Quiz 1 (first 4 lectures)

Question 1

what are “actionable signatures”?

Answer 1

information used to make treatment decisions (ex. genetic markers)

Question 2

polymorphisms in which 3 enzymes/CYPs determine ~50% of dose variance in pts taking warfarin?

Answer 2

VKORC1, CYP2C9, CYP4F2

Question 3

the FDA has approved ~_____ pharmacogenomic drug labels as of 2018

Answer 3

~150

(385 entries in 2020, 517 entries in 2023)

Question 4

ADME is part of

a. pharmacodynamics (PD)
b. pharmacokinetics (PK)

Answer 4

b. pharmacokinetics (PK)

Question 5

receptors, targets, signaling, and enzymes are part of

a. pharmacodynamics (PD)
b. pharmacokinetics (PK)

Answer 5

a. pharmacodynamics (PD)

Question 6

A and T are bonded with how many hydrogen bonds?

Answer 6

2

Question 7

G and C are bonded with how many hydrogen bonds?

Answer 7

3

Question 8

what is the diameter of DNA?

Answer 8

2 nm

Question 9

the entire human genome is more than ________ DNA base pairs?

Answer 9

3 billion

Question 10

gene vs genome

Answer 10

gene is a sequence of DNA or RNA which codes for a molecule that has a function; a genome is an organism’s complete set of DNA, including all of its genes

Question 11

how many protein coding genes are in the human genome?

Answer 11

~20,000

Question 12

what is the final product of a noncoding gene?

Answer 12

RNA (not a protein)

Question 13

which RNAs plays a role in regulating protein-coding gene expression?

a. transfer RNAs (tRNA)
b. ribosomal RNAs (rRNA)
c. microRNAs (miRNA)

Answer 13

c. microRNAs (miRNA)

Question 14

why do we have pairs of chromosomes?

Answer 14

one chromosome from each parent; this inc genetic diversity of the population; the different phenotypes lead to increased survival of the species

Question 15

true or false: mature mRNA do not have introns

Answer 15

true

Question 16

where does transcription occur in the cell?

Answer 16

nucleus

Question 17

what is added to end of the mRNA precursor in transcription?

Answer 17

poly A tail

Question 18

codon for start of translation

Answer 18

AUG (codes for methionine)

Question 19

3 stop codons

Answer 19

UAG, UAA, UGA

Question 20

what is another name for sequence variation?

Answer 20

polymorphism

Question 21

a polymorphism is a sequence variation at the same position of __________ chromosomes (diploid genome)

Answer 21

homologous

Question 22

true or false: polymorphisms are common in the genome of a single germ cell (haploid genome)

Answer 22

false (no polymorphisms in haploid genome)

Question 23

the DNA sequence(s) at a locus of one of the two homologous chromosomes

a. allele
b. genotype

Answer 23

a. allele

Question 24

what is the combination of alleles at the same locus of the homologous chromosomes in a genome/cell called?

Answer 24

genotype

Question 25

what is the genotype when someone has a pair of identical alleles at the same locus?

Answer 25

homozygous

Question 26

what is the genotype when someone has two different alleles at the same locus?

Answer 26

heterozygous

Question 27

what does hemizygous mean?

Answer 27

one allele is present and one is missing (a hemizygous genotype is also heterozygous)

Question 28

what is Mendel's Law of Segregation?

Answer 28

each parent passes a randomly selected allele (one of the two homologous chromosomes) to the offspring

Question 29

most common type of polymorphism (accounts for > 90% of all genetic variations)

Answer 29

single nucleotide polymorphism (SNP)

Question 30

difference between non-synonymous and synonymous SNP

Answer 30

non-synonymous will change AA in the protein, synonymous will not change AAs

Question 31

two examples of non-synonymous SNPs that we talked about

Answer 31

-missense SNP -> AA substitution (gain or loss of function) -nonsense SNP -> AA switches to stop codon (loss of function)

Question 32

example of synonymous SNP we talked about

Answer 32

silent SNP -> no AA change

Question 33

what SNP does a patient have if a sequence with a one base pair mutation now codes for Pro instead of His? a. missense b. nonsense c. silent d. intronic

Answer 33

a. missense (AA substitution)

Question 34

what is a copy number variation (CNV)? (I got this from internet)

Answer 34

when the # of copies of a particular gene varies from one person to the next

Question 35

if someone has 7 copy numbers of CYP2D6, will they need a lower dose or higher dose of CYP2D6 drugs?

Answer 35

higher dose bc they metabolize those drugs better

Question 36

which would be worse, an insertion/deletion of one nucleotide or 3 nucleotides?

Answer 36

one nucleotide bc this often causes a frameshift mutation leading to truncated protein for degradation

Question 37

which of the following is a protein? a. CYP2C19*17 b. CYP2C19.17

Answer 37

b. CYP2C19.17 (proteins use a dot, alleles use a star)

Question 38

which of the following should be italicized? a. CYP2C19*17 b. CYP2C19.17

Answer 38

a. CYP2C19*17 (Gene/allele is italicized. The star in the name means it is a gene, not a protein)

Question 39

what is minor allele frequency? (from internet)

Answer 39

frequency at which the second most common allele occurs in a given population

Question 40

difference between common/major/reference allele vs rare/minor/mutant allele

Answer 40

the common/major/reference occurs with frequency > 50% while the rare/minor/mutant allele occurs < 50%

Question 41

true or false: a rare allele is the same for every population

Answer 41

false (a rare allele in one population can be common in another population)

Question 42

which is the common allele and which is the rare allele in MDR1 3435T>C ?

Answer 42

T is common, C is rare allele

Question 43

what is a haplotype?

Answer 43

-a group of genes within an organism that were inherited together from a single parent -also refer to the inheritance of a cluster of SNPs

Question 44

what is linkage disequilibrium? a. random association of alleles at the same loci on the same chromosome b. non-random association of alleles at different loci on the same chromosome c. random association of alleles at different loci on different chromosomes d. non-random association of alleles at the same loci on different chromosomes

Answer 44

b. non-random association of alleles at different loci on the same chromosome

Question 45

what kind of linkage disequilibrium (LD) is there in each case? -when there are infinite recombinations -when there is no recombination -when recombination occurs in a portion of chromosomes

Answer 45

no LD complete/perfect LD incomplete LD

Question 46

R^2 value for complete/perfect LD

Answer 46

1

Question 47

R^2 value when there is no LD

Answer 47

0

Question 48

R^2 value when there is strong LD

Answer 48

0.8 or greater

Question 49

SNP1 and SNP2 has a linkage disequilibrium (LD) R2 value of 0.9. Which of the following is likely to be true: a. SNP1 and SNP2 are inherited independently of each other b. SNP1 and SNP2 have a high probability to be inherited together c. SNP1 and SNP2 have a low probability to be inherited together d. SNP1 and SNP2 are always inherited together

Answer 49

b. SNP1 and SNP2 have a high probability to be inherited together

Question 50

A missense mutation leads to ___ a. either gain-of-function or loss-of-function depending on the exact amino acid change b. protein-truncation c. loss-of-function d.gain-of-function

Answer 50

a. either gain-of-function or loss-of-function depending on the exact amino acid change

Question 51

How many base pairs have been identified in the whole human genome? a. ~3 million b. ~30 million c. ~300 million d. ~3 billion

Answer 51

d. ~3 billion