Biology Lab Final - Second Half Only

Which of the following is the first and most fundamental question to ask yourself during this stage for this type of task?

"Did I get the answer right?"

In the rbcL PCR of Leaf DNA Extraction protocol it uses a 2X Master Mix, what is contained in this mixture?

-Buffer -Ions -DNA nucleotides -Taq polymerase

In the big picture for DNA Barcoding what are the three steps before PCR?

-Specimen collection -Tissue sampling -DNA extraction

Primers are....

-bind to the template by complementary base pairing -short pieces of single-stranded DNA -designed specifically for the experiment -required for polymerization to occur

DNA barcoding is used to

-complete food inspections -identify species -identify invasive species in geographical regions

A recent paper, A taxonomic study of Quercus langbianensis complex based on morphology and DNA barcodes of classic and next generation sequences, describes the use of PCR in their Methods. Which of the following genes were used as barcoding genes? (select all that apply)

-internal transcribed spacer (ITS) -maturase K (matK) -ribulose-1,5-biphosphate carboxylase oxygenase (rbcL)

How many grams of agarose is required to make 40 ml of a 2% solution?

0.8

Put these in the correct order by matching each step with the corresponding number...

1. Grind the sample 2. Add RNAse and incubate 3. Add precipitation buffer and centrifuge 4. Add the lysate to a Qiashredder and spin 5. Add Ethanol wash Buffer AW1 to the Qiashredder and spin 6. Add solution to the DNA binding column 7. Wash the DNA binding column with AW2 8. Elute the DNA from the column

The following are steps that we have covered thus far in DNA Barcoding. Put these steps in order

1. Specimen collection 2. Tissue sampling 3. DNA extraction 4. PCR 5. Gel electrophoresis

When adding ethidium bromide to a gel, a stock solution is used and diluted in the total volume of gel. If the desired concentration in the gel is 0.5µg/ml, how many µl of a 10 mg/ml stock solution needs to be added to 30 ml of gel solution? Note: Look at your units. Use the C1V1 = C2V2

1.5 µl

If a procedure recalls adding 2.5 volumes of Buffer AW1 to the 400µl flow-through, then how much Buffer AW1 would you need?

1000

How much plant material is called for in the Qiagen DNeasy protocol?

10mg

To achieve greatest accuracy which pipette should be used to transfer 20 µ l?

2 - 20 µl

If you have a stock solution of PCR primers whose concentration is 100 nM, how many µl do you need to add to a total volume of 25 µl to have a final concentration of 10 nM? Concentration (start) x Volume (start) = Concentration (final) x Volume (final) C1V1 = C2V2

2.5

How many µl is 0.25 ml? Enter the number without units.

250

How many cycles are completed within PCR to create over a billion copies of DNA?

30

What is the reading on this p1000 pipettor?

300 µl

What is the approximate length of a cell (in µm) if 11 cells line up end to end across the 40X field of view. Note: The FOV using the 4X lens is 4.0 mm.

36

In order to run a gel, running buffer must be added to the gel box. If you need 400 ml of running buffer, how many ml of 10X buffer stock solution must be add to water to result in a 1X solution? C1V1 = C2V2

40 ml

Convert 0.0006 stomata/µm2 to stomata/mm2

600

When setting up a PCR reaction with the reagents listed in the table, how many microliters of water would you need to add to the TREE tube and the Control tube (respectively) to attain a Total Volume of 25 microliters?

8.5, 10.5

What is the temperature (degree C) used for denaturation in PCR?

95

Which of the following components/stages of metacognition is the most important?

All of the stages of metacognition are equally as important

Which of the following is NOT a benefit of thorough evaluating?

All of these are potential benefits of thorough evaluating -Keeps you from wasting time in the future -Shows strong and weak strategies that you used -Points out your strengths and weaknesses -Better performance on the next similar task -It informs future studying and/or projects

Which of the following were done in the monitoring stage for this example?

All of these were done in the monitoring stage for this example -Ensuring that you check off each of the variables you needed to from your plan -Recalling the plan while working -Making sure your actions align with the goal

Which of the following was NOT mentioned as a goal of the evaluating stage in this example

All of these were mentioned a goal of the evaluating process for this example -Evaluate the correctness of the solution -Make sure the solution matches the goal -Look at the strengths and weaknesses of your approach

What step should be labeled "A" in the graph below?

Annealing

In order to sequence the DNA barcoding region of your sample, a PCR reaction is performed to amplify the region of DNA that will be sequenced. This reaction depends on the selection of the PCR primers. To predict the size of the PCR product with a specific primer pair, a virtual PCR can be performed using _________________.

