Exercises: Gene expression

Explain in your own words what it means when a cell "expresses a gene", and why the final result of this expression is a protein.

Look at the diagram of a eukaryotic cell representing gene expression: labels ?1 and ?2 show where transcription and translation take place, without indicating which is which. State which process occurs at each labelled point and where in the cell it takes place.

What is the genetic code? Explain what a codon is and how many bases make it up.

Explain what a protein is and name three different functions that proteins carry out in living things, with an example of each one.

Define transcription: which molecule acts as the template, which molecule is made and in which part of the eukaryotic cell it takes place.

DNA never leaves the nucleus, but ribosomes are in the cytoplasm. Explain what problem this poses for making proteins and how messenger RNA solves it.

Explain what an amino acid is and how a protein is formed from them: what a polypeptide chain is and what determines the order in which the amino acids are joined.

During transcription, each base of the DNA template strand determines which base the mRNA will carry. State which base the mRNA will place opposite an A, a T, a G and a C of the template, remembering that RNA has no thymine.

State two differences between transcription and translation: the molecule produced in each process and the location where it occurs.

The template strand of a gene has the sequence 3'-TAC GGA TTT-5'. Write the sequence of the messenger RNA synthesised from it, keeping in mind that in RNA, thymine is replaced by uracil.

Explain the role of the ribosome and transfer RNA (tRNA) during translation: where does each bind and what does tRNA transport?

A messenger RNA carries the sequence 5'-AUG GCU CAA-3'. Reconstruct the sequence of the DNA template strand from which it was transcribed, indicating its direction.

These stages of the expression of a gene are out of order: the protein is finished; the mRNA leaves the nucleus; the mRNA binds to a ribosome; the DNA is transcribed. Put them in order and describe each one in a sentence.

Transcription and replication are similar because in both a DNA strand is "read" and a complementary molecule is made. Explain two fundamental differences between the two processes: what is copied in each case and which molecule is obtained.

Insulin is a protein of $51$ amino acids. Given that the mRNA also needs a stop codon, calculate the minimum number of nucleotides in the coding part of its mRNA and explain the calculation.

The ribosome reads the mRNA in consecutive codons, without skipping any bases. Reason what happens to all the codons following a point where an extra base has been inserted, and why it is said that the "reading frame shifts".

Two patients with point mutations in the same codon of their mature mRNA are analyzed; the original codon was GAA (encodes glutamic acid):

• In patient A, the codon mutates to GAG (encodes glutamic acid).

• In patient B, it mutates to GUA (encodes valine).

1. a) Based on the properties of the genetic code, justify why patient A shows no alteration while patient B presents a non-functional enzyme.
2. b) Could a "silent mutation" like the one in patient A exist if the genetic code were not degenerate? Justify your answer by deducing what consequences mutations would have in a hypothetical code with only one codon per amino acid.

A bacterium synthesizes an oligopeptide from the following mature mRNA fragment:

5'-... AUG GCC UUU UAA ...-3'

A mutagenic agent causes the deletion (loss) of the first nucleotide of the codon GCC (the first cytosine), resulting in the sequence: 5'-... AUG GCU UUU AA...-3'.

Given that:

• AUG = Methionine (start)

• GCC = Alanine; GCU = Alanine; UUU = Phenylalanine; UUA = Leucine

• UAA = Stop (termination)

1. a) Write the resulting amino acid sequence before and after the mutation.
2. b) Justify why a reading frameshift mutation (deletion or insertion) usually has much more severe consequences for protein function than a single base substitution mutation.

A student claims: "Since a neuron and a skin cell have completely different functions and shapes, their DNA molecules must be different; for example, the neuron has eliminated the genes for skin proteins that it does not need."

1. a) Refute the student's statement by explaining what we would actually find if we sequenced the genomic DNA of both cell types.
2. b) If the DNA is identical, predict and justify what differences you would expect to find when analyzing the types of mRNA and proteins present in the cytoplasm of both cells.

Imagine a hypothetical mutant cell in which mRNA molecules do not exist: ribosomes enter directly into the nucleus and translate proteins by directly reading the DNA double helix.

Evaluate this situation by proposing two serious biological drawbacks this mechanism would have: one related to the integrity and protection of the genetic material, and another related to response speed and amplification capacity when the cell needs to produce thousands of copies of a protein in a short time.

In electron micrographs of bacteria, it is frequently observed that several ribosomes attach to mRNA and begin translating it while RNA polymerase is still transcribing that same mRNA from DNA.

1. a) Justify why this simultaneous coupling of transcription and translation is impossible in a human cell.
2. b) If we clone a human gene directly into a bacterium just as it is extracted from the human nucleus (with its exons and introns), the bacterium is unable to produce the correct protein. Explain what causes this failure and which RNA processing step the bacterium lacks.

A human digestive enzyme has its optimal activity at 37 °C. If it is heated to 60 °C for five minutes and then cooled back to 37 °C, it completely loses its enzymatic activity and does not regain it. In contrast, if it is frozen at -20 °C and then thawed to 37 °C, it continues to function completely normally.

1. a) Justify at a molecular level the difference observed between heating and freezing the enzyme, explaining what happens to its three-dimensional structure and its active site in each case.
2. b) Why does the loss of tertiary structure prevent the enzyme from recognizing its substrate?

Thanks to genetic engineering, it is possible to introduce the human insulin gene into the bacterium Escherichia coli and have this bacterium produce insulin identical to ours.

1. a) What fundamental characteristic of the genetic code makes it possible for a bacterium to correctly interpret the instructions of a human gene? Justify what evolutionary conclusion about the common origin of all living things is drawn from this fact.
2. b) Imagine that the genetic code did not share this characteristic and was species-specific. What would happen upon introducing the human gene into the bacterium? Justify your deduction.

The human hemoglobin beta-chain gene in nuclear DNA is 1600 base pairs long, but the mature protein contains only 146 amino acids (the initial methionine is removed after translation).

1. a) Calculate how many nucleotides of the mature mRNA strictly encode this polypeptide chain (including the start and stop codons).
2. b) Justify what causes the large difference in length between the original gene of 1600 base pairs and the nucleotides you calculated.
3. c) The human genome contains about 20 000 genes, but our cells produce more than 90 000 different proteins. Explain through which mRNA maturation mechanism it is possible to generate multiple different proteins from a single gene.