Exercises: DNA and RNA

Explain what DNA is, what type of information it contains, and in which part of a eukaryotic cell most of this molecule is found.

Name the four nitrogenous bases of DNA and explain the base-pairing rule followed by the double helix.

The diagram shows a segment of a DNA double helix. State what markers 1 and 2 represent, and complete the missing bases on the rungs marked with ?, knowing that A always pairs with T and G with C.

Explain what a nucleotide is and name its three components. Which of them varies from one nucleotide to another and constitutes the "letter" of genetic information?

The DNA double helix resembles a spiral staircase. Explain which molecules form the "sides" of the staircase and which form the "rungs", and how the components of each rung are joined together.

Order these structures from smallest to largest and explain in one sentence what each one is: chromosome, cell, gene, nucleotide, nucleus.

In the DNA of a species, $22\ \%$ of the bases are thymine. Calculate the percentage of adenine, guanine and cytosine, and explain your reasoning.

The two strands of DNA are antiparallel: one runs along the double helix in the 5' to 3' direction and the other in the 3' to 5' direction. Explain with an analogy what it means for them to be antiparallel and what the 5' and 3' marks indicate.

State three differences between DNA and RNA: the sugar they contain, the number of strands and one of their nitrogenous bases.

Explain what a gene is and describe its relationship with DNA, chromosomes and proteins.

Before dividing, the cell copies all of its DNA through replication. Explain what this process consists of and why it is said to be semi-conservative: which strands form each daughter DNA molecule and what role complementary base pairing plays in making an exact copy.

In a DNA molecule, $18\ \%$ of the bases are guanine. Calculate the percentages of cytosine, adenine and thymine, and explain each step of your reasoning.

A DNA strand has the sequence 5'-ATG CCG TTA-3'. Write the sequence of the complementary strand, also indicating its direction, and explain what you took into account.

DNA replication occurs before the cell divides by mitosis. Explain why it is essential that it happens in that order and what would happen to the genetic information of the daughter cells if a cell divided without having copied its DNA first.

Compare how DNA is organised in a bacterium and in a eukaryotic cell: where it is found, how many chromosomes there usually are and what shape they have.

For decades, the hereditary material was thought to be proteins rather than DNA. Reason which three properties any molecule must fulfil in order to be the hereditary material and explain why DNA fulfils them.

An astrobiology team analyzes the genetic material of an extraterrestrial microorganism. They discover that it consists of two facing strands, but they observe two anomalies compared to terrestrial DNA: 1) the diameter of the double helix is not constant, but instead shows continuous widenings and narrowings; 2) both strands run in the same direction (both in the $5' \to 3'$ direction). Using the principles of purine/pyrimidine base complementarity and antiparallelism proposed by Watson and Crick, reason what type of chemical pairings would be causing these thickness irregularities and predict what physical or enzymatic difficulty a parallel double helix would present during cellular replication.

A laboratory analyzes the nitrogenous base composition of the genetic material extracted from three different viruses, obtaining the following results:

• Virus 1: $30\ \%$ adenine, $30\ \%$ thymine, $20\ \%$ guanine, $20\ \%$ cytosine.

• Virus 2: $30\ \%$ adenine, $20\ \%$ thymine, $22\ \%$ guanine, $28\ \%$ cytosine.

• Virus 3: $30\ \%$ adenine, $30\ \%$ uracil, $20\ \%$ guanine, $20\ \%$ cytosine.

Determine with reasoning for each virus: what type of nucleic acid it possesses (DNA or RNA) and whether its strand is single-stranded or double-stranded. Furthermore, justify why virus 2 does not contradict the laws of chemistry even though its percentages of adenine and thymine do not match.

In a laboratory, an experimental drug is tested on a cell culture. The compound binds irreversibly to histones, preventing the DNA from unwinding from the nucleosomes.

1. a) Predict which two molecular processes essential for the cell will be immediately blocked and justify why at the molecular level.
2. b) If an already replicated cell enters mitosis and manages to condense its chromosomes, but the drug prevents it from decondensing them at the end of telophase, what consequences will this have for the viability of the daughter cells during interphase?

The double-stranded DNA of two bacterial species is analyzed: species A comes from a deep-sea hydrothermal vent at $85\ ^\circ\text{C}$ and species B comes from soil at $20\ ^\circ\text{C}$. The analyses show that one of the samples contains $38\ \%$ cytosine and the other contains $19\ \%$ cytosine.

1. a) Deduce and justify which percentage corresponds to each bacterium, based on the molecular stability of the bonds between base pairs.
2. b) Calculate the percentage of all the other nitrogenous bases (adenine, thymine, and guanine) present in the DNA of the thermophilic bacterium in the sample.

The uninterrupted coding region of a eukaryotic gene consists of exactly $900$ base pairs (including the final stop codon).

1. a) Calculate how many amino acids will make up the protein translated from this gene.
2. b) Suppose an insertion mutation of a single nucleotide occurs at position number $301$. Predict what consequences this mutation will have on the final length of the amino acid chain and on its biological function, compared to a point substitution mutation at that same position $301$. Justify your prediction using the concepts of reading frame and premature stop codon.

A human metaphase chromosome measures about $5\ \mu\text{m}$, but the DNA strand it houses would measure about $5\ \text{cm}$ when stretched out (a $10\,000$-fold packaging).

1. a) If you apply an inhibitor of the enzyme RNA polymerase (responsible for transcription) to a cell in metaphase, you will see that it has barely any effect because RNA synthesis is already halted naturally. Justify this fact by relating it to the degree of chromatin compaction.
2. b) Explain why it is essential for the cell to achieve such a level of packaging during mitosis, and why it would be lethal for it to maintain that same degree of condensation permanently during interphase.

Certain cancer chemotherapy drugs (crosslinking agents) can covalently link the two strands of DNA. Imagine a hypothetical drug that acts by forming permanent covalent bonds between opposing nitrogenous bases of the double helix, replacing the usual hydrogen bonds.

1. a) Predict why this drug suddenly halts the division of tumor cells, explaining which enzymes and processes of replication or transcription are physically prevented.
2. b) Based on the case above, justify why biological selection maintained weak bonds (hydrogen bonds) between the two strands and strong bonds (covalent phosphodiester bonds) along each strand throughout evolution, instead of using only strong bonds or only weak bonds.

In the historic Hershey and Chase experiment (1952) with bacteriophages:

1. a) Predict what results would have been obtained in the bacterial pellet and in the supernatant liquid if the prevailing hypothesis of the time (that proteins constituted the hereditary material) had been correct.
2. b) Imagine that a student proposes repeating the experiment by labeling the viruses with nitrogen-15 ($^{15}\text{N}$, a stable isotope) instead of using phosphorus ($^{32}\text{P}$) and sulfur ($^{35}\text{S}$). Justify why this experimental design would be completely useless for determining whether the genetic material is DNA or protein.