Questions on the genetic code and transcription

Question 1

Describe how a molecule of pre-mRNA is produced from a gene in the nucleus of a eukaryotic cell.

Accepted Answer

B1 RNA polymerase binds to a promoter region at the start of the gene B1 the enzyme unwinds a short section of the double helix, breaking the hydrogen bonds between the paired bases B1 only one of the two exposed strands, the template strand, is read B1 free RNA nucleotides align against the template by complementary base pairing, with uracil pairing to adenine wherever thymine would have gone B1 RNA polymerase joins the aligned nucleotides by condensation into phosphodiester bonds, moving along the gene until it reaches a terminator sequence and releases the pre-mRNA

Question 2

Explain why a mature mRNA molecule is shorter than the gene it was transcribed from, and explain how one gene can give rise to more than one polypeptide.

Accepted Answer

B1 the pre-mRNA is a copy of the whole gene, introns included B1 spliceosomes cut the introns out and join the exons together, so the introns are not represented in the mature mRNA B1 in alternative splicing, different combinations of exons are retained in the mature mRNA B1 so several different mRNA molecules, and therefore several different polypeptides, can come from the same gene

Question 3

A single base is inserted into the coding sequence of a gene close to its start. The polypeptide produced is much shorter than normal and its amino acid sequence bears no relation to the original beyond the point of insertion. Suggest why, referring to two properties of the genetic code.

Accepted Answer

B1 the code is read in threes from a fixed starting point and is non-overlapping, so each base belongs to one triplet only B1 inserting a base pushes every subsequent base one place along, so every triplet after the insertion is read differently, which is a frame shift B1 the amino acid sequence after that point is therefore completely altered rather than altered in one place B1 a shifted reading frame produces stop codons at positions where there were none, so translation ends early and the polypeptide is short

Question 4

Compare the coding strand of a gene with the template strand, referring to which one is transcribed and how each one's sequence relates to the mRNA produced.

Accepted Answer

B1 the template strand is the strand that RNA polymerase actually reads and copies, whereas the coding strand is not transcribed at all B1 the mRNA produced is complementary to the template strand, base for base, whereas the mRNA has the same sequence as the coding strand except that every thymine in the coding strand is replaced by uracil in the mRNA B1 given the coding strand, the mRNA sequence can be written directly by substituting U for T, whereas given the template strand, the complementary sequence must first be taken before substituting U for T B1 only the template strand is exposed to complementary base pairing with the incoming RNA nucleotides during transcription, so only its sequence, not the coding strand's, physically determines which bases are added

Question 5

A textbook describes introns and other non-coding DNA as 'junk DNA' with no function. Evaluate this description, using what you know about non-coding DNA.

Accepted Answer

B1 for: introns and much other non-coding DNA does not code for a polypeptide, and it is removed from pre-mRNA by splicing before the mature mRNA is used, so it plays no part in specifying the sequence of the finished protein B1 against: a large proportion of eukaryotic DNA is non-coding, including introns, repeated sequences between genes and regions involved in switching genes on and off, and several of these regions have known regulatory or other roles rather than none at all B1 against: alternative splicing depends on retaining different combinations of exons from the same pre-mRNA, so which sequence is treated as exon and which as intron contributes to which mRNA molecules, and hence which polypeptides, a gene can produce B1 judgement: 'non-coding' is not the same claim as 'functionless', and describing all such DNA uniformly as junk overstates how much of it has been shown to do nothing, even though a function for every stretch of it has not been demonstrated either

Question 6

A student says that the genetic code being degenerate, with most amino acids specified by more than one triplet, shows it is a wasteful system that evolution has simply not got round to tidying up. Discuss this claim.

