IB DP Biology D2.2 Gene expression Study Notes - New Syllabus -2025
IB DP Biology D2.2 Gene expression Study Notes – New syllabus 2025
IB DP Biology D2.2 Gene expression Study Notes at IITian Academy focus on specific topic and type of questions asked in actual exam. Study Notes focus on IB Biology syllabus with guiding questions of
- How is gene expression changed in a cell?
- How can patterns of gene expression be conserved through inheritance?
Additional higher level: 3 hours
D2.2.1 – Gene Expression: How Genes Affect Phenotype
🧠 Key Concepts: Genotype & Phenotype
Genotype: The genetic information (DNA sequence) an organism has.
Phenotype: The observable physical and functional traits of an organism.
Gene expression: The process that converts genotype into phenotype by producing proteins.
🌿 Stages of Gene Expression
1. Transcription 📝
- A specific gene’s DNA sequence is copied to form messenger RNA (mRNA).
- Uses complementary base pairing: DNA bases guide the RNA sequence.
- mRNA carries the genetic code from the nucleus to ribosomes in the cytoplasm.
2. Translation 🧪
- mRNA is read by ribosomes to build a polypeptide chain (protein).
- The sequence of bases in mRNA determines the order of amino acids in the protein.
- Proteins may be made of one or more polypeptides, sometimes combined with other molecules.
3. Protein Function ⚙️
- Proteins shape the structure and function of cells and organisms.
- Some proteins affect visible traits (e.g., hair color, eye color).
- Many proteins act as enzymes, controlling biochemical reactions that affect phenotype.
🔍 Example: Lactose Digestion
- The enzyme lactase breaks down lactose in milk.
- Lactase production depends on gene expression.
- Without lactase, lactose isn’t digested properly, showing how gene expression affects phenotype.
📌 Gene Expression is Not Simply On or Off
Expression levels can vary; cells can produce different amounts of protein.
This variation influences how strongly a trait is shown.
| Stage | What Happens | Location | Outcome |
|---|---|---|---|
| Transcription | DNA sequence copied to mRNA | Nucleus | mRNA made |
| Translation | mRNA used to build polypeptide | Ribosomes (cytoplasm) | Polypeptide/protein formed |
| Protein Function | Protein acts to affect cell/organism | Various (cell/organelle) | Phenotype expressed |
Gene expression links genotype (DNA) to phenotype (traits).
It includes transcription, translation, and protein function.
Proteins, especially enzymes, carry out most of the effects genes have on organisms.
Expression can vary, affecting trait intensity, not just presence or absence.
D2.2.2 – Regulation of Transcription by DNA-Binding Proteins
🧠 What is Transcription Regulation?
Transcription regulation controls when and how much a gene is transcribed into mRNA.
This is essential to ensure proteins are made only when needed.
🌿 Key Players in Transcription Regulation
| Component | Role |
|---|---|
| Promoters | Specific DNA sequences near the gene where RNA polymerase binds to start transcription. |
| Enhancers | DNA sequences that can be far from the gene, increase the rate of transcription when bound by activator proteins. |
| Transcription Factors | Proteins that bind to promoters or enhancers to help start or regulate transcription. They can act as activators or repressors. |
🔬 How It Works
- RNA polymerase needs help from transcription factors to bind the promoter effectively.
- Activators bind enhancers and increase transcription by helping RNA polymerase.
- Repressors can block transcription by preventing RNA polymerase binding or recruiting other proteins to inhibit transcription.
📌 Why Is This Important?
- Allows cells to produce the right proteins at the right time.
- Enables different cell types to express different genes, despite having the same DNA.
- Essential for development, response to environment, and cell specialization.
Transcription is controlled by proteins binding to promoters, enhancers, and transcription factors.
Promoters start transcription; enhancers boost transcription.
Transcription factors regulate gene expression by activating or repressing transcription.
D2.2.3 – Control of mRNA Degradation as a Means of Regulating Translation
🧠 Why Regulate mRNA Degradation?
- mRNA molecules carry genetic information from DNA to ribosomes for protein synthesis (translation).
- The amount of protein produced depends not just on mRNA made but also on how long mRNA lasts.
- Controlling mRNA lifespan helps regulate how much protein is made.
🌿 How mRNA Degradation Works
- In human cells, mRNA can last anywhere from a few minutes to several days.
- When mRNA is no longer needed, it is broken down by enzymes called nucleases.
Faster degradation → less protein produced
Slower degradation → more protein produced
🔬 Significance of mRNA Stability
Allows cells to quickly adjust protein production in response to environmental or internal signals.
For example, if a protein is only needed temporarily, the cell can degrade its mRNA rapidly.
This adds a fine-tuning control over gene expression after transcription.
mRNA lifespan varies from minutes to days in human cells.
