Brainscape's Knowledge GenomeTM

Browse over 1 million classes created by top students, professors, publishers, and experts.


See full index

Pharmacogenomics > Lecture 1 + 2 > Flashcards

Lecture 1 + 2 Flashcards

1
Q

Actionable Signature

A

-info used to make tx decision
-genetic markers help dosing and efficacy
-ex VKOCR1, CYP2C9, CYP4F2 polymorphisms in pt taking warfarin
-150 pharmacogenomic drug labels in 2018 to 517 entries in 2023

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
2
Q

Genetic factors affect PK and PD

A

-PK (ADME)
-PD (receptor, targeting, enzymes, etc)

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
3
Q

DNA

A

-thin (2nm)
-linear polymer fiber, double helix
-ATGC
-A=T
-G≡C (3 H bonds)

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
4
Q

Genome

A

-complete set of one’s DNA
->3 billion base pairs in human
->21k genes
-contained in all cells w nucleus

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
5
Q

Genes

A

-seq of DNA or RNA that codes for a molecule that has a function
-can be a few hundred to 2 million BP long
-21k in humans, similar to mice
-protein coding or noncoding

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
6
Q

Protein coding genes

A

-expressed to be proteins
-1-3% of genome (~20,000genes)

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
7
Q

Noncoding genes

A

-final product is RNA not protein
-tRNAs (transfer aa to RNA to make protein)
-rRNAs (ribosome)
-microRNAs (miRNA): regulate protein-coding gene expression

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
8
Q

Gene nomenclature

A

-genes italicized, proteins not
-abbreviation, family based, or arbitraty assignment

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
9
Q

Structure of gene

A

-promoter
-5’ untranslated region (UTR)
-exons and introns
-3’ UTR

-flanking sequences

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
10
Q

Structure of real gene (SCN2A)

A
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
11
Q

Sequence position

A

-each nucleotide has unique position (locus) in reference genome

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
12
Q

Chromatin

A

-unwound
-interphase
-DNA available for transcription

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
13
Q

Chromosome

A

-tightly packed
-cell division
-DNA not in use

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
14
Q

Human genome

A

-46 chromosomes (23 pairs)
-karyotype

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
15
Q

karyotype

A

-complete pic of genome in cell

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
16
Q

Why chromosome pairs?

A

-half from each parent
-inc genetic diversity

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
17
Q

Expression of Genetic information (central dogma)

A
  1. Transcription (DNA to RNA)
  2. Translation (RNA to protein)

-viruses can go from RNA to DNA w reverse transcription or use RNA replication
-prion disease (virus replicating protein)

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
18
Q

Transcription

A

-mRNA maturation process
-mRNA precursor: DNA but w poly A tail and cut out introns
-matured mRNA: in cytoplasm with alll introns removed and poly a tail (AUCG)

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
19
Q

Translation

A

-RNA to protein
-starts with AUG (makes methionine)
-stops at UAG, UAA, UGA
-open reading frame (ORF)

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
20
Q

Open reading frame

A

-coding DNA seq (CDS)
-AUG to the codon before stop codon
-protein starts w methionine

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
21
Q

SLIDE 24-25

A

v important yes

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
22
Q

Genetic coding system

A

-64 codons (1 starts, 3 stop)
-20 amino acids
-chart

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
23
Q

start codon

A

-ATG

24
Q

Stop codons

A

-UAA
-UAG
-UGA

25
Q

Sequence variations (polymorphism)

A

-genetic variation at the SAME position of HOMOLOGOUS CHROMOSOMES
-NO polymorphisms in SINGLE GERM cell (haploid genome)
-ex: Single nucleotide polymorphism (SNP)
-

26
Q

allele

A

DNA seq at locus of ONE of two HOMOLOGOUS chromosome

27
Q
A
28
Q
A
29
Q

Genotype

A

combo of alleles at SAME locus of the homo chromo in a genome/cell

30
Q

Homozygote

A

pair of identical alleles at the locus
-genotype=homozygous

31
Q

Heterozygote

A

-2 diff alleles at same locus
-genotype = heterozygous

32
Q

Hemizygous

A

-one allele present while the other allele is missing
-genotype= HETEROZYGOUS

33
Q

Mendel’s Law

A

-each parent passes random allele to offspring (law of segregation)

34
Q

Single Nucleotide polymorphisms (SNP)

A

-one nucleotide is changed to another
-most common DNA seq variation
-55mil SNPs in SNP database

35
Q

most common polymorphisms

A

-SNPs

36
Q

cSNP

A

-SNP in coding region
-nonsynonymous or synonymous

37
Q

Non-synonymous SNP

A

-change aa in the protein
-missense (substitute)
-nonsense (stop codon)

38
Q

Missense SNP (cSNP)

A

-amino acid substitution
-can lead to gain or loss of function

39
Q

Nonsense SNP

A

-aa changes to stop codon
-usually loss of function

40
Q

Synonymous SNP

A

-does not change aa
-usually doesnt change function
-silent SNP = no aa change

41
Q

Noncoding region SNPs

A

-intronic
-SNPs in gene flanking regions and intergenic regions
-SNPs in UTR region

42
Q

Copy Number Variation (CNV)

A

-DNA region has 0-n copies in a population
-structural variation
-1kb-several Mb
-making each chromosome longer or shorter
-ex: CYP2D6 has 0-13 copies

43
Q

Insertion/Deletion (Indel)

A

-NTs present or absent from locus: 0 or 1 copy
-can be 1 to N NTs
-single indel is a specific form of SNP
-large ones are usually CNVs
-frameshift of reading fram = truncated protein

43
Q

Truncated protein

A

-loss of function
-sent to degradation

44
Q

Repetitive DNA variations

A

-Short Tandem Repeat (STR): short seq (1-1000bp) repeats N times (X)n
-Variable number of tandem repeat
-micro-satellite/mini-satellite (1-4bp)

-not starred

45
Q

Multi allelic polymorphisms (no star)

A

-often in the UTR region!!!!
-some cases of neurogenetive disorders like Huntington’s disease

46
Q

UGT1A1-53 (TA)n polymorphism (no star)

A

-(TA)n, n=5-8
-occurs in TATA box of promoter
-common alleles: 6 and 7
-Reduced UGT1A1 gene expression

47
Q

Reference comparison

A

-DNA: 1 copy of CYP2C19 in genome makes 100 copies mRNA
-100 copies of mRNA makes 1000 copies of protein
-1000 copies of proteins metabolize 10k drug molecules

48
Q

CNV comparison

A

-7 copies of CYP in genome = 700 mRNA = 7000 protein - 70k drug molecules metabolized
=gain of function

49
Q

Genen expression (repetitive DNA variation)

A

-1 copy CYP2C19 makes 50?
-loss of function

50
Q

Missense comparison

A
51
Q

Nonsense comparision

A

-1 to 100
-100 makes 1000 TRUNCATED proteins
=0 drug molecules metabolized
-loss of function

52
Q

rs number

A

-ID for SNPs
-assigned number follows

53
Q

Nomenclature

A

-gene/allele name: itallics
-protein name regular
-asterisk (gene) vs dot (protein)

54
Q

CYP2C19 nomenclature

A

-CYP2C191A (no SNPs, normal function)
-2D: splicing defect (99C>T) loss of function
-3A: nonsense (stop codon) loss of function
-17: missense, gain of function

55
Q

slide 17

A

slide 17
-*=different phenotypes= metabolize drug differently

Pharmacogenomics (3 decks)

Brainscape helps you reach your goals faster, through stronger study habits.
© 2025 Bold Learning Solutions. Terms and Conditions