DP IB Biology: HL Your notes

Mutations & Gene Editing

Contents
Gene Mutations
Consequences of Gene Mutations
Mutations & Genetic Variation
Gene Editing
Conserved Sequences

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 Gene Mutations
Your notes
Gene Mutations
A gene mutation is a change in the sequence of base pairs in a DNA molecule; this may
result in a new allele
Mutations occur all the time and at random
There are certain points in the cell cycle when mutations are more likely to occur, for
example, copying errors when DNA is being replicated (S phase of interphase)
As the DNA base sequence determines the sequence of amino acids that make up a
polypeptide, mutations in a gene can sometimes lead to a change in the
polypeptide that the gene codes for
Most mutations are harmful or neutral (have no effect) but some can be beneficial
Inheritance of mutations:
Mutations present in normal body cells are not inherited, they are eliminated from
the population once those cells die
Mutations within gametes are inherited by offspring, possibly causing genetic
disease

Substitution mutations
A mutation that occurs when a nucleotide base in the DNA sequence is randomly
swapped for a different base is known as a substitution mutation
A substitution mutation will only change the amino acid for the triplet (group of three
consecutive bases) where the mutation occurs; it will not have a knock-on
effect further along the gene/polypeptide

Substitution mutation diagram

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 An example of a substitution mutation altering the sequence of amino acids in the
polypeptide
Your notes
Insertion mutations
A mutation that occurs when a nucleotide (with a new base) is randomly inserted into
the DNA sequence is known as an insertion mutation
An insertion mutation changes the amino acid that would have been coded for by the
original base triplet, as it creates a new, different triplet of bases
Remember – every group of three bases in a DNA sequence codes for an amino acid
An insertion mutation also has a knock-on effect by changing the triplets (groups of
three bases) further on in the DNA sequence
This is sometimes known as a frameshift mutation
This may dramatically change the amino acid sequence produced from this gene and
therefore the ability of the polypeptide to function

Insertion mutation diagram

An example of an insertion mutation

Deletion mutations
A mutation that occurs when a nucleotide (and therefore its base) is randomly
deleted from the DNA sequence
Like an insertion mutation, a deletion mutation changes the amino acid that would have
been coded for
Like an insertion mutation, a deletion mutation also has a knock-on effect by changing
the groups of three bases further on in the DNA sequence
Like an insertion mutation, this is sometimes known as a frameshift mutation
This may dramatically change the amino acid sequence produced from this gene and
therefore the ability of the polypeptide to function

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Causes of Gene Mutations
Mutagenic agents are environmental factors that increase the mutation rate of cells Your notes
Radiation can cause chemical changes in DNA, this includes:
High-energy radiation such as UV light
Ionising radiation such as X-rays, gamma rays and alpha particles
Chemical substances can also caused changes to DNA, examples include
Benzo[a]pyrene and nitrosamines found in tobacco smoke
Mustard gas used as a chemical weapon in World War I
Mutagens can also come from inside the cell such as particular enzymes that either
break down DNA or produce substrates that are mutagenic
Some mutations may be produced at random, this can happen most frequently during
DNA replication and repair where errors in the nucleotide sequence are not detected by
the proofreading process carried out by DNA polymerase
If the polymerase detects that a wrong nucleotide has been added, it will remove
and replace the nucleotide before continuing with DNA synthesis
Most mutations do not alter the polypeptide or only alter it slightly so that its structure
or function is not changed
As the genetic code is degenerate (more than one triplet code codes for the same
amino acid) some mutations will not cause a change in the amino acid sequence

Randomness in Mutations
Mutations can occur anywhere in the base sequence of a genome on all chromosomes
in all organisms
This is how new strains of viruses or bacteria can come into existence
Some locations of the genome are more likely to mutate than others
Uncoiled DNA has a higher probability of encountering mutations than DNA tightly
coiled around a histone as it is more exposed
Many mutations occur in non-coding regions of DNA such as satellite DNA
Mutation hotspots are regions where mutations are more frequent. One hotspot is
where the nucleotide cytosine (C) is followed by guanine (G) and is called a CpG site
When methylation occurs here, C can mutate into Thymine (T) in a substitution
mutation
Where this occurs repeatedly it is known as a CpG island and is associated with
particular cancers such as colorectal cancer

