Introduction

In this experiment, we will test our hypothesis that says helices and strands are preferred by mother nature to build biomolecules. Apart from this, we will also be determining whether the structure of extended conformations is less stable than the structures of helices and strands.

Aim

To determine whether helices and strands are being preferred by nature for building biomolecules.

Theory

1. We hypothesized that the stability of extended conformation is lesser than the stability of helices and strands.

2. A strand is the single unit of multimeric molecules, for instance, DNA.

3. Helices have a three-dimensional spiral that contains a repetitive structure. The molecule of DNA has two intervene helices.

Helix Structure

Strands

Requirements

1. A computer

2. DeepView program

3. IsisDraw

4. Insight II

Procedure

Step 1: Using a computer, we first created a model peptide.

Step 2: This model peptide was created with the blocks of repeating pentapeptides, which are of the type [DAAAK]n and [AAAAA]n. Here, n is the number of blocks.

Step 3: After this, we extended the structures of the helix and strand.

Step 4: After measuring the peptides’ stability without and with the minimisation of energy, we compared the peptides’ stability without and with the minimisation of energy.

Step 5: We did this with the help of several programs like IsisDraw, Insight II, and DeepView.

Observations

1. From the experiment, we observed that helices followed by strands are the most stable conformation in nature and we also found out that the least stable structure is extended conformation.

2. After adding amino acid, we found that the gaps between the stability of extended conformation, strand, and helix increased.

Result

1. The analysis for the potential energy of some terms like Van der Waals, bond, torsion, electrostatic contribution, and angle showed us that the factor responsible for increasing the stability is Van der Waals.

2. The hypothesis in which we assumed that the structure of helices and strands would be more stable than the extended conformation was right.

3. Because of the formation of the anion-cation interaction between an acid, a base, D, and K, the peptides of [DAAAK](n) were more stable than the peptides of [AAAAA](n).

Precaution

1. Make sure all the programs run properly.

2. Record your observation carefully.

Conclusion

In this experiment, we hypothesized that helices and strands are the preferred structure of amino acids for forming biomolecules.

Viva Questions With Answers

Q.1 What was the aim of your experiment?

ANS. We aimed to determine whether helices and strands are the preferred structure for forming biomolecules. Apart from this, we also determined the stability of helices, strands, and extended conformation.

Q.2 Among helices, strands, and extended conformation, which one had the least stability?

ANS. Extended confirmations have the least stability while helices followed by strands showed the most stability.

Q.3 What happened to the structure after the addition of amino acids?

ANS. After adding more blocks of amino acid, the gap between the stability of extended conformation, helices, and strands increased.

Saquib Siddiqui

Saquib Siddiqui is a Mechanical Engineer and a content creator. He has special interest in science experiments and teaches the same to school and college students. He is also a technical lead at RUDE LABS PVT. LTD.