Questions on control of gene expression

Question 1

Discuss the claim that experiences during a person's lifetime leave epigenetic marks which are then inherited by that person's children.

Accepted Answer

B1 inheritance of marks from a cell to its daughter cells is not in doubt: when a cell replicates its DNA an enzyme copies the methylation pattern of the parent strand onto the new one, which is how a differentiated cell stays differentiated through hundreds of divisions B1 for the claim, there is human evidence of a kind: children conceived during the Dutch Hunger Winter of 1944 to 1945 show altered methylation at some loci decades later, and records from Överkalix suggest associations between a grandparent's food supply and a grandchild's health B1 against the claim, mammalian marks are erased twice, once in the primordial germ cells as gametes form and again in the zygote after fertilisation, so most marks acquired during a parent's life cannot reach the child B1 against the claim, imprinted genes, which are the clearest case of marks that do survive, have those marks wiped and reset each generation according to the sex of the parent, which is the opposite of an experience accumulating down a family line B1 weighing them: the human evidence is observational, a fetus in a starved uterus is directly exposed rather than inheriting anything, and no molecular route from a grandparent's diet to a grandchild's epigenome has been demonstrated, so this is an open question rather than an established mechanism

Question 2

Describe how the lac operon is switched on when lactose enters an Escherichia coli cell, naming the parts of the operon involved.

Accepted Answer

B1 the regulatory gene lacI is transcribed steadily whatever else is happening, and its product is the lac repressor, which binds to the operator B1 with the repressor on the operator, RNA polymerase cannot bind to the promoter, so the structural genes are transcribed only at a very low background rate B1 some of the lactose is converted to allolactose, which binds to the repressor's other binding site and changes the protein's tertiary structure, so the site that fitted the operator no longer fits it; a specification that simplifies the inducer to lactose accepts that name B1 the repressor leaves the operator, so RNA polymerase transcribes lacZ, lacY and lacA as one mRNA and the enzymes are made

Question 3

Explain why oestrogen can act on a gene inside the nucleus while a peptide hormone such as insulin cannot.

Accepted Answer

B1 oestrogen is a steroid and therefore lipid-soluble B1 it diffuses straight through the phospholipid bilayer without a channel or a carrier, so it reaches the inside of the cell and then of the nucleus B1 there it binds an oestrogen receptor, changing the receptor's tertiary structure and exposing its DNA-binding site, so the complex binds the oestrogen response element and transcription of the target gene increases B1 insulin is a peptide and is not lipid-soluble, so it binds a receptor on the outside of the membrane and its message is carried inwards by a second messenger instead

Question 4

A human body cell carries about 20 000 protein-coding genes. The table gives the number of them transcribed in a liver cell and in a neurone taken from the same person, and the number transcribed in both; the figures are constructed for this question rather than measured. Calculate the percentage of the genes transcribed in the liver cell that are also transcribed in the neurone, and calculate how many of the 20 000 genes are transcribed in neither cell.

Accepted Answer

M1 the shared genes are 7400 of the liver cell's 9200, so the percentage is 7400 ÷ 9200 × 100 A1 80.4%, accepting 80% M1 the number transcribed in at least one of the two cells is 9200 + 9600 − 7400 = 11 400, subtracting the shared genes because they would otherwise be counted twice A1 20 000 − 11 400 = 8600 genes transcribed in neither cell, although both cells carry all 20 000

Question 5

Compare the control of gene expression by a transcription factor with the control of gene expression by small interfering RNA, referring to the molecule each one binds, the stage at which each acts, and the direction in which each can change expression.

Accepted Answer

B1 a transcription factor is a protein that binds a specific base sequence of DNA, in or beside the promoter of the gene it controls, whereas one strand of siRNA, a short double-stranded RNA, pairs with a complementary base sequence in an mRNA molecule B1 a transcription factor acts at transcription, either helping RNA polymerase to bind and begin or obstructing it, whereas siRNA acts after transcription, guiding a protein complex that cuts the mRNA so it is never translated B1 a transcription factor can change transcription in either direction, since an activator raises the rate and a repressor lowers it, whereas RNA interference only reduces expression B1 in both cases the specificity comes from complementary binding to a particular sequence, but control at transcription is the cheaper of the two, because a gene left untranscribed costs the cell nothing while an mRNA destroyed by siRNA has already been paid for

Question 6

Describe how the plant hormone gibberellin switches on the genes for stem elongation, using the term DELLA protein in your answer.

Accepted Answer

B1 DELLA proteins normally bind the transcription factors for the stem elongation genes and prevent them from activating transcription B1 gibberellin binds its own receptor, and the hormone-receptor complex then attaches to the DELLA protein B1 the tagged DELLA protein is broken down by the cell's protein-degrading system B1 the transcription factors that DELLA had been holding are released, so transcription of the stem elongation genes increases and the stem elongates

Question 7

Explain how the birth of Dolly the sheep by nuclear transfer and the later production of induced pluripotent stem cells both provide evidence that a differentiated cell retains the whole genome.

