DP Biology HL D1.3 Mutations and Gene Editing

DP Biology HL D1.3 Mutations and Gene Editing - Full notes

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DP Biology HL | D1.3 Mutations and Gene Editing

DP BIOLOGY · THEME D: CONTINUITY AND CHANGE

D1.3

Mutations and Gene Editing

Full notes for HL · IB-style

Contents

1	What mutations are
2	Types of gene mutation
3	Causes of mutation: mutagens
4	Consequences of mutation
5	Mutation as the source of genetic variation
6	Gene knockout and CRISPR-Cas9 gene editing (HL only)
7	Conserved and highly conserved sequences (HL only)
8	Gene mutations defined
9	Base substitutions
10	Insertions and deletions
11	Causes of mutation
12	Randomness of mutations
13	Somatic and germ-line mutations
14	Mutations and cancer
15	Beneficial mutations
16	Gene knockout
17	CRISPR–Cas9 gene editing
18	Ethical issues of gene editing
19	Conserved and highly conserved sequences
20	Mixed review: worked problems
21	Additional exam-style practice
22	Detecting mutations
23	Mutation rate calculations
24	Practical: modelling mutations
25	Repair of DNA
26	Common misconceptions and links
27	Exam-style question with markscheme
28	Check your understanding
29	Summary and topic map

These are full teaching notes. Read each section in order, try the Think about it question before you read on, and do every Quick check before moving to the next section.

Before you start

Rate yourself on each statement now, and again after you've worked through the notes. Shade R (not yet), A (getting there) or G (confident).

I can…	R	A	G
define mutation and distinguish gene and chromosome mutations
explain base substitutions, insertions and deletions and their effects
explain the effects of mutagens such as radiation and chemicals
explain the consequences of mutations in germ cells and somatic cells, including cancer
explain why mutation is the original source of genetic variation
explain gene knockout as a research technique
explain how CRISPR-Cas9 edits genes and evaluate its uses
explain conserved sequences

Sections marked HL only (Sections 6 and 7) are Additional Higher Level content. Every other section is common to SL and HL.

Guiding questions

How do changes in DNA arise, and what are their consequences? How can scientists now change genes deliberately?

How this topic is examined

D1.3 is examined through base sequence exercises (predicting the effect of a substitution or frameshift), data on mutagens, and questions on the consequences of mutations. HL questions include CRISPR and gene knockout.

Be precise: a substitution changes one codon; an insertion or deletion of one base shifts the reading frame.

Command term	What the examiner wants
State / Identify	a brief answer with no explanation needed
Outline	a brief account or summary
Describe	a detailed account, including trends or features, without reasons
Explain	a detailed account including causes, reasons or mechanisms
Distinguish / Compare and contrast	give the differences (and similarities), point by point
Calculate	a numerical answer with working and units
Deduce / Suggest	reach a conclusion from data; propose a reasonable explanation
Evaluate / Discuss	weigh strengths and limitations and reach a judgement

How to use these notes

Each section teaches one part of the syllabus in full. You'll see these boxes throughout; each has one job:

Box	What it's for
Think about it	a question to get you thinking before a section; the answer comes in the section
Key point	the one idea you must not forget
Common mistake	an error examiners see every year, and how to avoid it
In the real world	where the biology shows up outside the classroom
Try this	something quick you can do yourself to test the idea
Worked example	full solutions with IB-style marks (M1 method, A1 answer, R1 reasoning)
Quick check	short questions to test yourself at the end of each section

1 What mutations are

A mutation is a change in the base sequence of DNA.

Think about it

Most mutations are harmless or harmful, yet without mutations evolution could not happen. How can both be true?

A mutation is a change in the base sequence of DNA. Gene mutations affect one or a few bases in a gene. Chromosome mutations affect the structure or number of whole chromosomes, such as the extra chromosome 21 in Down syndrome (A3.1).

Mutations occur randomly: there is no mechanism that directs a mutation to a particular gene or makes beneficial mutations more likely. However, some regions of DNA mutate more often than others (mutation 'hot spots'), and the rate of mutation is increased by mutagens.

2 Types of gene mutation

Substitution, insertion and deletion.

Base substitution: one base is replaced by another. Only one codon changes. The effect depends on the new codon: it may code for the same amino acid (a silent or same-sense mutation, because the code is degenerate); a different amino acid (a missense mutation, which may or may not change the protein's function, as in sickle cell anaemia, D1.2); or a stop codon (a nonsense mutation, producing a shortened, usually non-functional polypeptide).

