D2.2 Gene expression HL only

1. Transcription of the gene to mRNA, translation of the mRNA to a protein, then the function of that protein — These are the most common stages of gene expression. The protein product, often an enzyme, is what acts on the phenotype: here it could be an enzyme catalysing a step in pigment synthesis.
2. Direct action of the base sequence of the gene on the petal cells, without any protein product — A student who reads 'a gene for petal colour' literally picks this. DNA does not act on the phenotype directly; information in the gene has its effect through the protein made when the gene is expressed.
3. Transcription and translation of the gene to make the pigment molecule that colours the petal — A student who thinks the product of a gene is the characteristic itself picks this. Translation produces a polypeptide, not a pigment; the pigment is made by the function of the protein, for example an enzyme catalysing its synthesis.
4. Replication of the gene in every petal cell, so that copies of the gene produce the pigment — A student who confuses copying DNA with expressing it picks this. Replication copies the genome for cell division; expression begins with transcription of the gene into mRNA.

Syllabus statement D2.2.1 · Read this in Learn

1. The first part of the gene to be transcribed, which codes for the first amino acids of the polypeptide — A student who pictures the gene as one continuous piece of code picks this. The promoter lies upstream of the transcribed region and is not copied into mRNA, so it codes for nothing.
2. A protein that binds to an enhancer sequence and increases the rate of transcription of the gene — A student who thinks promoters are proteins picks this. The promoter is a DNA sequence; the proteins that bind to enhancers and promoters are transcription factors.
3. A sequence near the start of the gene to which transcription factors and RNA polymerase bind — The promoter is a specific base sequence in DNA. Transcription factors bind to it first, and this allows RNA polymerase to bind and begin transcription of the gene downstream.
4. A base sequence that RNA polymerase binds to by itself, with no other proteins required — A student who learned transcription as 'RNA polymerase binds and copies' picks this. In eukaryotic cells transcription factors must bind to the promoter before RNA polymerase can attach.

Syllabus statement D2.2.2 · Read this in Learn

1. More protein is made from gene Q, because each of its mRNA molecules is translated many times before degradation — An mRNA can be translated repeatedly for as long as it persists. With equal transcription, the long-lived mRNA of gene Q yields many more polypeptides, which is why control of mRNA degradation regulates translation.
2. The amount of protein made from each gene is the same, because their rates of transcription are equal — A student who thinks transcription rate alone sets the amount of protein picks this. Each mRNA from gene Q is translated for days, each from gene P for minutes, so far more protein is made from gene Q.
3. More protein is made from gene P, because its mRNA is used up and replaced much more rapidly — A student who thinks each mRNA delivers one message and is destroyed picks this. Faster turnover means each mRNA is translated fewer times, not that more protein is made.
4. The amount of protein from gene Q can be changed more quickly if its rate of transcription changes — A student who equates a stable mRNA with a better one picks this. Gene Q's mRNA keeps being translated for days after transcription changes, so it is gene P whose protein level can change quickly.

Syllabus statement D2.2.3 · Read this in Learn

1. Cells become different from each other because each type keeps only the genes it needs — A student who thinks differentiated cells discard unused genes picks this. Every body cell retains the complete genome; differentiation changes which genes are expressed, not which are present.
2. Cells become different from each other through changes in gene expression, not in DNA sequence — All the cells derive from one zygote and share a genome. Patterns of differentiation develop as different genes are switched on and off in different cells; the base sequences are not altered, so phenotype but not genotype changes.
3. Cells become different from each other through mutations that alter the sequences of their genes — A student who treats any developmental change in DNA activity as a mutation picks this. Epigenetic changes leave the base sequence unaltered, so genotype is unchanged while phenotype changes.
4. Cells become different from each other by expressing all of their genes at different rates — A student who assumes every gene is in use in every cell picks this. No cell expresses all of its genes; many genes are not transcribed at all in a given cell type.

Syllabus statement D2.2.4 · Read this in Learn

1. They have different genomes, because each has kept different genes — A student who thinks differentiation removes genes picks this. Both cells developed from the same zygote by mitosis and contain the same genome.
2. They have the same transcriptome, because both cells transcribe all of their genes — A student who assumes all genes are expressed everywhere picks this. No cell expresses all of its genes, and the two cell types transcribe different subsets, so their transcriptomes differ.
3. They have the same genome but different transcriptomes and proteomes — The genome is the same in all body cells. The two cells express different sets of genes, so the RNA present (transcriptome) and the proteins present (proteome) differ, and this is what makes them differentiated.
4. They have the same proteome, because the same genes code for the same proteins — A student who reads the proteome straight off the gene list picks this. Having the same genes does not mean making the same proteins; the proteome reflects which genes are expressed, which differs between the cells.

