Question

A primitive eukaryote was discovered that displayed a unique nucleic acid as its genetic material. Analysis provided the following information: (a) The general X-ray diffraction pattern is similar to that of DNA, but with somewhat different dimensions and more irregularity. (b) A major hyperchromic shift is evident upon heating and monitoring UV absorption at \(260 \mathrm{nm}\) (c) Base-composition analysis reveals four bases in the following proportions: \(\begin{array}{llr}\text { Adenine } & = & 8 \% \\ \text { Guanine } & = & 37 \% \\ \text { Xanthine } & = & 37 \% \\ \text { Hypoxanthine } & = & 18 \%\end{array}\) 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. Describe it briefly. (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 that either (i) both \(\mathrm{H}\) and \(\mathrm{X}\) are purines or both pyrimidines, or (ii) one is a purine and one is a pyrimidine? (d) About 75 percent of the sugars are deoxyribose, while 25 percent are ribose. Postulate a model for the structure of this molecule that is consistent with the foregoing observations.

Short answer

Question: Based on the given data and analysis, propose a model for the structure of this primitive eukaryote's genetic material and explain the base-pairing and nature of H and X. Answer: The genetic material of this primitive eukaryote is likely composed of a double-helix structure similar to DNA, but with some variations in dimensions and base proportions. H pairs with A and X pairs with G, where H is a pyrimidine and X is a purine. The structure is composed of stretches of a DNA-like molecule interconnected by small regions of an RNA-like molecule, with 75% deoxyribose sugars and 25% ribose sugars.

Step-by-step solution

Propose a general model

Since the given X-ray diffraction pattern is similar to that of DNA but with some irregularities and a constant diameter of about \(30 \AA\), we can assume that the genetic material has a double-helix structure, similar to the Watson-Crick model of DNA, but with some variations in the dimensions and proportions of the bases.

Base-pairing properties

The base composition analysis shows A=8%, G=37%, X=37%, and H=18%. We know that in a double-stranded genetic material, the adenine (A) pairs with a complementary base, and the same happens with guanine (G). In this case, G pairs with Xanthine (X), and Adenine (A) pairs with Hypoxanthine (H). This means that H must pair with A and X must pair with G to maintain a stable structure.

Determining purine or pyrimidine nature of H and X

Since the diameter of the double helix is constant, we can assume that the base pairing involves a purine paired with a pyrimidine, as seen in DNA (A pairs with T, and G pairs with C). In our case, Guanine (G) is a purine, and since we know that Xanthine (X) is also a purine, then Hypoxanthine (H) must be a pyrimidine in order to maintain the constant diameter of \(30 \AA\).

Proposing a model considering sugar composition

Given that 75% of the sugars are deoxyribose and 25% are ribose, we can propose a model in which the genetic material is composed of stretches of a DNA-like molecule (with deoxyribose sugars) interconnected by small regions of RNA-like molecule (with ribose sugars). These stretches are double-stranded, with base pairing between A and H (Adenine and Hypoxanthine) and between G and X (Guanine and Xanthine). The double-helix structure would be similar to DNA but with certain irregularities due to the presence of ribose sugars and different base pairing.

Key concepts

Nucleic Acid in Genetics

Nucleic acids are the molecules of heredity that store and transmit genetic information in living organisms. The two main types are DNA (deoxyribonucleic acid) and RNA (ribonucleic acid).

The structure of DNA and RNA is composed of long chains of nucleotides, each consisting of a sugar, a phosphate group, and a nitrogenous base. In the context of the exercise, we delve into an unusual nucleic acid with a unique composition.

The role of nucleic acids in genetics is fundamental, as they code for proteins and are responsible for the expression of traits. Their structure is pivotal for their function: the double-helical structure of DNA, composed of two complementary strands, allows for the replication and transmission of genetic information with high fidelity. Variations like those noted in the primitive eukaryote can give insights into evolution and the processes which govern genetic diversity.

Improving understanding involves exploring how the components of nucleic acids—sugars, bases, and phosphate groups—come together to form these complex but elegantly structured molecules. For instance, the sugar component can be deoxyribose (as in DNA) or ribose (as in RNA), and the proportions of these sugars can affect the overall structure, as evidenced by the discovered eukaryote which contains both.

X-ray Diffraction Pattern

X-ray diffraction is a powerful technique used to determine the three-dimensional structure of molecules, including nucleic acids. By passing X-rays through a crystallized sample and observing the pattern of diffracted rays, scientists can infer the spatial arrangement of the atoms within the molecule.

In genetics, the X-ray diffraction pattern of DNA provided the first clues to its double-helical structure, as famously discovered by Rosalind Franklin and used by Watson and Crick to develop their DNA model. The pattern is characterized by a series of 'X's which represent the specific way in which the various planes of atoms within the crystal scatter X-rays.

Role of X-ray Diffraction in Nucleic Acid Analysis

In the exercise's context, the diffraction pattern of the eukaryote's genetic material, though consistent with the helical pattern of DNA, exhibits irregularities and variations in dimensions. This suggests a deviation from the canonical B-form of DNA, indicative of unique structural characteristics. Understanding these patterns aids in constructing accurate models for such novel genetic materials.

To make this concept more accessible, one could compare the diffraction pattern to a fingerprint - while the general pattern might match DNA, the irregularities are unique to the new molecule, offering a diagnostic tool to visualize the shape and nature of this genetic material.

Base-Composition Analysis

Base-composition analysis is a biochemical technique that quantifies the percentages of the four nitrogenous bases that make up nucleic acids: adenine (A), guanine (G), cytosine (C), and thymine (T) in DNA or uracil (U) in RNA.

This analysis provides insight into the genetic structure and can infer properties about the organism’s genome. In the case of DNA, Chargaff’s rules state that A pairs with T (or U in RNA), and G pairs with C, maintaining a 1:1 ratio which contributes to the stability and consistency of the DNA's width.

Unique Base Pairs and Genetic Material Structure

In our exercise, the unique base composition, including Xanthine (X) and Hypoxanthine (H), deviates from the standard bases. Through the analysis, we deduce the pairing relationships and structural implications for the eukaryote’s genetic material.

For better grasp, consider the common pairing like a lock and key – A with T and G with C – form perfect matches. However, in the primitive eukaryote, the presence of X and H requires forming alternative, yet still complementary, 'locks' and 'keys', ensuring the double helix remains stable and functional. Drawing parallels to classic pairings helps simplify the understanding of these unique interactions within genetic material.