Question

Which of the following is not a factor that favors DNA symthesis? a. The release of pyrophosphate. b. The base-stacking interactions. c. The change of entropy when the free dNTP is added to the polynucleotide chain. d. The formation of hydrogen bonds. e. The hydrolysis of pyrophosphate that is released.

Short answer

Option c does not favor DNA synthesis.

Step-by-step solution

Understanding the Question

The question asks us to identify which option is *not* a factor that favors DNA synthesis. DNA synthesis involves forming a phosphodiester bond and adding nucleotides, which involves various molecular interactions and energy considerations.

Evaluating Option a

Option a states 'The release of pyrophosphate.' When a nucleotide is added to a growing DNA strand, a pyrophosphate group is released, which is energetically favorable and drives the reaction forward. Thus, this factor favors DNA synthesis.

Evaluating Option b

Option b refers to 'The base-stacking interactions.' Base-stacking interactions between nucleotides stabilize the DNA helix, thereby favoring the process of DNA synthesis.

Evaluating Option c

Option c considers 'The change of entropy when the free dNTP is added to the polynucleotide chain.' The addition of a nucleotide to a DNA chain decreases entropy, as it reduces disorder by forming a structured molecule. This decrease in entropy does not favor DNA synthesis.

Evaluating Option d

Option d involves 'The formation of hydrogen bonds.' Hydrogen bonds between complementary bases form as nucleotides are added, stabilizing the DNA structure and thus favoring DNA synthesis.

Evaluating Option e

Option e discusses 'The hydrolysis of pyrophosphate that is released.' The hydrolysis of pyrophosphate releases energy, which makes the addition of nucleotides energetically favorable, again promoting DNA synthesis.

Conclusion from Evaluations

Based on the evaluations, option c does not favor DNA synthesis due to the decrease in entropy associated with nucleotide addition.

Key concepts

phosphodiester bond

A phosphodiester bond is a crucial link in the backbone of DNA, connecting the sugar of one nucleotide to the phosphate group of the next. This bond forms between the 3'-OH group of one nucleotide and the 5' phosphate group of the next. The creation of this bond is catalyzed by enzymes like DNA polymerase.

During DNA synthesis, the formation of phosphodiester bonds is essential because it ensures the correct sequential attachment of nucleotides, thus creating a stable and continuous DNA strand. This process is energy-demanding but is driven forward by the release of pyrophosphate, making it highly favorable.

base-stacking interactions

Base-stacking interactions refer to the attractive forces between stacked nitrogenous bases in the DNA helix. Unlike other interactions, these are largely due to van der Waals forces and hydrophobic effects.

Stacking interactions contribute to the stability of the DNA double helix, helping maintain its structural integrity. These interactions are critical for DNA synthesis as they provide a stable framework that supports the binding of additional nucleotides. These interactions don't involve covalent bonds, but their role in maintaining DNA structure is vital.

hydrogen bonds

Hydrogen bonds are weak bonds that involve a hydrogen atom shared between two electronegative atoms, typically oxygen or nitrogen. In DNA, these bonds form between complementary bases of adenine with thymine, and guanine with cytosine.

Hydrogen bonds play a significant role in stabilizing the DNA helix, which is important for proper base pairing during DNA synthesis. Although individually weak, collectively they create a strong intermolecular linkage that is sufficient to keep the DNA strands together during replication.

pyrophosphate

When a nucleotide triphosphate is added to a DNA chain during synthesis, two phosphate groups are released as pyrophosphate. The release of this pyrophosphate is an exergonic reaction; it provides the necessary energy to drive the energetically unfavorable process of forming new phosphodiester bonds.

Pyrophosphate is rapidly hydrolyzed into two inorganic phosphates, releasing even more energy and helping to further push the DNA synthesis reaction forward. This makes pyrophosphate release a significantly favorable factor in the overall process of DNA replication.

entropy

Entropy in the context of DNA synthesis relates to the degree of disorder within the system. When a free deoxynucleotide triphosphate (dNTP) is added to the growing DNA strand, the overall entropy decreases because the system moves from a more disordered state (individual nucleotides) to a more ordered state (a neatly ordered DNA chain).

A decrease in entropy does not favor spontaneous processes, and thereby does not favor DNA synthesis inherently. However, this unfavorable change is counteracted by the energy-releasing reactions, like the hydrolysis of pyrophosphate, making the process feasible under cellular conditions.