IB Biology D2.2: Gene expression worked solutions

C. The proteome is the complete set of proteins a cell holds at one time. The genome is all of its DNA, the transcriptome is all of its mRNA, and a promoter is a stretch of non-coding DNA.

B. DNA wound tightly round histones is hard for RNA polymerase and transcription factors to reach, so transcription falls. Nucleosomes do not carry amino acids, join nucleotides or digest mRNA.

D. The bound repressor blocks the promoter, so RNA polymerase cannot start transcription. mRNA breakdown, ribosome function and DNA replication are not what a repressor on the promoter controls.

A. Methylation of cytosines in a promoter represses transcription. It does not change the base sequence, raise transcription or shorten the protein.

C. Most tags are removed so that the embryo can switch on the genes it needs. They are not duplicated, converted to mutations or all kept.

B. With the same base sequence, the difference must come from the environment changing epigenetic tags. Identical twins do not differ in chromosome number or gene order, and crossing over does not occur between two separate people.

D. The mRNA is broken down more slowly, so it lasts longer and more of its protein is made. Transcription is not stopped and the mRNA is still made and translated.

A. The tags are copied when the cell divides, so the gene stays silent in the daughter cells. The sequence is not mutated or deleted, and silence is not reversed by division alone.

C. The mRNA can be broken down by nucleases or blocked from translation before protein is made. If the mRNA is present, gene G is in the genome and was transcribed.

B. A band means the gene was transcribed in that tissue. Skin cells still have the gene; the gel does not show protein and says nothing about a difference in sequence.

(a) The promoter is the non-coding DNA sequence at which RNA polymerase binds to start transcription (1). (b) When tryptophan is plentiful it binds the repressor protein (1); the repressor then binds the DNA close to the promoter (1) and blocks RNA polymerase, so the genes for tryptophan synthesis are not transcribed and synthesis stops, which is negative feedback (1). The signal molecule acts on the protein, not on the DNA.

(a) \dfrac{12-100}{100}\times100 (1) =-88\%, that is a decrease of 88\% (1). (b) Methyl groups are added to cytosines in the promoter of gene R in Q (1); methylation of a promoter represses transcription, so RNA polymerase cannot easily start (1); less mRNA is made, 12 against 100 units (1). Since the base sequence is the same in both lines, the difference is epigenetic and not a mutation.

(a) 12 h is 12\div4=3 half-lives (1); 100\times\left(\tfrac12\right)^3=12.5\% (1). (b) Nucleases break down a short-lived mRNA quickly (1), so translation of it ends soon and the rate of making the protein changes quickly after transcription stops (1).

(a) Paternal DNA: 85-25=60 points; maternal DNA: 70-45=25 points (1); the paternal fall is more than twice the maternal fall (1). (b) Most tags are removed from the gamete DNA so that the embryo adopts the unmethylated state (1) and genes needed in early development can be expressed rather than kept silent (1). (c) Imprinted genes keep their tags, so methylation does not fall to zero (1).

(a) Identical 44% and non-identical 12% (1); 44\div12\approx3.7 times as high (1). (b) Identical twins share the same base sequence, so concordance below 100% shows that the environment, for example through epigenetic tags, changes expression (1). The much higher value for identical twins suggests that the sequence also contributes (1). (c) One limit: identical twins usually share their early environment, or only 200 pairs were studied, so the effect of the environment is not measured exactly (1).

(a) Gene G stays silent in the daughter cells (1) because the methyl tags remain or are copied onto the new DNA at mitosis, so the promoter stays methylated and transcription stays repressed (1). (b) A mutation changes the base sequence; here the sequence is unchanged and only a tag has been added (1). (c) Removal of the methyl groups, for example by a drug, or reprogramming that removes tags (1).

(a) \dfrac{47-34}{34}\times100 (1) =38\% (1). (b) Promoter methylation represses transcription (1), so less mRNA and less protein from gene R is expected in the high-pollution district (1). (c) Observational data show an association, not a cause; diet, income or other differences between districts could also change methylation (1).

(a) Gene G3, because X has its mRNA but not its protein (1). (b) Two of: nucleases break the mRNA down before translation; translation of the mRNA is blocked or slowed; the mRNA is made too recently for protein to have been made (2). (c) The genome, because both cell types belong to one animal and hold all four genes (1).

