CC Single Nucleotide Changes

Question 1

What is the most common type of genetic variation?

Answer 1

Single Nucleotide Polymorphisms (SNPs) (~75%)

Question 2

What are some examples of types of SNPs?

Answer 2

Substitution
Insertion/ Deletion

Question 3

What are the 3 effects that SNPs can have?

Answer 3

Synonymous
Non-Synonymous
Non-coding

Question 4

What synonymous SNPs mostly known as? What does this mean?

Answer 4

Silent SNPs
Same amino acid is still made, so no effect on protein sequence, no effect on phenotype.

Question 5

What can some synonymous SNPs do?

Answer 5

Change splicing or transcription, resulting in a phenotype (not silent)

Question 6

What can non-synonymous SNPs be?

Answer 6

Missense
Nonsense

Question 7

What does a missense non-synonymous SNP do?

Answer 7

Mutations change protein sequence, either to make a different amino acid

Question 8

What does a nonsense non-synonymous SNP do?

Answer 8

Mutations change protein sequence to make a STOP codon

Question 9

What other mutation can a non-synonymous SNP make?

Answer 9

Frameshift

Question 10

What is an example of a frameshift mutation?

Answer 10

An addition or deletion of a base within a coding sequence

Question 11

What is a read-through NS SNP mutation?

Answer 11

Converts a STOP codon into normal amino acid

Question 12

What could a non-coding SNP affect?

Answer 12

Gene splicing
Transcription
RNA stability

Question 13

What SNP is a risk factor for Alzheimers disease?

Answer 13

SNP in clusterin gene

Question 14

Give an example of a silent SNP (amino acid and its sequence):

Answer 14

UUA or UUG
leu

Question 15

Give an example of a missense SNP (amino acid and its sequence):

Answer 15

CCA or CAC
his or gin

Question 16

Give an example of a nonsense SNP (amino acid and its sequence):

Answer 16

UAC or UAA
tyr or STOP

Question 17

What can oxidative damage do?

Answer 17

Modify bases and following replication this can lead to transitions (purine – purine/ pyr-pyr) and transversion (pur – pyr)

Question 18

What other types of damage can cause the same outcomes as oxidative damage?

Answer 18

Hydrolysis
Alkylating Damage
Nitrous Acid

Question 19

What type of damage(s) can lead to a loss of bases and deletions?

Answer 19

Hydrolysis
UV damage

Question 20

What other damage can lead to sequence deletion?

Answer 20

Intrastrand damage

Question 21

What can replication slippage lead to?

Answer 21

Insertions

Question 22

What can does SNV stand for?

Answer 22

Single Nucleotide Variation

Question 23

What can SNVs lead to a gain or loss of?

Answer 23

A restriction site

Question 24

What does RFLP stand for?

Answer 24

Restriction Fragment Length Polymorphisms

Question 25

What do RFLPs do?

Answer 25

A restriction site containing a polymorphism (eg a SNP), where one version of the SNP creates or removes a restriction site

Question 26

What term is used to deScribe a set of SNPs that tend to always be transmitted together?

Answer 26

Haplotype

Question 27

What does the haplotypes being located close together on the chromosome prevent?

Answer 27

Recombination breaking them up

Question 28

What are haplotypes useful for?

Answer 28

Genetic studies that aim to identify novel disease genes

Question 29

What is an indel?

Answer 29

A genetic mutation where one or more nucleotides are inserted or deleted from a DNA sequence

Question 30

`What does CNV mean?

Answer 30

Copy Number Variation

Question 31

What does CNV typically refer to?

Answer 31

Indels (mostly larger ones, >100megabases)

Question 32

What are the 3 classes of tandem repeats in the satellite category?

Answer 32

Satellite DNA repeats Minisatellite DNA repeats Microsatellite DNA repeats

Question 33

What are Satellite DNA repeats associated with?

Answer 33

Centromeric regions of the genome

Question 34

What are minisatellite DNA repeats associated with?

Answer 34

Telomeres locations

Question 35

What are microsatellite DNA repeats widely distributed in?

Answer 35

Euchromatin

Question 36

What can variable number of tandem repeats (VNTRs) refer to?

Answer 36

Microsatellites and minisatellites

Question 37

What can short tandem repeats (STRs) or simple sequence repeats (SSRs) refer to?

Answer 37

Microsatellites

Question 38

What does satellite DNA overlap with?

Answer 38

The copy number variation

Question 39

What can replication slippage cause?

Answer 39

Increases or decreases in repeat number

Question 40

What happens when DNA sequences are tandemly repeated?

Answer 40

Instability

Question 41

What is a disease that can be associated with microsatellites?

Answer 41

Huntingtons disease (CAG)

Question 42

What are transposons ? How are they organised?

Answer 42

Major class of repetitive DNA Interspersed fashion

Question 43

What are the two classes of transposons?

Answer 43

DNA transposons Retrotransposons

Question 44

What do DNA transposons do?

Answer 44

Migrate directly without any copying of the sequence (cut-and-paste)

Question 45

What are the three types of retrotransposons?

Answer 45

Long interspersed nuclear element (LINEs) Short interspersed nuclear element (SINEs) Retrotransposons with long terminal repeats (LTRs)

Question 46

What does 'Transposition of LINEs is autonomous' mean?

Answer 46

Sequence of the LINE when transcribed makes all necessary proteins required for transposition to occur

Question 47

What is an example of a disease caused by LINEs?

Answer 47

Duchenne Muscular Dystrophy (Mutations in the dystrophin gene)