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PHRM 847 > Exam 1 Review > Flashcards

Exam 1 Review Flashcards

1
Q

How many codons are there in the genetic coding system?

A

64 codons

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2
Q

What are the 3 stop codons in the genetic coding system?

A
  • UAA
  • UAG
  • UGA
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3
Q

What is the start codon in the genetic coding system?

A

ATG

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4
Q

How many amino acids are there?

A

20 amino acids

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5
Q

What is a non-synonymous SNP?

A

changes amino acid in the protein

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6
Q

What is a missense SNP?

non-synonymous

A
  • Missense is an amino acid substitution
  • It could lead to either a gain of function or loss of function for the protein depending on what amino acid it changes to
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7
Q

What is a nonsense SNP?

non-synonymous SNP

A
  • Nonsense SNP changes an amino acid to a stop codon
  • This normally leads to a loss of function
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8
Q

What is a synonymous SNPP?

A
  • Does not change amino acids
  • Usually does not change the gene/protein function
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9
Q

What is a silent SNP?

synonymous SNP

A

non-amino acid change

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10
Q

Where must an SNP occur for the change in function to have a clinical effect?

A

SNP must be in an EXON because the exons are what are expressed.

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11
Q

What does the c in c.1297G>A indicate?

A

The change is in the coding DNA sequence

count from the first nucleotide of coding DNA sequence (ATG)

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12
Q

What does the p in p.Val433Met indicate?

A

The change is in protein position

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13
Q

Can a rare allele in one population be a common allele in another population?

A

Yes

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14
Q

What is linkage disequilibrium?

A

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

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15
Q

How does infinite recombination impact LD?

A

There is no LD

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16
Q

How does no recombination impact LD?

A

There is complete/perfect LD

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17
Q

How does recombination occurring in a portion of chromosomes impact LD?

A

There is incomplete LD

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18
Q

What does complete linkage mean?

A
  • Means that LD = 1
  • the DNA is inherited by segments (aka the alleles are ALWAY inherited together)
  • each segment is called a haplotype block
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19
Q

What does no linkage indicate?

A
  • LD = 0
  • The alleles are never inherited together
    The distance between the two loci is large
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20
Q

What does R^2 indicate?

A

How strong the correlation between two variables is

Measures the strength of LD

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21
Q

List what each R^2 value indicates about LD:

A
  • R^2 = 0 –> no LD
  • R^2 = 1 –? complete/perfect LD
  • R^2 > 0.8 –> strong LD
22
Q

Does p value measure strength of an association?

A
  • No
  • It can be affected by sample size. (Larger sample size, lower p )
  • It can be affected by allele frequency
23
Q

List what each p value indicates:

A
  • P > 0.1 no significant association
  • 0.05 < P < 0.1 marginal association
  • P < 0.05 significant association
  • P < 0.01 very significant association
24
Q

What is the P value used for whole genome sequencing data?

A

5x10^-8
- Corrected significant GWAS P value

25
Q

Describe what the various 95% CI values indicate:

A
  • 95% CI greater than1 –> significant risk effect
  • 95% CI contains 1 –> no statistical significance
  • 95% CI less than 1 –> significant protective effect
26
Q

What is polymerase chain reaction (PCR) used for?

A

DNA amplification

27
Q

What substrates are required for PCR?

A
  • DNA template
  • dNTPs (dATP, dGTP, dCTP, dTTP)
  • Primers: 2 short sequences specific to the region of interest
  • Buffer: pH, Mg2+
  • enzyme: Taq DNA polymerase
28
Q

What can DNA Chip sequencing detect?

A
  • KNOWN SNPs or targeted SNPs

High-throughput, but cheap

29
Q

What can Sanger Sequencing detect?

A
  • Can detect BOTH KNOWN AND UNKNOWN alleles
  • SNPs, indel, small CNV

low throughput, but more expensive per base pair

30
Q

What can next generation sequencing detect?

A
  • all known or unknown alleles
  • whole genome/whole exome
  • detects all kinds of polymorphisms

high-throughput, higher total cost

31
Q

Describe the functions of PCSK9:

A
  • PCSK9 decreases LDL receptor proteins via lysosomal degradation. LDL-R recycling is also blocked
  • Decreased LDLR leads to increased LDL-C concentrations (because they can’t bind to LDL-R)
32
Q

What is ICER?

