IB DP Biology D1.3 Mutations and gene editing Study Notes - New Syllabus -2025
IB DP Biology D1.3 Mutations and gene editing Study Notes – New syllabus 2025
IB DP Biology D1.3 Mutations and gene editing 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 do gene mutations occur?
- What are the consequences of gene mutation?
Standard level and higher level: 3 hours
Additional higher level: 2 hours
D1.3.1 – Gene Mutations: Structural Changes at Molecular Level
🧬 What Is a Gene Mutation?
A random change in the base sequence of a gene.
Different from intentional gene editing by scientists.
🌿 Types of Gene Mutations
| Type | Description | Effect on DNA |
|---|---|---|
| Substitution | One base replaced by another (e.g., G → T) | Single base change |
| Insertion | Extra base added into the sequence | Adds nucleotide, can shift reading frame |
| Deletion | Base removed from the sequence | Removes nucleotide, can shift reading frame |
📌 Key Points
- Insertions and deletions require breaks in DNA backbone.
- Multiple bases can be inserted/deleted at once.
- Mutations can affect gene function by altering protein sequences.
🧠 Summary Box:
Mutations = random base changes: substitution, insertion, deletion.
Can cause serious effects if they alter protein coding.
Mutations = random base changes: substitution, insertion, deletion.
Can cause serious effects if they alter protein coding.
D1.3.2 – Consequences of Base Substitutions
🧬 What Are Base Substitutions?
- A base substitution is when one nucleotide in DNA is replaced by another.
- When inherited, these are called single-nucleotide polymorphisms (SNPs).
- SNPs increase genetic diversity but may or may not affect protein function.
🌿 Effects of Base Substitutions
| Type of Mutation | Effect on Protein | Possible Outcome |
|---|---|---|
| Same-sense (Silent) | Codon changes but codes for same amino acid (due to genetic code degeneracy) | No change in protein function |
| Mis-sense | Codon changes and codes for different amino acid | May alter protein function—effects range from harmless to severe (e.g., sickle cell disease) |
| Nonsense | Codon changes to a stop codon | Early termination; incomplete, usually nonfunctional protein |
📌 Important Points
- Substitutions in non-coding DNA usually have no effect.
- Most base substitutions are neutral or harmful; beneficial ones are rare but drive evolution.
- SNPs can occur anywhere and some are linked to genetic diseases.
- Scientists use SNP patterns to predict genetic predispositions to diseases.
🧠 Summary Box:
Base substitutions can be silent, missense, or nonsense.
Only those affecting coding sequences change amino acid sequences.
SNPs are inherited substitutions contributing to genetic variation.
Effects range from no impact to disease-causing or rarely beneficial.
Base substitutions can be silent, missense, or nonsense.
Only those affecting coding sequences change amino acid sequences.
SNPs are inherited substitutions contributing to genetic variation.
Effects range from no impact to disease-causing or rarely beneficial.
D1.3.3 – Consequences of Insertions and Deletions
🧬 What Are Insertions and Deletions?
Insertions: Addition of one or more nucleotides into the DNA sequence.
Deletions: Removal of one or more nucleotides from the DNA sequence.
🌿 Effects on Polypeptides
| Type of Insertion/Deletion | Effect on Polypeptide |
|---|---|
| Frameshift mutations (1 or 2 nucleotides) | Shift the reading frame of codons during translation, changing every amino acid after the mutation; usually causes a nonfunctional protein. |
| Insertion/deletion of multiple of 3 nucleotides | Does not shift the reading frame but adds or removes whole amino acids; can cause major structural changes and affect protein function severely. |
| Major insertions or deletions | Usually cause the polypeptide to lose function completely due to large disruption in protein structure or sequence. |
📌 Key Points
- Insertions and deletions are generally more harmful than substitutions.
- Even small frameshift mutations can destroy protein function.
- Changes not causing frameshifts (multiples of three) can still have serious effects by altering protein shape.
🧠 Summary Box: Key Takeaway
Insertions and deletions often lead to nonfunctional proteins by either shifting the reading frame or altering amino acid sequence drastically.
