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150 L final Flashcards

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1
Q

List the major sections of a formal scientific manuscript

A

methods, results, discussion, and introduction

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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

what is the entryway into the process of science?

A

exploration and discovery

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3
Q

t/f DNA barcoding is useful to identify how much (%) of a product is made up of a particular ingredient.

A

false

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4
Q

What are the MAIN goals of an introduction to a scientific paper?

A

enable the reader to understand why the specific question/goal/aim of the study is important

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5
Q

scholarly literature

A

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

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6
Q

non scholarly literature

A

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

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7
Q

primary literature (def)

A

original research that is communicated “first-hand” by the people who collected and analyzed the data

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8
Q

primary literature (example)

A

journal articles

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9
Q

secondary literature (def)

A

second hand summary, sometimes peer reviewed, lacks method section, ok for citing`

an expert summary or synthesis of someone else’s original research that is communicated “second-hand” by people who did NOT collect or analyze the original data

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10
Q

secondary literature (example)

A

scientific books

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11
Q

tertiary literature (def)

A

‘third hand’ general background information, not written by experts and rarely peer reviewed, should be avoided

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12
Q

tertiary literature (example)

A

encyclopedia and textbooks

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13
Q

where and how to find scientific papers

A

scopus and jmu library

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14
Q

Broad Background (Beginning but immediately follows hook)

A

larger issue at hand and most general background on this issue

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15
Q

advantages of SCOPUS

A

free access to scholarly articles, content is curated for accuracy and authority, information is stable, specialized subject specific databases for the topic

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16
Q

specific background (middle)

A

specific organisms, system or technique being studied and why they are worth studying

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17
Q

very specific question/goal/aim (end)

A

the precise issue that the study is going to tackle

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18
Q

Hook (beginning)

A

argument or facts used to justify why anyone should care about the study. Used to appeal to the widest audience possible.

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19
Q

your question/aim/hypothesis

A

The proposed research would address this problem by making the first detailed examination of links between groundwater and concentrations of trace metals in avocados. We will test the hypothesis that heavy metal concentrations in groundwater affect their concentrations in avocados.

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20
Q

Which of the following BEST describes the general structure of an introduction

A

A upside down pyramid that starts with a hook to get the audience interested and all of the following information helps the reader to understand the specific aim of the study and its importance

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21
Q

CRAAP stands for?

A

Currency, Relevance, Authority, Accuracy, Purpose

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22
Q

currency in CRAAP

A

how up to date something is

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23
Q

What does peer-reviewed mean?

