DNA Replication Confusion Watch

RMNDK
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Alright can somebody shed some light on this...
I'm following the AQA Spec.

The role of polymerase, according to them, according to my teachers, my books, my notes and my memory is to bond adjacent nucleotides with a sugar-phosphate covalent to form the sugar phosphate backbone on the new strand.

I've been watching god knows how many videos, looked up however many sites and researched with my own biology texts I bought, and I'm inclined to believe it's DNA ligase that joins up the nucleotides by a nucleophilic substitution reaction.

I know AS modules always tweak information a bit, a little bit how GCSE bloody simplified everything there was to know, but this just bugs me. Somebody enlighten me with the truth.
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beyknowles
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(Original post by RMNDK)
:mad:
Alright can somebody shed some light on this...
I'm following the AQA Spec.

The role of polymerase, according to them, according to my teachers, my books, my notes and my memory is to bond adjacent nucleotides with a sugar-phosphate covalent to form the sugar phosphate backbone on the new strand.

I've been watching god knows how many videos, looked up however many sites and researched with my own biology texts I bought, and I'm inclined to believe it's DNA ligase that joins up the nucleotides by a nucleophilic substitution reaction.

I know AS modules always tweak information a bit, a little bit how GCSE bloody simplified everything there was to know, but this just bugs me. Somebody enlighten me with the truth.
"DNA ligase seals DNA backbone by producing a phosphodiester bond.
DNA polymerase synthesizes DNA.
If you want more information, look up DNA polymerase I (DNAP I).
DNAP I contains 3 functioning domains. 5'-->3' polymerase activity, 5'-->3' exonuclease activity, and 3'-->5' proofreading exonuclease activity.


DNA ligase uses a cofactor called NAD to create the phosphodiester bond.
Basically, the mechanism is similar to adding DNA nucleotides to a growing chain. The 3'OH attacks a pyrophosphate and the product releases a phosphate."

I quote Yahoo answers
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RMNDK
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(Original post by beyknowles)
"DNA ligase seals DNA backbone by producing a phosphodiester bond.
DNA polymerase synthesizes DNA.
If you want more information, look up DNA polymerase I (DNAP I).
DNAP I contains 3 functioning domains. 5'-->3' polymerase activity, 5'-->3' exonuclease activity, and 3'-->5' proofreading exonuclease activity.


DNA ligase uses a cofactor called NAD to create the phosphodiester bond.
Basically, the mechanism is similar to adding DNA nucleotides to a growing chain. The 3'OH attacks a pyrophosphate and the product releases a phosphate."

I quote Yahoo answers
Thank you. I hate it so much when they teach you incorrect stuff yet you've just got to accept the facts.
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kanra
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(Original post by RMNDK)
:mad:
Alright can somebody shed some light on this...
I'm following the AQA Spec.

The role of polymerase, according to them, according to my teachers, my books, my notes and my memory is to bond adjacent nucleotides with a sugar-phosphate covalent to form the sugar phosphate backbone on the new strand.

I've been watching god knows how many videos, looked up however many sites and researched with my own biology texts I bought, and I'm inclined to believe it's DNA ligase that joins up the nucleotides by a nucleophilic substitution reaction.

I know AS modules always tweak information a bit, a little bit how GCSE bloody simplified everything there was to know, but this just bugs me. Somebody enlighten me with the truth.
DNA replication is quite a bit more complicated than what they tell you at A level. The two DNA strands are replicated in different ways because polymerase can only add nucleotides to the OH group on an existing DNA strand, not the phosphate.

Basically, on one stand the nucleotides are added continuously, so you use DNA polymerase to make the sugar phosphate bond. On the other strand, DNA is synthesised as "fragments", and then ligase comes along and makes phosphodiester bonds in order to join these fragments together.
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RMNDK
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(Original post by kanra)
DNA replication is quite a bit more complicated than what they tell you at A level. The two DNA strands are replicated in different ways because polymerase can only add nucleotides to the OH group on an existing DNA strand, not the phosphate.

