1.3 Genome: (b) i Point mutations: nucleotide substitution, insertion and deletion

(b) Mutation Mutations are random changes in the genome. Mutations can alter alleles, genes, gene expression or chromosomes.

(i) Point mutations: nucleotide substitution, insertion and deletion

Mutation within genes and impact on protein structure. Regulatory sequence mutations can alter gene expression. Splice site mutations can alter post-transcriptional processing. Importance of point mutation in evolution.

MUTATIONS

A mutation is defined as a change in the structure or quantity of genetic material in an organism. Mutations are:

Spontaneous Random Rare events

BAD:Most mutations are harmful.

GOOD:1. Mutations result in the variations that create a heterozygous genotype

and allow a population to adapt to a changing environment. 2. Harmful mutations tend to be eliminated from a population by natural

selection against them. 3. Most mutations are recessive and are therefore not expressed until two

occur together in the homozygous recessive individual. When such a change occurs and the individual expresses the mutation in the phenotype that individual is known as a mutant.

The rate at which mutations occur can be increased by using mutagenic agents.

Examples of mutagenic agents:

Certain chemicals e.g. lead oxide, mustard gas Radiation e.g. UV-light, x-rays and gamma rays.

Experiment: Aim to compare the germination of cress seeds or growth of yeast cultures in response to mutagenic agents

Types of MutationsThere are 3 types of mutations. These are:

Gene Mutations/point mutations. Changes in the chromosome number Changes in the structure of one chromosome

Gene mutations (point mutations)

Gene mutations involve a change in one or more nucleotides on one DNA strand, which change gene structure.

One amino acid change can have a huge effect on the protein shape. In the following messages each letter represents a nucleotide.

This shows the normal order of the bases for one of the strands in the area highlighted in the DNA molecule.

Only one DNA strands is involved in protein synthesis. A change from the normal order of bases leads to different types of gene mutation.

Substitution: One base out and another swapped in.

Insertion: One base added in to the sequence causes a frame shift.

Deletion: One base is deleted from the sequence causing a frame shift

Inversion: Two bases swap position with the base immediately adjacent

Sometimes the point mutation only affects one gene e.g. Substitution and Inversion. The effects are less lethal

as there is more than one gene for each amino acid. Therefore the effects only show in the phenotype if theoriginal sequence was for an essential amino acid.

Example: Sickle cell anaemia

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The diagram above shows the difference in the synthesis of haemoglobin in normal DNA and abnormal DNA. The top strand shows the normal DNA, mRNA and amino acid sequences.

A single substitution mutation has changed the base sequence in the DNA. The base sequence on the mRNA produced by the DNA is altered.

As a result, a codon on the mRNA is altered. A different amino acid is inserted into the protein chain. The amino acid valine is inserted instead of glutamic acid, which is shown by the bottom strand of DNA. The protein synthesised is altered and no longer functions normally. These sequences result in sickle-shaped red blood cells. This blood disorder is known as sickle cell anaemia.

Phenylketonuria

The diagram represents part of the normal metabolic pathway involving the amino acid phenylalanine within human cells. The gene controls the synthesis of the enzyme and the enzyme converts the amino acid phenylalanine to tyrosine.

If a gene mutation occurs then individuals with this mutation can no longer produce the normal enzyme. This in turn means that they can no longer convert phenylalanine to tyrosine. The failure to bring about the normal enzyme conversion is called a metabolic block.

In newly born babies this metabolic block leads to the condition phenylketonuria (PKU). The effects of the condition if undetected and treated at birth are that:

phenylalanine concentration builds up within the body of the new born baby phenylaline is converted into toxic substances the toxic substances cause irreversible damage to the developing brain

FRAMESHIFTDue to the triplet nature of gene expression by codons, the insertion or deletion can result in a FRAMESHIFT. A frameshift is a change in the reading frame (the grouping of the codons). This means all of the triplet sequences after the mutation are changed resulting in a completely different translation from the original. Mutations resulting in a frame shift are lethal.

