Exercises: Nucleic acids

What three components form a nucleotide? State how a DNA nucleotide differs from an RNA nucleotide.

Name the nitrogenous bases found in DNA and RNA, and state which base is unique to each of them.

Look at the diagram of a nucleotide and identify the three structures labelled with the numbers 1, 2 and 3, stating the chemical name of each.

Explain the essential features of Watson and Crick's double-helix model: arrangement and direction of the two chains, position of the nitrogenous bases, and types of bonds holding the structure together.

In the DNA fragment in the diagram, only the bases of one of the strands are shown. Write the bases that should occupy the positions marked with ? on the complementary strand and state the rule you applied.

If a strand of DNA has the sequence 5'-ATGCCGTA-3', write the full sequence of the complementary strand indicating its polarity (5' and 3' ends) and explain what it means that the two strands are antiparallel.

In one strand of a DNA molecule, adenine accounts for $28\ \%$ of the bases and thymine accounts for $12\ \%$. Calculate the percentages of each nitrogenous base in the complementary strand and in the entire DNA molecule, reasoning each step using Chargaff's rules and explaining why the breakdown between guanine and cytosine within each strand separately cannot be known.

In a laboratory, three unknown nucleic acid samples (A, B, and C) are purified from subcellular fractions of a eukaryote and an animal virus:

• Sample A: It hydrolyses rapidly in an alkaline medium (basic pH). It contains a pentose with a hydroxyl group at the 2' carbon and the bases A, G, C, and U. It is isolated from the nucleus, the cytosol, and bound to the membrane of the rough endoplasmic reticulum.

• Sample B: It is resistant to alkaline hydrolysis; it contains thymine and the ratio $(\text{A}+\text{G})/(\text{T}+\text{C})$ is exactly equal to $1.0$. It is isolated both from inside the nucleus and from the mitochondrial matrix.

• Sample C: It comes from the virus. It contains deoxyribose and thymine, but its base analysis yields $34\ \%$ of A, $18\ \%$ of T, $28\ \%$ of G, and $20\ \%$ of C.

1. a) Reasonably identify what type of nucleic acid (DNA or RNA) each sample is based on its chemical composition (sugar and bases) and its reactivity.
2. b) Interpret the spatial structure of samples B and C: explain why sample B complies with Chargaff's rules and sample C does not, indicating whether each is single-stranded or double-stranded.
3. c) Compare the location and function of sample B with the three main types into which sample A is functionally organised within the eukaryotic cell.

Within the framework of astrobiology, an informational polymer isolated from a meteorite is analysed. The compound is a double-stranded nucleic acid made of deoxyribonucleotides joined by phosphodiester bonds. One of the scientists proposes that this molecule could have independently originated a primitive extraterrestrial metabolism, acting simultaneously as a genetic store and as a primeval metabolic catalyst, analogously to Earth's "RNA world" hypothesis.

1. a) Refute the scientist's proposal: justify, based on the molecular differences between RNA and DNA (presence of the 2'-OH group on the ribose and single-stranded vs. double-stranded structure), why this double-stranded DNA is much less suited than RNA to adopting conformations with catalytic activity (such as ribozymes).
2. b) Explain why the discovery that RNA possesses enzymatic activity resolved the classical paradox of the origin of life regarding which macromolecule arose first (nucleic acids or proteins).
3. c) If RNA exhibits greater functional versatility, reason what evolutionary advantages double-stranded DNA provided so that natural selection fixed it as the universal genetic material of cellular living organisms.

Unit challenge. Biomolecular audit of your pantry.

Have you ever wondered how the bioelements you study translate into what you eat every day? You are going to audit a real food item from your kitchen (legume, cereal, or dairy product) integrating all molecular levels.

1. Data collection: Select the food item and look up its nutritional breakdown per $100\text{ g}$ in the Irish Food Composition Database or on its label: water, bioelements, and mineral salts (such as $Na^+$ or $Fe^{2+}$), carbohydrates, lipids, and proteins.

2. Deduction of nucleic acids: Since nutritional tables do not quantify DNA/RNA, reason through and qualitatively estimate their presence considering the cellular origin (animal or plant tissue) and the degree of industrial processing.

3. Reasoned report: Prepare a table adapted to your usual serving size (e.g., $65.5\text{ g}$) and write a summary proposal justifying the cellular function of each fraction: osmotic homeostasis of water/ions, energy balance of carbohydrates versus lipids, structural/enzymatic function of proteins, and nucleotide recycling.

Evaluation criteria:

• Thoroughness in obtaining quantitative data and correctness of units.

• Deductive ability to justify the existence and role of the consumed genetic material.

• Conceptual accuracy when relating the chemical structure of each biomolecule to its metabolic role.