Insertion or deletion of one or two bases causes a frameshift: the reading frame of the codons is shifted from the point of the mutation onward, so every subsequent codon is changed. This usually produces a completely different, non-functional polypeptide, often with a premature stop codon. Insertion or deletion of three bases adds or removes one amino acid without a frameshift.

Original	THE CAT ATE THE RAT
Substitution	THE CAT ATE THE HAT (one word changed)
Insertion of one base	THE CAA TAT ETH ERA T (everything after shifts)
Deletion of one base	THE CTA TET HER AT (everything after shifts)

WORKED EXAMPLE 1 Predicting the effect of a mutation

An mRNA sequence reads AUG GCU UAC GGA. Using the codons Met (AUG), Ala (GCU), Tyr (UAC), Gly (GGA) and stop (UAA), predict the effect of (a) changing UAC to UAA; (b) deleting the first G of GCU.

Solution

(a) UAC → UAA: Tyr replaced by stop codon: nonsense mutation; polypeptide shortened to Met–AlaA1 R1

(b) Deletion: AUG CUU ACG GA...: every codon after AUG changes: frameshiftA1 R1

Quick check

1. Why can a substitution be silent?

2. Why are frameshift mutations usually more harmful than substitutions?

Answers: 1. the code is degenerate: the new codon may code for the same amino acid 2. they change every codon after the mutation

3 Causes of mutation: mutagens

Some agents increase the mutation rate.

Mutations occur spontaneously, mostly as errors in DNA replication that escape proofreading. Their rate is increased by mutagens: agents that damage DNA.

Radiation: ultraviolet (UV) radiation causes adjacent thymine bases to bond together (thymine dimers), distorting DNA; it is the main cause of skin cancer. Ionizing radiation such as X-rays, gamma rays and radiation from radioactive materials breaks DNA strands. After the Chernobyl nuclear accident in 1986, rates of thyroid cancer rose sharply among children exposed to radioactive iodine.

Chemical mutagens include many substances in tobacco smoke (such as benzopyrene), mustard gas, nitrosamines, some food contaminants such as aflatoxins, and certain chemotherapy drugs. Some viruses (such as HPV) can also cause mutations.

Quick check

1. Define mutagen.

2. How does UV radiation damage DNA?

Answers: 1. an agent that increases the mutation rate 2. forms thymine dimers

4 Consequences of mutation

Where the mutation happens determines who is affected.

Most mutations are neutral (no effect), especially those in non-coding DNA or silent substitutions. Many that do change a protein are harmful, because proteins are finely tuned to their function. A few are beneficial in a particular environment, giving an advantage that natural selection can favour.

Germ-line mutations occur in cells that form gametes. They can be passed to offspring and so to future generations; every cell of the offspring carries the mutation. Inherited diseases such as cystic fibrosis and sickle cell anaemia arise this way.

Somatic mutations occur in body cells. They are not inherited, but are passed to all cells descended from the mutated cell. Somatic mutations in genes that control the cell cycle can lead to cancer: uncontrolled cell division forming a tumour. Two classes of gene are involved: oncogenes (mutated versions of genes that stimulate division, now permanently 'on') and tumour suppressor genes (which normally stop division or trigger repair; mutation removes this brake). Several mutations are usually needed, which is why cancer risk increases with age.

	Germ-line mutation	Somatic mutation
Cells affected	gamete-producing cells	body cells
Inherited?	yes	no
Example consequence	cystic fibrosis in offspring	cancer in the individual

Quick check

1. Distinguish germ-line and somatic mutations.

2. What are oncogenes?

Answers: 1. germ-line: inherited; somatic: not inherited 2. mutated genes that stimulate uncontrolled cell division

5 Mutation as the source of genetic variation

Without mutation there would be no new alleles.

Mutations are the original source of all new alleles, and therefore of genetic variation. Meiosis and fertilization shuffle existing alleles into new combinations (D2.1, D3.2), but only mutation creates new ones.

Genetic variation is essential for evolution by natural selection (D4.1). Most mutations are harmful, but over millions of years and countless individuals, rare beneficial mutations accumulate and drive adaptation: examples include antibiotic resistance in bacteria, lactose tolerance in adult humans, and resistance to malaria in carriers of the sickle cell allele.

Key point

Mutations are random and mostly harmful or neutral, but they supply the raw material for evolution.

6 Gene knockout and CRISPR-Cas9 gene editing (HL only)

Deliberately changing genes to study or treat disease.

HL only

This section is Additional Higher Level content. SL students do not need it.

Gene knockout is a technique used to find the function of a gene by making it inactive and observing the effects. Libraries of knockout organisms (for example, mice, each with a different gene disabled) allow researchers to study genes involved in disease.