Results of frameshift: 1. The earlier in the sequence the deletion or insertion occurs, the more altered the protein.2. The reading of the codons after the mutation to code for different amino acids. 3. The first stop codon ("UAA", "UGA" or "UAG") encountered in the sequence could be altered. 4. The polypeptide being created could be abnormally short or abnormally long, and will not be functional.

Frameshift mutations are apparent in severe genetic diseases such as Cystic Fibrosis; they increase susceptibility to certain cancers.

QUESTIONS

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1. Complete the following diagram on the next page by inserting the appropriate letters (normal and mutant mRNA).

Normal Mutant

Transcription

b. Complete the following sentence:The example of a gene mutation, shown above, is called ________________. It is where one

_________________ is replaced by a different _________________.

c. How will this mutation affect the protein molecule produced?2. Complete the diagram by inserting the normal and mutant mRNA and add in the names of amino acids made (use the wheel diagram in your notes).

Normal Mutant

a) Complete the following sentence:

The example of a gene mutation, shown above, is called gene ________________.

It is where _____________________________________.

b) What effect does this mutation have on the amino acids in the protein molecule?

3. Complete the diagram by inserting the normal and mutant mRNA and add in the names of amino acids made:

Normal Mutant

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A G A G T C G G G G A T A G A T G C G G G G A T

DNAA

mRNAAA

AminoAcids

Transcription

Translation

C T T C A T

Glutamic acid

new amino acidAmino Acids

Translation

mRNA

DNA

Substituted nucleotide

A G A G T C G G G G A TDNAA

Transcription

a) Complete the following sentence:

The example of a gene mutation, shown above, is called gene ________________.

It is where _____________________________________.

b) What effect does this mutation have on the amino acids in the protein molecule?

4. Complete the diagram by inserting the normal and mutant mRNA and add in the names of amino acids made:

Normal Mutant

a) Complete the following sentence:

The example of a gene mutation, shown above, is called gene ________________.

It is where _____________________________________.- 5 -

A G A G T T C G G G G A

mRNAAAAminoAcids

Translation

A G A G T C G G G G A T A G A T C G G G G A T G DNAA

mRNAAA

AminoAcids

Transcription

Translation

b) What effect does this mutation have on the amino acids in the protein molecule?

Learning objectivesThe three types of mutations you need to know about are nucleotide substitution, insertion and deletion. By completing this exercise you should understand how these mutations affect protein structure.

This exercise uses the analogy of simple text to show you how different types of point mutations can impact on the final product: in this example it is if the sentence makes sense rather than the structure of a protein that is being examined.

Copy out the following three examples of text. Each word represents a triplet of bases, or codon, which codes for a different amino acid. To help you visualise the protein coding sequence the codons have been placed in a table, or reading frame. The part of the gene that codes for protein is referred to as the open reading frame.

Example 1Original the old man ran for the red busMutation The olb dma nra nfo rth ere dbus

Example 2Original the old man ran for the red busMutation the olm anr anf ort her edb us

Example 3Original the old man ran for the red busMutation The old nan ran for the red bus

1. For each example highlight or circle where the mutation has occurred.

2. For each example say whether it is a substitution, deletion and insertion.

3. Explain which has the greatest effect on the meaning of the sentence (or which would have the greatest effect on the final protein sequence).

4. Which mutations are frame-shift mutations? Explain why.

In a real gene there are potentially a number of regulatory sequences of DNA and possibly several exons on a chromosome that could be damaged, or changed, by a mutation. Post transcription there could be failure of exons to be correctly spliced, with huge consequences on the translation of the mRNA.

If a lethal or very damaging mutation occurs then the mutation will be removed from the gene pool or the chances of the mutated gene being reproduced will be less than that of the gene from an unaffected individual. In other words, essential genes and their expression are under stiff selection pressure to remain functional, hence they are conserved within a species and across species.

5. Explain why most single nucleotide polymorphisms, or point mutations, are found within …..non-coding regions of the genome.

