Exam 1 material

Question 1

What is the most common type of polymorphism? What is the frequency?

Answer 1

Single nucleotide polymorphism

Occurs in 1/300-750bp in the genome

Question 2

How many SNPs are deposited in the SNP database.

Answer 2

55M SNPs deposited

Question 3

What is the difference between Non-synonymous SNP and Synonymous SNP?

Answer 3

Non synonymous is changing amino acid in the protein

Synonymous SNP does not change amino acids, usually does not change gene function.

Question 4

What is the difference between Missense and Nonsense SNP?

Answer 4

Missense is amino acid substitution

Nonsense is amino acid changes to a stop codon.

Question 5

What is a silent SNP?

Answer 5

it is a synonymous SNP that has no amino acid change.

Question 6

What is a CNV?

Answer 6

Copy number variations. It is a polymorphism. It is a DNA region that has 0-n copies in a population. This makes a chromosome longer or shorter.
EX: CYP2D6, CYP2A6, SULT1A1, UGT2B17, GSTM1, GSTT1

Question 7

What is Indel?

Answer 7

It is a type of polymorphism that is an insertion/deletion. nucleotides are either present or absent from a locus: 0 or 1 copy. Can be 1 to N nucleotides.

Question 8

True or False

A gene/allele name can be recognized because it will be italicized.

Answer 8

True

Question 9

Will a protein name be italicized, bold or regular print?

Answer 9

Regular

Question 10

What does a * indicate?

Answer 10

Allele or haplotide

Question 11

what does a “ dot” indicate?

Answer 11

Protein isoform

Question 12

True or False

A single DNA variant can cause a disease.

Answer 12

True

Question 13

EGFR

Answer 13

Epidermal Growth Factor Receptor gene

Question 14

CYP3A4 - What does this mean?

Answer 14

Cytochrome p450 gene family 3 subfamily A gene #4

Question 15

What does C9ORF106 mean?

Answer 15

Chr 9 opening reading frame #106

Question 16

What is transcription and where does it occur?

Answer 16

It changes DNA into RNA in the NUCLEUS. There is now a U instead of T in RNA. 5’ cap and 3’ - polyA tail

Question 17

What is translation and where does it occur?

Answer 17

RNA into a protein. Occurs in the cytoplasm. Has a tart and stop codon. Start: AUG,
STOP: UAA, uAG, UGA

Question 18

Genetic coding system has how many codons and amino acids?

Answer 18

64 codons (3 stop and 1 initiation)
20 amino acids

Question 19

In Transcription, what are the CIS regulatory elements?

Answer 19

Promoter (usually about 500bp upstream of a gene, Enhancer (can be multiple sites in the gene or far away), Suppressor (multiple sites), Transcription start site (TSS: TATA box, CAAT box, transcription factor binding sites, Transcription stop signal.

Question 20

What are the Trans-regulatory elements in transcription?

Answer 20

Protein transcription factors (TFs), Non coding RNA’s (miRs) targeting 3’-UTR

Question 21

What makes the diversity and adaptability of humans to a changing environment?

Answer 21

Sequence Variation

Question 22

What is a polymorphism?

Answer 22

a sequence variation at the same position of homologous chromosomes (diploid genome)

Question 23

Is there a polymorphism in the genome of a single germ cell (haploid genome)?

Answer 23

NO!! Has to be diploid

Question 24

True or False: Polymorphism can lead to inter patient differences in response to a drug

Answer 24

True

Question 25

What is the significance of a UGT1A1-53 (TA)n polymorphism

Answer 25

Anticancer drugs can be metabolized by this.

Question 26

What controls blood levels of warfarin?

Answer 26

Cyp2c9

Question 27

What enzyme controls drug target for warfarin?

Answer 27

Vkorc1

Question 28

What polymorphism is single biggest predicted for warfarin dose?

Answer 28

Vkorc1