Nucleases break down mRNA to stop translation.
Controlling mRNA degradation is a key way cells regulate protein production.
This mechanism enables dynamic and timely responses in protein synthesis.
D2.2.4 – Epigenesis: Development of Cell Differentiation Patterns
🧠 What is Epigenesis?
- Epigenesis is the process by which cells in a multicellular organism develop different structures and functions.
- Organisms start from undifferentiated cells (like stem cells) that become specialized.
- This development creates the variety of cell types needed for tissues and organs.
🌿 How Does Cell Differentiation Occur?
- Through gene activation and gene silencing – some genes are turned on, others off.
- Controlled by chemical modifications to DNA or histone proteins associated with DNA.
- These modifications are called epigenetic tags.
🔬 Important: Genotype vs Phenotype in Epigenesis
| Aspect | Genotype | Phenotype |
|---|---|---|
| DNA sequence | Unchanged during epigenesis | Expression changes cause different traits |
| Effect of epigenetic tags | None | Alters which genes are expressed, changing cell function and appearance |
Epigenesis creates patterns of cell differentiation from the same DNA.
Regulated by epigenetic tags that switch genes on or off.
DNA sequences stay the same, so only phenotype is changed, not genotype.
D2.2.5 – Differences Between Genome, Transcriptome, and Proteome
🧠 What Are Genome, Transcriptome, and Proteome?
| Term | Definition | Key Points |
|---|---|---|
| Genome | The complete genetic information in a cell (all DNA). | Includes all genes, both coding and non-coding. Every cell of an organism has the same genome. |
| Transcriptome | All the mRNA molecules transcribed from the genome in a particular cell at a specific time. | Not all genes are transcribed at once → transcriptome is a subset of the genome. Changes over time and between cell types. |
| Proteome | The entire set of proteins produced by a cell. | Based on the transcriptome since proteins are made from mRNA. Protein levels do not always match mRNA levels because of additional regulation. |
🌿 Gene Expression and Cell Differentiation
- Cells do not express all their genes – only a specific pattern relevant to their function.
- The pattern of gene expression (which genes are turned on/off) controls how a cell differentiates (specializes).
- Differences in transcriptome and proteome between cells give rise to different cell types.
Genome: full set of DNA in every cell.
Transcriptome: the set of mRNAs produced at a given time – changes with cell type and conditions.
Proteome: proteins made by the cell – depends on transcriptome and regulation after transcription.
The pattern of gene expression determines cell specialization and function.
D2.2.6 – Methylation of Promoters and Histones as Epigenetic Tags
🧠 What Are Epigenetic Tags?
Epigenetic tags are chemical modifications that affect gene expression without changing the DNA sequence.
Two important examples are DNA methylation and histone methylation.
🌿 DNA Methylation
- Methylation means adding a methyl group (–CH₃) to cytosine bases in the promoter region of a gene.
- This represses transcription, meaning the gene is switched off or expressed less.
- The gene downstream of the methylated promoter is not expressed or expressed at a lower level.
🔬 Histone Methylation
- Histones are proteins around which DNA is wrapped (forming nucleosomes).
- Methylation of amino acids in histones can either repress or activate transcription.
- This helps control whether genes are accessible to the transcription machinery.
- Details of how this works are not required to be known.
Methylation of DNA promoters generally switches genes off by stopping transcription.
Methylation of histones can either turn genes on or off, affecting gene accessibility.
Both are key epigenetic mechanisms controlling gene expression without changing DNA sequence.
D2.2.7 – Epigenetic Inheritance: Passing on Gene Expression Changes
🧠 What is Epigenetic Inheritance?
It is the transmission of gene expression changes from one generation of cells (or organisms) to the next without altering the DNA sequence.
This means phenotypic changes can be inherited through mechanisms other than changes in DNA bases.
🌿 How Does It Happen?
- Epigenetic tags like DNA methylation and histone modifications can be maintained through cell division.
- During mitosis (cell division) and sometimes meiosis (formation of gametes), these tags can stay in place.
- Daughter cells or offspring inherit these tags, leading to similar gene expression patterns and phenotypes.
🔬 Why Is This Important?
Allows cells to maintain their identity (e.g., muscle cells remain muscle cells after division).
Can influence traits passed to offspring without DNA mutations.
Provides an additional layer of gene regulation across generations.
Epigenetic inheritance passes gene expression patterns without changing DNA sequence.
Maintained by epigenetic tags like DNA methylation and histone modification.
Explains how phenotypic traits can be inherited beyond classical genetics.
D2.2.8 – Environmental Effects on Gene Expression
🧠 How Environment Affects Gene Expression?
Environmental factors can change gene expression by altering epigenetic tags like DNA methylation.
