DNA Comparison of Potential Energy, RMS Deviation, Electrostatic Energy

In summary, the comparison of a normal DNA decamer molecule with one in which the two strands are only connected by two base pairs on one end revealed that the potential energies were negative for both, with the normal DNA having a much more negative value. The RMS deviations were positive for both, increasing over time, with the broken DNA having a much more positive value. The electrostatic energy for the broken DNA was also higher than that of the normal DNA. This is due to the molecules being closer together in the normal DNA, causing more hinderance and affecting the energies. However, the exact explanation for this difference is still unclear.
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Homework Statement


I am comparing a normal DNA decamer molecule with one in which the two strands are only connected by the two base pairs on one of the ends. It was determined that the potential energies of both DNA molecules are negative, with values for the normal DNA much more negative than broken DNA. It was also determined that root-mean-squared (RMS) deviations were positive for both DNA molecules (and increasing over time), with values for the broken DNA much more positive than those of the normal DNA. It was also determined that the electrostatic energy for the broken DNA was higher than that of the normal DNA.

I need help explaining why the potential energies, RMS deviations, and electrostatic energies are the way they are.

Homework Equations


N/A

The Attempt at a Solution



In the normal DNA, the molecules are closer to each other, allowing for more hinderance between the molecules, which affects the potential energies, RMS deviations, and electrostatic energies. I just do not know what else I can include in my answer.
 
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  • #2
I understand that the broken DNA molecules have more space between them but I am not sure how to explain this.
 
  • #3


Your explanation is a good start. Let's break down each component and discuss their role in the comparison of the two DNA molecules.

Potential Energy:
Potential energy is a measure of the energy stored in a system based on the position or configuration of its components. In the case of the DNA molecules, the potential energy is determined by the strength of the bonds between the nucleotides and the overall structure of the molecule. In the normal DNA molecule, the two strands are fully connected, allowing for a lower potential energy due to the strong bonds between the nucleotides. However, in the broken DNA molecule, the two strands are only connected by two base pairs, leading to a weaker overall structure and therefore a less negative potential energy.

RMS Deviation:
RMS deviation is a measure of the average distance between the atoms in a molecule compared to a reference structure. In this case, the reference structure is likely the ideal, fully connected DNA molecule. As time passes, the molecules in both the normal and broken DNA molecules will experience movement and fluctuations, leading to an increase in the RMS deviation. However, the broken DNA molecule, being less stable due to its weaker structure, will experience larger fluctuations and therefore have a higher RMS deviation compared to the normal DNA molecule.

Electrostatic Energy:
Electrostatic energy is a measure of the attraction or repulsion between charged particles. In the case of DNA molecules, the negatively charged phosphate groups on the nucleotides can interact with positively charged ions in the surrounding environment, leading to electrostatic energy. In the broken DNA molecule, with its weaker structure, there may be more exposure of the phosphate groups, allowing for more interactions and a higher electrostatic energy compared to the normal DNA molecule.

In summary, the potential energies, RMS deviations, and electrostatic energies of the two DNA molecules are affected by their overall structure, stability, and interactions with the surrounding environment. The normal DNA molecule, with its fully connected structure, has a lower potential energy, lower RMS deviation, and lower electrostatic energy compared to the broken DNA molecule, which has a weaker structure and more interactions with its surroundings.
 

1. What is DNA comparison?

DNA comparison is the process of analyzing and comparing the genetic sequences of two or more organisms to determine their similarities and differences.

2. What is potential energy in DNA comparison?

In DNA comparison, potential energy refers to the energy stored within the chemical bonds of DNA molecules. This energy can be used to drive biochemical processes and is an important factor in determining the stability and function of DNA.

3. What is RMS deviation in DNA comparison?

RMS deviation, or root-mean-square deviation, is a measure of the average distance between corresponding atoms in two molecules. In DNA comparison, it is used to quantify the structural differences between two DNA sequences.

4. What is electrostatic energy in DNA comparison?

Electrostatic energy in DNA comparison refers to the energy that results from the interaction between the positively charged hydrogen atoms and the negatively charged phosphate groups in DNA molecules. This energy is important for maintaining the overall structure of the DNA molecule.

5. How is DNA comparison used in scientific research?

DNA comparison is used in a variety of scientific research fields, including evolutionary biology, genetics, and medicine. It can help researchers understand the relationships between different species, identify genetic variations associated with diseases, and design targeted treatments for genetic disorders.

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