Basically, on one stand the nucleotides are added continuously, so you use DNA polymerase to make the sugar phosphate bond. On the other strand, DNA is synthesised as "fragments", and then ligase comes along and makes phosphodiester bonds in order to join these fragments together.
I get that one of the parent strands is a lagging strand because replication can only occur in a 5'-3' direction and so it creates, as you mentioned, Okazaki fragments. DNA ligase catalyses phosphodiester bonds between the fragments, removing the RNA primers and forming a sugar phosphate backbone.
The thing is I've learnt that the nucleotides randomly float free in the nucleoplasm. Upon encountering their complementary base the appropriate number of hydrogen bonds form and DNA polymerase bonds the nucleotides in the 5'-3' direction. For the other strand DNA ligase bonds it in groups (aka fragments). It's confusing me because I thought DNA ligase is required for the phosphodiester bonds for both daughter molecules, not just for the lagging strand. Or to put it another way, the role of polymerase was a proximity catalyst in DNA replication by bringing the new nucleotides to their complementary bases. :mad:
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swiftylol
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(Original post by RMNDK)
I get that one of the parent strands is a lagging strand because replication can only occur in a 5'-3' direction and so it creates, as you mentioned, Okazaki fragments. DNA ligase catalyses phosphodiester bonds between the fragments, removing the RNA primers and forming a sugar phosphate backbone.
The thing is I've learnt that the nucleotides randomly float free in the nucleoplasm. Upon encountering their complementary base the appropriate number of hydrogen bonds form and DNA polymerase bonds the nucleotides in the 5'-3' direction. For the other strand DNA ligase bonds it in groups (aka fragments). It's confusing me because I thought DNA ligase is required for the phosphodiester bonds for both daughter molecules, not just for the lagging strand. Or to put it another way, the role of polymerase was a proximity catalyst in DNA replication by bringing the new nucleotides to their complementary bases. :mad:
DNA Polymerase adds DNA to the leading strand continuously.

The lagging strand has DNA added to it by DNA polymerase in fragments. Because it's done in fragments, there's a resulting gap between the the DNA fragments on the lagging strand. DNA polymerase fills the gap, but is unable to join the the *new* (DNA that polymerase put there) and *old* (DNA that was there during the gap) DNA together. That's what DNA Ligase does.

Polymerase is basically an enzyme that recruits nucleotides and can make strings of long nucleotides without a problem, whilst Ligase has the job of joining together DNA fragments/pieces (it does this a lot in DNA repair). As far as I remember, ligase isn't required for leading strand synthesis because there are no gaps in the leading strand.

I'd need to draw it out to explain it better as well as I want to, but feel free to ask for clarification

I doubt this much details is required for AQA (I may be wrong, as the spec may have changed a bit)

Hope this helps
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RMNDK
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(Original post by swiftylol)
DNA Polymerase adds DNA to the leading strand continuously.

The lagging strand has DNA added to it by DNA polymerase in fragments. Because it's done in fragments, there's a resulting gap between the the DNA fragments on the lagging strand. DNA polymerase fills the gap, but is unable to join the the *new* (DNA that polymerase put there) and *old* (DNA that was there during the gap) DNA together. That's what DNA Ligase does.

Polymerase is basically an enzyme that recruits nucleotides and can make strings of long nucleotides without a problem, whilst Ligase has the job of joining together DNA fragments/pieces (it does this a lot in DNA repair). As far as I remember, ligase isn't required for leading strand synthesis because there are no gaps in the leading strand.

I'd need to draw it out to explain it better as well as I want to, but feel free to ask for clarification

I doubt this much details is required for AQA (I may be wrong, as the spec may have changed a bit)

Hope this helps

Thank you!
Bloody hell I hate my teacher. He was all like, "Oh the nucleotides simply float aimlessly until by chance they reach their complementary base. There's some cell signalling involved as well"
*******s. Thank you for consolidating my understanding. The AQA spec for biology annoys me, but I'll live with it now thanks you!
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kanra
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(Original post by RMNDK)
I get that one of the parent strands is a lagging strand because replication can only occur in a 5'-3' direction and so it creates, as you mentioned, Okazaki fragments. DNA ligase catalyses phosphodiester bonds between the fragments, removing the RNA primers and forming a sugar phosphate backbone.
The thing is I've learnt that the nucleotides randomly float free in the nucleoplasm. Upon encountering their complementary base the appropriate number of hydrogen bonds form and DNA polymerase bonds the nucleotides in the 5'-3' direction. For the other strand DNA ligase bonds it in groups (aka fragments). It's confusing me because I thought DNA ligase is required for the phosphodiester bonds for both daughter molecules, not just for the lagging strand. Or to put it another way, the role of polymerase was a proximity catalyst in DNA replication by bringing the new nucleotides to their complementary bases. :mad:
DNA polymerase also creates a phosphodiester bond between the 3'-OH end of the new strand and the incoming nucleotide. The difference is that DNA polymerase on the leading strand uses energy-rich triphosphates (ATP, GTP, CTP, TTP), which contain the energy needed to make the bond. Ligase makes the bond between the monophosphate of one fragment and the OH of another, and uses a high energy molecule to supply the energy needed to make the bond.