Research-based extension task

Within a DNA sequence several different codons can code for the same amino acid so a single base substitution may not result in the amino acid being changed, ie the protein would be normal. This is known as a silent mutation.

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A substitution may result in only one amino acid being changed without any major effects on the protein structure and hence function. However, if the mutation occurs at a critical point in the sequence, an amino acid vital in determining the proteins shape will no longer stabilise the protein and it will lose its function. This is a missense mutation.

Nonsense mutations introduce a stop codon early in the sequence, resulting in a shortened, usually non-functional, protein.

Mutations which do not have any effect on the protein’s function are also known as neutral mutations.

1. Can you find real-life examples of genetic disorders caused by missense, nonsense or frame -shift point mutations?

2. What is the frequency of these mutations?3. Are any of the mutations confined to a specific area or ethnic race?4. What are the symptoms associated with each mutation?5. Are any of the mutations beneficial or are they detrimental?

Look at this video clip: Embryo hope for inherited diseases: http://news.bbc.co.uk/1/hi/health/8621046.stm

Chromosome Mutations

Chromosome mutations involve the change in the structure of one chromosome; they involve a change in the number or sequence of genes in a chromosome.

The following are 4 types of chromosome mutations:1. Inversions2. Deletions3. Translocations4. Duplications.

Table summarising chromosome mutations. Each gene on a chromosome is given a letter or number.

Normal chromosome Mutation type Altered chromosome Effects

12345678

Deletion 1234678Gene 5 is missing Terminal

or harmfulTranslocation 12345678 + ABCDE = 12345 + ABCDE678

One section of chromosome joins to another chromosome

Inversion12543678

A segment of chromosome breaks off, turns around and joins again May be

beneficialDuplication 1234565678

Sets of genes become repeated

EXAMPLES OF CHROMOSOME STRUCTURE MUTATIONS:- 7 -

Sickle cells

Red blood cells

Present your results in the form of a spider diagram. In the centre of the page put a short appropriate title. Use colours to group information around the title. Each outer branch should have at least one diagram. Do not cut and paste text – write in your own words.

Why not start with sickle-cell trait?

1. Deletion on chromosome 5: results in Cri du Chat Syndrome: Symptoms: Severe learning difficulties, small head, widely spaced eyes and distinctive cry

2. Translocation: Results in problems during gamete formation, resulting in non-viable gametes or cancer

3. Duplication: - Formation of the 4 sub-units of haemoglobinNew DNA sequences means increased selective advantage.

4. Inversion: Results in problems during gamete formation, resulting in viable offspring which may have benificail characteristics

QUESTIONS ON CHROMOSOME MUTATIONS

Each of the diagrams, represent a type of chromosome mutation. For each, name the type of mutation and briefly describe what has happened.

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MUTATION TYPE:____________________________________________________________

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MUTATION TYPE:____________________________________________________________

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MUTATION TYPE:____________________________________________________________

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MUTATION TYPE:____________________________________________________________

___________________________________________

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_____________________________

Chromosome mutations-1. Change in the structure of a chromosome due to a change in the number/order of the genes i.e

translocation, inversion, duplication and deletion (TIDD)2. Can be a change in chromosome number due to spindle failure during meiosis.

Changes in the number of chromosomes within a cell

Normally during meiosis (gamete formation), homologous chromosomes come together and then segregate into separate cells. The gametes therefore end up with one of each type of chromosome.

Non-Disjunction

This is a chromosome mutation caused by spindle failure.Non-disjunction results in the addition or loss of one or more chromosome.

Changes in chromosome number occur when the spindle fibres fail to form properly which prevents the separation of the chromosomes during meiosis. This may effect one chromosome e.g. Down's Syndrome, or may be complete spindle failure as seen in polyploid plants. Failure of spindle formation is called non-disjunction.

Label the diagrams show the difference between normal meiosis and meiosis where non-disjunction has occurred.

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Normal meiosis

Non-disjunction

DISEASE EXAMPLE: 1 Down's syndrome

Down's Syndrome is due to non disjunction resulting in an individual with an extra chromosome 21. The affected individual is mentally retarded and has distinct physical features.