CRISPR-Cas9 is a gene-editing system adapted from a natural bacterial defence against viruses. It has two parts: Cas9, an enzyme that cuts both strands of DNA; and a guide RNA with a sequence complementary to the target DNA sequence. The guide RNA leads Cas9 to the exact site in the genome, where it makes a cut. The cell repairs the cut: imperfect repair often disables the gene (knockout); or, if a template DNA is supplied, the cell can insert a corrected or new sequence.

Uses: research into gene function; correcting disease-causing mutations, for example treatments for sickle cell disease and beta-thalassaemia approved in 2023; developing crops with improved traits; and controlling disease vectors such as mosquitoes. Concerns: off-target cuts in the wrong place; editing germ-line cells or embryos, which would affect future generations (the 2018 birth of gene-edited babies in China was widely condemned); and questions of equity and consent.

Figure 1. How CRISPR-Cas9 edits a gene.

7 Conserved and highly conserved sequences (HL only)

Some sequences barely change over evolution.

HL only

This section is Additional Higher Level content. SL students do not need it.

Conserved sequences are base or amino acid sequences that are similar or identical across many species, sometimes across all life. Highly conserved sequences, such as genes for ribosomal RNA, histones and key enzymes of respiration, have barely changed in hundreds of millions of years.

Sequences are conserved because they are functionally essential: almost any mutation in them is harmful and is eliminated by natural selection (purifying selection). Conserved sequences are useful for studying evolutionary relationships between distantly related organisms (A3.2) and help identify important functional regions of genes.

Quick check

1. What do Cas9 and the guide RNA each do?

2. Why are some sequences highly conserved?

Answers: 1. Cas9 cuts DNA; guide RNA directs it to the target sequence 2. mutations in them are harmful and selected against

8 Gene mutations defined

Changes in base sequence.

A gene mutation is a change in the base sequence of DNA. Mutations create new alleles and are the original source of genetic variation. Most are neutral, some harmful, a few beneficial.

WORKED EXAMPLE 2 Definition (basic)

Define gene mutation.

Solution

A change in the base sequence of a geneA1

9 Base substitutions

Single base changes.

A substitution replaces one base with another. It may be silent (same amino acid), missense (different amino acid, e.g. sickle cell: GAG → GTG, glutamic acid → valine) or nonsense (stop codon, producing a shortened protein).

WORKED EXAMPLE 3 Classifying (standard)

Codon UCA (Ser) changes to UCG (Ser), then to UAA (stop). Classify each mutation.

Solution

UCA → UCG: silentA1

UCA → UAA: nonsenseA1

10 Insertions and deletions

Frameshifts.

Inserting or deleting one or two bases shifts the reading frame, changing every codon downstream and usually producing a non-functional protein. Inserting or deleting three bases adds or removes one amino acid without a frameshift.

WORKED EXAMPLE 4 Frameshift (exam level)

Explain why deleting one base usually has a greater effect than a substitution.

Solution

Reading frame shifts after the deletionR1

All downstream codons change; may introduce early stop codonR1

Quick check

1. Why does deleting three bases have a smaller effect than deleting one?

Answers: 1. no frameshift; only one amino acid removed

11 Causes of mutation

Mutagens and errors.

Mutations arise spontaneously (replication errors) or from mutagens: ionizing radiation (X-rays, gamma rays), UV radiation (forms thymine dimers), and chemical mutagens (benzene, chemicals in tobacco smoke, some viruses).

WORKED EXAMPLE 5 UV (standard)

Explain how UV radiation causes mutations.

Solution

Causes adjacent thymines to bond (thymine dimers)R1

Errors during repair or replication alter the sequenceR1

In the real world

Chernobyl and Hiroshima survivors showed increased cancer rates due to mutations caused by ionizing radiation.

12 Randomness of mutations

Not directed by need.

Mutations occur randomly: any base can mutate, and mutation is not directed towards what the organism needs. Some regions (hot spots) mutate more often. Natural selection, not mutation, determines which alleles become common.

Quick check

1. Do bacteria mutate in order to become resistant to antibiotics?

Answers: 1. no: resistance mutations occur randomly; antibiotics select resistant bacteria

13 Somatic and germ-line mutations

Inherited or not.

Somatic mutations occur in body cells and are not passed to offspring, but can cause cancer. Germ-line mutations occur in cells that produce gametes and can be inherited by offspring.

WORKED EXAMPLE 6 Inheritance (standard)

Explain why a mutation in a skin cell is not inherited.

Solution

Skin cells are somatic; they do not produce gametesR1

14 Mutations and cancer

Oncogenes and tumour suppressors.

