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Midterm Flashcards

1
Q

how many stop codons are there

A

3

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2
Q

what are the stop codons

A

UAA
UAG
UGA

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3
Q

what are the two types of SNPs

A

non-synonymous SNP
synonymous SNP

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4
Q

what is a non-synonymous SNP

A

changing amino acid in the protein

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5
Q

what are the two non-synonymous SNPs

A

missense SNP
nonsense SNP

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6
Q

what is a missense SNP

A

amino acid substitution that could lead to either gain or loss of function

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7
Q

what is a nonsense SNP

A

amino acid changes to a stop codon and normally leads to loss of function

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8
Q

what is a synonymous SNP

A

does not change amino acids and does not change gene/protein function

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9
Q

what is MDR for

A

nucleotide coding

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10
Q

what is CYP for

A

protein sequence

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11
Q

what does c. CYP refer to

A

means to count from the first nucleotide of coding DNA sequence

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12
Q

what does p. CYP refer to

A

means to know protein sequence

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13
Q

what does MAF mean

A

minor allele frequency

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14
Q

what is RAF

A

rare allele frequency

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15
Q

how do rare alleles transfer amongst populations

A

rare alleles are mostly rare in one population and then common allele in another population

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16
Q

what is LD

A

linkage disequilibrium

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17
Q

what is linkage disequilibrium

A

non-random association of alleles at different loci on the same chromosomes

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18
Q

R2 = 0 meaning

A

infinite recombination
no LD

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19
Q

R2 = 1

A

no recombination
complete/perfect LD

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20
Q

R2 >= 0.8

A

recombination partial chromosome
incomplete LD

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21
Q

P > 0.1

A

no presumption against null
no significant association

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22
Q

0.05 < P < 0.1

A

low presumption against null
marginal association

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23
Q

P < 0.05

A

strong presumption against null
significant association

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24
Q

P < 0.01

A

very strong presumption against
very significant association

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24
how do P values measure strength of association
they do not measure the strength of an association relationship
24
how are p values affected
by sample size by allele frequency
25
why do p values need corrections
large number of tests for many SNPs vs a single phenotype so there is a much higher probability of a false positive
25
what is the bonferroni correction
P = 0.05/N (total SNPs tested)
26
what is the correction P value for GWAS
5x10^8
27
CI of significant risk
greater than 1
28
CI with no statistical significance
containing 1
29
CI with significant protective effect
less than 1
30
what are polymerase chain reactions used for
technique for DNA amplification amplify specific region from the genome for making billions of copies detectable enzymatic reaction
31
what are the substrates for polymerase chain reactions
DNA template dNTPs primers: 2 short sequences specific to region of interest buffer: pH, Mg2+ enzyme: Taq DNA polymerase
32
what is a DNA chip used for
identify known and unknow alleles high throughput
33
when to use DNA chip
low/medium cost overall large scale used for research
34
what is sanger sequencing
detects both known and unknown alleles SNPs, indel, small CNV low throughput
35
when to use sanger sequencing
higher cost used for Pgx testing
36
what is next generation sequencing
simultaneously sequence DNA of multiple individuals with customizable capacities detect all known or unknow alleles and all kinds of polymorphisms
37
when to use next generation sequencing
high throughput higher cost whole genomes/exomes
38
how does PCSK9 work
PSCK9 secreted and binds to LDL-r then routes them for lysosomal degradation rather than recycling inhibitors prevent this from happening
39
how does loss of PCSK9 make people healthier
it means there are more LDL receptors that are working and being recycled, therefore, more LDL is being taken up out of the blood stream
40
what do RNA interference drugs do
reduce mRNA levels
41
what are RNA interference drugs
antisense oligonucleotides, ASO
42
what does mRNA medicine do
introduce exogenous mRNA into the body, so cells can make proteins based on the introduced mRNA
43
what is an example of mRNA medicine
covid vaccine
44
what do monoclonal antibody and antibody-drug conjugate do
y shape protein that specifically binds to its target to block the function of that target protein: or to help recognize a specific group of cells that express the target protein
45
what are monoclonal antibody drugs
PD1 PD-L1
46
what do gene therapies do
virus as a vehicle to deliver genes
47
what is a gene therapy example
Luxturna vaccine
48
what are stem cells for
generate any cell type in the body to replace damaged tissue
48
what is CRISPR for
gene editing and mutation repair
49
how do AAV vaccines work
transgene packaged into AAV vectors delivered one time via IV infusion: AAVs carry transgene to target liver transgene is delivered to nucleus of liver cells to enable production of therapeutic protein
50
what is the AAV drug name
zelgensma
51
what does zelgensma contain
AAV9 capsids that contain a SMN1 transgene along with synthetic promoters
52
what are PD-1 blocker drugs
pembrolizumab, nivolumab, cemiplimab
53
what are PD-L1 blocker drugs
atezolizumab, avelumab, durvalumab
54
what is synthetic lethality
when DNA has breakage and cell dies
55
why do we induce synthetic lethality
to cause cell death in cancer cells and tumors
56
what are BRCA1 drugs
olaparib, niraparib, talazoparib, rucaparib
57
what are KRAS drugs
binimetinib, trametinib, cobimetinib
58
what is AMG510
small molecule that specifically and irreversibly inhibits KRAS G12C by locking it in an inactive GDP-bound state to slow cell growth and proliferation
59
what is KRAS
gene that plays large role in pathways with cell growth and division. mutations in this gene are frequently found in colorectal, lung, and pancreatic cancer

Genomics (1 decks)

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