But honestly, I think that's a lot more detail than you need for A level (unless they've massively changed the syllabus since 2 years ago...)
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RMNDK
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(Original post by kanra)
DNA polymerase also creates a phosphodiester bond between the 3'-OH end of the new strand and the incoming nucleotide. The difference is that DNA polymerase on the leading strand uses energy-rich triphosphates (ATP, GTP, CTP, TTP), which contain the energy needed to make the bond. Ligase makes the bond between the monophosphate of one fragment and the OH of another, and uses a high energy molecule to supply the energy needed to make the bond.

But honestly, I think that's a lot more detail than you need for A level (unless they've massively changed the syllabus since 2 years ago...)
Yeah I know that this is way past the A Level Syllabus. It's just for my own benefit because I decided to make a little project about DNA replication and when I learnt more about how the enzymes catalyse the reactions, I realised quite how wrong my teacher has been teaching me. It's like with GCSE. I hated the fact that we learnt over-simplified topics like the structure of the atom. Even though it's part of the syllabus, I'd much rather know at least information that has been satisfactorily simplified to an acceptable degree yaknow
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kanra
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(Original post by RMNDK)
Yeah I know that this is way past the A Level Syllabus. It's just for my own benefit because I decided to make a little project about DNA replication and when I learnt more about how the enzymes catalyse the reactions, I realised quite how wrong my teacher has been teaching me. It's like with GCSE. I hated the fact that we learnt over-simplified topics like the structure of the atom. Even though it's part of the syllabus, I'd much rather know at least information that has been satisfactorily simplified to an acceptable degree yaknow
I get what you mean, and it's really good that you're looking beyond the syllabus! I'm doing a biochemistry degree now, and "Molecular Biology of The Cell" by Alberts, and "Molecular Biology" by Weaver are really popular first year books - they have clear diagrams and good explanations, so it might be worth having a look there if you ever want more information
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RMNDK
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(Original post by kanra)
I get what you mean, and it's really good that you're looking beyond the syllabus! I'm doing a biochemistry degree now, and "Molecular Biology of The Cell" by Alberts, and "Molecular Biology" by Weaver are really popular first year books - they have clear diagrams and good explanations, so it might be worth having a look there if you ever want more information
Oh wow really!!? How is it? Biochemistry is one of the courses I'm interested in applying for Uni for next year.
I'll definitely be sure to check out those books you've recommended, thank you.
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kanra
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(Original post by RMNDK)
Oh wow really!!? How is it? Biochemistry is one of the courses I'm interested in applying for Uni for next year.
I'll definitely be sure to check out those books you've recommended, thank you.
It's pretty challenging! But that's part of what makes it interesting. First and second year tend to be a bit more of a mixed bag, since you don't pick modules (or at my university anyway) so there's stuff you like and stuff you don't like. Third year is the one everyone looks forward to though!

Have you thought of which universities you might apply for?
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RMNDK
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(Original post by kanra)
It's pretty challenging! But that's part of what makes it interesting. First and second year tend to be a bit more of a mixed bag, since you don't pick modules (or at my university anyway) so there's stuff you like and stuff you don't like. Third year is the one everyone looks forward to though!

Have you thought of which universities you might apply for?
xD You're right that does sound fun though. It's always been an interesting topic because it's so vast and applicable to many other fields of science.
Yeah I've heard about that, in your third year you get to pick the modules you want to specialise in.
I have Warwick, Birmingham and Nottingham in mind, Warwick especially for Biochemistry. What university are you currently studying at may I ask?
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kanra
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(Original post by RMNDK)
xD You're right that does sound fun though. It's always been an interesting topic because it's so vast and applicable to many other fields of science.
Yeah I've heard about that, in your third year you get to pick the modules you want to specialise in.
I have Warwick, Birmingham and Nottingham in mind, Warwick especially for Biochemistry. What university are you currently studying at may I ask?
Sounds good! Warwick is supposed to be really pretty! And a great university too of course!

I'm at Imperial right now
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AdamskiUK
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Guyton and Hall's Guide to Medical Physiology is a solid starting block for further reading, too.
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RMNDK
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(Original post by kanra)
Sounds good! Warwick is supposed to be really pretty! And a great university too of course!

I'm at Imperial right now
Yeah I went to their open day and the campus looks so nice and naturey xD Definitely my top for Biochemistry.
Oh wow! Well done, that's a great university! Good luck with your degree then!
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kanra
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(Original post by RMNDK)
Yeah I went to their open day and the campus looks so nice and naturey xD Definitely my top for Biochemistry.
Oh wow! Well done, that's a great university! Good luck with your degree then!
Thank you! And good luck with your applications!
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