Lecture 15: Mutations

Question 1

define a mutation

Answer 1

change genes from one allelic form to another, sometimes leading to the creation of entirely new alleles

Question 2

when do genes mutate?

Answer 2

genes mutate randomly, at any time and in any cell of an organism

Question 3

how often do genes mutate?

Answer 3

very rarely; on average 1.2x10^-8 mutations/gene/gamete in humans

Question 4

what causes a gene to mutate?

Answer 4

spontaneous:
- arise in absence of known mutagen (polymerase errors, reactive oxygen species etc)
- provide ‘background rate’ of mutation

induced (by geneticist -> mutagenesis)
- action of mutagen alters nucleotide sequence

Question 5

what types of mutations can and can’t be passed onto progeny?

Answer 5

only mutations in germline cells can be transmitted to progeny; somatic mutations cannot be transmitted

Question 6

inherited mutations appear as —- in populations

Answer 6

alleles

Question 7

state 3 observations of mutation rates

Answer 7

• mutations affect phenotype rarely
• different genes mutate at different rates (mutation rates range from less than 10^-9 to more than 10^-3/gene/gamete)
• mutation rate can increase after exposure to a mutagen (eg UV light, certain chemicals)

Question 8

define a substitution

Answer 8

a base is replaced by one of the other 3 bases

Question 9

indels

Answer 9

deletions - block of one or more nucleotide (base) pairs is lost
insertion - block of one or more nucleotide (base pairs is added)

Question 10

what are the two types of base substitutions?

Answer 10

transition:
purine to purine (A<->G) or pyrimidine to pyrimidine (C<->T)

transversioin:
purine to pyrimidine or pyrimidine to purine

Question 11

purines

Answer 11

guanine, adenine

Question 12

pyrimidines

Answer 12

thymine, cytosine

Question 13

why do we study mutations?

Answer 13

• they act as markers for genes
• mutations can disrupt gene function. this allows for the study of how the wild-type gene works

Question 14

wild-type allele

Answer 14

the form found in nature (or in a standard laboratory stock); an allele whose frequency is 1% or more of the population

Question 15

mutant allele

Answer 15

the form that has changed due to a mutation; an allele whose frequency is less than 1% of the population

Question 16

forward mutation

Answer 16

changes wild-type allele to a different allele

Question 17

reverse mutation (reversion)

Answer 17

causes novel mutation to revert back to wild-type allele

Question 18

which is higher - rate of forward or rate of reverse mutation

Answer 18

rate of forward mutation is almost always higher than rate of reverse mutation (except TEs)

Question 19

depurination

Answer 19

the hydrolysis of a purine base from the deoxyribose-phosphate backbone, leading to an apurinic site

Question 20

how often does depurination occur?

Answer 20

100 times/hour in every human cell

Question 21

deamination

Answer 21

the removal of an amino group from a cytosine, leading to the conversion of cytosine to uracil

Question 22

how is deamination fixed?

Answer 22

by uracil-DNA glycosylase
- most of the time, it is easy for cells to recognise deamination as uracil is only meant to be in RNA, not DNA

Question 23

how does deamination affect DNA strands resulting from replication?

Answer 23

• after replication, one of the strands will be normal (CG) and the other will be mutant (UA) as adenine base pairs with uracil
• after another round of replication, one of the strands will be (TA) and the other will be (UA)

overall, there is a C-G to T-A transition mutation

Question 24

give examples of radiation that may cause mutations

Answer 24

naturally occurring radiation such as cosmic rays and x rays often lead to mutations like deletions

Question 25

what kind of mutation does UV light cause and how?

Answer 25

- UV light (especially UV-B and UV-C) primarily causes pyrimidine dimers - induces covalent bonds between adjacent pyrimidines (especially thymine-thymine dimers, but also C-T and C-C).

Question 26

describe how oxidation leads to mutation

Answer 26

- oxidative damage can occur to any of the 4 base pairs - ROS oxidize guanine into 8-oxoG. 8-oxoG mispairs with adenine during replication. This causes a G:C → T:A transversion in the next round of replication.

Question 27

describe how DNA polymerases may lead to mutation

Answer 27

- DNA polymerases may lead to DNA replication mistakes - this is caused by the incorporation of an incorrect during replication

Question 28

how often do DNA replication mistakes occur?

Answer 28

DNA polymerase has very high fidelity, so such errors are exceedingly rare

Question 29

where do indel mutations tend to occur?

Answer 29

in regions of repeated bases during replication or crossing over in meiosis

Question 30

trinucleotide repeat expansion

Answer 30

DNA polymerase can slip or misalign on the template strand, forming a loop of extra repeats on the new strand, leading to expansion

Question 31

trinucleotide repeat contraction

Answer 31

DNA polymerase can slip or misalign on the template strand, forming a loop of extra repeats on the template strand, leading to contraction

Question 32

give examples of diseases caused by intel mutations of regions with repeated bases

Answer 32

Fragile X-syndrome, Huntington and other disorders of the nervous system

Question 33

define genetic code

Answer 33

- dictionary used to translate nucleic acids to a amino acids - codon language - redundant (multiple codons per amino acid)

Question 34

why is redundancy of the genetic code important?

