IB DP Biology: Gene expression and epigenetics (HL) (DP Biology)

This study guide covers gene expression and epigenetics, section D2.2 (statements D2.2.1 to D2.2.11) of the IB Biology guide, first assessment 2025. The whole section is additional higher level (HL only): the guide states that there is no SL content in it. It sits in Theme D, Continuity and change, and builds on what you already know about transcription and translation.

Work through it with the revision notes and the practice questions. The course hub and the printable checklist track the rest of the course. If you are unsure where your gaps are, try the free 10-minute diagnostics. For earlier ideas on cells and genes, see the Theme A guide.

What this unit covers

Section	What you must be able to do	Tier
D2.2.1	Explain gene expression as the way gene information affects phenotype	HL only
D2.2.2	Explain regulation of transcription by sequence-specific DNA-binding proteins: promoters, enhancers, transcription factors	HL only
D2.2.3	Explain how control of mRNA degradation regulates translation	HL only
D2.2.4	Define epigenesis and explain why phenotype but not genotype changes	HL only
D2.2.5	Compare genome, transcriptome and proteome of individual cells	HL only
D2.2.6	Explain methylation of promoter DNA and of histones as epigenetic tags	HL only
D2.2.7	Explain epigenetic inheritance to daughter cells or offspring	HL only
D2.2.8	Give examples of environmental effects on gene expression, including air pollution and methyl tags	HL only
D2.2.9	Explain the consequence of removing most, but not all, epigenetic tags from ovum and sperm, using tigons and ligers	HL only
D2.2.10	Interpret monozygotic twin studies of environmental effects on gene expression	HL only
D2.2.11	Give one hormone example and one biochemical example (lactose or tryptophan in bacteria) of external factors changing expression	HL only

D2.2.1 Gene expression and phenotype

Gene expression is the process by which the information in a gene has an effect on the phenotype. In the most common pathway there are three stages:

1. Transcription: RNA polymerase makes an mRNA copy of the gene.
2. Translation: a ribosome reads the mRNA and builds a polypeptide.
3. Function of the protein product, for example an enzyme that catalyses a reaction in the cell.

The phenotype is the result of that function. A gene that is never transcribed has no effect, however good its base sequence. Some genes give RNA products that are not translated, but the guide’s emphasis is on the three stages above.

D2.2.2 Regulating transcription

DNA-binding proteins that recognise particular base sequences switch genes on and off.

• A promoter is the DNA sequence next to a gene where RNA polymerase attaches.
• An enhancer is a sequence, often some distance from the gene, where regulatory proteins bind and raise the rate of transcription.
• A transcription factor is a protein that binds a specific sequence (in a promoter or enhancer) and either helps or blocks the attachment of RNA polymerase.

Because each transcription factor recognises its own sequence, a cell can control many genes independently. A cell makes a given protein only if the right transcription factors are present and bound.

Worked example: a hormone-controlled gene

Cells were grown with or without a glucocorticoid hormone (a steroid). Reporter-protein activity was measured (arbitrary units).

Cell type	No hormone	Hormone added
With receptor	15	270
Without receptor	14	16

For cells with the receptor, activity rises 270 / 15 = 18 times, a 1700% increase ((270 − 15) / 15 × 100). Cells without the receptor barely change (14 to 16). So the response needs the receptor, which acts as a transcription factor once the hormone has bound it.

D2.2.3 Degrading mRNA

Translation depends on mRNA being present. Cells therefore regulate protein output by controlling how long mRNA lasts. In human cells mRNA may persist from minutes up to days before nucleases break it down. An mRNA with a short life gives a short burst of protein and lets the cell change quickly. An mRNA with a long life keeps producing protein from one transcript.

mRNA decay is usually described by a half-life: the time for the amount to fall by half.

Worked example: finding a half-life

Transcription of gene X was stopped at time 0 and mRNA was measured.

Time (h)	0	3	6	9	12
mRNA (units)	640	320	160	80	40

The amount halves every 3 hours, so the half-life is 3 h. Another mRNA, with half-life 8 h, has 100 × (1/2)³ = 12.5% left after 24 h (three half-lives). Check: 24 / 8 = 3.

D2.2.4 Epigenesis

Epigenesis is the process by which the cells of a multicellular organism come to follow different patterns of differentiation. Cells from one zygote end up as neurons, muscle fibres, and many other types. The guide stresses that epigenetic changes leave the order of bases untouched. Phenotype changes, genotype does not.

D2.2.5 Genome, transcriptome and proteome

• The genome is all the DNA of a cell. In an organism, nearly all cells carry the same genome.
• The transcriptome is all the mRNA molecules present in a cell at a given time.
• The proteome is all the proteins present in the cell.

Every cell leaves some genes unexpressed, and which genes it does express decides how it differentiates. So genomes are the same but transcriptomes and proteomes differ between cell types.

Worked example: comparing cells

A genome has 20 000 protein-coding genes (data supplied). Transcripts from two cell types were counted.

