Gene expression connects DNA, transcription regulation, epigenetic control, transcript stability, proteomes and environmental signals to phenotype in living cells and tissues.
Gene expression is the regulated use of DNA information to produce a functional RNA or protein.
Control can act before transcription, during RNA processing or stability, and during translation. The combined controls set where, when and how much product a cell makes.
Trace: regulatory signal; DNA access; RNA amount; translation; functional output.
A liver cell expresses a detoxification gene strongly after exposure to a chemical, while a neuron keeps it mostly silent.
A gene being present in DNA does not mean it is expressed in every cell.
This objective is assessed through structured response, commonly using Explain.
Explain
Build the answer around this relationship: DNA information affects phenotype through gene products.
Representative question
One important chemical in the mobilization of stem cells is a protein, CXCL12, which maintains the stem cells inside the bone marrow. The breakdown of CXCL12 causes the mobilization of stem cells to the blood vessels.
The graph below shows the mobilization of stem cells and the production of mRNA for CXCL12 when the bone marrow is treated with two different chemicals (isoprenaline and clenbuterol).
Explain how the amount of mRNA for CXCL12 gives an indication of the amount of protein CXCL12 produced.
mRNA is translated to protein / involved in protein synthesis
Transcriptional regulation changes whether RNA polymerase starts and how often a gene is transcribed.
Transcription factors bind regulatory DNA and alter access to the promoter. Activators can recruit machinery; repressors can block it or close chromatin, changing mRNA abundance.
Identify: regulatory sequence; factor; promoter access; predicted change in transcription.
A repressor bound near a promoter can reduce mRNA production without changing the gene’s coding sequence.
Transcriptional regulation is not the only control; mRNA degradation and translation can still alter protein output.
This objective is assessed through structured response, multiple choice, commonly using Suggest / Explain.
Suggest / Explain
Promoters mark where RNA polymerase can bind to begin transcription, while transcription factors bind specific DNA sequences to activate or repress transcription.
Treating promoters as translation start sites instead of RNA polymerase binding regions.
Representative question
Explain how gene expression can be regulated during transcription to determine an organism's phenotype.
a. transcription factors bind to DNA and can be activators or repressors OR
transcription factors promote or block transcription;
b. protein/transcription factor/TF binds to promoter to activate transcription OR
promoter indicates where RNA polymerase binds to begin transcription;
c. transcription factor/activator/protein binds to enhancer to increase the rate of transcription
OR
transcription factor/repressor/protein binds to silencer to decrease the rate of transcription;
d. epigenic tags can alter gene expression / methylation can alter gene expression;
e. methylation of cytosine in the DNA of a promoter represses transcription;
f. methylation of amino acids/protein in histones can cause transcription to be repressed or activated;
g. thereby regulating the production of proteins from the gene
OR
proteins from gene expression display/create phenotypic traits;
h. gene expression may be altered by (steroid) hormones/biochemicals that act as chemical signals to activate receptors that promote transcription;
i. alteration of methyl tags on DNA in response to air pollution or in response to the environment;
j. valid example of gene regulation;
7
Marking guidance:
max
mRNA degradation determines how long a transcript remains available for translation and therefore affects protein output.
Protective structures and RNA-binding factors can slow degradation, while nucleases remove transcripts. A stable message supports repeated translation; a short-lived message produces a brief pulse.
Predict output by comparing: transcript production; degradation rate; lifetime; translation opportunity.
If two cells make equal mRNA amounts but one degrades the message twice as quickly, it can produce less protein.
More transcription does not always mean more protein when rapid degradation removes the message.
Epigenetic regulation changes gene expression through reversible or persistent changes in chromatin state rather than changing nucleotide sequence.
DNA methylation, histone modification and chromatin remodeling can make regulatory regions more or less accessible. This changes transcription probability while the underlying sequence remains.
Separate: sequence; chromatin mark; accessibility; transcriptional effect.
Adding a repressive chromatin mark near a promoter can reduce transcription even though the gene’s bases are unchanged.
Epigenetic does not mean permanent or independent of environment; marks can be added, removed or maintained.
The genome is an organism’s DNA, the transcriptome its RNA molecules at a time, and the proteome its proteins at a time.
All cells in one organism usually share the genome, but cell type and conditions change which genes are transcribed and translated. Therefore transcriptome and proteome are dynamic subsets and products.
Compare samples by asking: DNA content; RNA expression; protein abundance; time and cell type.
A muscle and liver cell can share a genome but have different transcriptomes and proteomes because different genes are active.
A transcript detected does not guarantee the corresponding protein is abundant or functional.
This objective is assessed through multiple choice, commonly using State / Calculate / Explain.
State / Calculate / Explain
Build the answer around this relationship: The genome is the complete genetic information.
Assuming the genome and proteome are identical in all tissues.
Representative question
Which statement correctly describes genome and proteome?
Only the genome but not the proteome can be analysed using gel electrophoresis.
The genome and the proteome are the same in all tissues in an organism.
In cells of different tissues, the genome is the same while the proteome varies.
Only mutations in the proteome but not in the genome cause any variability.
C
Epigenetic tags such as DNA methylation or histone modification can change chromatin accessibility and gene expression.
Tags recruit proteins that compact or loosen chromatin. A closed promoter is harder for transcription machinery to reach; an open region is more accessible, though context matters.
Read a tag effect by identifying: tag; chromatin state; DNA accessibility; expression outcome.
If methylation recruits a chromatin-compacting protein beside a promoter, RNA polymerase has less access and the gene’s transcript level falls.
One tag does not have one universal effect at every genomic location; neighboring marks and proteins matter.
This objective is assessed through structured response, commonly using Outline / Suggest / Explain.
