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Spring 2024 (All Classes Except Therapeutics+ Lab) > Pharmacogenomics Quiz 1 > Flashcards

Pharmacogenomics Quiz 1 Flashcards

1
Q

What is an “actionable signature”?

A

Information used to make a treatment decision

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2
Q

As of 2018, how many pharmacogenomic drug labels have been approved by the FDA?

A

150

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3
Q

As of 2023, how many pharmacogenomic drug entries have been approved by the FDA?

A

517

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4
Q

What can genetic markers distinguish about patients?

A

-Who is most likely to respond to a drug
-Who is most likely to develop side effects
-Who should not take the drug
-The best dose they should take

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5
Q

What is Pharmacokinetics (PK)?

A

What the BODY does to the drug

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6
Q

What is Pharmacodynamics (PD)?

A

What the DRUG does to the body

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7
Q

What are the 4 roles of a pharmacist in pharmacogenomics?

A

RECOMMENDING (or scheduling) pharmacogenomics testing to help with drug and dosage selection

DESIGNING patient-specific drug and dosage regimen based on their genetic profile that also considers the PK and PD of the drug

EDUCATING patients, pharmacists, and health care professionals about pharmacogenomics and indications for clinical pharmacogenomic testing

COMMUNICATING genetic drug therapy recommendations to the health care team (includes documenting interpretation of results in patient’s health record)

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8
Q

What is an intrinsic factor?

A

A genetic/ physiological factor

(intrinsic to a person)

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9
Q

What is an extrinsic factor?

A

An environmental factor

(extrinsic to a person)

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10
Q

What are the 4 nucleobases of DNA?

A

Adenine (A)

Thymine (T)

Guanine (G)

Cytosine (C)

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11
Q

What nucleobase bonds with Adenine (A)

A

Thymine (T)

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12
Q

What nucleobase bonds with Guanine (G)?

A

Cytosine (C)

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13
Q

How many hydrogen bonds form between Adenine (A) and Thymine (T)?

A

2 hydrogen bonds

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14
Q

How many hydrogen bonds form between Guanine (G) and Cytosine (C)?

A

3 hydrogen bonds

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15
Q

Which DNA base pairs bind more strongly to each other? A + T or C + G

A

C + G

A + T form 2 hydrogen bonds whereas C + G form 3 hydrogen bonds

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16
Q

How many pairs of chromosomes do humans have?

A

23

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17
Q

What is a genome?

A

An organism’s complete set of DNA (including all of its genes)

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18
Q

How many DNA base pairs make up the human genome?

A

3 billion DNA base pairs

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19
Q

A copy of the entire genome is contained where in the human body?

A

In all cells that have a nucleus

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20
Q

How many base pairs are in a kilobase (kb)?

A

1000 bp

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21
Q

How many base pairs are in a megabase (Mb)?

A

1 million bp

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22
Q

How many total genes are found in the human genome?

A

21,000 (about 20,000)

*this is actually lower than previously expected, similar to the # found in mice

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23
Q

What is a gene?

A

A sequence of DNA or RNA which codes for a molecule that has a function

-Made up of DNA

-Act as instructions to make molecules

**evolving concept

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24
Q

What is a protein coding gene?

A

A gene that is expressed to be a protein

(type of classification of genes)

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25
Q

What % of the human genome are protein-coding sequences?

A

1-3%

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26
Q

What is a noncoding gene?

A

A gene who’s final product is an RNA (not a protein)

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27
Q

What is a Transfer RNA (tRNA)?

A

RNA that transfers amino acids to the RNA template to make proteins

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28
Q

What is Ribosomal RNA (rRNA)?

A

The RNA component of a ribosome

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29
Q

*What is microRNA (miRNA)?

A

RNA that plays an important role in regulating protein-coding gene expression

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30
Q

True or False: Symbols for genes are italicized, but symbols for proteins are not

A

TRUE

*important part of gene nomenclature

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31
Q

True or False: DNA always has a promoter region

A

True

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32
Q

What is the function of the promoter region in DNA?

A

Determines what tissue the gene will be expressed in

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33
Q

What is the 5’UTR in DNA and what is its function?

A

(5’ Untranslated region)

Has a regulatory function
(if some cells need more of a protein or less of a protein, or need a protein to go to a certain location, this region regulates it)

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34
Q

Where is the 5’UTR found?

A

Exists in DNA and mRNA but NOT IN PROTEIN

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35
Q

Which region is removed to make mRNA and eventually, a protein?

(Intron or Exon)

A

Intron (non-coding)

-exons (coding) remain and are eventually made into proteins

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36
Q

Which region is a coding region that contains information to encode a protein. This region is not removed from a gene.