Intentional changes to base sequences

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No known mechanisms exist where cells are able to intentionally mutate or change their
DNA base sequence
Your notes
Proofreading processes exist to change a mutation back into its original sequence but
no mechanism exists for making a deliberate change to a base or sequence of bases
with the purpose of changing a trait of the organism

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 Consequences of Gene Mutations
Your notes
Consequences of Base Substitutions
Base substitutions are a mutation that occurs when a base in the DNA sequence is
randomly swapped for a different base
A substitution mutation can only change the amino acid for the triplet in which the
mutation occurs; it will not have a knock-on effect on the rest of the sequence
A base substitution can result in single nucleotide polymorphisms, frequently called
SNPs (pronounced “snips”)
These represent a difference in a single DNA nucleotide. E.g. a SNP may replace the
nucleotide cytosine (C) with the nucleotide thymine (T) in a certain stretch of DNA
SNPs occur normally throughout a person’s DNA
They occur once in every 300 nucleotides on average, which means there are
roughly 10 million SNPs in the human genome
SNPs are commonly found in the non-coding regions of DNA between genes
They can act as biological markers, helping to locate genes that are associated with
disease

The effect of SNPs

Substitution mutations can take three forms which may or may not change the amino
acid of a polypeptide chain:
Silent mutations – the mutation does not alter the amino acid sequence of the
polypeptide (this is because certain codons may code for the same amino acid as
the genetic code is degenerate)
Missense mutations – the mutation alters a single amino acid in the polypeptide
chain (sickle cell anaemia is an example of a disease caused by a single substitution
mutation changing a single amino acid in the sequence)
Nonsense mutations – the mutation creates a premature stop codon (signal for the
cell to stop translation of the mRNA molecule into an amino acid sequence), causing
the polypeptide chain produced to be incomplete and therefore affecting the final
protein structure and function (cystic fibrosis is an example of a disease caused by a
nonsense mutation, although this is not always the only cause)

Consequences of Insertions & Deletions

Insertions and deletions are two types of point mutations, which are mutations that
involve a change in the DNA base sequence at a single location
An insertion occurs when an extra nucleotide is incorporated into the DNA
sequence during replication
A deletion mutation occurs when a nucleotide is missed or absent from the
replicated strand

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 These mutations are often considered more harmful than substitutions, because they
impact on the way the rest of the sequence is read by mRNA or the ribosome
Your notes
Insertions and deletions of nucleotides can also have the effect of a frameshift
mutation
This causes a complete change to the entire amino acid sequence of a protein after the
mutation site and can cause the polypeptide to cease to function
This happens because of the way the translated mRNA is read by the ribosomes
The mRNA is read in codons (groups of 3 nucleotides) so if an additional 1 or 2
nucleotides are added or removed, the sequence is ‘shifted’
The ribosome still reads the sequence of triplet codons along the length of mRNA
which means the entire mRNA and resulting protein are completely different
The result of frameshift mutation means the entire DNA sequence following the mutation
will be incorrectly read. This can result in the addition of the wrong amino acids to the
polypeptide chain and/or the creation of a codon that stops the protein from growing
longer
Although a frameshift mutation during translation is rare (10−5 to 10−7 per codon), the
effects are generally catastrophic for the resulting protein
The same can be said for large insertions and deletions of nucleotides of the DNA
sequence
Consequences of Mutations Diagram

Insertion and deletion mutations can cause a frameshift in the sequence of bases which
can drastically alter the amino acid coded for. The resulting protein may be very different
to the original intended.

Mutations in Germ & Somatic Cells

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 The effect of a mutation can vary depending on whether it occurs in a germ cell or
somatic cell
Your notes
A germ cells use meiosis to produce gametes
Somatic cells use mitosis to produce cells all over the body which can grow into
tissues and organs

Germ cells
If a mutation occurs in a germ cell it can be passed on to the offspring and next
generation
Cells involved in inheritance of genetic information, eggs, sperm and zygote, are
know as the germ line
A mutation that occurs in sperm cells could potentially affect the zygote of that
offspring and all cells developed from that zygote will contain the mutation
A female that has inherited a mutation will contain the mutation in the germ cells of
their ovaries which will be passed onto future offspring

