Exam 3 Flashcards
1
Q
CD3
A
T cells
2
Q
CD4
A
T helper
3
Q
CD8
A
cytotoxic
4
Q
CD19
A
B cells
5
Q
Flow Cytometry
A
cell sorting/counting,
6
Q
FSC
A
forward scatter, size of cell
7
Q
SSC
A
side scatter, granularity
8
Q
Direct ELISA
A
- Patient antigen added
- Enzyme added
- WASH
- Signal added
(Antigen Test - Infection)
9
Q
Indirect ELISA
A
- Pre-coated Antigen
- Add Primary Antibody Sample
- WASH
- Add labeled antibody
- WASH
- Signal added
(Antibody Test - Immunity)
10
Q
ELISA
A
Enzyme Linked Immunosorbent Assay
11
Q
Artificially Acquired Immunity
A
vaccine
12
Q
Naturally Acquired Immunity
A
antibody response, vertical transmission
13
Q
Acyclovir
A
inhibits viral DNA polymerase
14
Q
Vidarabine
A
inhibits viral DNA polymerase
15
Q
Cidofovir
A
inhibits viral DNA polymerase
16
Q
Docosanol
A
inhibits host cell membrane
17
Q
Tamiflu
A
neuraminidase
18
Q
Molnupiravir
A
induce mutations (nucleoside)
19
Q
HIV Decrease Cell Counts of ___.
A
T-reg/Th cells
20
Q
HIV
A
+ssRNA, reverse transcriptase
21
Q
HIV glycoprotein
A
gp120
22
Q
HIV binds ___.
A
CD4/CCR5
23
Q
Integrase
A
integrates HIV into genome
24
Q
Protease
A
cleaves poly proteins -> viral capsid
25
PB1
RNA polymerase
26
PB2
cap snatcher, steals 5' cap, tricks host
27
NP
cap attacher
28
Hemagglutinin
Influenza coat protein
29
Neuraminidase
Influenza pruni out silica acid, cannot bind coat protein
30
Strain A Influenza
Spanish, Bird Flu, H1N1
31
Strain B Influenza
seasonal flu
32
Strain C Influenza
less serious, rare
33
Biosafety Level 1
not known to consistently cause disease in healthy adults (V. fischeri)
34
Biosafety Level 2
associated with human disease; potential hazard if percutaneous injury, ingestion, or mucous exposure occurs (Salmonella, E. coli, S. aureus)
35
Biosafety Level 3
Indigenous or exotic agents with potential for aerosol transmission; disease may have serious or lethal consequences (plague/herpes)
36
Biosafety Level 4
dangerous/exotic agents that pose high risk of life-threatening disease, aerosol-transmitted lab infections, or related agents with unknown (Ebola, smallpox)
37
PCR Steps
1. Denaturation
2. Primer Annealing
3. Elongation by DNA Polymerase
38
Denaturation Temperature
94C for 1 minute
39
Primer Annealing Temperature
56C for 1.5 minutes
40
Elongation Temperature
72C for 1 min
41
If you add a human DNA polymerase to a PCR reaction, will the reaction take place?
No, adding human DNA polymerase to a PCR reaction would likely not lead to successful DNA amplification. PCR relies on heat-stable DNA polymerases, such as Taq polymerase
42
qPCR
fluorescent label to PCR to visualize replication in real-time and quantify nucleic acids
43
qPCR Fluorescence
SYBR Green
44
Intercalating Dye
sybr green, binds dsDNA and fluoresce upon binding
45
Probe-based Dye
hybridizes to sDNA
46
Cycle Threshold
equal to the number of cycles needed to produce enough fluorescence to cross a baseline threshold of fluorescence, lower number = higher amount of DNA
47
True or false: A sample that registers a Ct value of 25 has much less DNA in it than a sample that registers a Ct of 15.
True
48
CRISPR
Clustered Regularly Interspaced Short Palindromic Repeats
49
Bacterial CRISPR/Cas
used to remember a viral attack and prepare for future attack
50
Stages of CRISPR
1. Acquisition
2. CRISPR RNA Biogenesis
3. Interference
51
Acquisition
if cell survives infection, it adds portions of viral genome the CRISPR region, added closest to CAS genes
52
RNA Biogenesis
CRISPR region transcribed to yield large RNA containing repeats and spaces. Cas proteins associate with this RNA and process it into mature crRNA
53
Interference
CAS-crRNA complexes associate with viral mRNA or DNA, cleave these nucleic acids, preventing the virus from replicating
54
Gene Editing
design specific guide RNAs that an hybridize to any gene of interest, modify the Cas9 protein to modify gene expression
55
Cas9
protein that can cut DNA
56
End-Point PCR v qPCR
qualitative vs quantitative
lower vs higher sensitivity
57
cDNA
made from mRNA via reverse transcriptase
58
qPCR COVID Testing
1. RNA Extraction
2. Reverse Transcriptase -> cDNA
3. qPCR Amplification
4. Detection (Ct)
59
Inconclusive COVID Test
One value = 40, one value less than 40
60
Negative COVID Test
Both values 40
61
Positive COVID Test
Both values less than 40
62
Genome vs Metagenome
complete set of one vs. totality of genetic material
one vs multi species
63
Sanger vs NGS
low v high throughput
long v short read
slower v faster
64
Flow Cell
apparatus to amplify and sequence amplicons from DNA
65
Major Advantages of NGS
Massively Parallel (all sequence fragments)
Deep Sequencing (replicates)
High Throughput (simultaneously)
66
Library Preparation
Fragmentation/PCR, index/barcode
67
Cluster Formation
PCR of sequence fragments on the flow cell produce replicate sequences
68
dNTPs
deoxynucleoside tri-phosphates
69
Taq Polymerase
isolated from a thermophilic bacterium Thermus aquatics, able to withstand protein denaturing conditions
70
Primers
complementary to the sequence for amplification
71
Thermocycler
machine that facilitates the temperature changes associated with steps of a PCR cycle, one cycle = one round of DNA replication
72
Gel Electrophoresis
used to identify DNA fragments based size, DNA is negatively charged so it will migrate toward the positive electrode
73
Ladder
helps quantify DNA
74
Bridge Amplification
produces clusters of replicate sequences
75
Deeper
more replicates produced, the larger the cluster
76
Sequencing by Synthesis
sequence is determined in real time while nucleotides are added
77
Breadth
how much of the genome you are sequencing, number of nucleotides
78
Virion Shapes
polyhedral, helical, complex, spherical (flu)
79
True or False: A non-nucleoside reverse transcriptase inhibitor binds the reverse transcriptase while a nucleoside reverse transcriptase inhibitor is incorporated into HIV’s dsDNA, causing a faulty and unstable DNA strand.
True
80
Docosanol
HSV, targets the host cell membrane, prevents viral attachment
81
Tamiflu
inhibits neuraminidase, prevent viral release from host cell
82
Molnupiravir
COVID, nucleoside analogs that induce mutations
