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Bio 150 Lab > Bio 150 Lab Final Exam > Flashcards

Bio 150 Lab Final Exam Flashcards

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
Q

how to use a pipette

A

vertical position
correct volume is middle to top volume range

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23
Q

3 basic steps of PCR

A

denature, anneal, extend

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24
Q

anneal

A

temperature reduced to 55 and the PCR primer anneal/ base pair with the DNA template

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24
Q

denature

A

heat is increase to 94 and the hydrogen bonds break so the two strands separate

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25
Q

extend

A

heated up to 72. TAQ polymerase binds to the primers and new DNA begins to be synthesized

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26
Q

major ingredients in PCR reaction

A

DNA template
PCR primers
DNA polymerase
Deoxyribonucelotide (dNTPs)

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27
Q

dna template role in PCR reaction

A

dna is copied

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27
Q

PCR primers role in PCR reaction

A

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
Q

what primers are needed for PCR reaction

A

forward and reverse

29
Q

DNA polymerase role in PCR reaction

A

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
Q

dNTPs

A

monomers/ building blocks of DNA. DNA polymerase links dNTPs together into a new DNA strand

31
Q

how is exponential growth related to PCR

A

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
Q

why are positive and negative controls needed?

A

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
Q

what goes into the master mix

A
  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
Q

DNA purity

A

other substances in DNA extracts that are not DNA (ie: salts and proteins)

35
Q

PCR inhibitor

A

molecules that interfere with DNA amplification in PCR

36
Q

DNA concentration

A

can not be to high or to low otherwise the PCR reaction will fail

37
Q

factors that reduce DNA purity

A

dna extract solution carried over from extraction process like ethanol, proteins and lipids

38
Q

how DNA concentration influences the likelihood of PCR success

A

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
Q

how DNA purity influences the likelihood of PCR success

A

to many other substances may be read

40
Q

how does spectrophotometry work

A

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
Q

A260:A280 ratio

A

1.8

41
Q

A260:A230 ratio

A

2-2.2

42
Q

ideal DNA concentration for PCR

A

50-250 ng/ul

43
Q

wavelength DNA is absorbed at

A

260 nm

44
Q

is the A260:A280 ratio is low and DNA concentration is high what should happen to the sample?

A

it should be diluted

44
Q

if the ratios are too low what should happen to the sample?

A

it should be kept but a new DNA extraction should be done

45
Q

wavelength proteins are absorbed at

A

280 nm

46
Q

wavelength salts are absorbed at

A

230 nm

47
Q

wavelength carbs are absorbed at

A

230 nm

48
Q

what does A260/A280 measure

A

proteins

48
Q

what does A260/A230 measure

A

sugars and carbs

49
Q

equation to dilute a sample of known DNA concentration

A

(starting concentration)(starting volume)= (final concentration)(final volume)

50
Q

main goals of gel eletrophoresis

A

to see if a PCR produced a product and see if the product size is the expected size

51
Q

why we use a marker (ladder)

A

the size of PCR products can be estimated in other lanes

52
Q

why we use GelRed stain

A

DNA intercalator and flourences under UV light

53
Q

why we use positive controls

A

to know the size

54
Q

why we use negative controls

A

to see if there are contaminations

55
Q

typical size (bp) of a DNA barcode sequence

A

.5-.8 kp

56
Q

primer dimers

A

they form when annealing occurs between primers

57
Q

how can you tell primer dimers

A

the bottom of the gel is very blurry

58
Q

gDNA (definition)

A

too much template added to the reaction, low molecular weight, fragmented DNA may anneal and self prime increasing concentration

59
Q

gDNA (spotting it)

A

long smears that are vertical

60
Q

how to increase gDNA

A

dilute the template and repeat PCR

61
Q

major steps of DNA barcoding

A

specimen, collection data, tissue sample, photos, run a gel, DNA subway

62
Q

steps of running a gel

A

extract DNA, PCR amplification, sequence

63
Q

parts of DNA subway

A

sequence viewer, sequence trimmer, pair builder, consensus builder, blastin, muscle, phylip nj, phylip ml

64
Q

primer sets for plants, inverterbae/ animals, frogs/ bacteria, fungi

A

plants: Rbcl
inverterbae/ animals: COI
frogs/ bacteria: 16s
fungi: ITS

65
Q

single read

A

before the sequence is trimmed

66
Q

trimmed read

A

after the sequence has been trimmed

67
Q

consensus sequence

A

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
Q

bit score

A

summary statistic based on the length of the alignment and number of mismatches

68
Q

aln. length

A

length of sequence used to make match

69
Q

e score

A

likelihood that the match BLAST made between our query sequence and your match could happen by chance

69
Q

mismatches

A

number of non common bases between query and bit score

Bio 150 Lab (1 decks)

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