Somatic cells
Somatic cell mutations are not inherited by offspring, instead these mutations are
associated with cancers
Cancers demonstrate how important it is that cell division is precisely controlled, as
cancers arise due to uncontrolled mitosis
Cancerous cells divide repeatedly and uncontrollably, forming a tumour (an irregular
mass of cells)
Cancers start when a mutation occurs in the genes that control cell division
If the mutated gene is one that causes cancer it is referred to as an oncogene
Mutations are common events and don’t lead to cancer most of the time
Most mutations either result in early cell death or result in the cell being destroyed
by the body’s immune system
As most cells can be easily replaced, these events usually have no harmful effect on
the body
The mutations that result in the generation of cancerous cells do not result in early cell
death or in the cell being destroyed by the body’s immune system

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 Mutations & Genetic Variation
Your notes
Mutations & Genetic Variation
Differences exist between organisms of the same species
These differences are known as variation
Examples of variation include:
Coat colour in mammals
Body length in fish
Flower colour in flowering plants
Variation results from small differences in DNA base sequences between individual
organisms within a population
There are several sources of these differences in DNA base sequences:
Mutation
Meiosis
Random fertilisation during sexual reproduction

Mutations
The original source of genetic variation is mutation
Mutation results in the generation of new alleles which can influence evolution of a
species
Mutations that take place in the dividing cells of the sex organs lead to changes in the
alleles of the gametes that are passed on to the next generation
A new allele may be advantageous, disadvantageous or have no apparent effect
An advantageous allele is more likely to be passed on to the next generation
because it increases the chance that an organism will survive and reproduce
A disadvantageous mutation is more likely to die out because an organism with
such a mutation is less likely to survive and reproduce
Mutations in a species are, in the long term, essential for evolution by natural selection
Note that a mutation taking place in a body, or somatic, cell will not be passed on to
successive generations, and so will have no impact on natural selection
Mutation is the only source of variation in asexually reproducing species

NOS: Commercial genetic tests can yield information

about potential future health and disease risk. One

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possible impact is that, without expert interpretation,
this information could be problematic Your notes
There are two types of genetic testing available
Clinical or medical genetic testing
This is carried out through healthcare providers such as doctors, nurse
practitioners, or genetic counselors
Healthcare providers determine which test is needed, order the test from a
laboratory, collect the DNA sample, send the DNA sample to a laboratory for
testing and analysis, and importantly they share the results with the patient
and ensure understanding of the test results and the implications to the
individual and their families
Commercial genetic testing provides genetic tests marketed directly to
customers
The test kits can be bought online or in stores
Customers send the company a DNA sample and receive their results directly
from the genetic company or lab
Commercial genetic testing provides people access to their genetic
information without necessarily involving a healthcare provider
This can pose some problems
Commercially available genetic tests are not scientifically validated and
can give inaccurate results
Unexpected information that a customer receives about their health, family
relationships, or ancestry may be stressful or upsetting
People may make important decisions about disease treatment based on
inaccurate or misunderstood information from their test results
Individuals often are not provided with genetic counseling

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 Gene Editing
Your notes
Investigating Gene Function
The entire set of genetic material of an organism is known as its genome
Biologists now know the entire human genome (they have worked out all the genes that
are found in humans)
The Human Genome Project (completed in 2003) was the name of the international,
collaborative research effort to determine the DNA sequence of the entire human
genome and record every gene in human beings
This was a very important breakthrough but following this scientists now want to know
what each gene codes for and the effect of a gene on an organism; this will help us
better treat and prevent disease

Gene knockout
One way to find out the effect and function of a gene on an organism is to remove it
from the genome or make the gene unusable; this technique is called gene knockout
The organism that has had its genes "knocked out" is called a knockout organism
Common knockout organisms are laboratory mice
Scientists create knockout organisms to study the impact of removing a gene from an
organism, which often allows them to then learn something about that gene's function
This is classed as a genetic engineering technique
A genetic library of knockout organisms exists, such as for the fungal species
Saccharomyces cerevisiae, to
understand the mechanism of action of a drug
target specific biological processes or deficiencies
Conditions that have been studied using gene knockout techniques include
obesity
diabetes
cancer likelihood
addiction
cardiovascular disease