A karyotype is a display of matching chromosomes showing their number, form and size.

Look at the karyotypes of a normal individual and a Down's syndrome individual. Which is which? Underneath each karyotype comment on whether it is normal or down’s and explain your choice.

Questions:

1. Explain how Down’s syndrome occurs?2. What is Down's syndrome caused by the presence of?

Non-Disjunction of the sex chromosomes

DISEASE EXAMPLE: 2 Turners's syndromeNo sex chromosome fuses with normal X gamete.Zygote chromosome complement 2n = 45 (44 + X)

Always female Infertile as – ovaries fail to develop.

Klinefelter’s Syndrome

XX egg fertilised by normal sperm Y, or normal X egg is fertilised by an XY sperm. Zygote formed 2n = 47 (44+XXY). Individuals are always male and have male

organs. They are infertile – testes develop to half normal size and fail to produce sperm.

‘Complete’ non-disjunction or polyploidy

This is due to the failure of all spindle fibres during meiosis in a gamete mother cell. This results in 2 gametes which are diploid and two with no chromosomes.

Complete non-disjunction will result in diploid gametes i.e. they have two of each chromosome instead of one of each pair (the gametes which gain no chromosomes will die)

Diagram showing complete non-disjunction

If a diploid gamete (2n) fuses with a normal haploid gamete (n) a triploid (3n) individual is formed. This individual has three sets of chromosomes.Complete the diagram below by inserting the chromosomes, showing the joining of a ‘2n’ gamete with an ‘n’ gamete where n=2.

If the diploid gametes are fertilised by a normal haploid gamete a triploid known as a polyploidy plant is produced.

The organism shown above cannot produce gametes and is therefore sterile, as meiosis cannot occur because homologous pairs cannot be formed.

Diploid Gamete Mother Cell

Mitotic Division

Meiotic Division

All chromosomes go into one cell

Gametes without chromosomes die

Diploid gametes 2n

2n

gameten

gamete

Cell Division

Sterile organism

If two diploid gametes fuse a tetraploid (4n) individual is formed. The organism has four sets of chromosomes. It is fertile as they are able to form homologous pairs.

Often these polyploidy plants have an economical advantage, for example they may have/be:

Larger plants Increased seed and fruit size Resistance to disease Increased yield Hybrid Vigour (better in some way than the parent plants)

Example of Polyploidy

An example of polyploidy is in the species of grass, Spartina townsendii, which is formed by crossing Spartin stricta and Spartina alterniflora.

Spartina townsendii is fertile but it is formed as a result of the cross between S. stricta and S. alterniflora which are two different species.

Remember: When two different species are crossed the resulting offspring should not be fertile!

Complete the polyploidy example below by inserting the correct numbers for the haploid and diploid state.Polyploid example

Spartina stricta Spartina alterniflora2n=56 2n=72

N= n=Sterile Hybrid

2n=Spindle failure causing

polyploidy

Spartina townsendii2n=n=

Explain why the hybrid is sterile.

Formation of human chromosome 2 and evolution of monkey and homosapiens

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Mutations Dictionary

Chromosome mutations-Can be a change in chromosome number due to spindle failure during meiosis. Or a change in the structure of a chromosome due to a change in the number/order of the genes i.e translocation, inversion, duplication and deletion (TIDD)

Down’s Syndrome-An example of a chromosome mutation involving a change in the number of chromosomes. Down’s syndrome individuals have 47 chromosomes instead of 46 due to non-disjunction happening at pair 21.