(Intron or Exon)

A

Exon

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37
Q

What is the professor’s favorite gene?

A

SCN2A

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38
Q

Note:

A

Review Lecture 2 Slide 9

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39
Q

What is a sequence position?

A

The unique position of a nucleotide in the reference genome

(The starting point and ending point of a gene in the genome)

(location of a gene)

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40
Q

What is a locus?

A

The unique position of a nucleotide in the reference genome

(similar to sequence position)

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41
Q

What is chromatin?

A

Unwound DNA with proteins

(accessible for transcription)

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42
Q

What is a chromosome?

A

Tightly packed DNA

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43
Q

How does packing/unpacking DNA affect gene expression?

A

If you want to express only one gene, you have to unpack DNA

(otherwise it is too tightly packed to only do one)

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44
Q

How many chromosomes does a human have?

A

46

(23 pairs)

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45
Q

What is a non-sex chromosome called?

A

Autosome

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46
Q

What is a karyotype?

A

A complete picture of the genome in a cell

(done on unborn fetuses to detect for disease)

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47
Q

Why are chromosomes paired up into homologous chromosomes?

A

-One chromosome comes from the mother and one from the father and they pair

-Main reason is to increase genetic diversity of the population to increase survival

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48
Q

What disease has the first CRISPR medication been developed to target?

A

Sickle cell disease

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49
Q

How is genetic information expressed (AKA Central Dogma) (what is the pathway it takes)?

A

Previous thinking:
DNA (replicates) -> Transcription -> RNA -> Translation -> Protein

Now:
-DNA replicates and is transcribed to RNA
-Transcription is reversible!
-RNA is able to replicate and then is translated to protein
-Protein replicates itself through prion

*see Lecture 2 Slide 14

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50
Q

What is the process of changing DNA to RNA?

A

Transcription

*reversible

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51
Q

What is the process of changing RNA to protein?

A

Translation

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52
Q

True or False: RNA is less stable than DNA

A

TRUE

53
Q

What process of the central dogma results in the creation of viruses such as coronavirus?

A

RNA replication

(RNA is less stable than DNA, more likely to have mutations and change when it replicates)

*coronavirus is an RNA based virus and does not have DNA

54
Q

Instead of a Thymine (T) nucleobase, what is present in RNA instead?

A

Uracil (U)

55
Q

What is missing in a matured mRNA?

A

Introns

56
Q

When matured mRNA is formed, where is it exported to?

A

Exported from the Nucleus to the Cytoplasm

57
Q

When DNA is transcribed to matured mRNA, what intermediate form is it changed to first?

A

mRNA precursor

**introns have not yet been cut out but are starting to

58
Q

What is the start codon?

A

AUG

(ATG in DNA)

59
Q

What amino acid does the start codon (AUG) code for?

A

Methionine

60
Q

What is the “open reading frame”?

A

The sequence from the start codon to the codon before the stop codon

61
Q

What is a “premature stop”?

A

When a protein has a stop codon in the wrong place

-causes the reading frame to stop prematurely and leads to disease

62
Q

True or False: Only the first ATG is the start codon

A

True
-if there is another ATG in the sequence, it is not a start codon
(only the first ATG starts a protein)

63
Q

True or False: Any UAA, UAG, OR UGA us a stop codon regardless of its position in a sequence

A

TRUE
-anytime one of these codons appears, it is a stop codon
-there should not be any of these codons in the middle of a protein (otherwise it is a “premature stop”)

64
Q

How many total codons are there?

A

64

65
Q

How many amino acids are there?

A

20 amino acids

66
Q

What is a benefit of having multiple codons code for the same amino acid?

A

Increases resistance to genetic changes

67
Q

What is a polymorphism?

A

A sequence variation at the same position in homologous chromosomes

-influences diversity and adaptability of humans to a changing environment

68
Q

Can polymorphisms affect the genome of single germ cells (haploid cells)?

A

NO
-only affect homologous chromosomes and occurs in both

69
Q

True or False: all polymorphisms cause disease

A

False, only cause disease when they affect the function of a protein

70
Q

What is a Single Nucleotide Polymorphism (SNP)?

A

A single nucleotide is changed to another

*most common DNA sequence variation

*often changes the amino acid coded for

(ex: A changed to C in a codon)
(ex: CTA changed to CTC)

71
Q

*What is an allele?

A

The DNA sequence at a locus of ONE of the two homologous chromosomes

(each chromosome can have a different or identical version of the allele)

72
Q

*What is a genotype?

A

The combination of alleles at the same locus of the homologous chromosomes in a genome/cell

73
Q

What is a homozygote?

