Question

Newsdate: March \(1,2030 .\) A unique creature has been discovered during exploration of outer space. Recently, its genetic material has been isolated and analyzed, and has been found to be similar in some ways to DNA in chemical makeup. It contains in abundance the 4 -carbon sugar erythrose and a molar equivalent of phosphate groups. In addition, it contains six nitrogenous bases: adenine(A), guanine(G), thymine(T), cytosine (C), hypoxanthine (H), and xanthine (X). These bases exist in the following relative proportion: \(A=T=H \quad\) and \(\quad C=G=X\) X-ray diffraction studies have established a regularity in the molecule and a constant diameter of about \(30 \AA\). Together, these data have suggested a model for the structure of this molecule. (a) Propose a general model of this molecule, and briefly describe it. (b) What base-pairing properties must exist for \(\mathrm{H}\) and for \(\mathrm{X}\) in the model? (c) Given the constant diameter of \(30 \AA\), do you think either (i) both \(\mathrm{H}\) and \(\mathrm{X}\) are purines or both pyrimidines, or (ii) one is a purine and one is a pyrimidine?

Short answer

Answer: The most likely base pairing pattern for the unique molecule is A-H, C-X, and G-T, with one base in each pair being a purine and the other being a pyrimidine.

Step-by-step solution

(Step 1: Establish the main structure of the molecule)

Based on the information provided, the molecule contains erythrose as a 4-carbon sugar and a molar equivalent of phosphate groups. This implies that the main structure is a sugar-phosphate backbone, similar to DNA. The nitrogenous bases must attach to this backbone.

(Step 2: Incorporate the nitrogenous bases)

We know there are six nitrogenous bases: adenine(A), guanine(G), thymine(T), cytosine (C), hypoxanthine (H), and xanthine (X). The given proportions are A=T=H and C=G=X. This means that the bases attach to the sugar-phosphate backbone in pairs: A-H, C-X, and G-T.

(Step 3: Propose a general model of the molecule)

Based on the information, we can propose a double-stranded helical molecule with a sugar-phosphate backbone and paired nitrogenous bases (A-H, C-X, and G-T). This is similar to the structure of DNA but with unique bases.

(Step 4: Determine base-pairing properties for H and X)

For H and X, they must pair with their respective counterparts: A and C, respectively. This means that H must form hydrogen bonds with A, and X must form hydrogen bonds with C, similar to the base-pairing rules of DNA.

(Step 5: Purines, pyrimidines, or both?)

For this question, we must consider the constant diameter of 30 Å (angstroms) in the molecule. DNA base pairs, consisting of one purine and one pyrimidine, have a similar diameter, 20 Å. Given that the diameter is constant, it's more likely that one base is a purine and one is a pyrimidine in each pair in our molecule (A-H, C-X, and G-T). So, we will go for option (ii), that is one is a purine and one is a pyrimidine. In conclusion, we have proposed a general model for the molecular structure by incorporating the information given and determining the base-pairing properties for H and X. Based on the constant diameter, our best estimate is that one base in each pair is a purine and the other is a pyrimidine.

Key concepts

Nitrogenous Bases

Nitrogenous bases are essential components of the genetic material in many organisms, including this unique space creature. In the model proposed, there are six nitrogenous bases: adenine (A), guanine (G), thymine (T), cytosine (C), hypoxanthine (H), and xanthine (X). These bases are crucial because they store and transfer genetic information.

Each nitrogenous base can be classified into two categories: purines and pyrimidines. Purines, like adenine and guanine, have a double-ring structure. Pyrimidines, such as thymine and cytosine, have a single-ring structure. Hypoxanthine and xanthine, although not commonly found in standard DNA contexts, can be purines or pyrimidines depending on their structure, which determines their role and pairing in the genetic code.

The proportion of these bases in the creature's genetic material is given as: A = T = H and C = G = X. This means that the bases exist in equal amounts within each group, influencing the molecular structure and stability of the genetic material.

Molecular Structure

The molecular structure of this genetic material resembles DNA, yet it is unique due to its components. Just like DNA, this molecule features a double-stranded helical formation. This means that it is composed of two strands winding around each other, which provides stability and ensures accurate replication of genetic material.

This helical structure is supported by the sugar-phosphate backbone and the specific pairing of nitrogenous bases. The regularity and a constant diameter of about 30 Å, as observed in x-ray diffraction studies, suggest a consistent spatial arrangement. This diameter is essential in understanding how each nitrogenous base pairs with another, maintaining the structural integrity and function of the molecule.

Such a precise and consistent structure proposes that the unique genetic material could potentially perform similar biological functions to DNA, aiding processes like replication and transcription by providing an ordered and accessible blueprint for cellular machinery.

Sugar-Phosphate Backbone

The sugar-phosphate backbone is a fundamental aspect of the structure of genetic materials, serving as the framework to which nitrogenous bases attach. In this unique molecular structure, the backbone consists of erythrose, a 4-carbon sugar, and phosphate groups. These components alternate and form a long chain that provides structural support to the entire molecule.

The sugar-phosphate backbone is crucial because it prevents the molecule from breaking apart, thereby preserving the genetic information. Phosphate groups link the sugars through phosphodiester bonds, forming a stable chain. This configuration allows the nucleotide bases to project inwardly, facilitating base pairing and genetic coding.

In cellular processes, the backbone's flexibility aids in the molecule's interaction with various enzymes and other cellular components. Its strength and resilience are vital for maintaining integrity during replication and transcription.

Base Pairing Rules

Base pairing rules define how nitrogenous bases align and connect in genetic material, ensuring accurate genetic encoding and replication. In this model, because A = T = H and C = G = X, each pair must adhere to specific pairing properties that allow the helical structure to maintain its constant diameter of approximately 30 Å.

Normally, in DNA, purines pair with pyrimidines to maintain the helical structure's uniformity. This implies that for each unique pair like A-H and C-X, one must be a purine and the other a pyrimidine. It can be inferred that hypoxanthine and xanthine should pair with adenine and cytosine, respectively, forming hydrogen bonds similar to those found in DNA base-pairs.

This pairing is vital for ensuring that the genetic material can correctly and efficiently be transcribed and replicated, as it allows for the double helix to unwind and expose the nucleotides for informational transfer, without distorting the structural stability of the genetic material.