These mutations usually have severe or lethal consequences for protein activity.
Insertions and deletions often lead to nonfunctional proteins by either shifting the reading frame or altering amino acid sequence drastically.
These mutations usually have severe or lethal consequences for protein activity.
D1.3.4 – Causes of Gene Mutation
🧬 What Causes Gene Mutations?
Gene mutations happen randomly, but DNA is generally stable.
Mutation rate increases during DNA replication due to occasional base-pairing errors that may not get fixed.
External factors called mutagens increase mutation rates.
🌿 Types of Mutagens
| Mutagen Type | Description | Examples |
|---|---|---|
| Radiation | High-energy radiation causes chemical changes in DNA | Gamma rays, X-rays, alpha particles (from radioactive radon), short-wave UV radiation (sunlight) |
| Chemical Mutagens | Chemicals that chemically alter DNA bases or cause breaks | Polycyclic aromatic hydrocarbons, nitrosamines (in tobacco smoke), mustard gas |
📌 Key Points
- Mutagens increase mutation frequency, raising risk of harmful mutations.
- Mutations can also result from errors in DNA replication or repair.
- Understanding mutagens helps explain causes of genetic diseases and cancer.
🧠 Summary Box:
Gene mutations arise naturally but are increased by mutagens both radiation and chemicals.
DNA replication errors and faulty repair also cause mutations.
Examples of mutagens include UV light, X-rays, tobacco smoke chemicals, and mustard gas.
Gene mutations arise naturally but are increased by mutagens both radiation and chemicals.
DNA replication errors and faulty repair also cause mutations.
Examples of mutagens include UV light, X-rays, tobacco smoke chemicals, and mustard gas.
D1.3.5 – Randomness in Mutation
🧬 Key Features of Mutations
- Mutations are random, unpredictable changes in DNA.
- Organisms cannot direct mutations to create beneficial traits.
- The chance a mutation happens is independent of its effects whether harmful, neutral, or beneficial.
🌿 Where Do Mutations Occur?
- Mutations can happen anywhere in the genome.
- Some bases or positions have a higher probability of mutating than others.
- DNA regions (coding vs. non-coding) differ in mutation likelihood due to their usage and structure.
📌 Important Points
- There is no natural mechanism that purposefully changes a specific base to improve traits.
- Beneficial mutations are rare; most are neutral or harmful.
- Mutations in somatic cells affect only the individual and are not inherited.
- Mutations in germ-line cells (gametes) can be passed on but are not tested or “filtered” before inheritance.
🧠 Summary Box:
Mutations occur randomly without intent or direction.
Their randomness means most are neutral or harmful; beneficial mutations are exceptions.
Only mutations in germ cells are inherited, but there is no mechanism to test or select beneficial mutations during an organism’s life.
Mutations occur randomly without intent or direction.
Their randomness means most are neutral or harmful; beneficial mutations are exceptions.
Only mutations in germ cells are inherited, but there is no mechanism to test or select beneficial mutations during an organism’s life.
D1.3.6 – Consequences of Mutation in Germ Cells and Somatic Cells
🧬 Mutations in Germ Cells
- Occur in cells that produce gametes (sperm and eggs).
- Can be passed on to offspring as new alleles.
- These inherited mutations may:
- Provide a beneficial trait (rare).
- Cause genetic diseases (more common).
- Important to minimize mutations in germ cells to prevent inherited disorders.
🌿 Mutations in Somatic Cells
- Occur in body cells other than gametes.
- Are not inherited by offspring.
- Usually have limited effects; damaged cells can be replaced.
- Can cause cancer if mutations affect proto-oncogenes:
• Proto-oncogenes control normal cell division.
• Mutation converts them into oncogenes which cause uncontrolled cell growth.
• Leads to tumor formation and cancer.
📌 Key Points
| Cell Type | Mutation Effect | Inheritance | Example Outcome |
|---|---|---|---|
| Germ cells | New alleles passed to offspring | Yes | Genetic diseases or rare benefits |
| Somatic cells | Affects only individual cells | No | Cancer, cell death, tissue repair |
🧠 Summary Box:
Mutations in germ cells affect future generations.
