Mutations

Question 1

Single nucleotide polymorphism (SNPs “snips”)

Answer 1

• single bases substitution
• 2/3 of SNPs are C to T changes
• transitions (purine to purine or pyrimidines to pyrimidines) are more common than transversions (purine to pyrimidines)

Question 2

Missense mutations

Answer 2

• one amino acid is substituted for another (normally by a single base change)
• e.g. GGC (glycine) to TGC (cysteine)
• substitutions of e.g. a valine to alanine may be tolerated in non-critical (not the active site) regions of the protein

Question 3

Silent mutations

Answer 3

• a single base substitution which doesn’t substitute the amino acid
• e.g. GGA changed to GGG (both glycine)
• some can disrupt RNA splicing and result in heritable diseases

Question 4

Nonsense mutations

Answer 4

• an amino acid codon is changes to a stop codon
• e.g. GGA (glycine) to TGA (stop)
• mRNAs that contain a PTC will be degraded by “nonsense mediated decay” - a protective mechanism

Question 5

Frameshift mutations

Answer 5

• the reading frame of mRNA is altered in some way
• insertion, deletion (of bp that are not in multiples of 3) or slice site mutations
• a stop codon is often found in alternative reading frame causing the ribosome to terminate translation prematurely
• mRNAs that contain a PTC will be degraded by “nonsense mediated decay” - a protective mechanism

Question 6

Causes of base changes

Answer 6

• sequence changing during replication
• chemicals can induce mutations
• exposure to radiation

Question 7

Tautomeric shift

Answer 7

• proton (H+) briefly changes position
• altered base pairing properties
• can behave as an altered template base during DNA
  replication (C pairs with an A and T pairs with a G)

Question 8

Chemical mutant base change

Answer 8

Nitrous acid replaces amino group with keto groups
C –> U pairs with A
A –> H pairs with C
G –> X pairs with C

Ethyl methane sulphate EMS causes removal of purine rings
apurinic sites can be paired with any base during replication - are unpredictable

Question 9

Consequence of mutations

Answer 9

About 1-2% of DNA is protein coding

• mutations close or within genes are most likely to cause disease
• type and location of mutation will determine its consequences

Question 10

IQ

a heterocyclic aromatic amine food mutagen

Answer 10

Found in cooked meats and cigarette smoke condensates

• disrupts the packaging of DNA bases & causes mostly single base deletions at GC base pairs
• intercalation of IQ forces the bases further apart leading to misreading by DNA polymerase and deletion of a single base

Question 11

Ionising radiation

Answer 11

• radiation that produces ions during interaction with cellular molecules
  e. g. UV, X-Rays, nuclear power plant accidents, radon gas
• is unavoidable

Question 12

UV light effects

Answer 12

• UVB exposure induces the production of vitamin D in the skin, over exposure causes sunburn and some types of cancer
• UVA, UVB, UVC can all cause damage to collagen fibres leading to skin ageing
• UVA and UVB destroy vitamin A in the skin,
  UV light protons cause adjacent thymine bases to pair - the diners often resolve spontaneously through a process known as photo-reactivation

Question 13

DNA repair processes

Answer 13

Most errors are corrected by “proof reading” - mis paired 3’ base in newly synthesised strand is detected and corrected by polymerase 99% of the time

Question 14

Nucleotide mismatch repair

Answer 14

• enzymes detect mismatched bases in the newly synthesised strand (after replication) and replace them
• a “patch” of DNA sequence is replaced

Question 15

IQ

a heterocyclic aromatic amine food mutagen

Answer 15

Found in cooked meats and cigarette smoke condensates

• disrupts the packaging of DNA bases & causes mostly single base deletions at GC base pairs
• intercalation of IQ forces the bases further apart leading to misreading by DNA polymerase and deletion of a single base

Question 16

Ionising radiation

Answer 16

• radiation that produces ions during interaction with cellular molecules
  e. g. UV, X-Rays, nuclear power plant accidents, radon gas
• is unavoidable

Question 17

UV light effects

Answer 17

• UVB exposure induces the production of vitamin D in the skin, over exposure causes sunburn and some types of cancer
• UVA, UVB, UVC can all cause damage to collagen fibres leading to skin ageing
• UVA and UVB destroy vitamin A in the skin,
  UV light protons cause adjacent thymine bases to pair - the diners often resolve spontaneously through a process known as photo-reactivation

Question 18

DNA repair processes

Answer 18

Most errors are corrected by “proof reading” - mis paired 3’ base in newly synthesised strand is detected and corrected by polymerase 99% of the time

Question 19

Nucleotide mismatch repair

Answer 19

• enzymes detect mismatched bases in the newly synthesised strand (after replication) and replace them
• a “patch” of DNA sequence is replaced

Question 20

Excision repair

Answer 20

Types of damaged bases 
- oxidised bases
- alkylated bases
- de-aminated bases
- uracil 
Are repaired by base excision repair

Question 21

Cancer

Answer 21

Failure of DNA repair mechanisms can result in cancer
- humans: MLH1, MSH2 and MSH6 encode for mismatch repair enzymes
- the genes are commonly mutated in cases of hereditary non-polyposis colorectal cancer
Tumour is result of growth advantage with 6 new characteristics
- divide independently (no need for internal growth signals)
- ignore external antigrowth signals
- avoid apoptosis (programmed cell death)
- divide indefinitely
- stimulate sustained angiogenesis (blood supply for nutrients)
- invade tissues and establish secondary tumours

Question 22

Successive advantage

Answer 22

• mutations affect functions which raise the probability of successive mutations occurring
• all cancer cells exhibit chromosomal instability and microsatellite instability
  Inherited breast cancer genes - BRCA1 or BRCA2

Question 23

Oncogenes

Answer 23

• retro-viruses have genes that are able to transform cells into a cancerous phenotype
• several human genes have sequence similarities to vital oncogenes (Proto-oncogenes)
• key amino acid substitutions can activate the proto-oncogenes into cancer causing oncogenes

Question 24

Heritable or sporadic

Answer 24

• inherited cancer genes tend to harbour recessive mutations
• development of cancer is a dominant pattern of inheritance
  Initiation of tumour formation requires that both copies be mutated or that the functional wild-type copy be deleted

Question 25

SSCP mutation scanning

Answer 25

• identify the mutated region of the gene - perform targeted DNA sequencing
• amplified DNA is heated to denature, then rapidly cooled - the individual strains will adopt a sequence-specific partly double stranded forms
• the DNA is electrophoresed in polyacrylamide gel and detected by staining with silver (3D protein haves will have different mobilities in the gel)

Question 26

Obtaining foetal DNA

Answer 26

• Amniocentesis (amniotic fluid cells) - performed at 15-20 weeks gestation with ultrasound guidance - 0.5-1% risk of causing a miscarriage
• Chorion villus biopsy - performed at 10-13 weeks gestation with ultrasound guidance - tissue sample from placenta - 2% risk of causing a miscarriage
• Foetal DNA in mother’s blood - can be isolated from mothers blood along with mothers DNA - largely a research tool