BLASTn

At what cycle does the desired fragments start to appear?

Cycle 3

When the thermocycler temperature is at 72 degrees Celsius, ___________.

DNA polymerase adds complimentary nucleotides to the DNA strand

When extracting DNA, we normally wear gloves because ______________ will fragment DNA into smaller pieces at room temperature?

DNAse

It is not beneficial to physically write/type out my self-evaluation, as I will definitely remember them next time I approach a similar question or task.

False

Metacognition is a linear process and integrating all the components of metacognition at once exemplifies this idea.

False

The planning stage will look the same regardless of what the task is that you are approaching.

False

Smaller DNA fragments migrate _____ and further over a given period of time than larger fragments.

Faster

What is the function of the tool shown on the left?

Grinding

In the procedure of electrophoresis, what molecular component of the DNA allows it to move through the gel?

Phosphate

Which of the following genes has been used to "barcode" plants?

RbcL (Ribulose-1,5-bisphosphate carboxylase oxygenase large subunit)

What does the evaluating stage NOT entail?

Simply moving on to the next task after coming to a solution

Which of the following enzyme(s) is/are used in PCR?

Taq polymerase

What does 'elute' mean in context of DNA extraction?

The process of releasing DNA from a column using warm water or buffer.

Read the Introduction of the paper A taxonomic study of Quercus langbianensis complex based on morphology and DNA barcodes of classic and next generation sequences. What is the Purpose of their work?

To revise the taxonomy of Quercus langbianensis.

Certain tasks may require you to define important terms in your plan, helping to ensure that you fully understand the task at hand.

True

Extensive research and listing out information that you find are a component of this planning process. Doing this will save you time during the monitoring process.

True

It is best to evaluate my work as soon as possible, so that it is fresh on my mind at the time and I will benefit most from my time spent evaluating.

True

Monitoring effectively will help you to identify mistakes early on and help reduce errors down the line.

True

The answers to the question examples given in this video will impact your study choices immediately, as opposed to far in the future like our previous examples.

True

The effectiveness of your monitoring depends on the thoroughness of your plan from the previous stage.

True

The evaluating process can look different depending on the type of task, problem, or project.

True

While it is still beneficial to go through only certain parts of the metacognitive process at one, the metacognitive process is most effective when you use all three aspects at once.

True

What is the theme of the Department of Biology?

Understanding our World • Healing our World

As you have likely taken exams in your lecture course, do you feel that you employed more of these strategies since being trained on them? (Note: both are credited responses, so answer honestly)

Yes

Which of the following is the main component of gels that are used to separate DNA?

agarose

When spinning your samples in the microcentrifuge, it is most important to

balance the centrifuge by putting another tube with equal weight across from yours

Gel electrophoresis is best for separating DNA

between 200-10,000 bases.

One of the main differences in the Qiagen protocol and the protocol demonstrated by Jason from the DNA Learning Center is that the Qiagen protocol uses

column purification

Which type of monomers are required for elongation in PCR?

deoxynucleotide triphosphates

Micropipettors are used with

disposable plastic tips

In order to see the DNA molecules in the gel, __________ is added to the gel which fluoresces under UV light.

ethidium bromide

The screen shot above illustrates the result of the rbcL PCR primers match in the NCBI database. The Range 1 result is the match of the ______________ primer and the Range 2 is the match of the ____________ primer.

forward; reverse

What if the function of a thermocycler?

heats and cools to create a reaction

Before the development of electrophoresis to separate macromolecules, ____________ was used to isolate DNA.

high speed centrifugation

What is unique about the DNA Polymerase used in PCR?

it can hold up to high levels of heat

What is the purpose of the comb when making a gel is to

make the wells.

DNA moves within the gel from

negative to positive electrode

Which pipettor should you use to add 9.5 µl of water to a reaction tube?

p10

Which pipettor should you use for transferring 150 µl of solution from one tube to another?

p200

Which part of the DNA molecule allows the separation of DNA fragments using gel electrophoresis.

phosphates in the backbone

When dispensing liquids from micropipettes,

push slowly to the 1st stop and then push the remaining liquid out by pushing past the 2nd stop

What are PCR primers?

single stranded DNA complementary to the template

In gel electrophoresis DNA is separated by _____________.

size

What is the goal of PCR?

to amplify DNA

A DNA ladder is used

to measure the number of bases in a DNA molecule.

In the rbcL PCR of Leaf DNA Extraction protocol it uses a control. What is the purpose of using a control?

to test the reaction tube for contamination

Before running the gel, DNA is mixed with dye and loaded into _______ by the use of a pipette.

wells