Mutations in somatic cells affect only the individual, often causing cancer.
Cancer results from mutations in genes controlling the cell cycle.
Mutations in germ cells affect future generations.
Mutations in somatic cells affect only the individual, often causing cancer.
Cancer results from mutations in genes controlling the cell cycle.
D1.3.7 – Mutation as a Source of Genetic Variation
🧬 What Are Alleles?
An allele is a different version of a gene.
Alleles differ because of changes in the DNA base sequence.
🌿 How Does Mutation Create Genetic Variation?
- A mutation is a change in the base sequence of a gene.
- Mutation creates new alleles by altering existing ones.
- This is the original source of all genetic variation in populations.
📌 Genetic Variation and Evolution
- Genetic variation is increased by:
- Mutations (new alleles)
- Meiosis and sexual reproduction (mixing alleles)
- Natural selection depends on genetic variation — without it, evolution can’t happen.
- Variation allows populations to adapt to changing environments.
🌱 Why Is Mutation Important?
- Most mutations are neutral or harmful to individuals.
- However, some mutations provide useful traits that improve survival or reproduction.
- Without mutations:
• Genetic diversity would decline over generations.
• Populations would lose the ability to evolve.
• Species risk extinction when environments change.
📊 Real-World Note: Genetic Testing
Commercial genetic tests reveal risks for diseases.
But without expert advice, interpreting this data can be confusing or misleading.
🧠 Summary Box:
Mutation is the starting point for genetic variation by creating new alleles.
Genetic variation fuels natural selection and evolution.
Mutation is essential for species to adapt and survive environmental changes.
Loss of mutation-driven variation can lead to extinction.
Mutation is the starting point for genetic variation by creating new alleles.
Genetic variation fuels natural selection and evolution.
Mutation is essential for species to adapt and survive environmental changes.
Loss of mutation-driven variation can lead to extinction.
Additional Higher Level
D1.3.8 – Gene Knockout: Investigating Gene Function by Making Genes Inoperative
🧬 What Is Gene Knockout?
A technique used to study the function of a gene by deliberately making it nonfunctional (inoperative).
Helps scientists understand what traits or processes a gene controls.
🌿 How Does Gene Knockout Work?
- A gene is replaced or disabled in the genome of an organism.
- Resulting organisms lack a working copy of that gene – called knockout organisms.
- By observing the changes (phenotype), researchers can infer the gene’s role.
📌 Model Organisms and Knockout Libraries
- Widely used in model species like mice and yeast.
- There are libraries of knockout organisms available for many genes in some species.
- Example:
- Piezo2-knockout mice urinate less often, showing the gene’s role in bladder pressure sensing.
- Humans missing PIEZO2 have similar bladder control issues.
🧠 Why Is Gene Knockout Important?
Helps identify gene functions when unknown.
Powerful for studying genetic diseases.
Enables targeted research on how specific genes affect traits.
🧠 Summary Box:
Gene knockout is a research tool that disables a gene to reveal its function.
Knockout organisms are key for understanding gene roles and disease mechanisms.
Libraries of knockouts speed up genetic research in model species.
Gene knockout is a research tool that disables a gene to reveal its function.
Knockout organisms are key for understanding gene roles and disease mechanisms.
Libraries of knockouts speed up genetic research in model species.
D1.3.9 – Use of CRISPR Sequences and Cas9 in Gene Editing
🧬 What Is CRISPR-Cas9?
- CRISPR stands for Clustered, Regularly Interspaced, Short Palindromic Repeats.
- It’s a natural system found in many prokaryotes used to cut DNA at specific sites.
The system includes:
- CRISPR regions in the genome (repeats + unique spacers).
- The enzyme Cas9, which cuts DNA guided by RNA.
🌿 How CRISPR-Cas9 Works
- Guide RNA (gRNA) directs Cas9 to the target DNA sequence.
- Cas9 makes a two-strand break at the target site.