Cancer results from mutations in genes controlling the cell cycle: proto-oncogenes become oncogenes (stimulating division), and tumour suppressor genes (such as p53) are inactivated. Several mutations are usually needed.

Quick check

1. Why does cancer risk increase with age?

Answers: 1. mutations accumulate over time

15 Beneficial mutations

Raw material for evolution.

Some mutations increase fitness: lactase persistence in adults (dairy-farming populations), the CCR5-Δ32 deletion giving resistance to some HIV strains, and antibiotic resistance in bacteria.

WORKED EXAMPLE 7 Lactase persistence (exam level)

Explain how lactase persistence became common in some populations.

Solution

Mutation allowed lactase production in adultsR1

Advantage in dairy-farming populations: selected and increased in frequencyR1

16 Gene knockout

Finding gene function.

Knockout organisms (often mice) have a specific gene inactivated. Comparing them with normal organisms reveals the gene's function. Knockout libraries exist for many model organisms.

Quick check

1. How can a knockout mouse show a gene's function?

Answers: 1. changes in phenotype reveal what the gene normally does

17 CRISPR–Cas9 gene editing

Precise cuts.

CRISPR–Cas9 uses a guide RNA complementary to a target DNA sequence to direct the Cas9 nuclease, which cuts both strands. Cell repair mechanisms then disable the gene or insert a new sequence. It originated as a bacterial defence against viruses.

WORKED EXAMPLE 8 Mechanism (exam level)

Outline how CRISPR–Cas9 edits a gene.

Solution

Guide RNA binds complementary target sequenceR1

Cas9 cuts the DNA at that siteR1

Repair disrupts the gene or inserts a new sequenceR1

In the real world

In 2023, the first CRISPR-based therapy (Casgevy) was approved to treat sickle cell disease and beta thalassaemia.

18 Ethical issues of gene editing

Somatic versus germ-line.

Somatic gene editing affects only the patient; germ-line editing changes the DNA of embryos and future generations. Concerns include safety (off-target effects), consent of future generations, equity of access, and 'designer babies'.

WORKED EXAMPLE 9 Ethics (exam level)

Discuss germ-line gene editing.

Solution

For: could eliminate inherited diseasesR1

Against: off-target effects; changes inherited; ethical concerns about enhancementR1

19 Conserved and highly conserved sequences

Why some genes barely change.

Some sequences are nearly identical across species (highly conserved), such as genes for histones and ribosomal RNA, because mutations in them are harmful and are removed by natural selection. Conserved sequences are useful for studying evolutionary relationships.

Quick check

1. Why are histone genes highly conserved?

Answers: 1. most mutations disrupt essential functions and are selected against

20 Mixed review: worked problems

Bringing the ideas together.

WORKED EXAMPLE 10 Mixed problem (exam level)

Explain how one base substitution causes sickle cell anaemia.

Solution

GAG → GTG in the β-globin geneR1

Glutamic acid replaced by valineR1

Haemoglobin polymerizes at low O2, distorting red cellsR1

21 Additional exam-style practice

Paper 1 and Paper 2.

WORKED EXAMPLE 11 Paper 1 question (standard)

Which mutation is most likely to cause a frameshift? A. substitution B. insertion of one base C. insertion of three bases D. silent mutation

Solution

BA1

WORKED EXAMPLE 12 Paper 2 question (exam level)

Distinguish between somatic and germ-line mutations.

Solution

Somatic: body cells, not inherited, may cause cancerR1

Germ-line: gametes, inherited by offspringR1

22 Detecting mutations

Sequencing and screening.

DNA sequencing identifies mutations directly; genetic screening tests for specific alleles (BRCA1/2 for breast cancer risk; carrier testing for cystic fibrosis). Results raise issues of privacy and how to act on risk information.

Quick check

1. Give one ethical issue raised by genetic screening.

Answers: 1. privacy/insurance discrimination; anxiety; decisions about pregnancy

23 Mutation rate calculations

How often?

Mutation rate can be expressed per base per generation. Humans have about 60 new mutations per genome per generation (about 1 × 10−8 per base).

WORKED EXAMPLE 13 Estimate (standard)

At 1 × 10−8 per base per generation, how many new mutations in a 3 × 109 base genome?

Solution

3 × 109 × 10−8M1

= 30 per haploid genome (about 60 per diploid)A1

24 Practical: modelling mutations

Sentence analogy.

Writing a sentence with three-letter words (THE CAT SAW THE DOG) and then substituting, inserting or deleting letters shows why frameshift mutations are so damaging.