A

incremental cost-effectiveness ration

33
Q

What is QALY?

A

quality-adjusted life-year

34
Q

Explain RNA interference (antisense oligonucleotides (ASO)) drugs:

A
  • blocking the mRNA directly to reduce the protein being made from that particular mRNA
  • halts the process of creating a disease-causing protein
  • Onpattro (patisiran) - an RNAi drug for people with hereditary transthyretin-mediated amyloidosis (rare and deadly)
35
Q

Explain mRNA medicine:

A
  • introduce exogenous mRNA into the body so cells can make proteins based on the introduced mRNA
  • COVID-19 vaccine
36
Q

Explain monoclonal antibodies and antibody-drug conjugates (ADCs):

A
  • A type of Y shape protein that specifically binds to its target (target protein) to block the function of that target protein OR help to recognize a specific group of cells (cancer cells) that express the target protein
  • PD1 and PD-L1 drugs are common mabs
37
Q

Explain gene therapy drugs:

A
  • virus as a vehicle to deliver gene
  • FDA-approved adeno-associated virus (AAV) drug Luxturna to treat a rare form of inherited vision loss
38
Q

Explain CRISPR-mediated gene-editing and mutation-repair:

just give an example

A
  • a trial of an experimental CRISPR-Cas9 therapy for the blood disorder B-thalassemia has been launched
39
Q

Explain stem cell (iPSCs) therapy:

A
  • most are still being developed
  • has the potential to generate many cell types in the body to replaced damaged tissue
40
Q

What are the 4 steps in mRNA medicine?

A
  1. scientists generated an mRNA sequence that codes for the virus spike protein
  2. the RNA sequence, a blueprint for making the spike, is swathed in a lipid coating for delivery
  3. Once it arrives, cells read the information in the mRNA sequence to produce millions of copies of the spike protein
  4. the protein fragments spur the immune system to produce antibodies that can protect when a real virus enters the body
  • making the exogenous mRNA stable is key
  • finding the right coating to deliver them into the cell is critical
41
Q

Explain the process of gene therapy with adeno-associated virus (AAV):

A
  1. Transgene is packaged into AAV vectors
  2. Through a one-time IV infusion, AAVs carrying the transgene target the liver
  3. In the liver, AAV vectors deliver transgene to the nucleus of liver cells to enable production of therapeutic protein
42
Q

What kind of drug is zolgensma?

A
  • Gene therapy with AAV
  • biologic drug consisting of AAV9 capsids that contain a SMN1 transgene along with synthetic promoters

this drug increases SMN1 to increase survival of motor neurons

43
Q

How does the CRISPR/Cas9 DNA editing technique work?

A
  1. A cell is transfected with an enzyme complex containing: guide molecule, healthy DNA copy, and DNA-cutting enzyme
  2. A specially designed synthetic guide molecule finds the target DNA strand
  3. An enzyme cuts off the target DNA strand
  4. the defective DNA strand is replaced with healthy copy
44
Q

List the PD-L blockers:

A
  • pembrolizumab (Keytruda)
  • nivolumab (Opdivo)
  • cemiplimab (Libtayo)
45
Q

List the PD-L1 blockers:

A
  • atezolizumab (Tecentriq)
  • avelumab (Bavencio)
  • durvalumab (Imfinzi)
46
Q

What is synthetic lethality and why do we induce it?

A
  • The combination of two separate mutations (BRAC and PARP) lead to cell death while either mutation alone is not lethal.
  • We can exploit this to selectively kill cancer cells while sparing normal cells.
47
Q

List the BRAC1 inhibitors:

A
  • niraparib
  • olaparib
  • rucaparib
  • talazoparib
48
Q

List the drugs that target the KRAS mutation:

A
  • binimetinib
  • trametinib
  • cobimetinib
49
Q

What is MRTX849/AMG-510 and what does it do?

A
  • Lumakras/sotorasib
  • Blocks KRAS signaling and promotes apoptosis in KRAS G12C

ONLY FOR G12C

50
Q

List the CDK4 and CDK6 inhibitors:

A
  • palbociclib
  • ribociclib
  • abenaciclib

PHRM 847 (8 decks)

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