairs per
turn (ex. 9 instead of 10.5) = +Lk
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Effect of Fixed DNA Ends
Molecular Biology of the Cell, 4th Ed.
Function of Topoisomerases?
Molecular Biology of the Cell, 4th Ed.
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Topoisomerase I
Releases strain from over- or under-winding of the DNA Forms a single-stranded break, and changes linking
number by 1
ATP independent
Molecular Cell Biology, 4th Ed.
Topoisomerase II (ex. DNA Gyrase)
Releases strain from underwinding of the DNA Forms a double-stranded break, and changes linking
number by 2
ATP dependent
Molecular Cell Biology, 4th Ed.
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