- This allows scientists to edit genes by cutting and replacing DNA sequences (“search and replace”).
📌 Gene Editing Process Using CRISPR-Cas9
| Step | Description |
|---|---|
| 1. Guide RNA binds Cas9 | The gRNA binds Cas9 and leads it to the matching DNA sequence. |
| 2. Cas9 locates target DNA | Cas9 moves along DNA to find the sequence complementary to gRNA. |
| 3. DNA cut | Cas9 cuts both DNA strands at the target location, creating a break. |
| 4. DNA repair & editing | The cell repairs the break, allowing insertion, deletion, or replacement of DNA sequences. |
🌱 Prime Editing (Advanced CRISPR Technique)
Uses a modified Cas9 enzyme linked to reverse transcriptase.
Employs a prime editing guide RNA (pegRNA) with:
- Guide sequence for target binding.
- Primer binding site.
- RNA template for new DNA sequence.
- Cas9 nicks one DNA strand, and reverse transcriptase writes new DNA using the RNA template.
- This enables precise DNA changes without double-strand breaks.
🧠 Applications and Ethical Considerations
CRISPR is a powerful tool to:
- Edit genes in crops, animals, and humans.
- Potentially treat genetic diseases.
- Raises ethical issues about gene editing, especially in humans.
- Regulatory systems vary globally, prompting efforts for international harmonization of genome editing rules.
🧠 Summary Box:
CRISPR-Cas9 enables precise, targeted gene editing using guide RNA and Cas9 enzyme.
Prime editing improves precision by using a modified enzyme to add new DNA sequences.
This technology is revolutionizing genetics but requires careful ethical and regulatory oversight worldwide.
CRISPR-Cas9 enables precise, targeted gene editing using guide RNA and Cas9 enzyme.
Prime editing improves precision by using a modified enzyme to add new DNA sequences.
This technology is revolutionizing genetics but requires careful ethical and regulatory oversight worldwide.
D1.3.10 – Hypotheses for Conserved or Highly Conserved Sequences in Genes
🧬 What Are Conserved Sequences?
Conserved sequences are DNA sequences that are identical or very similar across species or groups of species.
Highly conserved sequences remain unchanged or very similar over long evolutionary times, spanning many species, often across whole classes like mammals or vertebrates.
🌿 Where Are Conserved Sequences Found?
- In protein-coding genes.
- In regions producing ribosomal RNA (rRNA) or transfer RNA (tRNA).
- In sequences regulating gene expression.
📌 Hypothesis 1: Functional Importance
- These sequences code for essential gene products or regulate important functions.
- Because these functions are crucial, natural selection preserves these sequences.
- Even as species evolve, these sequences remain largely unchanged.
- Example: Some genes conserved across all mammals or vertebrates.
🌱 Conserved Non-Coding Elements
- These are conserved DNA regions that do not code for proteins.
- Their function is less clear but conservation suggests important roles.
- They may be involved in gene regulation or other vital processes.
🧠 Hypothesis 2: Low Mutation Rate Regions
- Some conserved sequences might appear conserved because they are in genome regions with naturally lower mutation rates.
- These sequences may change less due to fewer mutations, not necessarily due to functional constraints.
📊 Example: HACNS1 Gene
- Contains 546 base pairs.
- Highly conserved in many birds and mammals for hundreds of millions of years.
- Shows rapid changes in human evolution, possibly linked to unique human traits.
- Suggests conserved sequences can evolve when advantageous.
| Hypothesis | Explanation | Key Point |
|---|---|---|
| Functional Constraint | Important gene functions preserve sequences | Natural selection maintains sequences |
| Low Mutation Rates | Some sequences conserved due to fewer mutations | Conservation not always functional |
🧠 Key Takeaway:
Conserved sequences either reflect essential biological functions or lie in genome regions with fewer mutations.
Understanding conservation helps reveal gene importance and evolutionary history.
Conserved sequences either reflect essential biological functions or lie in genome regions with fewer mutations.
Understanding conservation helps reveal gene importance and evolutionary history.