Bio 150 lab final JMU
Page 1 of 16
What goes in the green circle of this flow chart depicting the process of science?
Testing Ideas
Which of the following is NOT an item that belongs in the process of science flow chart?
Benefits and Outcomes
Community Analysis and Feedback
Research
Testing Ideas
Exploration and Discovery
Research
Which of the following is the typical "entryway" into the process of science?
Testing Ideas
Community Analysis and Feedback
Benefits and Outcomes
Exploration and Discovery
Exploration and Discovery
xamples of "Exploration and Discovery"
Finding inspiration
Asking Questions
Exploring the literature
Making Observations
Sharing data and ideas
Page 2 of 16
Which of the following did we do in lab 1?
Exploration and Discovery
Where does this go in the Process of Science flow chart?
You find an article on the web that explains how DNA barcoding is being used to
identify cockroaches in Arizona and this gives you the idea to test what kinds of
cockroaches are in Virginia (note: you have not yet actually tested anything)
Exploration and Discovery
(T/F) An anuran is a frog
True
(T/F)a frog larva and a tadpole are the same thing
True
"Science question"
addressing issues/questions using data
"non-science questions"
addressing issues/questions using values/judgements/beliefs
examples of question that can be addressed using science
What% of sushi is mislabelled at restaurant X?
example of question that cannot be addressed using science
Should DNA barcoding be used to regulate the nutritional supplement industry?
parts of a lab report
title, abstract, introduction, methods, results, and discussion
Page 3 of 16
What is a "proposal" for a scientific study?
receive monetary grants to fund their research
Typical contents of a scientific grantproposal include an explanation of:
-why the area of study is important
-work previously done, emphasizing why it is inadequate,
-research you plan to do, and how it would advance knowledge beyond its current state.
-the specific question/hypothesis you will test
-how your research will specifically address or test this question/hypothesis (methods)
-the budget/materials that justify the need for the funding you are requesting
-a timetable to complete the project
-the references used in the proposal (aka a "works cited" section).
What is/are the goal(s) of an introduction to a scientific paper or project proposal?
Enable the reader to understand the specific question/goal/aim of the study and why it is
important
broad background
larger issues at hand and most general background
Specific background
specific organism, system or techniques and why their worth studying
very specific question/goal
precise topic study is focusing on
hook
Page 4 of 16
appealing facts
structure of intro
An 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
Scholarly literature is typically structured like what
lab report
Scholarly literature is typically published where and has lots of what
journal and jargon
how long are scholarly literature
very long
whats craap stand for?
Currency, Relevance, Authority, Accuracy, Purpose
What does peer-reviewed mean?
Other experts in the field have verified the integrity of the information
Which is a disadvantage of scholarly literature?
less accessible to non-experts
According to your lab manual, citations:
-main purpose is to provide the exact information that a reader needs to locate the sources
used by an author
-are a standardized way of listing the sources used in a publication
Page 5 of 16
What are advantages of scholarly literature?
reliable, detailed, transparent with sources of info
According to your lab manual, what are the 2 main things that citing your sources
accomplishes?
-provides readers with an "in-road" to the literature surrounding a particular topic
-establishes the source of facts that are stated in a paper and therefore the legitimacy (or
illegitimacy) of these statements
This is a short summary of a scholarly article that will help you identify whether the
article is relevant. Whats it called?
Abstract
Which of the following best depicts the format for citations within the text
(Author(s), Year)
Which of the following best depicts the format of citations in the Literature cited
section
Author(s). (Year). Title. Journal, Vol. Pgs.
Currency
when was the information published?
Relevance
Is the information appropriately related to the topic you are interested in?
Authority
Page 6 of 16
is there an author? What are their credentials and affiliations? Could they bebiased or have an
agenda?
Accuracy
are sources of the information cited? Is this fact or opinion?
Purpose
Is this article clearly biased or trying to sell your something? What are theaffiliations of the
source?
descriptive studies
not testing a hypothesis, but simply making observations
non-experimental (or observational)
not manipulate any variable, but merely gathers data needed to test a hypothesis
empirical
it relies on measurements of the real world
balanced experimental design
making sure that you have an equal number of independent samples for each
group/treatment you are studying
(T/F)Pipettors are most accurate in the middle to top end of their volume range.
true
How can contamination be prevented in the laboratory?
-Using barrier pipette tips, changing the tips
-Keeping test tubes and pipette tip boxes closed as much as possible
Page 7 of 16
1.23 mL (milliliters) = _______ µL (microliters)
1230 µL
μL stands for microliter , which is ______liters:
10^-6 L
(T/F)Test tubes should always be placed into a centrifuge with the hinges facing inward.
False
(T/F)For the greatest accuracy in pipetting, one person should hold the pipettor while a
second person holds the test tube the person is pipetting into or out of.
False
Never hold the pipettor _______
horizontally
(T/F)The alkaline lysis DNA extraction procedure uses high pH and heat to break open
cells and release the DNA.
true
(T/F)During the crude alkaline lysis DNA extraction procedure for animal samples, many
proteins are precipitated and the DNA remains in solution
True
What is the main purpose of PCR?
to amplify DNA
Which of the following is NOT a term that can be used for the DNA that you want to
make copies of in a PCR?