Any seven of: gene expression is how the information in a gene has an effect on the phenotype, through transcription and translation to a working protein (1); transcription factors are proteins that bind specific base sequences (1); a repressor bound to a promoter blocks RNA polymerase (1); an activator bound to an enhancer promotes transcription (1); methylation of cytosine in the promoter represses transcription (1); methylation of histones, and so the packing of nucleosomes, changes access to the gene (1); nucleases break down mRNA, which limits translation (1); an external signal such as a hormone, or lactose or tryptophan in bacteria, acts through a regulatory protein (1); the tags are copied to daughter cells, so patterns of differentiation persist (1); the base sequence is not changed (1). A named example earns the point only if it is attached to one of these ideas.

(a) Methylation falls from 62% at day 0 to 12% at day 12 while mRNA rises from 10 to 90 units, an inverse relationship (2: values for both variables, and the inverse pattern). (b) \dfrac{90-10}{10}\times100 (1) =800\% (1). (c) A less methylated promoter is more accessible, so RNA polymerase can bind and start transcription (1) and more mRNA is made (1). (d) At day 8 mRNA is 48\div10=4.8 times the day-0 value but protein is 15\div8\approx1.9 times (1: values); two of: translation takes time after transcription; protein accumulates slowly; nucleases break mRNA down before it is translated (1).

(a) At age 3: 52-52=0; at age 30: 61-53=8; at age 60: 74-55=19 (all three values, 2). (b) \dfrac{74-52}{52}\times100 (1) =42\% (1). (c) The twins have the same base sequence, so the divergence is not caused by a mutation (1); the environment changed the methylation, an epigenetic tag, so expression differs as the twins grow apart (1). (d) One pair only, and the lifestyles differ in many ways besides pollution (diet, exercise, disease), so the data show an association and not a cause (1).

(a) Normal cell without S: R is bound to the DNA and blocks RNA polymerase, so mRNA is only 2 units and enzyme 3 units (1); with S, S binds R, R leaves the DNA (1), and RNA polymerase transcribes, giving 85 units of mRNA and 120 units of enzyme (1). (b) In the mutant R cannot bind the DNA, so the promoter is never blocked (1); the gene is transcribed with or without S (about 82 and 84 units) (1). (c) The mRNA column is the transcriptome and the enzyme column is part of the proteome (1).

(a) Both hybrids carry the same two sets of base sequences (1), so the difference cannot be caused by the sequence, for example by dominant alleles (1). (b) Imprinted genes keep their tags and only one copy is active, depending on the parent that supplied it (1); a growth gene that is methylated and silent when it comes from one species is active when it comes from the other (1); so the two crosses express different amounts of the growth gene, and the hybrids differ in size (1). (c) Most tags are removed soon after fertilisation, but imprinted genes keep theirs, which is why the parental origin still matters (1).

(a) Both cells have the same genome (1); different transcription factors are active in the two cells, so the myosin gene is transcribed in muscle but not in the neurone (1); an activator binds the enhancer or promoter of the myosin gene in muscle and mRNA is made (1). (b) Translation: a ribosome builds the myosin polypeptide from the mRNA (1). (c) In the neurone the myosin gene is silent because the activator is absent, or because its promoter is methylated and transcription is repressed (1); the pattern is kept when the cell divides, so the neurone lineage stays specialised (1).

(a) Only target cells contain the receptor for oestradiol, so only they respond (1); other cells have the same hormone passing by but nothing to bind (1). (b) The hormone–receptor pair enters the nucleus and binds to specific base sequences in the DNA (1), where it acts as a transcription factor and raises or lowers transcription of particular genes (1); the mRNA is then translated into more or less of a protein (1). (c) A steroid hormone is lipid-soluble (non-polar), so it passes through the phospholipid bilayer directly (1).

(a) Methylation of the promoter represses transcription (1), so no tumour-suppressor protein is made, which has the same effect as losing the gene (1). (b) The tags remain or are copied at mitosis, so the daughter cells inherit the silent gene (1) and the cells keep dividing without the brake (1). (c) A mutation changes the base sequence, whereas the sequence here is normal and only a tag is present (1). (d) A drug that removes methyl groups from the promoter could restore transcription of the tumour-suppressor gene, so the protein is made again (1).