Accepted Answer

B1 for the student's claim: sixty-one triplets are shared between only twenty amino acids, which is forty-one more than the minimum needed, so in terms of the sheer number of triplets in use there is apparent redundancy B1 against: triplets sharing an amino acid tend to differ mainly in their third base, so a substitution mutation at that position is often silent, leaving the protein completely unchanged rather than harming it B1 against: because degeneracy makes many mutations silent, it reduces how often a random copying error or mutagen actually changes the protein an organism produces, which is a protective effect rather than a wasted one B1 judgement: describing the redundancy as unused waste ignores this protective consequence; degeneracy is better understood as a feature that has been retained because it reduces the impact of mutation, not as an oversight evolution failed to remove

Question 7

The coding strand of a short section of a gene reads GAT CCA TTG. Give the base sequence of the template strand, written base for base beneath the coding strand, give the base sequence of the mRNA transcribed from this section, and give the rule that relates the mRNA sequence to the coding strand.

Accepted Answer

B1 template strand CTA GGT AAC, each base complementary to the coding strand A1 mRNA GAU CCA UUG B1 the mRNA matches the coding strand, with uracil in place of every thymine

Question 8

A base substitution changes the third base of one mRNA codon, and the polypeptide produced is completely unchanged. Explain how this is possible.

Accepted Answer

B1 the genetic code is degenerate: most amino acids are specified by more than one triplet B1 triplets sharing an amino acid tend to differ in the third base, so the new codon can specify the same amino acid as the old one B1 the primary structure is then identical, so the polypeptide is unchanged, and the substitution is called silent

Question 9

State what is meant by a gene, state what is meant by its locus, and state how the genome differs from the proteome.

Accepted Answer

B1 a gene is a sequence of DNA bases that codes for a polypeptide, or for a functional RNA molecule such as a tRNA B1 the locus of a gene is its specific position on a chromosome B1 the genome is the complete set of DNA in a cell, whereas the proteome is the full range of proteins that cell is able to produce

Question 10

Describe the difference between an exon and an intron, and describe what happens to each during splicing.

Accepted Answer

B1 an exon is a section of a gene that ends up represented in the mature mRNA, whereas an intron is a non-coding section that does not B1 the pre-mRNA produced by transcription contains both exons and introns, since it is a copy of the whole gene B1 spliceosomes cut the introns out of the pre-mRNA and join the exons together, producing the mature mRNA that leaves the nucleus

Question 11

Explain why the terminator sequence at the end of a gene and a stop codon in an mRNA molecule are two different things, even though both are commonly called 'stops'.

Accepted Answer

B1 the terminator is a sequence in the DNA of the gene itself, recognised by RNA polymerase, which causes the enzyme to detach and release the finished pre-mRNA, ending transcription B1 a stop codon is a triplet in the mature mRNA, read by the ribosome during translation, which causes translation of the polypeptide to end B1 the terminator therefore acts on RNA polymerase and finishes making the RNA copy, while a stop codon acts on the ribosome and finishes making the polypeptide

Question 12

Mitochondrial DNA interprets a small number of triplets differently from nuclear DNA in the same cell. Suggest what this shows about the claim that the genetic code is universal, and suggest why the near-universality of the code across most organisms is still significant for genetic engineering.

Accepted Answer

B1 the code is not absolutely universal, since mitochondria interpret a few triplets differently from the interpretation used by the nuclear genome of the very same cell, so 'universal' should be read as 'almost universal' B1 despite that exception, the code is read the same way across the great majority of triplets and the great majority of organisms, including between organisms as different as bacteria and humans B1 that near-universal agreement is what allows a gene taken from one species to be transcribed and translated correctly by the machinery of an unrelated species, which is what genetic engineering that inserts a human gene into a bacterium depends on

Question 13

State what is meant by saying that the genetic code is degenerate, and state what is meant by saying that it is non-overlapping.

Accepted Answer

B1 degenerate: most amino acids are specified by more than one triplet B1 non-overlapping: each base belongs to one triplet only, and the triplets are read one after another

Question 14

DNA uses four bases read in triplets. Calculate the total number of different triplets, and the number left to specify amino acids once the stop signals are set aside.

Accepted Answer

M1 the number of triplets is 4 raised to the power 3, which is 64 A1 three of the 64 are stop signals, leaving 61 that specify amino acids

Question 15

Name the enzyme that carries out transcription, and name the structures that remove introns from pre-mRNA.

Accepted Answer

B1 RNA polymerase, which is not the enzyme that replicates DNA B1 spliceosomes, which cut the introns out and join the exons together