BIOL1007 Lecture Notes - Lecture 6: Phosphodiester Bond, Pyrophosphate, Polymerization
19 May 2018
School
Department
Course
Professor
Describe the general properties of the polymerisation of information containing biolpolymers
DNA -> DNA/RNA through set of enzymes polymerases
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RNA and DNA polymerases (naming based on product made not template used)
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Reverse transcriptases - DNA polymerases which DNA from an RNA template
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Copying DNA
DNA polymerases only (make DNA)
Common characteristics of DNA and RNA polymerases
RNA polymerases only (make
RNA)
Need primer to start
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Proof read the last nucleotide added (3'
to 5' exonuclease activity, nuclease chops
off last nucleotide just added if it is wrong
ie. Doesn't base pair properly, base
pairing is wrong)
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Use deoxynucleotide triphosphates
(dNTPs: dATP, dGTP, dTTP, dCTP) as
substrate
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This process makes a new template for
the cell, so copying must be accurate
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There's only one double-stranded copy of
the genome in the 2 new cells (only have
one complete copy of the genome)
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Mistake = systematic error in next cell,
everytime it copies DNA it will make the
same mistake
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e.g. killer python
Head (with KP) is 5' phosphate
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Tail = 3' OH
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Made of jelly - H bonds need to cool to
set
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ALWAYS copy new strand 5' to 3' (new nucleotide is adding
to the 3' OH end)
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Only work in one direction
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Use nucleotide triphosphates as substrate
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ONLY ADD nucleotide monophosphate to the 3'OH end of
the growing chain
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Require template
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Form a phosphodiester bond (forming bond on the
backbone, joining phosphate and nucleotide to growing
chain)
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Release pyrophosphate (PPi)
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DON'T need primer to start
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Do NOT proof read last
nucleotide added -> so NO 3'
to 5' exonuclease activity
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Use ribonucleotide
triphosphates (NTPs: ATP,
GTP, CTP, UTP) as substrate
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Doesn't have to be as
accurate as DNA, as many
copies transcribed
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Mistake = random RNA,
doesn't effect next copying
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5' to 3' polymerase activity
DNA polymerases activity
1.
The dNTP which base pairs to template, is added
by the POLYMERASE
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Each nucleotide added sequentially directed by
the template
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2.
Screen clipping taken: 24/08/2017 8:17 AM
Correct dNTP which base pairs to the template
added by polymerase
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Mouse shows phosphodiester bond formed
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3.
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4.
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Eventually wholelstrand is copied
Use ribonucleotide triphosphates
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NO PRIMER
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RNA polymerases activity
Semi molecular level
L6 - Copying DNA
Wednesday, 23 August 2017
11:10 PM
Mod 1 Information transfer Page 1
Phosphate 3' and 5' paired opposite to parent strand ie. 3' aligns with 5' and vice versa
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Hydroxyl attacks phosphate
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Removal drives the reaction (THINK OF EQUIL like chem)
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Pyrophosphate released (product of the reaction), which breaks down into 2 phosphate
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On a super molecular level
Screen clipping taken: 24/08/2017 6:12 PM
Mod 1 Information transfer Page 2
Screen clipping taken: 24/08/2017 6:12 PM
Outline the general mechanism for copying DNA to DNA before cell division, replication. List
the unique problems associated with replication and describe the strategies used by the cell to
overcome these
Challenges of replication
Once in a lifetime activity - either off or on
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Just before cell division, must be coordinated, make sure cell is ready to divide
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Whole genome (both strands) copied ONCE
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Both strands copies at the SAME TIME and SAME PLACE
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Polymerases work in one direction 5' to 3' (2 strands with opposite orientation and need to copy both from the same site
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We have a lot of OriCs
○
OriC - origin of replication of the chromosome (where it starts)
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Strands pulled apart
1.
Replication forks formed, bidirectional = direction of the forks
2.
End with 2 complete copies of the genome (one strand from parent, one newly synthesised, called semi-conservative)
3.
Thick black line = backbone
•
Helicase unwinds DNA, breaks H bonds/base pairing (pulling apart 2 strands)
1.
DNA polymerase - sticks onto chromosome for whole process
2.
Leading strand - New strand moves continuously
3.
Lagging strand - need to use primers, primase added by primase (DNA polymerase)
4.
dNTP - fills in gaps in lagging strand, discontinuous synthesis, results in fragments
5.
Screen clipping taken: 24/08/2017 6:19 PM
Problems
BREAKS DOWN
INTO 2
PHOSPHATES
Mod 1 Information transfer Page 3
Document Summary
Describe the general properties of the polymerisation of information containing biolpolymers. Dna -> dna/rna through set of enzymes polymerases. Rna and dna polymerases (naming based on product made not template used) Reverse transcriptases - dna polymerases which dna from an rna template. Do not proof read last nucleotide added -> so no 3" to 5" exonuclease activity. Doesn"t have to be as accurate as dna, as many copies transcribed. Mistake = random rna, doesn"t effect next copying. Always copy new strand 5" to 3" (new nucleotide is adding to the 3" oh end) Only add nucleotide monophosphate to the 3"oh end of the growing chain. Form a phosphodiester bond (forming bond on the backbone, joining phosphate and nucleotide to growing chain) Proof read the last nucleotide added (3" to 5" exonuclease activity, nuclease chops off last nucleotide just added if it is wrong ie. doesn"t base pair properly, base pairing is wrong)
