Quiz 1 (first 4 lectures) Flashcards
what are “actionable signatures”?
information used to make treatment decisions (ex. genetic markers)
polymorphisms in which 3 enzymes/CYPs determine ~50% of dose variance in pts taking warfarin?
VKORC1, CYP2C9, CYP4F2
the FDA has approved ~_____ pharmacogenomic drug labels as of 2018
~150
(385 entries in 2020, 517 entries in 2023)
ADME is part of
a. pharmacodynamics (PD)
b. pharmacokinetics (PK)
b. pharmacokinetics (PK)
receptors, targets, signaling, and enzymes are part of
a. pharmacodynamics (PD)
b. pharmacokinetics (PK)
a. pharmacodynamics (PD)
A and T are bonded with how many hydrogen bonds?
2
G and C are bonded with how many hydrogen bonds?
3
what is the diameter of DNA?
2 nm
the entire human genome is more than ________ DNA base pairs?
3 billion
gene vs genome
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
how many protein coding genes are in the human genome?
~20,000
what is the final product of a noncoding gene?
RNA (not a protein)
which RNAs plays a role in regulating protein-coding gene expression?
a. transfer RNAs (tRNA)
b. ribosomal RNAs (rRNA)
c. microRNAs (miRNA)
c. microRNAs (miRNA)
why do we have pairs of chromosomes?
one chromosome from each parent; this inc genetic diversity of the population; the different phenotypes lead to increased survival of the species
true or false: mature mRNA do not have introns
true
where does transcription occur in the cell?
nucleus
what is added to end of the mRNA precursor in transcription?
poly A tail
codon for start of translation
AUG (codes for methionine)
3 stop codons
UAG, UAA, UGA
what is another name for sequence variation?
polymorphism
a polymorphism is a sequence variation at the same position of __________ chromosomes (diploid genome)
homologous
true or false: polymorphisms are common in the genome of a single germ cell (haploid genome)
false (no polymorphisms in haploid genome)
the DNA sequence(s) at a locus of one of the two homologous chromosomes
a. allele
b. genotype
a. allele
what is the combination of alleles at the same locus of the homologous chromosomes in a genome/cell called?
genotype
what is the genotype when someone has a pair of identical alleles at the same locus?
homozygous
what is the genotype when someone has two different alleles at the same locus?
heterozygous
what does hemizygous mean?
one allele is present and one is missing (a hemizygous genotype is also heterozygous)
what is Mendel’s Law of Segregation?
each parent passes a randomly selected allele (one of the two homologous chromosomes) to the offspring
most common type of polymorphism (accounts for > 90% of all genetic variations)
single nucleotide polymorphism (SNP)
difference between non-synonymous and synonymous SNP
non-synonymous will change AA in the protein, synonymous will not change AAs
two examples of non-synonymous SNPs that we talked about
-missense SNP -> AA substitution (gain or loss of function)
-nonsense SNP -> AA switches to stop codon (loss of function)
example of synonymous SNP we talked about
silent SNP -> no AA change
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
a. missense (AA substitution)
what is a copy number variation (CNV)? (I got this from internet)
when the # of copies of a particular gene varies from one person to the next
if someone has 7 copy numbers of CYP2D6, will they need a lower dose or higher dose of CYP2D6 drugs?
higher dose bc they metabolize those drugs better
which would be worse, an insertion/deletion of one nucleotide or 3 nucleotides?
one nucleotide bc this often causes a frameshift mutation leading to truncated protein for degradation
which of the following is a protein?
a. CYP2C19*17
b. CYP2C19.17
b. CYP2C19.17
(proteins use a dot, alleles use a star)
which of the following should be italicized?
a. CYP2C19*17
b. CYP2C19.17
a. CYP2C19*17
(Gene/allele is italicized. The star in the name means it is a gene, not a protein)
what is minor allele frequency? (from internet)
frequency at which the second most common allele occurs in a given population
difference between common/major/reference allele vs rare/minor/mutant allele
the common/major/reference occurs with frequency > 50% while the rare/minor/mutant allele occurs < 50%
true or false: a rare allele is the same for every population
false (a rare allele in one population can be common in another population)
which is the common allele and which is the rare allele in MDR1 3435T>C ?
T is common, C is rare allele
what is a haplotype?
-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
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
b. non-random association of alleles at different loci on the same chromosome
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
no LD
complete/perfect LD
incomplete LD
R^2 value for complete/perfect LD
1
R^2 value when there is no LD
0
R^2 value when there is strong LD
0.8 or greater
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
b. SNP1 and SNP2 have a high probability to be inherited together
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
a. either gain-of-function or loss-of-function depending on the exact amino acid change
How many base pairs have been identified in the whole human genome?
a. ~3 million
b. ~30 million
c. ~300 million
d. ~3 billion
d. ~3 billion
