Lecture 8

Question 1

Define polymorphism

Answer 1

two or more allies of a gene in a population

Question 2

Define SNPs

Answer 2

single base differences- single nucleotide polymorphism

Question 3

Define indels

Answer 3

insertion or deletion

Question 4

What is copy number variation caused by?

Answer 4

large insertion or deletion in one chromosome

Question 5

Describe DNA sequencing

Answer 5

• Chain-termination – accurate, low throughput 800 bases
• Next generation sequencing – extremely high throughput, 100 bases, small sequences – most popular, good for SNP detection, poor for CNVs
• Single molecule – high error rates and cost, 10,000 bases, how molecules are arranged

Question 6

How can SNPs be detected?

Answer 6

DNA hybridisation techniques

Question 7

How different from each other are individuals?

Answer 7

Watsons genome contains 3.3 millions SNPS, approx. 10million common SNPS in humans

Question 8

Describe indels

Answer 8

analysed using PCR and gel electrophoresis, STRs are multi allelic, used in genetic profiling, less than SNPS

Question 9

Describe genetic variation regions on phenotypic effects

Answer 9

• Intergenic region: no effect
• Non-coding regions – silent and may affect gene expression
• Protein coding region – effects

Question 10

Describe base substitutions

Answer 10

silent, neutral (affects sequence but not properties), mis-sense or nonsense(stop codons)

Question 11

Describe mutations

Answer 11

rare alleles, mutant are useful for genetics, normal allele is termed wild type

Question 12

Define mendelian disease

Answer 12

mutations of a single gene- rare disease

Question 13

What mechanisms do cells have to prevent mutation?

Answer 13

• Proofreading DNA polymerase
• Postreplication mistmatch repair
• DNA repair by homologous recombindation
• Cell cycle checkpoints

Question 14

What are the environmental factors that cause mutations?

Answer 14

radiation and chemical mutagens

Question 15

Transitions

Answer 15

substituting pyrine for pyrine or pyrimidine for pyrmidine

Question 16

Transversions

Answer 16

pyrine (2 ring) to pyrimidine (3 ring structure)

Question 17

What do mutations cause thymines to do?

Answer 17

covalently link to produce a photodimer caused by UV light, photolyase and light can reverse this,

Question 18

Intercalating agents

Answer 18

insert between base pairs  frameshift

Question 19

Base analogues

Answer 19

incoroporated into DNA in place of normal base, mis pairing

Question 20

Base modifying agents

Answer 20

covalently modify the DNA causing mis pairning
• Deaminating agents remove amino groups – 5-methylcytosine to thymine
• Hydroxlyating agents add hydroxyl groups
• Aklyating agents add alkyl groups

Question 21

Alkylating agents

Answer 21

• ENU converts G to A, MMS acts similarly but by addition of a methyl group

Question 22

What generates STR variation

Answer 22

replication slippage

Question 23

Describe mutations in coding regions

Answer 23

Mutations in coding regions:
• Mutant genes- non functional or unstable proteins
• Diploid have mostly recessive mutations

Question 24

Describe temperature sensitive mutations

Answer 24

mutant protein is less stable at non-permissive temperature, very useful for studying essential cell functions eg yeast