This means the environment can influence phenotype without changing the DNA sequence.
🌿 Example: Air Pollution and the Epigenome
Air pollution exposes cells to harmful chemicals such as:
- Particulate matter
- Nitrous oxides
- Ozone
- Polycyclic aromatic hydrocarbons (PAHs)
These pollutants can reduce DNA methylation across the genome.
Reduced methylation can lead to changes in gene expression.
🔬 Effects on Health
Changes in gene expression can increase the production of immune system proteins.
This may contribute to diseases linked to inflammation such as:
- Asthma
- Heart disease
During pregnancy, pollution can alter methylation of important genes.
These changes can affect fetal development and early childhood health.
Environmental factors like air pollution can alter gene expression via epigenetic changes.
DNA methylation levels can be reduced, leading to altered gene activity.
This influences immune responses and can increase risk of diseases.
Epigenetic effects can impact development during pregnancy and childhood.
D2.2.9 – Consequences of Removal of Most but Not All Epigenetic Tags from Ovum and Sperm
🧠 Epigenetic Tag Removal in Gametes
- During the formation of sperm and egg cells, about 99% of epigenetic tags (like DNA methylation) are removed.
- However, some epigenetic tags persist and are passed on to offspring.
- This inheritance of epigenetic tags is called genomic imprinting.
🌿 What is Genomic Imprinting?
- In genomic imprinting, one allele of a gene is silenced (imprinted), so only the other allele is expressed.
- This differs from Mendelian inheritance, where both alleles can be active or recessive alleles require two copies to be expressed.
- Example: If the dominant allele is silenced, a recessive mutation can show up.
🔬 Example: Angelman Syndrome
- Normally, a child with one dominant and one recessive allele shows the dominant trait.
- If the father’s allele is imprinted (silenced), only the mother’s recessive allele is expressed.
- This can cause diseases like Angelman syndrome.
🌿 Imprinting in Lion-Tiger Hybrids (Ligers and Tigons)
| Hybrid Type | Parentage | Phenotype (Size) | Reason |
|---|---|---|---|
| Liger | Lion father + Tiger mother | Very large, bigger than both parents | Paternal imprinting favors large size |
| Tigon | Tiger father + Lion mother | Smaller than both parents | Maternal imprinting limits growth |
Lions and tigers imprint genes differently due to evolutionary pressures.
Lions: Male genes promote larger offspring, females limit size for survival.
Tigers: Less competition, so imprinting effects differ.
Most epigenetic tags are erased in gametes, but some remain and cause genomic imprinting.
Imprinting leads to expression of only one allele, affecting phenotype.
This explains differences in size in lion-tiger hybrids (ligers vs tigons).
Shows how epigenetics can influence inheritance beyond DNA sequence.
D2.2.10 – Monozygotic Twin Studies: Effects of Environment on Gene Expression
🧠 Types of Twins
| Type | Formation | Genetic Similarity |
|---|---|---|
| Dizygotic (Fraternal) | Two eggs fertilized separately | Share ~50% of genes |
| Monozygotic (Identical) | Single embryo splits into two individuals | Share 100% identical genes |
🌿 Monozygotic Twin Studies
- Identical twins share exactly the same DNA.
- Differences between them show how the environment affects gene expression and phenotype.
- Studies compare traits, disease susceptibility, and epigenetic changes.
🔬 Why Are These Studies Important?
Help separate genetic influences from environmental influences on traits.
Show that despite identical genes, twins can have different:
– Physical features
– Health conditions
– Behaviors
Differences arise mainly due to environmental effects on gene expression (like diet, lifestyle, pollutants).
Monozygotic twins have identical genomes.
Differences in their traits highlight environmental effects on gene expression.
Twin studies are powerful tools to understand nature vs nurture.
D2.2.11 – External Factors Impacting Gene Expression
🧠 How External Factors Affect Gene Expression
Certain hormones and biochemicals can change which genes are turned on or off.
This controls protein production and cell behavior based on external signals.
🌿 Example 1: Hormone – Insulin
Insulin is a hormone that regulates blood sugar levels.
When insulin is present, it activates genes involved in:
– Glucose uptake
– Glycogen synthesis
This changes the pattern of gene expression to help cells store glucose.
🌿 Example 2: Biochemical – Lactose in Bacteria
In bacteria like E. coli, the presence of lactose turns on genes for enzymes that digest lactose.
The lac operon is switched on only when lactose is available.
If lactose is absent, these genes remain off to save energy.
External factors like hormones and biochemicals can regulate gene expression.
Insulin influences genes for glucose metabolism in humans.
Lactose controls bacterial gene expression via the lac operon.
This regulation allows organisms to adapt to their environment efficiently.