DNA Synthesis Mechanism Quiz

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Questions and Answers

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?

  • 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?

  • 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?

<p>The primer. (A)</p> Signup and view all the answers

What is the critical chemical group on the primer that is essential for extension during DNA synthesis?

<p>The 3'-hydroxyl group. (B)</p> Signup and view all the answers

Which of the following molecules is NOT required as a substrate for DNA synthesis?

<p>dUTP (C)</p> Signup and view all the answers

What is the relationship between the primer and template strands at the primer:template junction?

<p>The primer is shorter than and complementary to the template. (D)</p> Signup and view all the answers

Which end of the primer is extended during DNA synthesis?

<p>The 3' end. (C)</p> Signup and view all the answers

During DNA synthesis, which end of the primer is extended?

<p>The 3' end (A)</p> Signup and view all the answers

What type of reaction is involved in forming the phosphodiester bond during DNA synthesis?

<p>SN2 reaction (A)</p> Signup and view all the answers

Which molecule acts as a leaving group during the formation of the phosphodiester bond?

<p>Pyrophosphate (A)</p> Signup and view all the answers

What is the role of the template strand in DNA synthesis?

<p>To determine which nucleotide is added to the primer strand (A)</p> Signup and view all the answers

What is the role of pyrophosphatase in DNA synthesis?

<p>To hydrolyze pyrophosphate into two phosphate molecules (B)</p> Signup and view all the answers

What is the net effect of nucleotide addition and pyrophosphate hydrolysis on phosphate bonds?

<p>Two high-energy phosphate bonds are broken (B)</p> Signup and view all the answers

Why is DNA synthesis considered to be effectively irreversible?

<p>The rapid hydrolysis of pyrophosphate renders the reverse reaction highly unfavorable (B)</p> Signup and view all the answers

What is the change in free energy (DG) for the net reaction of nucleotide addition and pyrophosphate hydrolysis?

<p>–7 kcal/mol (D)</p> Signup and view all the answers

Flashcards

DNA Synthesis Direction

DNA synthesis occurs by adding nucleotides to the 3' end of a primer strand.

Pyrophosphatase

The enzyme that breaks down pyrophosphate (PPi) into two inorganic phosphates (Pi).

Nucleotide Addition

The reaction that adds a nucleotide to a growing DNA strand.

Energy Source for DNA Synthesis

The energy required for DNA synthesis comes from the hydrolysis of pyrophosphate (PPi) into two inorganic phosphates (Pi).

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Antiparallel Orientation

The template strand and the newly synthesized strand run in opposite directions.

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DNA Synthesis Mechanism

The process of DNA synthesis involves attaching a new nucleotide to the 3' end of the primer strand using the template strand as a guide.

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Phosphodiester Bond Formation

The chemical reaction that links nucleotides together to form a DNA strand.

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3' Hydroxyl Group Attack

The 3' end of the primer has a hydroxyl group (OH) that attacks the phosphate of the incoming nucleotide, forming a phosphodiester bond.

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What are dNTPs?

Deoxynucleotide triphosphates (dNTPs) are the building blocks of DNA, consisting of a deoxyribose sugar, a nitrogenous base (adenine, guanine, cytosine, or thymine), and three phosphate groups.

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What are the three phosphate groups in a dNTP?

The a-phosphate is the phosphate group closest to the deoxyribose sugar, while the b-phosphate and g-phosphate are the middle and outer phosphate groups, respectively.

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What is a primer:template junction?

A primer:template junction is a specific arrangement of DNA where a short, single-stranded primer is annealed to a longer, single-stranded template.

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What is the role of the template strand in DNA synthesis?

The template strand serves as a guide for DNA synthesis, dictating which nucleotides are added to the newly synthesized strand.

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What is the role of the primer strand in DNA synthesis?

The primer is a short, single-stranded DNA molecule that initiates DNA synthesis by providing a free 3'-OH group for the first nucleotide to attach to.

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What is essential for a primer to function in DNA synthesis?

The primer must have a free 3'-OH group at the end that is adjacent to the single-stranded region of the template. This free 3'-OH is where new nucleotides are added.

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How is DNA synthesized?

DNA polymerase adds new nucleotides to the free 3'-OH end of the primer, extending the chain in a 5' to 3' direction.

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Why are both a primer and a template required for DNA synthesis?

Both the primer and the template are essential for DNA synthesis. The primer provides the starting point for the new DNA strand, while the template dictates the sequence of nucleotides to be added.

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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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