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Questions and Answers
Which phosphoryl group in a deoxynucleoside triphosphate is closest to the deoxyribose molecule?
Which phosphoryl group in a deoxynucleoside triphosphate is closest to the deoxyribose molecule?
- delta-phosphate
- b-phosphate
- a-phosphate (correct)
- g-phosphate
What is the specific required arrangement of DNA strands necessary for DNA synthesis?
What is the specific required arrangement of DNA strands necessary for DNA synthesis?
- A primer:template junction. (correct)
- A single-stranded DNA helix.
- A double-stranded DNA helix.
- A triple stranded DNA complex.
What is the function of the template strand in DNA synthesis?
What is the function of the template strand in DNA synthesis?
- To form the covalent linkage with the incoming nucleotide.
- To provide the free 3'-OH for nucleotide addition.
- To provide the single stranded DNA sequence that directs nucleotide addition. (correct)
- To serve as the substrate for the reaction.
What part of the primer:template junction is chemically modified during DNA synthesis?
What part of the primer:template junction is chemically modified during DNA synthesis?
What is the critical chemical group on the primer that is essential for extension during DNA synthesis?
What is the critical chemical group on the primer that is essential for extension during DNA synthesis?
Which of the following molecules is NOT required as a substrate for DNA synthesis?
Which of the following molecules is NOT required as a substrate for DNA synthesis?
What is the relationship between the primer and template strands at the primer:template junction?
What is the relationship between the primer and template strands at the primer:template junction?
Which end of the primer is extended during DNA synthesis?
Which end of the primer is extended during DNA synthesis?
During DNA synthesis, which end of the primer is extended?
During DNA synthesis, which end of the primer is extended?
What type of reaction is involved in forming the phosphodiester bond during DNA synthesis?
What type of reaction is involved in forming the phosphodiester bond during DNA synthesis?
Which molecule acts as a leaving group during the formation of the phosphodiester bond?
Which molecule acts as a leaving group during the formation of the phosphodiester bond?
What is the role of the template strand in DNA synthesis?
What is the role of the template strand in DNA synthesis?
What is the role of pyrophosphatase in DNA synthesis?
What is the role of pyrophosphatase in DNA synthesis?
What is the net effect of nucleotide addition and pyrophosphate hydrolysis on phosphate bonds?
What is the net effect of nucleotide addition and pyrophosphate hydrolysis on phosphate bonds?
Why is DNA synthesis considered to be effectively irreversible?
Why is DNA synthesis considered to be effectively irreversible?
What is the change in free energy (DG) for the net reaction of nucleotide addition and pyrophosphate hydrolysis?
What is the change in free energy (DG) for the net reaction of nucleotide addition and pyrophosphate hydrolysis?
Flashcards
DNA Synthesis Direction
DNA Synthesis Direction
DNA synthesis occurs by adding nucleotides to the 3' end of a primer strand.
Pyrophosphatase
Pyrophosphatase
The enzyme that breaks down pyrophosphate (PPi) into two inorganic phosphates (Pi).
Nucleotide Addition
Nucleotide Addition
The reaction that adds a nucleotide to a growing DNA strand.
Energy Source for DNA Synthesis
Energy Source for DNA Synthesis
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Antiparallel Orientation
Antiparallel Orientation
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DNA Synthesis Mechanism
DNA Synthesis Mechanism
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Phosphodiester Bond Formation
Phosphodiester Bond Formation
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3' Hydroxyl Group Attack
3' Hydroxyl Group Attack
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What are dNTPs?
What are dNTPs?
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What are the three phosphate groups in a dNTP?
What are the three phosphate groups in a dNTP?
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What is a primer:template junction?
What is a primer:template junction?
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What is the role of the template strand in DNA synthesis?
What is the role of the template strand in DNA synthesis?
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What is the role of the primer strand in DNA synthesis?
What is the role of the primer strand in DNA synthesis?
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What is essential for a primer to function in DNA synthesis?
What is essential for a primer to function in DNA synthesis?
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How is DNA synthesized?
How is DNA synthesized?
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Why are both a primer and a template required for DNA synthesis?
Why are both a primer and a template required for DNA synthesis?
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Study Notes
DNA Synthesis Requirements
- DNA synthesis needs four deoxynucleoside triphosphates: dGTP, dCTP, dATP, and dTTP.
- These triphosphates have three phosphate groups attached to the deoxyribose sugar (a-, b-, and g-phosphate).
- A primer:template junction is also crucial.
- The template provides the single-stranded DNA (ssDNA) sequence that dictates new nucleotide addition.
- The primer, shorter than the template, is complementary and has a free 3'-OH group next to the ssDNA template section.
- Only the primer part is chemically altered during synthesis; the template gives the nucleotide selection instructions.
- Both are essential for all DNA synthesis.
Mechanism of DNA Synthesis
- DNA synthesis extends the 3' end of the primer.
- The 3'-OH on the primer attacks the a-phosphate of the incoming nucleoside triphosphate (dNTP).
- This forms a phosphodiester bond, extending the DNA chain.
- Pyrophosphate (b- and g-phosphates) is released.
- Pyrophosphatase rapidly hydrolyzes pyrophosphate into two phosphate molecules.
- The template strand determines which incoming dNTP pairs with it.
Driving Force of DNA Synthesis
- The simple addition reaction has a low free energy change (-3.5 kcal/mol).
- The subsequent hydrolysis of pyrophosphate to two phosphates (-7kcal/mol) by pyrophosphatase is energetically favorable.
- The net free energy change of the coupled reaction (adding nucleotide and hydrolyzing pyrophosphate) is large and negative (-7 kcal/mol), effectively making the reaction irreversible (high Keq >105).
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