L14 Gene Mutations

Front 1

What is a mutation?

Back 1

Mutation is a hereditary change in DNA - if it occurs in germlinewill be passed on to offspring

Front 2

Do all organisms carry mutant alleles?

Back 2

Every organism carries mutant alleles, whether they manifest indistinct phenotypes or not.

Front 3

When do new mutations occur?

Back 3

New mutations can occur in every generation.

Front 4

Why do gene mutations arise?

Back 4

Gene mutations occur within individual genes as a result ofchange in nucleotide sequence which can have consequence interms of protein structure or gene expression.

Front 5

What are some causes of mutations?

Back 5

Many causes of mutation

– DNA replication errors

– Spontaneous mutations

– Chemicals and irradiation (e.g. ultra violet light)

Front 6

What are somatic mutations?

Back 6

Somatic mutations are ones that occur in any cell of the body apart fromgerm cells (egg and sperm). These mutations can not be inherited byoffspring. Somatic mutationscan lead to cancer

Front 7

What are germ-line mutations?

Back 7

Germ-line mutations - occur in gametes. These mutations are inheritedby offspring

Front 8

Why are dominant mutations easier to study?

Back 8

Dominant mutations are easier to detect than recessive mutations andso are easier to study.

Front 9

Do mutation frequencies differ among organisms?

Back 9

Mutation frequencies differ considerably among organisms.

Front 10

Do mutation frequencies vary among genes of a single species?

Back 10

Mutation frequencies vary among genes of a single species

Front 11

Do larger genomes have higher mutation frequencies?

Back 11

Each species has an average mutation frequency; those with largergenomes have, on average, higher mutation frequencies.

Front 12

Do some genes have higher mutation frequencies and why might this be?

Back 12

Mutation frequencies for some genes are considerably higher thanothers in a given genome; genes that have elevated mutationfrequencies are called hotspots of mutation. One reason formutational hotspots is large gene size

Front 13

What is mutation frequency defined as in diploids?

Back 13

In diploids mutation frequency is defined as the number of mutationalevents in a given gene over a defined period of time (most often perDNA replication cycle or per cell generation)

Front 14

What are Base-pair substitution mutations?

Back 14

the replacement of one nucleotide base pair by another

Front 15

What are transition mutations?

Back 15

Transition mutations: one purine replaces another, or one pyrimidinereplaces another.

A ↔ G (purine ↔ purine) (A·T ↔ G·C)

C ↔ T (pyrimidine ↔ pyrimidine) (C·G ↔ T·A)

Front 16

What are transversion mutations?

Back 16

Transversion mutations: a pyrimidine is replaced by a purine or viceversa.

Front 17

What is a silent mutation?

Back 17

1. Silent mutation: a base-pair change that does not alter the resultingamino acid sequence due to the redundancy of the genetic code

Front 18

What is a missense mutation?

Back 18

Missense mutation: a base-pair change that results in an amino acidchange in the protein

Front 19

What is a nonsense mutation?

Back 19

Nonsense mutation: a base-pair change that creates a stop codon inplace of a codon specifying an amino acid

Front 20

Define a synonymous or silent mutation

Back 20

Synonymous or silent mutation

– changes one codon for an amino acid to another codon forthat amino acid

– no change in amino acid (silent mutation)

Front 21

Define missense mutation

Back 21

Missense mutation

– changes codon for one amino acid to codon for anotheramino acid

– also called nonsynonymous mutation

– the effect of changing an amino acid will depend on the roleof that amino acid in protein function

Front 22

What is a neutral mutation?

Back 22

Missense mutations differ in severity

– conservative amino acid substitution substitutes chemicallysimilar amino acid, less likely to alter function often called aneutral mutation

e.g. alanine (-CH3) for glycine (-H)

Front 23

What would be the effect of a nonconservative mutation?

Back 23

Missense mutations differ in severity

– nonconservative amino acid substitution substituteschemically different amino acid, more likely to alter function

– consequences for protein depend on the function of theamino acid within the 3D structure

e.g. glycine (-H) for glutamate (-CH2-CH2-COO-)

Front 24

Where in the three letter code is more likely to produce a change in amino acid?