A

An individual that has a pair of identical alleles at the locus

(genotype is homozygous)

74
Q

What is a heterozygote?

A

An individual has two different alleles at the same locus

(genotype is heterozygous)

75
Q

What is a hemizygote?

A

An individual where one allele presents while the other allele is missing on the other chromosome

(genotype is hemizygous)

*their genotype is also considered heterozygous

76
Q

What is Mendel’s Law (of segregation)?

A

Every individual possesses two alleles and each parent passes one of them (randomly selected) onto the offspring

77
Q

What is the most common DNA sequence variation/ polymorphism?

A

Single nucleotide polymorphism (SNP)

(>90% of all genetic variations)

78
Q

What are the two types of Single Nucleotide Polymorphisms (SNPs) that can occur in the coding region (cSNP)?

A

Non-synonymous SNP

Synonymous SNP

79
Q

What is a non-synonymous SNP?

A

A single nucleotide polymorphism where the amino acid is changed in the protein

80
Q

What is a synonymous SNP?

A

A single nucleotide polymorphism where a change in a nucleotide does not result in a change in the amino acid coded for

-the gene/protein function is normally not changed

(silent SNP)

81
Q

What are the 2 types of non-synonymous SNPs?

A

Missense SNP

Nonsense SNP

82
Q

What is a Missense SNP?

A

A nucleotide change leads to an amino acid substitution
(but does not change to a stop codon)

(either leads to gain- or loss-of-function for the protein depending on what amino acid it changes to)

83
Q

What is a Nonsense SNP?

A

A nucleotide change leads to an amino acid being changed to a stop codon

(normally leads to loss-of-function only!)

84
Q

True or False: You can look at a codon and tell if it is gain- or loss-of-function

A

FALSE

-You cannot tell just by looking at it!!

*Have to check its function!

*ONLY can tell if it is missense or nonsense, nonsense is typically loss-of-function

**IF THERE IS A QUESTION ON THE EXAM asking about missense SNP and whether it is gain- or loss-of-function, the answer is: need more information

85
Q

If a question on the exam gives you a missense SNP and asks if it is gain- or loss-of-function with no other information, what is the answer?

A

NEED MORE INFORMATION

-cannot tell without information about how it is functioning

86
Q

If a question on the exam gives you a nonsense SNP and asks if it is gain- or loss-of-function, what is the answer?

A

Loss-of-function

87
Q

True or False: Many newborns require both alleles to have a mutation in order to develop a disease

A

True

88
Q

What is a truncated protein?

A

A protein that has been shortened by a nonsense SNP mutation

89
Q

What is a copy number variation (CNV)?

A

Sections of the genome are repeated and the number of repeats varies between individuals

-A DNA region (a part or even one or more entire genes) has 0-n copies in a population

90
Q

How does copy number variation (CNV) affect the way a patient metabolizes a drug?

A

-Can change the number of enzymes a patient has to metabolize a drug

(0 copies= patient cannot metabolize a drug)

(Many copies (ex: 7)= patient metabolizes drug too fast)

91
Q

What is an insertion/deletion polymorphism (Indel)?

A

An extra nucleotide is added or deleted from a locus

-Can be 1 to n nucleotides

**this is very bad because it changes the reading frame (frameshift) and affects all amino acids after it

-Can be an SNP
-Large ones are CNVs

92
Q

What affect does a frameshift have on the resulting protein?

A

Often leads to a truncated (loss-of-function) protein for degradation

93
Q

What is the only scenario in an insertion/deletion (Indel) polymorphism where a frameshift does not occur?

A

When 3 nucleotides are added or deleted (or any multiple of 3)

-in this case, an amino acid is inserted or deleted without affecting the others downstream

94
Q

What are the parts of the nomenclature of a gene?

A

Species -> Superfamily -> Family -> Subfamily -> Isoform -> *Allele/haplotype

EX: Human CYP2C19*17

Species: Human
Superfamily: CYP
Family: 2
Subfamily: C
Isoform: 19
Allele/Haplotype: *17

*Note: this entire thing should be italicized

*Note: GENE NAME only includes: Superfamily, Family, Subfamily, and Isoform

95
Q

Regarding nomenclature, what should be italicized?

A

Gene/ allele name

**not a protein name!!

96
Q

Regarding nomenclature, when would we use a * vs a .

A

For genes/alleles: use a *before the allele/haplotype

For proteins: use a . before the allel/haplotype

Ex Gene: italicized CYP2C19*17

Ex Protein: CYP2C19.17

97
Q

*Note

A

Review lecture 3 slide 18 for nomenclature

98
Q

What does a * in the nomenclature refer to?