Page 8 of 16
Template DNA (or template)
Expansion DNA (or DNA expansion)
DNA extract (or extracted DNA)
Expansion DNA (or DNA expansion)
Short, single stranded pieces of DNA that are designed to base pair (or match up with) a
specific segment of DNA you want to copy are called:
Primers
During the annealing step...
Primers bind to the newly separated DNA strand
In sequential order, what are the three steps of PCR?
Denature DNA, Anneal Primers, Extend DNA
What is a necessary "ingredient" for a PCR to proceed.
DNA polymerase (or Taq polymerase)
Template DNA
Forward Primer
Nucleotides
Reverse Primer
If no primers were included in your PCR the reaction would not work because:
The DNA polymerase would not amplify the specific region of DNA you want to be amplified
During PCR, DNA polymerase (or Taq polymerase) starts copying at
Primers attached to the end of the desired DNA sequence
Page 9 of 16
The three main stages of the PCR process are usually repeated around 30 times over
several hours. Approximately how many copies of the target region of original DNA
molecule are made during that time?
1 billion
What kind of primer do plants use?
RbcL
What kind of primer do invertebrate animals use?
MT-CO1
What kind of primer do fungi use?
ITS
What kind of primer do fish use?
MT-CO1
What kind of primer do non-fish vertebrates use?
MT-CO1
What is the total volume of the master mix
30 μL
what volume of pcr reactants do we use in the master mix?
15 μL
what volume of primer mix do we use in the master mix?
1 μL
Page 10 of 16
what volume of water do we use in the master mix?
12 μL
what volume of DNA extract do we use in the master mix?
2 μL
How long is the denature time?
30 sec
How long is the annealing time?
30 sec
how long is the extension time?
1:30
What temp do you denature at?
94 C
What temp do you anneal at?
55 C
What temp do you extend at?
72 C
Electrophoresis is used to:
-Determine the presence of DNA fragments of certain size
-Determine the size of DNA fragments
-Separate DNA fragments
Page 11 of 16
The rate at which DNA migrates through the gel is determined by
-Molecular size of the DNA
-Conformation of DNA
DNA possesses: (kind of charge)
net negative
Why do we run our H2O control (aka negative control) from our PCR reactions on the
gel?
It enables you to tell if your PCR was contaminated by DNA that was not from your sample
(T/F) Once you've loaded your gel you can throw away the remaining PCR product.
False
(T/F)You should be sure to include loading dye in each well of your gel (except the well
with marker/ladder).
True
1000 base pairs =
= 1 kilobase
Since dideoxy (Sanger) sequencing is based on chain termination, why are normal
dNTPs (deoxyribonucleotides like A, T, G, and C) also included in the reaction?
to produce a range of sizes of DNA synthesis products that terminate at variety of lengths
The dideoxyribonucleotides (ddNTPs) used in DNA sequencing work to ______
stop the growth of a DNA strand at a particular base (A, T, G, or C)
Page 12 of 16
The final step in a Sanger DNA sequencing reaction is to run the DNA fragments on a
gel. What purpose does this serve?
It separates DNA fragments generated during the sequencing reaction based on onenucleotide differences in their size.
What would be the most likely outcome of a Sanger dideoxy DNA synthesis reaction if
ddNTPs were present in large numbers relative to the number of dNTPs (normal A's, T's,
G's, and C's)?
Most daughter strands would be very short.
(T/F)Each student that has PCR product for sequencing should have 2 sequential
sequencing tubes. One tube for a reverse read and one tube for a forward read.
True
(T/F)You should be sure to put BOTH a forward AND reverse primer in EACH
sequencing tube.
False
how long should the dna strands be?
0.4-0.5 kb
Which of the following is NOT a substop in the "ANALYZE SEQUENCES" stop of the DNA
subway blue line?
Select data
PHYLIP NJ
Pair builder
MUSCLE
Page 13 of 16
Pair builder
What is the main goal of the "sequence viewer" substop?
visualize your sequence and determine if you have an accurate or inaccurate read
What is the main goal of the "MUSCLE" substop?
This aligns your sequence with other sequences that you select (to look for sequence
similarity)
What symbol will you see in the sequence viewer if you have inaccurate sequence?
exclamation point in a triangle to the left of your sequence
What are the benefits of building a consensus sequence?
it is more accurate and longer than a single read
Is it better to have a higher or lower number for aln. length?
Higher=better match
Is it better to have a higher or lower number for bit score?
Higher=better match
Is it better to have a higher or lower number for mismatches?
lower=better match
Is it better to have a higher or lower number for e?
lower=better match
Which of the following can be very helpful in comparing levels of polymorphism a
MUSCLE alignment?
Page 14 of 16
% sequence similarity
What does branch length mean in the phylip nj tree?
nothing
What does branch tip mean in the phylip nj tree?
individual taxa
What does node mean in the phylip nj tree?
common ancestor
1st step of dna subway
assembling sequences (sequence viewer, consensus sequences)
2nd step of dna subway
add sequences (BLASTN sequences, reference data)
3rd step of dna subway
Analyze sequences (MUSCLE, trees)
Shannon Diversity accounts for what 2 things
species richness and evenness
Page 15 of 16
All the best!!
For any queries email and
discounted documents:
alldocs4sale@gmail.com
Page 1 of 16