Back 24

Many amino acids have more than one codon.A mutation in the first letter of the three letter code is morelikely to produce a change in amino acid.

Front 25

Define a nonsense mutation

Back 25

Nonsense mutation– change codon for amino acid into translation termination(stop) codon

Front 26

What is the effect of a nonsense mutation?

Back 26

Nonsense mutation results in premature termination oftranslation. truncated polypeptides often are nonfunctional

Front 27

What is a frameshift mutation?

Back 27

Addition or deletion of one ormore bases changes thereading frame and alters allthe amino acids downstreamof the mutation

Front 28

What are regulatory mutations?

Back 28

Some point mutations alter the amount (but not the amino acidsequence) of protein product produced by a gene

Front 29

What do these regulatory mutations affect?

Back 29

These regulatory mutations affect regions such as

a. Promoters and other regulatory protein binding sites

b. Introns

c. regions coding for 5′-UTR and 3′-UTR segments on mRNA

Front 30

What are promotor mutations?

Back 30

Mutations that alter consensus sequence nucleotides of promoters arecalled promoter mutations

Front 31

What do these interfere with?

Back 31

These interfere with efficient transcription initiation.

Front 32

How might the level of transcription be affected?

Back 32

Some promoter mutations cause mild to moderate reductions intranscription levels, whereas others may abolish transcription, somemutations can even enhance transcription.

Front 33

What does efficient splicing of introns from pre-mRNA in eukaryotes require?

Back 33

In eukaryotes, messenger RNA (mRNA) is transcribed as pre-messengerRNA (pre-mRNA) which is processed to remove intron regions.Efficient splicing of introns from pre-mRNA requires specific sequences atthe intron-exon boundaries.

Front 34

What are splicing mutations?

Back 34

Mutations that alter that alter nucleotides required for efficient splicingat intron-exon junctions are called splicing mutations.

Front 35

What can splicing mutations result in?

Back 35

These can result in splicing errors and the production of mutantproteins due to the retention of intron sequences in the mature mRNA.

Front 36

What are cryptic splice sites?

Back 36

Some base-pair substitution mutations produce new splice sites thatreplace or compete with authentic splice sites during mRNA processing.Leads to new possible forms of protein product.

Front 37

What are forward mutations?

Back 37

Forward mutation: converts a wild-type allele to a mutant allele

Front 38

What are reverse mutations?

Back 38

Reverse mutations or reversions: convert mutant alleles to wildtypeor near wild-type

Front 39

What is true reversion?

Back 39

True reversion: wild-type DNA sequence is restored by a secondmutation within the same codon

Front 40

What is Second-site reversion?

Back 40

Occurs by mutation in a different gene and together the two mutationsrestore the organism to wild-type

Front 41

What happens in induced mutation?

Back 41

Induced mutation

• action of mutagen, an environmental agent that altersnucleotide sequence

• process of inducing mutations by mutagens is calledmutagenesis

Front 42

What happens in spontaneous mutations?

Back 42

Spontaneous mutation

• arise in absence of known mutagen

• may be caused by errors in DNA replication

• provide “background rate” of mutation

• important for evolution

Front 43

What are the 3 types of spontaneous mutation?

Back 43

1.DNA replication errors

2.Spontaneous nucleotide base changes

– causes mispairing of DNAnucleotides during DNA replication

3.DNA nucleotide lesions

– causes mispairing of DNA nucleotides duringDNA replication

for example Depurination – removal of purine group

Deamination – removal of amino group

Front 44

What happens in DNA replication errors and what normally corrects them?

Back 44

DNA polymerase can insert the wrong nucleotide.This is corrected by the ‘proof reading’ 3’ to 5’ exonuclease function of theDNA polymerase 99% of the time.

Front 45

What causes trinucleotide repeat disorders?

Back 45

The trinucleotide repeat disorders are caused by DNA polymeraseslipping during DNA replication and increasing the number of trinucleotide repeats within a gene which results in longer stretches of thesame amino acid within the protein.

Front 46

What is an example of a trinucleotide repeat disorder?

Back 46

Example - Huntington’s disease (autosomal dominant) - caused byincrease in length of a polyglutamine region in the Huntingtin protein28 CAG repeats - normal

36 or more CAG repeats - disease symptoms

Front 47

What are tautomers?