A

Other experts in the field have verified the integrity of the information

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24
what are scientific testable questions
addressed the issues/ questions using data
25
what are non scientific testable questions
addresses issues/ questions using values, beliefs or judgements
26
what is independent variable
variation does not depend on another variable
27
dependent variable
does depend on variation of independent variable
28
control
designed to show change ( is not manipulated)
29
descriptive study
scientist is not testing a hypothesis; they are simply making observations
30
non experimental study
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
31
Which of the following is a major advantage of a subject specific database (like Scopus) over Google Scholar?
Scopus has better filters than Google Scholar to help narrow down your results
32
This is a short summary of a scholarly article that will help you identify whether the article is relevant. This short summary will save you a lot of time, because you won't have to read an entire article before discovering it is not relevant to your topic or interests.
abstract
33
Which of the following best depicts the format of citations in the references section of the Ferrito et al. paper? Note: references are found at the end of the paper.
Author(s). (Year). Title. Journal, Vol. Pgs.
34
Which of the following best depicts the format for citations within the text of Ferrito et al.'s introduction?
Author(s) last name(s), Year
35
What are the 2 main things that citing your sources accomplishes?
Citing your sources establishes the source of facts that are stated in a paper and therefore the legitimacy (or illegitimacy) of these statements Citing your sources provides readers with an "in-road" to the literature surrounding a particular topic
36
Which of the following statements is correct regarding in text citations in the Ferrito et al. paper?
In text citations are most often at the end of sentences
37
According to the formatting used in the Ferrito et al. paper, which of the following is a properly formatted reference?
Kringle, K., Claus, S., & St. Nick, O. (2003). Evidence for the presence of Santa Claus in North American Chimneys. J North Pole Research, 270, 421-431.
38
According to the formatting used in the Ferrito et al. paper, which of the following is a properly formatted citation?
Though difficult, there is mounting evidence that Santa is accessing North American homes via chimneys (Kringle, Claus, & St. Nick, 2003).
39
experimental study
hypothesis tested, variable is manipulated to measure response of dependent variable, good at establishing casual relationships
40
what studies require independent and dependent variables?
experimental and non experimental studies
41
a non experimental study that does not determine causation
correlation
42
pipettor parts
plunger, tip ejector, shaft, pipette tip
43
how to use a pipette
vertical position correct volume is middle to top volume range
44
units used for pipetting
microliters
45
why are there so many protocols for pipetting?
to avoid contamination
46
C​urrency​
when was the information published?
47
R​elevance
Is the information appropriately related to the topic you are interested in?
48
A​uthority​
is there an author? What are their credentials and affiliations? Could they bebiased or have an agenda
49
A​ccuracy​
are sources of the information cited? Is this fact or opinion?
50
P​urpose
​Is this article clearly biased or trying to sell your something? What are theaffiliations of the source?
51
empirical
it relies on measurements of the real world
52
This is an enzyme whose function is to synthesize new DNA by attaching nucleotides that are complementary to a single strand of DNA.
DNA polymerase
53
The building blocks of DNA are:
nucleotides
54
Nucleotides are added to the growing DNA strand during the _________ phase
extension
55
During the annealing step...
Primers bind to the newly separated DNA strand
56
the following that is a necessary "ingredient" for a PCR to proceed. Forward Primer
DNA polymerase Reverse Primer Template DNA Nucleotides
57
What primer set would be used to amplify each organism’s genome (Fungi, Plant, Vertebrate)
fungi- ITS plant- RncL animal- MT-CO1
58
A typical reaction would consist of:
15 µL PCR reactants 1 µL Primer Mix 12 µL H2O + 2 µL DNA extract
59
what volume of PCR reactants would you add to your master mix if you wanted to amplify 6 samples?
105 microliters
60
What volume of DNA extract would you add to your master mix before you distribute it to individual PCR tubes if you wanted to amplify 6 samples?
this doesnt go in the master mix
61
This is the volume of master mix that will go into an individual PCR reaction tube (before any DNA is added)
28 microliters
62
Which of the following would be a GOOD region of the genome to use for DNA barcoding?
a region that has lots of copies in the genome
63
Why are the primers we use to DNA barcode often referred to as "universal" primers?
they work across a wide variety of taxa
64
in the context of our labs, what does "bp" stand for?
base pairs
65
What is NCBI Genbank?
One of the world's largest DNA sequence Databases
66
You want to develop primers for the blue and red regions of the following DNA template sequence: 5'-ATGCAATTGCAGTCGATTGCTCGATCGATCTTCGAAATTTCCCGAGCTTCGATCGC-3' Which of the following is the appropriate Reverse Primer sequence?
5'-GCGATCGAAGCTCG-3'
67
What would the resulting gel look like if your primers did not match a DNA sequence found in your organism or sample? Correct!
there would be no bands
68
Electrophoresis is used to:
-Separate DNA fragments -Determine the size of DNA fragments -Help determine the success of a PCR reaction
69
The rate of migration of DNA within an agarose gel in the gel electrophoresis technique is primarily based on what factor?
the size of the DNA fragments
70
Which of the following provides evidence that electric current is running through your gel (check all that apply)
-bubbles rise from the electrodes -you can see the loading dye move from the well into the gel
71
When two bands from two different samples line up on a gel this means
The samples share a fragment of DNA that is the same length
72
Why do we run our H2O control (aka negative control) from our PCR reactions on the gel?
t enables you to tell if your PCR was contaminated by DNA that was not from your sample
73
t/f You should be sure to include marker/ladder in each well of your gel
false
74
Why do we dye our gels with intercalating agents like Gel Red dye or Ethydium bromide?
This dye stains the double stranded DNA in our gel
75
To carry out Sanger sequencing, a mix is needed containing: dideoxyribonucleotide (ddNTPs)
DNA polymerase Primer DNA template four deoxyribonucleotides (A, T, C, G)
76
The primer used in Sanger sequencing
has a nucleotide sequence complementary to the area that flanks the region you want to sequence
77
What volume of PCR product goes into an individual sequencing tube?
8 ul
78
t/f You should remove the rubber cap of the sequencing tube before injecting your sample DNA or primer.
false
79
t/f You should use 2 sequential sequencing tubes for each sample that successfully amplified. One tube for a reverse read and one tube for a forward read.
true
80
t/f You should be sure to put BOTH a forward AND reverse primer in EACH sequencing tube.
False You only put a forward OR reverse primer in each tube
81
What is the main goal of the "sequence viewer" substop?
visualize your sequence and determine if you have an accurate or inaccurate read
82
What is the main goal of the "PHYLIP NJ" substop?
Creates a phylogenetic tree based on your DNA sequence(s)
83
trace file
this depicts the raw results of automated sanger sequencing. typically include lots of colored humps that represent each nucleotide
84
base call
the nucleotide at a given position in your DNA sequence according to the results of automated sanger sequencing
85
phred score
a measure of the quality of the identification of the nucleobases generated by automated DNA sequencing
86
consensus sequence
combination of trimmed forward and reverse DNA sequences that is typically more accurate than each sequence alone.
87
accession number
unique identifier # given to each sequence in the blast database
88
muscle
an alignment of multiple DNA sequences that allows you to visualize similarities and differences between the DNA sequences
89
blast
basic local alignment search tool- used to find matching DNA sequences from a database
90
Which of the following would you use to remove "bad calls" from your original sequence?
trim sequence
91
A260:A280 ratio
1.8
92
A260:A230 ratio
2-2.2
93
ideal concentration for PCR
50-250 ng/ul
94
wavelength dna is absorbed at
260
95
3 basic steps of pcr
denature, anneal, extend
96
anneal
temperature reduced to 55 and the PCR primer anneal/ base pair with the DNA template
97
denature
heat is increase to 94 and the hydrogen bonds break so the two strands separate
98
extend
heated up to 72. TAQ polymerase binds to the primers and new DNA begins to be synthesized
99
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
100
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
101
what primers are needed for PCR reaction
A forward and reverse
102
dNTPs
A monomers/ building blocks of DNA. DNA polymerase links dNTPs together into a new DNA strand
103
A short branch length on a PHYLIP ML tree means:
species are closely related
104
What numbers are associated with the concentration of DNA, salt contaminents, and protein contaminents
DNA: A260 SALT: A230 PROTEIN: A280
105
list the 8 major levels of the Linnean taxonomic hierarchy
domain, kingdom,phylum,class,order, family,genus,species
106
the typical size (bp) of a DNA barcode sequence
400–800 bp

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