Frameshift mutations-Type of gene mutations, which lead to a major change in the gene’s DNA i.e. insertion and deletion

Gene mutations-type of mutation, which involves a change in one or more of the actual nucleotides in a strand of DNA. Four types of gene mutation are deletion, insertion, substitution and inversion (DISI)

Karyotype-a display of the complete set of chromosomes (which shows their number, form and size)

Klinefelter’s syndrome-this is a condition that arises when non-disjunction happens in the sex chromosomes. An XX egg is fertilised by a normal Y sperm then the resulting zygote has the chromosome complement 44 + XXY. Such individuals are always male and possess male sex organs. However they are infertile.Mutagenic agents-Factors that can artificially increase the rate of mutation e.g. chemicals (such as mustard gas) and radiation (gamma rays, X-rays and UV light)

Mutant-When a mutation is actually expressed in the phenotype, the affected individual is called this.

Mutation-A change in the structure or quantity of genetic material in an organism. Mutation is the only source of new variation

Non-disjunction-this can occur during meiosis and results in gametes with extra/less chromosomes than normal. During the first meiotic division, spindle failure results in failure to separate a pair of homologous chromosomes. As in Down’s syndrome

Point mutations- Type of gene mutations which lead to a minor change in the gene’s DNA i.e. inversion and substitution

Polyploidy-Rare in animals, more common in plants. When all the spindle fibres in a gamete mother cell fail during meiosis and none of the homologous pairs become separated. Results in gametes with double the number of chromosomes. Fertilisation of these abnormal gametes results in mutant plants which have complete extra sets of chromosomes.

Sickle cell anaemia-due to a type of gene mutation called substitution that results in the formation of sickle–shaped red blood cells. An example of when a point mutation (which is usually not that harmful) can occasionally cause a major defect

Turner’s syndrome- this is a condition that arises when non-disjunction happens in the sex chromosomes. A gamete with no X/Y chromosomes is fertilised by a normal X gamete then the resulting zygote has the chromosome complement 44 + XO. Such individuals are always female and are infertile.

Chromosome and Gene Mutation Questions

1) With the aid of an example, state clearly the difference between the terms mutation and mutant?2) What name is given to the process by which a spindle fibre fails during

meiosis and one or more of the gametes produced receive an extra chromosome?3a) If a normal human sperm fertilises an egg containing an extra copy of chromosome 21, what is the diploid number of the zygote formed?

b) What name is given to the condition suffered by a person who develops from an abnormal zygote of this type?

c) What relationship exists between the age of the mother and the incidence of this condition occurring?4a) What is meant by the term Polyploidy?b) Explain how a Polyploid Plant containing 3 separate sets of chromosomes could have arisen?

c) State 2 ways in which polyploid plants can be of an economic importance.

5) State the 4 different chromosome mutations

6) What name is given to a change that involves a chromosome breaking in two places and a segment of genes dropping out?

7) Name the type of change that involves a chromosome breaking in two places and then the affected length of genes rotates through 180°C before rejoining?

8) Name the type of change that involves a section of one chromosome breaking off and joining onto another non-homologous one?9) Name the 4 different gene mutations10) Classify these four gene mutations into "frameshift" and "point" mutations11) Is frameshift or point mutations most likely to lead to the formation of a protein that is greatly changed and non-functional?12) Name two mutagenic agents?

Variation – MutationsActivity I can find I can do

this in my notes

this

State that a mutation is an error in the amount or structure of genetic material in an organism State that mutations in nature occur at random and at low frequencyDefine the term ‘mutagen’ and give examplesState that mutations can be grouped under three headings:1. alteration to the sequence of bases making up a gene2. alteration to chromosome structure3. alteration to chromosome numberState that alterations to base sequence can be of 4 types:Substitution; insertion; deletion; inversionDescribe what is involved in each of the above examplesState the effect of a gene mutation would have on an amino acid sequence and subsequently a protein

State that alterations to chromosome structure can occur in one of these ways:deletion; inversion; duplication; translocationDescribe what is involved in each of the above examplesState that the number of chromosomes in a cell can be altered by non-disjunction during meiosis/mitosisExplain what happens to spindle fibres and chromosomes when non-disjunction occursCompare the chromosome number of people with & without Down’s SyndromeState that polyploidy arises when non-disjunction involves whole sets of chromosomes because all the spindle fibres failState the benefit of polyploidy to crop breedersExplain what a karyotype is