Worked Problems

1. The following diagram represents a sequence of nucleotides surrounding an RNA coding sequence.

RNA coding sequence

(a) Is the RNA coding sequence likely to be from a bacterial cell or from a eukaryotic cell? How can you tell?

(b) Which DNA strand will serve as the template strand during transcription of the RNA coding sequence?

(a) Bacterial and eukaryotic cells use the same DNA bases (A, T, G, and C); so the bases themselves provide no clue to the origin of the sequence. The RNA coding sequence must have a promoter, and bacterial and eukaryotic cells do differ in the consensus sequences found in their promoters; so we should examine the sequences for the presence of familiar consensus sequences. On the bottom strand to the right of the RNA coding sequence we find AAATAT, which, written in the conventional manner (5' on the left), is 5'-TATAAA-3'. This sequence is the TATA box found in most eukaryotic promoters. However, the sequence is also quite similar to the —10 consensus sequence (5' - TATAAT - 3') found in bacterial promoters.

Farther to the right on the bottom strand, we also see 5'-GCGCGCC-3', which is the TFIIB recognition element

(BRE) in eukaryotic RNA polymerase II promoters. No similar consensus sequence is found in bacterial promoters; so we can be fairly certain that this sequence is a eukaryotic promoter and RNA coding sequence.

(b) The TATA box and BRE of RNA polymerase II promoters are upstream of the RNA coding sequences; so RNA polymerase must bind to these sequences and then proceed downstream, transcribing the RNA coding sequence. Thus RNA polymerase must proceed from right (upstream) to left (downstream). The RNA molecule is always synthesized in the 5': 3' direction and is antiparallel to the DNA template strand; so the template strand must be read 3':5'. If the enzyme proceeds from right to left and reads the template in the 3': 5' direction, the upper strand must be the template, as shown here.

Template strand

Template strand

- Direction of transcription

- Direction of transcription

2. Suppose that a consensus sequence in the regulatory promoter of a gene that encodes enzyme A were deleted. Which of the following effects would result from this deletion?

(a) Enzyme A would have a different amino acid sequence.

(b) The mRNA for enzyme A would be abnormally short.

(c) Enzyme A would be missing some amino acids.

(d) The mRNA for enzyme A would be transcribed but not translated.

(e) The amount of mRNA transcribed would be affected. Explain your reasoning.

The correct answer is part e. The regulatory protein contains binding sites for transcriptional activator proteins. These sequences are not part of the RNA coding sequence for enzyme A; so the mutation would have no effect on the length or amino acid sequence of the enzyme, eliminating answers a, b, and c. The TATA box is the binding site for the basal transcription apparatus. Transcriptional activator proteins bind to the regulatory promoter and affect the amount of transcription that takes place through interactions with the basal transcription apparatus at the core promoter.

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