Outline / Suggest / Explain
Build the answer around this relationship: Promoter DNA methylation usually represses transcription.
Describing histone methylation when the question specifically asks about DNA methylation.
Representative question
Explain how methylation of nucleosomes affects DNA transcription.
a. methylation of amino acids/histones;
b. (can cause) transcription to be inhibited/repressed/activated / OWTTE;
c. methylation of cytosine causes transcription to be repressed/inhibited;
d. (repressed as histones) restricts access to the DNA;
e. (activated as) allows transcription factors to bind to DNA;
f. methylation of promoter (DNA) represses transcription
g. results in decreased gene (downstream) expression/gene silencing / OWTTE;
b. Accept "transcription more difficult".
d. Accept other wording such as "less accessible".
2
Marking guidance:
max
Epigenetic marks can be copied or re-established after cell division, allowing daughter cells to retain aspects of gene-expression state.
Maintenance enzymes recognize marks on parental chromatin and help place corresponding marks on new chromatin. This provides cellular memory without changing DNA sequence.
Trace: parental mark; maintenance during replication; daughter chromatin; continued expression state.
If a muscle-lineage gene is repressed before mitosis, maintenance enzymes can restore that repression on daughter chromosomes, so both daughter cells retain the same identity.
Persistence is not guaranteed across all cell divisions or generations; marks can be erased or reset.
External factors can alter gene expression by changing signaling pathways, transcription factors, chromatin marks or RNA stability.
Cells sense temperature, nutrients, stress or hormones and convert those signals into molecular changes. The DNA sequence can remain constant while output changes with conditions.
Separate cause and response: environmental factor; sensor or signal; regulatory change; phenotype.
When oxygen becomes scarce, a cell’s sensor pathway activates transcription of anaerobic-metabolism genes, increasing the proteins that maintain ATP production without changing DNA sequence.
An environmental effect on expression is not automatically an inherited mutation; distinguish regulation from sequence change.
This objective is assessed through essay response, multiple choice, commonly using Compare / Suggest / Discuss.
Compare / Suggest / Discuss
Build the answer around this relationship: Environmental conditions can alter gene expression.
Treating altered expression as a necessary DNA base-sequence mutation.
Representative question
Using the data in the bar chart, discuss the evidence for Arabidopsis plants adapting to different daylight regimes by changing the pattern of gene expression.
a. «mRNA» transcripts differ in plants grown in long days and short days
b. indicates different genes are being expressed
c. plants adapt to different daylight regimes by altering gene expression
d. short day length causes struggle to get enough light to photosynthesize and more «mRNA» transcripts related to photosynthesis
OR
plants produce large leaves rapidly when grown in long days which may result in more transcripts for biotic stress
Marking guidance:
Accept an example of such a transcript from the bar chart
Accept other valid reason.
3 max
Epigenetic states are changeable because enzymes can erase, add or remodel DNA and histone marks.
Signals and developmental programs recruit enzymes that alter chromatin. Removing a repressive tag can reopen a promoter, while adding one can silence it, changing expression without rewriting DNA.
Explain reversibility by naming: original mark; modifying enzyme or signal; accessibility change; expression change.
A differentiation signal can remove a repressive histone mark near a muscle gene and allow transcription.
Reversibility does not mean every epigenetic change is quickly or completely erased.
This objective is assessed through multiple choice.
Some marks, such as imprints, may be retained in specific cases and can affect offspring phenotypes.
Representative question
Very soon after fertilization, parental epigenetic methylation is reversed in the DNA. Later, tissue-specific epigenetic modifications are made to the embryonic DNA. The graph follows the degree of methylation from different sources during embryonic development.
According to the graph, what are the changes in DNA methylation during embryonic development?
Only the paternal DNA becomes demethylated.
The maternal DNA becomes demethylated first.
The methylation patterns of the parents' DNA are erased before fertilization.
The methylation patterns of both parents are erased after fertilization.
D
Studies of monozygotic twins compare genetically similar individuals to estimate how environment and epigenetic differences contribute to traits.
If twins differ despite near-identical DNA, differing environments, developmental history or epigenetic states are possible explanations. Concordance and study design determine the strength of inference.
Evaluate a twin result by checking: shared genes; shared environment; age and exposure; trait concordance; alternative causes.
Twins may both inherit risk alleles but develop different symptoms after different exposures, suggesting environment modifies expression or phenotype.
Twin differences do not prove a purely environmental cause; measurement error and non-shared biology also matter.
This objective is assessed through data analysis, multiple choice, commonly using Identify / Compare / Analyse.
Identify / Compare / Analyse
Build the answer around this relationship: Monozygotic twins share essentially the same genome.
Using only numerical values without comparing identical and non-identical twins.
Representative question
Analyse the data to find whether it supports the hypothesis that genetic factors cause some people to have a much higher chance of cocaine dependence than others.
hypothesis supported as identical twins are more likely to behave the same for abuse and dependence than non-identical twins; identical twins have the same genotype / OWTTE; hypothesis not supported as environment is the major factor for trying cocaine; not known if similar results may be due to similar environment; not enough data for valid statistical analysis/OWTTE;
External factors influence phenotype when they change cellular signals that regulate transcription, translation or protein activity.
Hormones, nutrients, temperature and stress activate receptors and pathways. These pathways alter regulatory proteins and gene output, linking an environmental condition to a cellular response.
Trace: external factor; receptor or sensor; intracellular pathway; gene or protein change; phenotype.
A hormone entering a cell can bind a receptor that activates transcription of proteins needed for a metabolic response.
A factor may affect phenotype through protein activity without changing gene expression, so identify the actual pathway.