WORKED EXAMPLE 14 Analogy (standard)

What does regrouping show?

Solution

Every word after the deletion changes (frameshift)R1

Try this

Delete the first E from 'THE CAT SAW THE DOG' and regroup into three-letter words. What happens to the meaning?

25 Repair of DNA

Cells fix damage.

Cells have repair systems: proofreading by DNA polymerase, mismatch repair, and excision repair (removing thymine dimers). Defects in repair genes (such as in xeroderma pigmentosum) greatly increase cancer risk.

Quick check

1. Why do people with defective DNA repair have high skin cancer risk?

Answers: 1. UV damage is not repaired, so mutations accumulate

26 Common misconceptions and links

Students often think…	Actually…
mutations are always harmful	most are neutral; some beneficial
mutagens target specific genes	mutations are random
somatic mutations are inherited	only germ-line mutations are inherited
CRISPR only removes genes	it can disable, correct or insert sequences

How D1.3 connects to the rest of the course

Topic	Connection
D1.2 Protein synthesis	codons and sickle cell
D1.1 Replication	errors and proofreading
D2.1 Cell division	cell cycle control and cancer
D4.1 Natural selection	variation
D3.2 Inheritance	alleles

27 Exam-style question with markscheme

Try this under exam conditions (about 15 minutes) before reading the markscheme.

Figure 2. Mutant bacterial colonies after different UV exposure times (minutes).

(a) Distinguish between a substitution and a frameshift mutation. [2]

(b) Explain why a substitution may have no effect on the protein. [2]

(d) Explain why mutation is important for evolution. [2]

(e) Outline how CRISPR-Cas9 could correct a mutation. [3]

Markscheme

Part	Answer	Marks
(a)	substitution changes one codon	A1
	frameshift (insertion/deletion) changes all following codons	A1
(b)	genetic code degenerate	R1
	new codon codes for same amino acid	R1
(c)	UV forms thymine dimers / damages DNA	R1
	mutations in genes controlling cell division	R1
	uncontrolled division forms tumour	R1
(d)	creates new alleles	R1
	variation for natural selection	R1
(e)	guide RNA complementary to target	R1
	Cas9 cuts DNA at the target	R1
	repair using supplied correct template	R1

Examiner's comments. In (c), the best answers linked damage specifically to genes controlling the cell cycle.

28 Check your understanding

Section A: multiple choice

1. A mutation is

A. a change in the base sequence of DNA B. a change in phenotype only C. always harmful D. an extra chromosome only

2. A frameshift is caused by

A. a substitution B. a silent mutation C. insertion or deletion of one base D. translation

3. A nonsense mutation creates

A. a start codon B. a stop codon C. a silent change D. a frameshift

4. Somatic mutations are

A. always inherited B. only in gametes C. always beneficial D. not passed to offspring

5. UV radiation causes

A. chromosome loss B. thymine dimers C. extra genes D. frameshifts only

6. The original source of new alleles is

A. mutation B. meiosis C. fertilization D. natural selection

7. In CRISPR, the guide RNA

A. cuts DNA B. repairs DNA C. is a protein D. directs Cas9 to the target sequence

Section B: structured

8. Explain the possible effects of a base substitution. [4]

9. Distinguish germ-line and somatic mutations. [3]

10. Explain how mutations can lead to cancer. [3]

11. Evaluate the use of CRISPR-Cas9 in humans. [4]

Answers

1. A 2. C 3. B 4. D 5. B 6. A 7. D

8. Silent (same amino acid), missense (different amino acid, function may change), nonsense (stop codon).

9. Germ-line in gamete-forming cells, inherited; somatic in body cells, not inherited, may cause cancer.

10. Mutations in oncogenes or tumour suppressor genes; loss of cell cycle control; tumour.

11. Treats genetic disease (sickle cell); but off-target effects, germ-line ethics, consent, cost.

29 Summary and topic map

Idea	Remember
Mutation	change in DNA base sequence; random
Substitution	silent, missense, nonsense
Insertion / deletion	frameshift
Mutagens	UV, ionizing radiation, chemicals
Consequences	germ-line inherited; somatic, cancer
Variation	mutation is the source of new alleles
HL	gene knockout; CRISPR-Cas9; conserved sequences

Before the exam, make sure you…

•predict effects using codons
•distinguish germ-line from somatic
•link mutagens to DNA damage
•evaluate gene editing ethically

Mutations and Gene Editing on one page

Cover this page with a sheet of paper and try to rebuild it from memory. Whatever you can't recall is what to revise next.

Figure 3. Topic map for Mutations and Gene Editing.

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