This week we will work in a Virtual Lab related to Gel Electrophoresis.
First it is important to check what are the parts of the Lab Report, so here you have a template to remember each one.
Lab Report Template
Title: * a brief, concise, yet descriptive title
Example: "Types of Invertebrates Found in Pond Water"
Introduction: (State the problem or question to be answered)
* What question(s) are you trying to answer?
* Not all experiments start with a question, some start with an observation and questions develop from further observations
* Include any preliminary observations or background information about the subject
Example: How many different types of insects are found in pond water? Does the location of the pond change the types of insects that live there? Does water quality affect the number of organisms?
Hypothesis:
* Write a possible solution for the problem or an explanation for the observation
* Make sure this possible solution is a complete sentence.
* Make sure the statement is testable, an if-then statement is recommended to illustrate what criteria will support your hypothesis (and what data would not support the hypothesis).
* Identify the manipulated (independent) variable and the responding (dependent) variable.
Example: Ponds located near populated areas will have less organisms than ponds found in isolated areas. The manipulated variable is the pond location, the responding variable is the number of organisms.
Materials:
* Make a list of ALL items used in the lab. Draw the to be sure you recognize each of them. Alternatively, materials can be included as part of the procedure.
Example: Pond water, strainers, microscopes, field guides, petri dishes
Procedure:
* Write a paragraph (complete sentences) which explains what you did in the lab as a short summary.
* You may choose to add details (step-by-step) of your procedure in such a way that anyone else could repeat the experiment.
Example: Water was sampled from each pond and examined under the microscope. A field guide was used to identify the types of organisms found and estimations of numbers were recorded.
Data:
* This section should include any data tables, observations, or observations
* You may attach a separate sheet(s) if necessary.
* All tables, graphs and charts should be labeled appropriately (X and Y axis)
Conclusions:
* Accept or reject your hypothesis.
* EXPLAIN why you accepted or rejected your hypothesis using data from the lab.
* Include a summary of the data - averages, highest, lowest..etc to help the reader understand your results. Try not to copy your data here, you should summarize and reference KEY information.
* List one thing you learned and describe how it applies to a real-life situation.
*Discuss possible errors that could have occurred in the collection of the data (experimental errors) and suggest ways the experiment could be improved.
After this please open , READ and print the worksheet in the following link.
WORKSHEET ON LAB ON ELECTROPHORESIS
Later, enter into the Virtual Lab
VIRTUAL LAB LINK
Finally, this information taken from: https://www.khanacademy.org/science/biology/biotech-dna-technology/dna-sequencing-pcr-electrophoresis/a/gel-electrophoresis
will help you to understand the characteristics and uses of this procedure.
Gel electrophoresis
A technique used to separate DNA fragments and other macromolecules by size and charge.
Key points:
- Gel electrophoresis is a technique used to separate DNA fragments according to their size.
- DNA samples are loaded into wells (indentations) at one end of a gel, and an electric current is applied to pull them through the gel.
- DNA fragments are negatively charged, so they move towards the positive electrode. Because all DNA fragments have the same amount of charge per mass, small fragments move through the gel faster than large ones.
- When a gel is stained with a DNA-binding dye, the DNA fragments can be seen as bands, each representing a group of same-sized DNA fragments.
Introduction
Suppose you have just done a PCR reaction, making many copies of a target DNA region. Or perhaps you’ve done some DNA cloning, trying to "paste" a gene into a circular DNA plasmid.
Now, you want to check and see whether your PCR worked, or whether your plasmid has the right gene in it. What technique can you use to visualize (directly observe) the fragments of DNA?
Gel electrophoresis
Gel electrophoresis is a technique used to separate DNA fragments (or other macromolecules, such as RNA and proteins) based on their size and charge. Electrophoresis involves running a current through a gel containing the molecules of interest. Based on their size and charge, the molecules will travel through the gel in different directions or at different speeds, allowing them to be separated from one another.
All DNA molecules have the same amount of charge per mass. Because of this, gel electrophoresis of DNA fragments separates them based on size only. Using electrophoresis, we can see how many different DNA fragments are present in a sample and how large they are relative to one another. We can also determine the absolute size of a piece of DNA by examining it next to a standard "yardstick" made up of DNA fragments of known sizes.
What is a gel?
As the name suggests, gel electrophoresis involves a gel: a slab of Jello-like material. Gels for DNA separation are often made out of a polysaccharide called agarose, which comes as dry, powdered flakes. When the agarose is heated in a buffer (water with some salts in it) and allowed to cool, it will form a solid, slightly squishy gel. At the molecular level, the gel is a matrix of agarose molecules that are held together by hydrogen bonds and form tiny pores.
At one end, the gel has pocket-like indentations called wells, which are where the DNA samples will be placed:
Before the DNA samples are added, the gel must be placed in a gel box. One end of the box is hooked to a positive electrode, while the other end is hooked to a negative electrode. The main body of the box, where the gel is placed, is filled with a salt-containing buffer solution that can conduct current. Although you may not be able to see in the image above (thanks to my amazing artistic skills), the buffer fills the gel box to a level where it just barely covers the gel.
The end of the gel with the wells is positioned towards the negative electrode. The end without wells (towards which the DNA fragments will migrate) is positioned towards the positive electrode.
How do DNA fragments move through the gel?
Once the gel is in the box, each of the DNA samples we want to examine (for instance, each PCR reaction or each restriction-digested plasmid) is carefully transferred into one of the wells. One well is reserved for a DNA ladder, a standard reference that contains DNA fragments of known lengths. Commercial DNA ladders come in different size ranges, so we would want to pick one with good "coverage" of the size range of our expected fragments.
Next, the power to the gel box is turned on, and current begins to flow through the gel. The DNA molecules have a negative charge because of the phosphate groups in their sugar-phosphate backbone, so they start moving through the matrix of the gel towards the positive pole. When the power is turned on and current is passing through the gel, the gel is said to be running.
Based on similar diagram in Reece et al.start superscript, 2, end superscript
As the gel runs, shorter pieces of DNA will travel through the pores of the gel matrix faster than longer ones. After the gel has run for awhile, the shortest pieces of DNA will be close to the positive end of the gel, while the longest pieces of DNA will remain near the wells. Very short pieces of DNA may have run right off the end of the gel if we left it on for too long (something I've most definitely been guilty of!).
Visualizing the DNA fragments
Once the fragments have been separated, we can examine the gel and see what sizes of bands are found on it. When a gel is stained with a DNA-binding dye and placed under UV light, the DNA fragments will glow, allowing us to see the DNA present at different locations along the length of the gel.
The bp next to each number in the ladder indicates how many base pairslong the DNA fragment is.
A well-defined “line” of DNA on a gel is called a band. Each band contains a large number of DNA fragments of the same size that have all traveled as a group to the same position. A single DNA fragment (or even a small group of DNA fragments) would not be visible by itself on a gel.
By comparing the bands in a sample to the DNA ladder, we can determine their approximate sizes. For instance, the bright band on the gel above is roughly 700 base pairs (bp) in size.
Check your understanding
Four lanes are numbered on the gel above. (A lane is a corridor through which DNA passes as it leaves a well.)
Which lane matches each description below?
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