Back 47

DNA nucleotide bases can occasionally convert to alternative structurescalled tautomers, with slight differences in bonding and placement ofhydrogens

Front 48

what can these Spontaneous Nucleotide Base Changes be?

Back 48

amino (normal structure for adenine and cytosine) ↔ imino (rare)

keto (normal structure for thymine and guanine) ↔ enol (rare)

amino is C−NH2

imino is C=NH

keto is C=O

enol is C−OH

Front 49

What can tautomeric shifts lead to?

Back 49

Tautomeric shifts can lead to base-pair mismatches and incorporation ofincorrect bases during replication

Front 50

What is the most common form of replication error?

Back 50

tautomeric shifts

Front 51

What causes induced mutations?

Back 51

Induced mutations are produced by interactions between DNA andphysical, chemical, or biological agents that generate mutations

Front 52

What are the types of induced mutation?

Back 52

1.Nucleotide base analogs

2.Deaminating agents – remove NH2 group3.Alkylating agents - add methy (-CH3) or ethyl group (-CH2-CH3)

4.Hydroxylating agents – add hydroxyl group (-OH)

5.Oxidative agents - addition of oxygen or removal of hydrogen

6.Intercalating agents

7.Radiation induced DNA damage – ultraviolet light, X-rays, gamma rays, cosmic rays

Front 53

What is an example of base analogs?

Back 53

Base analogs are similar to nitrogenous bases of DNA, but have alteredpairing properties

e.g. 5-bromouracil (5-BU) replaces thymine and causes a AT > GCtransition

Front 54

What is an example of an alkylating agent?

Back 54

Alkylating agents modify base structure by adding methyl or ethylgroups which can result in altered base pairing

e.g. EMS (ethyl methanesulfonate)

Front 55

What is an example of intercalating agents?

Back 55

Intercalating agents are flat, planar molecules intercalate between basepairs distorting the DNA helix which disrupts DNA replication and causesaddition or deletion of nucleotides leading to frameshift mutations.

e.g. proflavin, acridine orange, ethidium bromide.

Front 56

What DNA repair mechanisms?

Back 56

There are a number of ways organisms try to repair DNA damage usingcorrect base on the damaged DNA strand.

Front 57

What is photoreactivation repair?

Back 57

DNA damage repaired byphotoreactivation enzyme (PRE)which cleaves the thymine dimerbond. In E. coli this enzyme is calledphotolyase.

Front 58

What is Base excision repair?

Back 58

Base excision repair performed bya base specific DNA glycolsylase(in this example uracil DNAglycosylase), AP endonuclease,DNA polymerase and DNA ligase.Uracil is recognised as anoncomplementary base pair andreplaced with the complementarybase (C).

Front 59

What is Nucleotide excision repair?

Back 59

Repairs lesions which distort DNA e.g.thymine dimers.In E. coli the UVRA, UVRB and UVRCproteins recognise the lesion and excises13 nucleotides.

DNA polymerase I then synthesises thenew DNA strand

and DNA ligase joins thesingle stranded nick

Front 60

Human diseases can be caused by mutations in genes that encodeproteins involved in DNA repair mechanisms. What is an example of such a disease?

Back 60

Xeroderma pigmentosum - individuals areusually homozygous recessive for a faultyrepair gene. Sufferers are photosensitiveand if their skin is exposed to lightdevelops freckles and patches of intensepigment leading to warty growths that aremalignant and usually fatal.

Front 61

What causes Xeroderma pigmentosum?

Back 61

Xeroderma pigmentosum diseasesymptoms are caused by mutant alleles ofsix different genes whose protein productsare involved in DNA repair in humans

Front 62

What can mutations in human genes whose proteins are involved in DNA repair mechanisms cause?

Back 62

Mutations in human genes whose proteins are involved in DNA repairmechanisms can cause hereditary cancer.

Front 63

What are some examples of these mutations?

Back 63

BRCA2 - hereditary breast cancer

MSH2 - Hereditary colorectal cancer

MLH1 - Hereditary colorectal cancer

Front 64

What other mutations can cause cancer?

Back 64

Somatic mutations in human genes whose proteins are involved in DNArepair mechanisms can cause cancer as well.