Accepted Answer

B1 Dolly was produced by transferring a nucleus from an adult, differentiated mammary gland cell into an egg cell whose own nucleus had been removed B1 that single transferred nucleus directed the development of a complete sheep with every cell type in its body, not only mammary gland cells B1 induced pluripotent stem cells are produced by treating a differentiated adult cell with a small set of transcription factors, without removing or replacing any of the cell's own genes B1 those factors switch previously silent genes back on, which shows that the differentiated cell had kept the whole genome and had merely stopped transcribing most of it

Question 8

Compare control of gene expression by the lac operon in a bacterium with control of gene expression by oestrogen in a eukaryotic cell, referring to how many genes are switched together and to whether an operon is involved.

Accepted Answer

B1 the lac operon switches three structural genes on together, transcribed as a single mRNA from one promoter, whereas the oestrogen receptor complex acts separately at each target gene's own promoter B1 eukaryotic genes with related functions are typically scattered across different chromosomes rather than grouped into an operon, so a eukaryotic cell has no equivalent structure for switching several genes on together in one transcript B1 in both systems a protein changes shape when it binds a small molecule, allolactose or oestrogen, and that change alters its ability to bind DNA B1 both mechanisms work by changing whether RNA polymerase can access a promoter

Question 9

Explain how small interfering RNA stops a protein being produced from a gene that has already been transcribed.

Accepted Answer

B1 double-stranded RNA in the cytoplasm is cut into fragments about twenty-one nucleotides long, and one strand of each fragment is loaded into a protein complex B1 the complex uses that single strand as a search template and pairs with any mRNA whose bases are complementary to it B1 the mRNA is cut and broken down, so it is never translated and no polypeptide is made, even though transcription of the gene did happen

Question 10

A drug occupies the hormone-binding site of the oestrogen receptor without changing the receptor's shape. Suggest the effect of this drug on transcription of an oestrogen-responsive gene, and suggest why it affects breast tissue far more than liver tissue.

Accepted Answer

B1 oestrogen can no longer bind, because the drug is occupying its binding site B1 the receptor's tertiary structure is therefore not altered, so no hormone-receptor complex able to bind the oestrogen response element forms and transcription of that gene is not increased B1 only cells that make the receptor can respond to oestrogen at all, and breast tissue carries far more of it than liver tissue does, so there is much less for the drug to interfere with in the liver

Question 11

State what kind of molecule a transcription factor is, state where it binds, and state what it does to the rate of transcription of a gene.

Accepted Answer

B1 a transcription factor is a protein B1 it binds to a specific base sequence of DNA, usually in or near the promoter of the gene it controls B1 it increases or decreases the rate of transcription of that gene, depending on whether it is an activator or a repressor

Question 12

A mutation abolishes the DNA-binding site of a transcription factor that normally activates several different genes. Suggest the effect on those genes, and suggest why this mutation could affect more genes than a mutation in one of the target genes' own promoters would.

Accepted Answer

B1 with no functional DNA-binding site the factor cannot bind the promoters of the genes it normally activates, so it can no longer raise their transcription above a low background rate B1 one transcription factor can regulate many different genes at once, so losing that single factor removes its effect from every gene it controls B1 a mutation in one target gene's own promoter would instead prevent transcription factor binding at that one gene only, leaving every other gene the factor controls unaffected

Question 13

Outline the difference between a transcription factor acting as an activator and one acting as a repressor, referring to the direction each one changes the rate of transcription.

Accepted Answer

B1 an activator is a transcription factor that increases the rate of transcription of the gene it binds near B1 a repressor is a transcription factor that decreases the rate of transcription of the gene it binds near B1 both are proteins that bind a specific base sequence of DNA near the promoter of the gene they control, and which one a factor is depends only on the direction of its effect

Question 14

Give two examples of mechanisms that control gene expression before or during transcription, and give one example of a mechanism that controls gene expression after transcription has already happened.

Accepted Answer

B1 a transcription factor, such as the lac repressor or the oestrogen receptor complex, acts at transcription by altering whether RNA polymerase can bind the promoter B1 DNA methylation and histone acetylation also act before transcription, by changing how accessible the promoter is to RNA polymerase and transcription factors B1 small interfering RNA acts after transcription, degrading an mRNA that has already been made so that no protein is produced despite transcription having occurred

Question 15

State the effect that increased methylation of a promoter has on transcription of the gene, and state the effect of decreased acetylation of the histones around it.

Accepted Answer

B1 heavy methylation of the promoter reduces or prevents transcription of that gene B1 decreased acetylation also reduces transcription, because the histones regain positive charge and the chromatin condenses

Genes transcribed	Number of protein-coding genes
in the liver cell	9200
in the neurone	9600
in both the liver cell and the neurone	7400