Examiner Tips and Tricks

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 You are not required to know or understand the techniques involved in creating a
knockout organism
Your notes
Gene Editing Techniques
Gene, or genome, editing allows genetic engineers to alter the DNA of organisms
by inserting, deleting or replacing DNA at specific sites in the genome known to cause
disease.
It differs from genetic engineering in that it involves the modification of the existing
DNA of an organism rather than the insertion of DNA from another organism.
Note that the term 'genome' refers to all of the DNA, or genetic information, found
inside a cell.
Gene editing enables the scientists to be more accurate in their manipulation of the
genome
Older gene editing techniques include
Modifying viruses to insert DNA, e.g. into the gene causing a disease
This sometimes resulted in DNA being inserted into other genes causing
unforeseen consequences
Liposomes (small spheres of lipid molecules) containing the normal version of a
gene being sprayed into noses
This was only a short-term solution as the epithelial cells lining the nasal
passageway were short-lived
Today scientists have developed new gene editing techniques, the most commonly
used one being CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats)
This technique involves using the natural defense mechanism bacteria (and some
archaea) have evolved to cut the DNA strands at a specific point as determined by a
guide RNA attached to an enzyme (Cas9)
Once cut scientists can then either insert, delete or replace faulty DNA with normal
DNA
Gene editing is involved in gene therapies (e.g. developing treatments for cystic fibrosis
and sickle cell anaemia).
Gene therapy is the treatment of a genetic disease by altering the person’s
genotype
As scientists learn more about the human genome (from the Human Genome Project)
and the proteome and have the technology to process large quantities of data through
computational biology, they can gain a better understanding of which genes are
responsible for genetic diseases and where they are located,and therefore what base
changes need to occur to treat or cure the disease

Gene editing techniques diagram

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 Your notes

CRISPR is an example of a gene editing technique

Examiner Tips and Tricks

You are not required to know the role of the CRISPR–Cas system in prokaryotes.
However, you should be familiar with an example of the successful use of this
technology.

NOS: Certain potential uses of CRISPR raise ethical

issues that must be addressed before implementation
Genetic engineering practices raise a number of ethical issues that need to be
considered
Issues may arise around consent for genetic data
Insurance companies may require data on genetic testing results
The need for legal control over how data is used, particularly data involving human
genomes
Fortunately, decisions based on the morality of genetic engineering tend to be made on
a worldwide scale
Ethics committees exist which must approve all experiments carried out and they gain
advice and guidance from world-leading experts

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Countries have their laws in place to protect participants in genetic technology
research
Your notes
International committees have been formed to discuss and debate the issues raised
and make recommendations to governments, and scientists so that any policies made
have considered the ethics involved
One such committee is The International Commission on the Clinical Use of Human
Germline Genome Editing
The World Health Organisation (WHO) plays an important role in creating guidance for
best practices and issue guidelines
The challenge is to ensure that all policymakers and countries work together to
coordinate regulations
These international regulations are applied to all gene editing processes including
CRISPR

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 Conserved Sequences
Your notes
Conserved Sequences
A conserved sequence is a section of DNA or RNA that shows minimal mutations over
time
A conserved sequence tends to be identical or similar across a species or a group of
species
Sequences that show little to no mutations over long periods of evolution are called
highly conserved sequences
Examples of such sequences include those that lead to DNA replication, transcription
and translation, and proteins involved in cellular respiration
Sequences for DNA helicases, tRNA and ribosomes
Sequences for the respiratory proteins cytochrome c and ferredoxin
A number of hypotheses exist for the mechanisms that lead to conserved sequences
and high conserved sequences
One is that the functional requirements of the gene are those that the organism
cannot survive without
The other is that some sequences of DNA are subject to slower mutation rates

Functional requirements
Conserved sequences and highly conserved sequences exist within genes that code
for proteins that are essential for an organism's survival such as transcription and
translation
If these processes were unable to take place, due to mutations in the genes that code
for essential proteins, then the cell would cease to survive
Therefore the functional requirements of the cell maintain the conserved sequence
and minimise mutations, as any mutations created would not be passed on to future
generations
We can hypothesise that natural selection maintains conserved sequences by
necessity and and does not let any mutations pass to future generations

Slower mutation rates

This hypothesis suggests that certain sections of gene sequences are less prone to
mutations and the mutation rate is much slower than in other areas of the genome
Mutation rate is how many changes there is to the DNA sequence over time
It can be measured as
The number of base pair changes in a single gene at each generation or cell
division

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 Or, the number of base pair changes in the whole genome per generation
DNA repair and proofreading mechanisms are very active in coding regions of the
genome, and within genes that have high functionality Your notes
It is thought that areas where there are lower mutation rates do not have lower
mutation but that they are spotted and corrected more frequently and so do
not show up in sequenced DNA
Error correcting and proofreading is less active in areas of non-coding DNA so here
higher rates of mutation are found

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