Syllabus statement D2.2.5 · Read this in Learn

1. Transcription of the gene downstream is repressed, so it is not expressed — Methylation of cytosine in a promoter is an epigenetic tag that represses transcription and therefore the expression of the gene downstream, without any change in the base sequence.
2. Translation of the gene's mRNA is blocked, because ribosomes cannot read methylated codons — A student who pictures methyl groups as obstacles on the message picks this. The tag is on the DNA of the promoter and acts at transcription, so no mRNA is made in the first place.
3. The base sequence of the gene is altered, so a different polypeptide is produced from it — A student who thinks methylation is a mutation picks this. A methylated cytosine is still cytosine and still pairs with guanine; the sequence, and so the genotype, is unchanged.
4. Transcription of the gene is increased, because the methyl tag marks it for expression — A student who takes a tag to be a label for use picks this. Methylation of the promoter has the opposite effect: it switches transcription of the gene off.

Syllabus statement D2.2.6 · Read this in Learn

1. Expressed, because epigenetic tags are lost whenever DNA is replicated — A student who thinks only the base sequence survives cell division picks this. Methylation patterns can be maintained through mitosis, which is how differentiated cells produce daughter cells of the same type.
2. Not expressed, because the methylation has changed the base sequence of the gene — A student who treats methylation as a mutation picks this. The daughter cells do inherit the silenced state, but the base sequence of gene G is not altered; only the tag is passed on.
3. Not expressed, because the methyl tags remained in place through mitosis — Epigenetic tags such as promoter methylation can remain in place during mitosis, so the daughter cells inherit the same pattern of gene expression. The base sequence of gene G is unchanged; this is epigenetic inheritance.
4. Not expressed in the person's children, because the tags pass to offspring — A student who thinks acquired epigenetic changes go to the next generation picks this. A tag in a skin cell is passed only to that cell's daughter cells; reaching offspring would require the tag to be in a gamete.

Syllabus statement D2.2.7 · Read this in Learn

1. The diet alters epigenetic tags, so the two castes express different sets of the same genes — This is an environmental effect on gene expression: the food a larva receives changes tags such as DNA methylation, altering which genes are switched on, so genetically alike larvae develop different phenotypes.
2. Larvae fed worker jelly lose the genes that are needed for queen development — A student who thinks unused genes are discarded picks this. Workers keep the whole genome; the genes for queen development are present but not expressed.
3. Royal jelly contains a mutagen that alters the base sequence of the larva's growth genes — A student whose only model for an environmental effect is mutation picks this. Diet acts on gene expression through epigenetic tags; the DNA sequence of a queen is the same as that of her worker sisters.
4. The diet cannot cause the difference, so the caste of each larva must be fixed at fertilization — A student who thinks gene activity is set at conception picks this. The larvae are genetically alike and the stem states that the caste depends on the diet given, so the environment must be acting on gene expression.

Syllabus statement D2.2.8 · Read this in Learn

1. So that no epigenetic tag from either parent is able to affect the offspring's cells — A student who thinks the gametes are wiped completely clean picks this. Most but not all tags are removed; some remain, and these affect how certain genes are expressed according to the parent that supplied them.
2. So that the cells of the embryo can develop a fresh pattern of differentiation — Removing most of the tags from the gametes means the embryo is not committed to the expression patterns of the parents' cells, so its cells can differentiate into every cell type. The tags that are not removed are the exception that makes ligers and tigons differ.
3. So that the base sequence of the offspring's DNA is restored to normal — A student who thinks tags alter the sequence picks this. Epigenetic tags do not change the base sequence, so there is nothing in the sequence to restore; removing tags changes only the pattern of expression.
4. So that every gene in the zygote is switched off until it is needed — A student who takes tags to be 'on' labels picks this. Many tags, such as promoter methylation, repress genes, so removing them does not switch every gene off; it resets the pattern so that a new one can be established.

