Jagger slides lecture 1.2

Question 1

1.2

Question 2

1) Define Single Nucleotide Polymorphisms (SNPs)
2) What does it usually have?
3) Where do most occur?

Answer 2

1) Multiple versions of nucleotide base at single location “substitution
2) Usually has but two alleles
3) Non-coding portions of DNA

Question 3

1) More than 100K ________ SNP’s have been discovered
2) Half of these do not alter the amino acid sequence (called “________________”)
3) Those that alter amino acid sequence are “________________”

Answer 3

1) exonic
2) synonymous
3) nonsynonymous

Question 4

List 2 significant changes caused by Single Nucleotide Polymorphisms (SNPs)

Answer 4

1) Altering or introducing a stop codon
2) Altering a splice site where introns/exons are altered

Question 5

1) How many base pairs can Indels (Insertion / deletion polymorphisms) occur in?
2) How many alleles do most “simple” indels have? What does this mean?
3) What is another type of indel besides “simple”? What are these?

Answer 5

1) as few as one base pairs, and as many as ~1000
2) Two; basically, the presence or absence of the inserted/deleted segment
3) “Microsatellite”; have multiple short repeats of the inserted segment

Question 6

1) Give an example of a microsatellite indel
2) What does this make? What are these called?

Answer 6

1) Instead of a single instance of TGT, you see TGTTGTTGTTGTTGT
2) Many different alleles, depending upon how many repeats there are. Called STR polymorphisms
(“short tandem repeat”; tandem means “length”)

Question 7

1) What can be unique and used to identify individuals and families
2) Microsatellite loci are known to researchers and number in the _____________

Answer 7

1) Microsatellite indels
2) thousands

Question 8

What is involved in DNA fingerprinting?

Answer 8

Microsatellite indels

Question 9

1) Mobile Element Insertion Polymorphisms consist of what? Give examples
2) What happens to these? What is this called?
3) What is this process called? What is it similar to?

Answer 9

1) Repetitive elements (think Alu and LINE)
2) Transcribed into RNA, then reverse transcribed back into the DNA code, but at a different locus; retrotranscription
3) Insertion (i.e. transposition); processed pseudogenes

Question 10

1) What are Copy Number Variants?
2) What are the largest of these called?
3) The allelic variation comes from what?

Answer 10

1) Up to hundreds of thousands of base pairs long
2) “segdups” (segmental duplications)
3) The number of copies

Question 11

Regarding copy number variants:
1) True or false: The larger the number of copies inserted, the more variation
2) If these do include genetic material, what can they do? Why is this a big deal?

Answer 11

1) True
2) Alter gene dosage; it’s like giving yourself multiple copies of a given gene

Question 12

1) Define inversion polymorphism
2) When does it often happen?

Answer 12

1) A portion of the sequence is “flipped around”
2) During recombination
(recombination is the same thing as “crossing over”)

Question 13

1) What are the two general types of inversion polymorphisms?
2) What can inversion polymorphisms result in?

Answer 13

1) Pericentric (includes centromere) vs paracentric (doesn’t)
2) Duplication or deletion of DNA located between regions of homology, causing genetic disease

Question 14

1) Many chromosome mutations are produce a change in the number of what?
2) What is this caused by?
3) What does this result in? Maternal or paternal?
4) In what chromosomes is this nearly always lethal? Why?

Answer 14

1) Chromosomes
2) Chromosome missegregation during meiosis I or II
3) Aneuploidy; maternal or paternal (often maternal)
4) autosomal; “gene dosing”

Question 15

1) Give 3 examples of regional mutations. When do all of these predominantly happen?
2) Give an example of where this can happen

Answer 15

1) Large duplications, deletions, or inversions; during recombination
2) At spontaneous breaks in the DNA

Question 16

Single gene mutations:
Include base pair substitution, indels, can occur in what two ways?

Answer 16

1) During DNA replication
2) After failure to repair damaged DNA

Question 17

Frameshift mutations: When the insertion / deletion number of nucleotides is not a multiple of three, what happens?

Answer 17

Everything downstream is messed up

Question 18

1) Define placental mosaicism
2) Define somatic mosaicism
3) Define germline mosaicism
4) When does segmental mosaicism occur? Give an example

Answer 18

1) In the extraembryonic tissue but not in baby
2) In the body and not gametes
3) In the germline only
4) Only part of the body is affected; neurofibromatosis 1

Question 19

True or false: Mosaicism might and will occur due to X-inactivation

Answer 19

True

Question 20

List 4 different types of mosaicism

Answer 20

1) Placental
2) Somatic
3) Germline
4) Segmental

Question 21

1) Define hemochromatosis
2) What is its penetrance and expressivity?
3) What inheritance pattern does it have?

Answer 21

1) Disease of iron overload resulting in mutation of the HFE gene
2) Incomplete penetrance and variable expressivity
3) Autosomal recessive inheritance pattern