Answer 34

this protects against the negative impacts of mutations

Question 35

silent (synonymous) mutation

Answer 35

altered codon resulting from the mutation specifies the same amino acid

Question 36

missense mutation

Answer 36

altered codon resulting from the mutation specifies a different amino acid

Question 37

southern blot

Answer 37

identifies specific DNA sequences

Question 38

northern blot

Answer 38

identifies (m)RNA sequences

Question 39

western blot

Answer 39

identifies protein sequences

Question 40

two types of missense mutations

Answer 40

conservative: - substitutes chemically similar amino acid - less likely to alter function or structure of protein non-conservative: - substitutes chemically different amino acid - more likely to alter function or structure of protein

Question 41

nonsense mutation

Answer 41

introduction of a (early) stop codon (TAG, TAA, TGA)

Question 42

frameshift mutation

Answer 42

- the insertion or deletion of nucleotides in a DNA sequence not in multiples of three - shifts the reading frame used during translation, drastically altering the resulting protein

Question 43

intragenic suppressor mutation

Answer 43

a second mutation that occurs within the same gene as a previous mutation and restores, at least partially, the original function that was lost or disrupted by the first mutation

Question 44

two types of mutations outside the coding sequence

Answer 44

- mutations in promoter or termination signal sites - splice donor/acceptor site mutations

Question 45

splice donor/acceptor site mutations

Answer 45

- disrupts splice donor/acceptor site, resulting in incorrect retention/excision of intron - often leads to large additions or deletions that may cause frameshift

Question 46

loss-of-function mutation

Answer 46

result in reduced or abolished protein activity

Question 47

what is the typical inheritance mode of loss of function mutations?

Answer 47

loss-of-function mutations are usually recessive

Question 48

two types of loss-of-function mutations

Answer 48

- null (amorphic) mutations - completely block function of gene product (eg deletion of an entire gene) - hypomorphic mutations - gene product has weak, but detectable, activity

Question 49

haplosufficiency

Answer 49

- when one WT allele reaches threshold for the WT phenotype, the WT allele is haplosufficient - even with one mutant allele, we still see the WT phenotype - recessive mutations

Question 50

haploinsufficiency

Answer 50

- when one WT allele does not reach the threshold for the WT phenotype, the WT allele is haploinsufficient - heterozygotes are affected - dominant mutations

Question 51

give an example of haploinsufficiency

Answer 51

polydactyly - phenotype is seen in individuals with only one mutant copy

Question 52

incomplete dominance

Answer 52

phenotype varies with the amount of functional gene product

Question 53

gain of function mutations

Answer 53

enhance a function or confer a new activity

Question 54

what mode of inheritance do gain of function mutations typically have?

Answer 54

they are typically dominant

Question 55

two types of gain-of function mutations

Answer 55

hypermorphic mutations: - generate excessive gene product or more potent gene product neomorphic mutations: - generate gene product with new functions or ectopically expressed at inappropriate time or place, generating a novel phenotype

Question 56

give an example of a hypermorphic mutation

Answer 56

achondroplasia - caused by a hypermorphic allele of the FGFR3 gene, which leads to increased receptor activity. - this overactive FGFR3 inhibits bone growth, resulting in the characteristic short stature.

Question 57

give an example of a neomorphic allele

Answer 57

mutation in Antennapedia gene of drosophila causes ectopic expression of a leg-determining gene in structures that normally produce antennae

Question 58

antimorphic/dominant negative mutations

Answer 58

- usually occur in genes that encode multimeric proteins - produce a mutant gene product that interferes with the function of the normal (wild-type) protein

Question 59

How did Garrod use mutations to understand gene function in phenylketonuria (PKU)?

Answer 59

- proposed that genes control metabolism by encoding specific enzymes. - In PKU, a mutation in the gene for phenylalanine hydroxylase leads to a loss of enzyme function, causing a buildup of phenylalanine. - This showed that mutations can block metabolic pathways, linking gene defects to biochemical function

Question 60

compare a normal pathway to alkaptonuria

Answer 60

normal pathway: phenylalanine -> tyrosine -> p-hydroxyphenylpyruvate -> homogentisic aid (HA) -> maleylacetoacetic acid -> CO + H2O in alkaptonuria: - HA oxidase nonfunctional - HA accumulates (toxic) - turns urine black in air - pathway stops

Question 61

how can we analyse biosynthetic pathways?

Answer 61

- compounds that are used latest in the pathway will support the growth of the most mutants - compounds that are used earliest in the pathway will support the growth of the fewest mutants