Syllabus statement D2.2.9 · Read this in Learn

1. The methylation differences show that the older twins' DNA base sequences had changed — A student who treats methylation as a mutation picks this. Methyl tags alter gene expression without altering the base sequence, so the twins remain genetically identical.
2. The older pairs cannot have been monozygotic, because identical twins are alike in every respect — A student who takes 'identical' to cover gene activity as well as genome picks this. Monozygotic twins have the same DNA but can develop different epigenetic tags, which is exactly what makes them useful for this kind of study.
3. Differences in the twins' environments over time altered their patterns of gene expression — Monozygotic twins share a genome, so differences in methylation cannot be genetic. The growth of the differences with age, and especially with time apart, shows the environment acting on gene expression through epigenetic tags.
4. The older twins who lived together must have differed genetically, since their environments were the same — A student who equates environment with the home picks this. Twins living together still differ in diet, illness, habits and exposures, and monozygotic twins do not differ genetically.

Syllabus statement D2.2.10 · Read this in Learn

1. The pigment melanin, which the gene codes for — A student who treats the characteristic as the gene product picks this. Melanin is not a protein and is not coded for by any gene; it is produced by the function of the enzyme that the gene codes for.
2. The enzyme tyrosinase, made by translation — The direct product of gene expression is the polypeptide made by translation of the gene's mRNA: here the enzyme tyrosinase. Its function, catalysing a step in melanin synthesis, is what affects the phenotype.
3. The skin colour that the gene determines — A student who thinks genes act directly on the phenotype picks this. Skin colour is the eventual effect; it is reached only through transcription, translation and the function of the enzyme.
4. More copies of the gene in each skin cell — A student who confuses replication with expression picks this. Expressing a gene does not make more copies of it; it makes mRNA and then a polypeptide.

Syllabus statement D2.2.1 · Read this in Learn

1. The deleted sequence coded for a transcription factor, so less is now made — A student who confuses the DNA sequence with the protein that binds it picks this. The stem states that the sequence was non-coding; an enhancer is a binding site for transcription factors, not a gene for one.
2. The deletion is unrelated, because a sequence so far away cannot affect the gene — A student who judges influence by distance along the DNA picks this. Looping of the DNA brings proteins bound at a distant enhancer into contact with those at the promoter, so distant sequences do regulate transcription.
3. The deleted sequence was part of the transcribed region, so a shorter mRNA is made — A student who thinks control sequences upstream of a gene are transcribed along with it picks this. Transcription begins downstream of the promoter, so a non-coding sequence 20 000 base pairs upstream is never copied into mRNA; it is a control sequence (an enhancer) whose loss reduces the rate of transcription, not the length of the transcript.
4. The deleted sequence was an enhancer to which activator proteins bound — Enhancers can lie thousands of base pairs from the gene they regulate. Transcription factors bound to the enhancer increase the rate of transcription, so deleting it lowers the rate even though the promoter is intact.

Syllabus statement D2.2.2 · Read this in Learn

1. The cell has lost the 9 000 genes for which no mRNA could be detected in the study — A student who thinks unused genes are discarded picks this. The genes were identified in the cell's genome; they are present but not transcribed in this cell type.
2. The weak correlation must be an error, because each mRNA gives the same amount of protein — A student who extends one gene–one polypeptide to quantities picks this. mRNAs differ in how often they are translated and how quickly they are degraded, so a weak correlation is expected.
3. The transcriptome is fixed, so the 9 000 silent genes cannot be expressed in this cell later — A student who treats the transcriptome as a fixed property picks this. The transcriptome is a snapshot; genes that are silent now can be switched on if conditions or signals change.
4. The cell transcribes only some of its genes, and protein amounts are also regulated after transcription — Transcripts from only 11 000 of 20 000 genes show that the cell does not express all of its genes. The weak correlation shows that the proteome is not a copy of the transcriptome: translation rate, mRNA degradation and protein turnover also set protein amounts.

Syllabus statement D2.2.5 · Read this in Learn

1. The finding on active genes must be an error, because methylation only ever represses transcription — A student who has learned methylation as a single off switch picks this. That rule holds for cytosine in a promoter, but methylation of amino acids in histones can repress or activate transcription.
2. Methylation of histones can either activate or repress transcription, depending on the tag — Methyl groups on different amino acids of a histone are different epigenetic tags, and the guide states that histone methylation can cause transcription to be repressed or activated. The details of how this is achieved are not required.
3. The methyl groups must be on the DNA wound around the histones, because histones are not modified — A student who merges histone methylation with DNA methylation picks this. Histones are proteins, and the tags described are on their amino acids, not on DNA bases.
4. Methylation of histones activates transcription, so the silenced genes were switched off by another tag — A student who thinks tags label genes for use picks this. The data show histone methylation on silenced genes as well as active ones, so histone methylation can repress as well as activate.