Cell	Different genes transcribed
Liver cell	9 000
Red blood cell precursor	3 000

Liver: 9 000 / 20 000 × 100 = 45%. Precursor: 3 000 / 20 000 × 100 = 15%. Both cells hold all 20 000 genes (same genome), but the liver cell expresses three times as many. A protein in the proteome also needs translation, and mRNA life (D2.2.3) affects it, so transcriptome and proteome do not match perfectly.

D2.2.6 Epigenetic tags

An epigenetic tag is a chemical group added to DNA or to histone proteins that changes expression without changing the base sequence. DNA is wound round histones in nucleosomes.

• Methylation of cytosine in a promoter represses transcription, so the gene downstream is not expressed.
• Methylation of amino acids in histones can repress or activate transcription, depending on the amino acid and the site. You do not need to know how this works.

Worked example: a methylated promoter

A reporter gene was put under a promoter with different treatments.

Promoter	Reporter activity
Unmethylated	840
Methylated	63
Methylated, then treated with a methyl-removing drug	420

Methylation lowers activity by (840 − 63) / 840 × 100 = 92.5%, or 13.3-fold. Removing methyl groups restores activity to 420 / 840 × 100 = 50% of the unmethylated level, which is 6.7 times the methylated level. This supports a causal role for methylation, because an intervention reversed the effect. The drug restored only part of the activity, so some methyl groups probably remained.

D2.2.7 Epigenetic inheritance

A change in phenotype can be passed to daughter cells or offspring without any change in nucleotide sequence. This can happen if tags, for instance methyl groups on DNA or modified histones, stay attached through mitosis or meiosis. Mitotic inheritance keeps a differentiated cell line stable. Inheritance through meiosis would carry tags to offspring.

D2.2.8 Environmental effects on expression

The environment can change tags and so expression. The guide’s example is that methyl tags on DNA change when people breathe polluted air: studies have linked exposure to pollutants with changed DNA methylation in cells of exposed people. When you evaluate such data, remember that an association does not prove cause, and that people differ in diet, age and smoking.

D2.2.9 Removal of tags and tigons and ligers

Most epigenetic tags are removed from the ovum and sperm, so the zygote starts largely reset. Not all are removed. Some tags marking whether a gene came from the father or the mother remain, and affect which copy is expressed.

Tigons and ligers show this. A liger has a lion father and tiger mother; a tigon has a tiger father and lion mother. The two hybrids differ in phenotype (ligers tend to be larger) even though both inherit one set of chromosomes from each species. A proposed explanation is that the tags kept on some growth-related genes differ between lions and tigers, so a gene is expressed to a different extent depending on which species supplied it and through which parent. Present this as an outline of an epigenetic origin, not a proven mechanism.

D2.2.10 Monozygotic twin studies

Monozygotic twins develop from one zygote and share the same genome. Differences between them, at least in expression, must come from the environment. The guide limits you to environmental effects on gene expression.

Worked example: methylation in twin pairs

Mean difference in methylation at one site between twins in a pair (data supplied):

Age of pairs (years)	3	28	50
Mean difference (percentage points)	2.1	5.4	9.8

From age 3 to 50 the difference rises by 9.8 − 2.1 = 7.7 points, and the 50-year-old pairs differ 9.8 / 2.1 = 4.7 times more. The pattern suggests that identical genomes drift apart in expression as different environments accumulate. These are different groups of twins, not the same twins followed over time, so age is not the only possible factor.

D2.2.11 External factors on expression

The guide limits you to one hormone and one biochemical; lactose or tryptophan in bacteria are suitable choices.

Hormone example. A steroid hormone such as a glucocorticoid enters the cell and binds a receptor. The hormone-receptor complex enters the nucleus, binds a specific sequence and acts as a transcription factor (see the worked example in D2.2.2).

Lactose in bacteria. In E. coli the genes for lactose use lie together and are controlled by a repressor protein. With no lactose, the repressor binds the operator and stops RNA polymerase. When lactose is present, a lactose-derived molecule binds the repressor, which releases the operator, and the genes are transcribed. Tryptophan works the other way: tryptophan binds the repressor and lets it block the genes, so the cell stops making tryptophan when supplied with it.

Worked example: lactose data

β-galactosidase activity (units):

Strain	No lactose	Lactose
Wild type	2	1400
Repressor cannot bind operator	1380	1420

Wild type rises 1400 / 2 = 700-fold with lactose. The mutant is high either way (1420 / 1380 = 1.03, almost no change). So the mutant repressor no longer blocks the operator, and expression no longer depends on lactose.

Common errors

• Writing that epigenetic tags change the DNA sequence.
• Saying all tags are removed from gametes; most, not all, are.
• Calling methylation of histones always repressive; it can activate or repress.
• Saying cells of one organism have different genomes; the transcriptomes differ.
• Treating a correlation between pollution and methylation as proof of cause.

Official syllabus

IB Biology guide, first assessment 2025, International Baccalaureate Organization, section D2.2 Gene expression (additional higher level).