Exercises: Gene expression

Define transcription and translation and state where in the eukaryotic cell each of these processes takes place.

What is a codon? State how many nucleotides make it up, how many distinct codons exist, and how many different amino acids they encode in total.

Look at the diagram of the flow of genetic information. State which molecules are labelled A, B and C, which processes occur at arrows 1 and 2, and what the area surrounded by the dashed line represents.

From the DNA template strand 3'-TACGGAACT-5', obtain the resulting mRNA sequence indicating its polarity, and state the maximum number of amino acids this fragment can encode.

Based on the following genetic code table:

1. a) Translate the following $\text{mRNA}$: $5'\text{-AUGGCUUAA-}3'$, and indicate the resulting amino acid sequence.
2. b) Explain what role the first and the last codon of the fragment play.

Differentiate the functions of mRNA, tRNA and rRNA in protein synthesis, indicating what each type of RNA contributes to the process.

Consider the following fragment of the coding sequence of an mRNA that is translated into a cytoplasmic protein:

$5'\text{--- AUG - UCU - UCC - UCA - UCG --- } 3'$

(Note: the four codons following the AUG start codon all code for the amino acid serine).

1. a) Based on this specific case, justify why the genetic code is degenerate and demonstrate that this property is not equivalent to saying that the code is "ambiguous".
2. b) Suppose that two independent point mutations are introduced: Mutant 1 changes the second codon from UCU to UCC; Mutant 2 changes the third codon from UCC to UAC (which codes for tyrosine). Compare the impact of both mutations on the amino acid sequence of the protein and classify each mutation according to its functional effect.
3. c) Reason what adaptive advantage is conferred by the fact that the degeneracy of the genetic code is almost always concentrated at the third base of each triplet (wobble hypothesis) rather than at the first or second, in the face of spontaneous point mutations.

The following diagram represents a functional ribosome during the elongation phase of translation:

1. a) Justify and deduce the polarity ($5'$ and $3'$ ends) of the mRNA strand and the direction in which the ribosome will move along it.
2. b) Write the sequence of the anticodon of the tRNA marked with a question mark (?), mandatory specifying its $5'\to 3'$ polarity, and reason which amino acid it carries knowing that the GCU codon codes for alanine.
3. c) In a mutant strain, a suppressor tRNA is produced that is capable of recognizing the UAA codon by inserting the amino acid tyrosine. Predict what will happen to translation and to the length of the resulting protein when the ribosome reaches the position marked with the stop codon compared to the wild-type cell.

In the human genome, the fibronectin gene contains numerous exons and introns. In fibroblasts, it gives rise to an insoluble protein isoform that forms part of the extracellular matrix, whereas in hepatocytes it originates a soluble isoform that circulates in the blood plasma.

1. a) Justify the molecular mechanism by which a single genomic DNA sequence can give rise to these two proteins with such different functions and locations.
2. b) A patient presents a point mutation consisting of a transition (G to A) at the splicing acceptor site of intron 4 of this gene. Predict two possible alterations in the structure of the resulting mature mRNA and their consequences for the synthesized protein.
3. c) If we clone this intact human gene (with all its introns and exons) into a plasmid and introduce it into Escherichia coli, reason whether the bacterium will synthesize functional human fibronectin.