Syllabus statement D2.2.6 · Read this in Learn

1. Air pollution acted as a mutagen, changing the genes in the blood cells — A student whose only model of environmental action on DNA is mutation picks this. The base sequences were the same in both groups, so the genes were not mutated; what differed was the epigenetic tags.
2. The two groups must have differed genetically before any exposure to pollution — A student who believes gene activity is fixed from conception picks this. The base sequences examined were the same in both groups; the difference lay in tags that the environment can alter.
3. The altered tags will be inherited by the children of the exposed people — A student who assumes acquired epigenetic changes pass to offspring picks this. The tags were observed in blood cells; nothing in the study shows that they are present in gametes or survive to the next generation.
4. Air pollution altered gene expression without altering genotype — Altered methyl tags with an unchanged base sequence is exactly an environmental effect on gene expression: the pattern of expression, and so the phenotype of the cells, changed while the genotype did not.

Syllabus statement D2.2.8 · Read this in Learn

1. The two hybrids inherit different combinations of lion and tiger alleles for the genes controlling growth — A student who expects every inherited difference to be genetic picks this. The stem states that both hybrids receive one lion set and one tiger set; the alleles are the same combination, supplied by different parents.
2. Some tags on growth genes survive in the sperm and ovum, so a gene's expression depends on its parent of origin — Most but not all epigenetic tags are removed from the gametes. Tags that remain on growth-related genes differ between lion and tiger sperm and ova, so the same genes are expressed differently in the liger and the tigon.
3. All epigenetic tags are removed from the gametes, so the difference must come from the uterus — A student who thinks the gametes are wiped clean picks this. If every tag were removed, the reciprocal hybrids would carry the same tags; it is the tags that are not removed that make parent of origin matter.
4. Tags acquired by the body cells of the lion father during his life were passed to the liger — A student who thinks acquired changes in body cells reach offspring picks this. The tags that matter are those present in the sperm and ovum; tags in a parent's somatic cells are not transmitted.

Syllabus statement D2.2.9 · Read this in Learn

1. Lactose is the raw material from which the bacteria build the new enzyme — A student who explains more enzyme by more raw material picks this. Enzymes are proteins built from amino acids; lactose is the substrate, and its role here is to switch on transcription of the enzyme's gene.
2. Lactose acts as a transcription factor, binding directly to the gene's promoter — A student who jumps from the signal straight to the DNA picks this. Transcription factors are proteins; lactose acts by binding to the repressor protein, not to the DNA.
3. Lactose stops the bacteria from transcribing the gene coding for the repressor — A student who thinks the repressor is removed by not making it picks this. The repressor is made continuously; lactose changes the shape of repressor molecules that already exist so that they release the operator.
4. Lactose binds to the repressor protein, which releases the operator — Lactose (as its isomer allolactose) binds to the lac repressor and changes its shape so that it can no longer bind to the operator. RNA polymerase can then transcribe the lac operon genes, and beta-galactosidase is synthesized.

Syllabus statement D2.2.11 · Read this in Learn

1. It binds to a receptor protein, and the hormone–receptor complex acts as a transcription factor — Estrogen binds to a receptor inside the cell; the complex binds to specific base sequences in DNA and alters transcription of target genes. The hormone therefore acts through a protein that binds DNA, as all regulation of transcription does.
2. It binds directly to the promoters of its target genes in place of a transcription factor — A student who leaves out the receptor picks this. Regulation of transcription is by proteins binding to DNA; estrogen has to bind to a receptor protein, and it is the complex that binds the DNA.
3. It activates enzymes already in the cell by binding to their active sites, without any transcription — A student who reaches for enzyme activation picks this. Estrogen's effect on the pattern of gene expression is a change in which genes are transcribed, so new proteins are made rather than existing enzymes activated.
4. It adds methyl tags to cytosine in the promoters of target genes, switching them on — A student who thinks a methyl tag marks a gene for use picks this. Promoter methylation represses transcription, and the hormone acts through a receptor that becomes a transcription factor, not by methylating DNA.

Syllabus statement D2.2.11 · Read this in Learn