Brainscape's Knowledge GenomeTM

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


See full index

Year 3 - Biotech (2nd half) > 1 - Intro > Flashcards

1 - Intro Flashcards

1
Q

Define pharmacogenomics

A

General study of all of the different genes that determine drug response

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

How can genetic variations affect PK?

A
  • Drug uptake channels
  • Transporters
  • Drug metabolizing enzymes (CYP), etc.
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
3
Q

How can genetic variations affect PD?

A
  • Drug receptors
  • Receptor gated channels
  • Enzyme targets
  • Second messengers
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
4
Q

Define allele

A

2 copies of a gene, one from each parent

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

Define locus

A

Region on a chromosome

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

Define genotype

A
  • Entire genetic makeup of the cell/ organism

- 2 alleles for a specific gene or group of genes

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

Define haplotype

A
  • Group of alleles (or polymorphisms) on the same chromosome that are inherited together
  • Can refer to a combination of alleles or to a set of SNPs found on the same chromosome
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
8
Q

Define wild type

A
  • Normal sequence of the gene in the population

- Gene that is most often expressed in the population

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

Define polymorphism

A

Variation in DNA sequence present in 1% or more of the population

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

What are the types of polymorphisms?

A
  • Single nucleotide polymorphism (SNP)
  • Variable number tandem repeats (VNTR) – more than 1 nucleotide change (in tandem repeats)
  • Gene insertion or deletion
  • Multiple copies of a gene
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
11
Q

Types of single nucleotide polymorphisms (SNP)

A
  • Nonsense mutation -> premature stop codon SNP
  • Silent mutation -> synonymous SNP (nucleotide change that still results in the same AA)
  • Missense mutation -> non-synonymous SNP
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
12
Q

What is the difference between SNP deletions and insertions?

A
  • Deletion SNP will cause frame shift; almost certainly results in premature stop codon
  • Insertion SNP will cause frame shift; typically results in premature stop codon
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
13
Q

What can VNTR’s cause?

A
  • No effect on activity
  • Result in frame shift (causing no activity)
  • No frame shift but no activity
  • Loss of some activity
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
14
Q

What is a gene deletion and what does it cause?

A
  • Deletion of thousands of base pairs

- Results in loss of gene (no activity)

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

What is a gene duplication and what does it cause?

A
  • Duplication of the sequence of a gene

- Results in more activity, but the increase in activity isn’t always linear w/ increasing copies of said gene

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

Define intron

A

Removed from gene and doesn’t appear in final mRNA

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

Define exon

A

Sequence that makes up the final mRNA

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

What can polymorphisms w/in introns cause?

A
  • May not change gene activity but could change gene expression
  • In the intron-exon boundary, may result in splice variant
19
Q

What can polymorphisms w/in exons cause?

A

Likely affect gene activity (unless a synonymous SNP)

20
Q

What can be caused by improper splicing?

A
  • Mutation could result in the forced formation of a splice variant (splice variant may still have activity)
  • Mutation could also truncate the protein (almost certainly will result in an inactive protein)
21
Q

Define promoter

A

DNA sequence where transcription factors bind to initiate transcription (+1 is the position of first base of the primary RNA transcript)

22
Q

Define enhancer

A
  • DNA sequence that binds proteins that increase the rate of transcription
  • Usually located far upstream or downstream of the gene
  • Can be more than 1 for a given gene
  • Can also be found w/in introns
23
Q

What can polymorphisms in the promoter cause?

A
  • Can alter transcription of the gene
  • Could reduce transcription but also possible that the gene won’t express at all (may occur by reducing binding of transcription factors)
  • However, depending on the polymorphism, transcription may also increase
24
Q

What can polymorphisms in the enhancer regions cause?

A
  • Can affect transcription of the gene
  • Enhancers are sometimes found w/in introns (another reason why polymorphisms w/in introns can affect transcription of genes)
  • The polymorphism can disrupt the enhancer
25
Q

What is caused from a nonsynonymous SNP in exons?

A

Usually results in a malfunctioning protein – may have no activity or lower activity

26
Q

What can SNPs in introns cause?

A
  • Have no affect
  • Decrease transcription
  • Influence splicing producing a truncated protein or a splice variant
  • Disrupt enhancer sequences decreasing transcription
27
Q

What is caused from a synonymous SNP w/in exons?

A

No impact on protein sequence but can change expression of the gene

28
Q

Changes to a reading frame will eventually result in ____

A

A stop codon

29
Q

What is caused from tandem repeats of multiples of 3 bases?

A
  • Won’t cause a shift in reading frame

- Will introduce additional AA’s into the protein, it it occurs in an exon

30
Q

What is caused from deletions of multiples of 3 bases?

A
  • Won’t cause a frame shift

- Will delete AA’s from the protein sequence, if occurs in an exon

31
Q

What is caused from tandem repeats/deletions in multiples of other than 3 bases?

A

Will result in frame shift and eventually a stop codon

32
Q

What do mutations outside of the reading frame (ie: before the start or after the stop codons) NOT cause?

A

Frame shifts

33
Q

What is the mutation of CYP 2C19 *2 and what does it cause?

A
  • 681 G > A

- Results in splicing defect and no activity

34
Q

What is the mutation of CYP 2C19 *3 and what does it cause?

A
  • 636 G > A

- Results in insertion of a stop codon and no activity

35
Q

What are CYP 2C19 *2 through *8 referred to as?

A

Defective

36
Q

What is the mutation of CYP 2C19 *17 and what does it cause?

A
  • 806 C > T

- Increased activity

37
Q

What metabolizes omeprazole?

A

CYP 2C19

38
Q

What are the 3 types of CYP 2C19 w/ respect to omeprazole metabolism?

A
  • *1 / *1 = homozygous = EM
  • def / *1 = heterozygous = IM
  • def / def = homozygous = PM
39
Q

What does a PM of CYP 2C19 for omeprazole cause?

A
  • Omeprazole metabolized into inactive metabolite
  • PM causes much higher intragastric pH for a longer period of time b/c higher omeprazole concentration and lower inactive metabolite concentration
  • Example of when it’s good to have defective alleles
40
Q

Define linkage disequilibrium

A

When 2 or more alleles appear together in greater or lower frequency than would be expected by random chance

41
Q

Briefly describe CYP 2D6 *5

A

Polymorphism where thousands of base pairs are missing, resulting in the effective deletion of the CYP 2D6 gene => PM

42
Q

Give an example of gene duplication

A
  • CYP 2D6 *2XN
  • Extra copies of CYP 2D6 gene are present (N = 2, 3, 4, 5, 13) => more enzyme is produced
  • Results in UM
43
Q

Define phenotype

A

The net effect of the activities of the 2 copies of the genes an individual has

Year 3 - Biotech (2nd half) (7 decks)

Brainscape helps you reach your goals faster, through stronger study habits.
© 2024 Bold Learning Solutions. Terms and Conditions