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Bio 150 Lab > Bio 150 Lab Final Exam > Flashcards

Bio 150 Lab Final Exam Flashcards

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1
Q

main parts of the flow chart

A

exploration, testing ideas, community analysis and feedback, benefits and outcomes

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2
Q

community analysis and feedback examples

A

replication, publication, discussing with colleagues, theory building

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3
Q

testing ideas examples

A

gather and interpret data

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4
Q

benefits and outcomes examples

A

develop technology, inform policy, and build knowledge

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4
Q

exploration and discovery examples

A

explore the literature, ask questions, make observations, share data and ideas, find inspiration

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5
Q

what is the entryway into the process of science?

A

exploration and discovery

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6
Q

what part of the flow chart did we do on the first day of class?

A

exploration and discovery

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7
Q

scholarly literature

A

disseminate information, peer-reviewed, reliable but not always accessible

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8
Q

non scholarly literature

A

want to make money, not as reliable, not peer reviews, more accessible

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9
Q

primary literature

A

original research from original people, usually peer reviewed, best for citing, has a methods section (example: journal articles)

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10
Q

secondary literature

A

second hand summary, sometimes peer reviewed, lacks method section, ok for citing. (example: scientific books)

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11
Q

tertiary literature

A

third hand’ general background information, not written by experts and rarely peer reviewed, should be avoided. (example: tertiary literature, encyclopedia and textbooks)

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12
Q

what does CRAAP stand for

A

currency
relevance
accuracy
authority
purpose

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13
Q

scientific testable questions

A

addressed the issues/ questions using data

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14
Q

non scientific testable questions

A

addresses issues/ questions using values, beliefs or judgements

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14
Q

independent variable

A

variation does not depend on another variable

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15
Q

dependent variable

A

does depend on variation of independent variable

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16
Q

control

A

designed to show change

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17
Q

descriptive study

A

scientist is not testing a hypothesis; they are simply making observations

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18
Q

non experimental study

A

variable is not manipulated and just gathering data to test a hypothesis, examine if there is a relationship between the two variables but not a casual relationship, hypothesis is tested

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19
Q

experimental study

A

hypothesis tested, variable is manipulated to measure response of dependent variable, good at establishing casual relationships

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20
Q

what studies require independent and dependent variables?

A

experimental and non experimental studies

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21
Q

correlation

A

a non experimental study that does not determine causation

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22
Q

pipettor parts

A

plunger, tip ejector, shaft, pipette tip

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22
how to use a pipette
vertical position correct volume is middle to top volume range
23
3 basic steps of PCR
denature, anneal, extend
24
anneal
temperature reduced to 55 and the PCR primer anneal/ base pair with the DNA template
24
denature
heat is increase to 94 and the hydrogen bonds break so the two strands separate
25
extend
heated up to 72. TAQ polymerase binds to the primers and new DNA begins to be synthesized
26
major ingredients in PCR reaction
DNA template PCR primers DNA polymerase Deoxyribonucelotide (dNTPs)
27
dna template role in PCR reaction
dna is copied
27
PCR primers role in PCR reaction
PCRs will anneal to the template DNA and that will be the starting point for DNA replication. They also select the region of DNA that will be amplified
28
what primers are needed for PCR reaction
forward and reverse
29
DNA polymerase role in PCR reaction
an enzyme that can synthesize new DNA. TAQ polymerase is used because it can withstand the heat and allows us to perform repeated rounds of DNA replication
30
dNTPs
monomers/ building blocks of DNA. DNA polymerase links dNTPs together into a new DNA strand
31
how is exponential growth related to PCR
the theoretical number of copies of DNA produced in a PCR reaction from a single template can be calculated as 2 to the # of pcr cycles
32
why are positive and negative controls needed?
the positive control will tell you if DNA was amplified and demonstrates all reaction components are present and working the negative control will tell you if there are contaminants
33
what goes into the master mix
1. 15 ul x the number of samples + 1 extra sample 2. dna extract DOES NOT go into the master mix 3. 28 ul of mix will go into individual PCR reaction tubes before any DNA is added
34
DNA purity
other substances in DNA extracts that are not DNA (ie: salts and proteins)
35
PCR inhibitor
molecules that interfere with DNA amplification in PCR
36
DNA concentration
can not be to high or to low otherwise the PCR reaction will fail
37
factors that reduce DNA purity
dna extract solution carried over from extraction process like ethanol, proteins and lipids
38
how DNA concentration influences the likelihood of PCR success
not enough can cause the reaction to fail because enough copies might not be produced to much might cause amplification to stop before exponential phase of the reaction is reached
39
how DNA purity influences the likelihood of PCR success
to many other substances may be read
40
how does spectrophotometry work
it increases the amount and wavelength of light absorbed/ transmitted through a sample; it will give the concentration of different compounds in a solution
41
A260:A280 ratio
1.8
41
A260:A230 ratio
2-2.2
42
ideal DNA concentration for PCR
50-250 ng/ul
43
wavelength DNA is absorbed at
260 nm
44
is the A260:A280 ratio is low and DNA concentration is high what should happen to the sample?
it should be diluted
44
if the ratios are too low what should happen to the sample?
it should be kept but a new DNA extraction should be done
45
wavelength proteins are absorbed at
280 nm
46
wavelength salts are absorbed at
230 nm
47
wavelength carbs are absorbed at
230 nm
48
what does A260/A280 measure
proteins
48
what does A260/A230 measure
sugars and carbs
49
equation to dilute a sample of known DNA concentration
(starting concentration)(starting volume)= (final concentration)(final volume)
50
main goals of gel eletrophoresis
to see if a PCR produced a product and see if the product size is the expected size
51
why we use a marker (ladder)
the size of PCR products can be estimated in other lanes
52
why we use GelRed stain
DNA intercalator and flourences under UV light
53
why we use positive controls
to know the size
54
why we use negative controls
to see if there are contaminations
55
typical size (bp) of a DNA barcode sequence
.5-.8 kp
56
primer dimers
they form when annealing occurs between primers
57
how can you tell primer dimers
the bottom of the gel is very blurry
58
gDNA (definition)
too much template added to the reaction, low molecular weight, fragmented DNA may anneal and self prime increasing concentration
59
gDNA (spotting it)
long smears that are vertical
60
how to increase gDNA
dilute the template and repeat PCR
61
major steps of DNA barcoding
specimen, collection data, tissue sample, photos, run a gel, DNA subway
62
steps of running a gel
extract DNA, PCR amplification, sequence
63
parts of DNA subway
sequence viewer, sequence trimmer, pair builder, consensus builder, blastin, muscle, phylip nj, phylip ml
64
primer sets for plants, inverterbae/ animals, frogs/ bacteria, fungi
plants: Rbcl inverterbae/ animals: COI frogs/ bacteria: 16s fungi: ITS
65
single read
before the sequence is trimmed
66
trimmed read
after the sequence has been trimmed
67
consensus sequence
combination of trimmed and reverse DNA sequences that is typically more accurate than each sequence alone; allows you to make a more accurate DNA barcoding sequence
68
bit score
summary statistic based on the length of the alignment and number of mismatches
68
aln. length
length of sequence used to make match
69
e score
likelihood that the match BLAST made between our query sequence and your match could happen by chance
69
mismatches
number of non common bases between query and bit score

Bio 150 Lab (1 decks)

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