A

A certain SNP that is present that results in a certain functional change

99
Q

What is an ultrarapid metabolizer?

A

A patient who metabolizes a drug with normal or increased activity

100
Q

What genotype results in an ultrarapid metabolizer?

A

Two increased activity alleles (17/17)
or
One functional allele + one increased-activity allele (1/17)

101
Q

What is an extensive metabolizer?

A

A patient who metabolizes a drug with homozygous wild-type or normal activity

102
Q

What genotype results in an extensive metabolizer?

A

Two functional alleles (1/1)

103
Q

What is an intermediate metabolizer?

A

A patient who metabolizes a drug with heterozygous or intermediate activity

104
Q

What genotype results in an intermediate metabolizer?

A

One functional allele + one loss-of-function allele (1/2-8)

One loss-of-function allele + one increased-activity allele (2-8/17)

105
Q

What is a poor metabolizer?

A

A patient who metabolizes a drug with homozygous variant, mutant, low, or deficient activity

106
Q

What genotype leads to a poor metabolizer?

A

Two loss-of-function alleles (2-8/2-8)

107
Q

What is the Increased Activity Allele?

A

*17

108
Q

What is the Functional Allele?

A

*1

109
Q

What are the Loss-of-Function Alleles?

A

2-8

110
Q

What mutation does CYP2C19*1A correlate to?

(note the *1A)

A

None, no change in gene

-Normal function

111
Q

What mutation does CYP2C19*2D correlate to?

(note the *2D)

A

Splicing defect

Loss-of-Function

112
Q

What mutation does CYP2C19*3A correlate to?

(note the *3A)

A

Nonsense (stop codon)

Loss-of-function

113
Q

What mutation does CYP2C19*17 correlate to?

(note the *17)

A

Missense (point mutation)

Gain-of-function

114
Q

What is “Minor Allele Frequency”

A

The frequency that an unlikely phenotype (ultrarapid metabolizer, extensive metabolizer, etc.) appears in the population

-know how to calculate
-expressed as a %

115
Q

What number represents the number of homologous chromosomes when calculating allele frequency?

A

For a given population of N individuals, the number of homologous chromosomes is 2N

(each individual has 2 homologous chromosomes paired)

116
Q

What is the equation for Allele Frequency?

A

N= Q+R+S

N= # of individuals in population

Q= Number of homozygous people with one allele (T/T)

R= Number of heterozygous people (T/C)

S= Number of homozygous people with other allele (C/C)

117
Q

How do we find the % of an allele in a given population?

A

First: Find the total number of the allele

Ex: T allele= 2Q + R

(Q= # of people with T/T
and
R= # of people with T/C)

Next: Find the % of the allele in the total population

Ex: T allele % = (2Q+R)/2N

N= number of individuals in the population
(note: 2N = the total number of homologous chromosomes/alleles in the population since each person has 2)

118
Q

What is the equation to calculate Minor Allele Frequency? (AKA an Allele %)

A

Allele% = Homozygote % + (1/2) Heterozygote %

*note: must know the genotype frequencies to do this

119
Q

True or False: Allele frequencies usually stay stable in a population

A

True

120
Q

True or False: A rare allele in one population can be a common allele in another population

A

True

121
Q

What is a haplotype?

A

A group of genes within an organism that were inherited together from a single parent

Also refers to the inheritance of a cluster of single nucleotide polymorphisms (SNPs)

122
Q

What is linkage disequilibrium (LD)?

A

Non-random association of alleles at different loci on the same chromosome

123
Q

When there is infinite recombination, how does this affect linkage disequilibrium?

A

No Linkage Disequilibrium

(distance between two loci is so long that every time recombination occurs, they will be recombined a lot of the time. Almost independent segregation occurs)

124
Q

When there is no recombination, how does this affect linkage disequilibrium?

A

Complete/Perfect Linkage Disequilibrium

(distance between two loci is so short that every time recombination occurs, they are always switched together 100% of time, never recombined)

125
Q

When recombination occurs in a portion of chromosomes, how does this affect linkage disequilibrium?

A

Incomplete Linkage Disequilibrium

126
Q

What does R^2 measure regarding Linkage Disequilibrium (LD)?

A

How strong the correlation is between two variables (strength of LD)

*varies from 0 to 1

127
Q

What does an R^2 of 0 mean?

A

No Linkage Disequilibrium (LD)

128
Q

What does an R^2 of 1 mean?

A

Complete/Perfect Linkage Disequilibrium (LD)

129
Q

An R^2 of what value is considered a strong Linkage Disequilibrium (LD)?

A

> or = 0.8

Spring 2024 (All Classes Except Therapeutics+ Lab) (9 decks)

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