Biology - Lab II Midterm Review
What are JoVE videos? Have you watched the assigned videos on aseptic technique, pipetting, and making solutions?
Journal of Visualized Experiments (JoVE)
Solutions in LAB
Molarity (Mol solute/L solvent), % Concentration grams/100ml = %W/V or Vol/Vol = %V/V, c1v1=c2v2(solution of desired concentration or volume can be made using a known concentration)v1=c2v2/c1, serial dilution is taking the known concentration of a solution and diluting in increments in order to keep track of concentrations as they are being diluted, this is done until the desired concentration is achieved
Explain how to make 1 liter of a 1 molar solution of NaCl. How would you make 300 ml?
To make a 1 liter solution containing 1 molar of NaCl you would need to weigh out 58.44 grams of NaCl (molar mass = 58.44 grams/mol) and mix this into the solution. Since there is 58.44g(1 mol) in 1 L of fluid and you need to figure out the concentration needed for 300ml, first make the units the same (1000ml = 1L) 300ml X 1L/1000ml = 0.3L, 58.44g/L X 0.3L = 17.53 g NaCl needed to be added to the 300mL solvent
Explain how to make 100 ml of 40% glucose.
Assuming this 40% is by mass in grams, glucose has a molar mass of 180.2g/mol, with this knowledge we can than convert these 40 grams into moles 40g x 1 mol/180.2 g = 0.222 moles glucose, we can than convert the 100ml into l, 100ml x 1l/1000ml = 0.1L, we than divide the moles of glucose by 0.1l = 0.222 mol glucose/0.1l = a concentration of 2.22mol/l
What does BIO-HEROES stand for?
Biological Hands-on Explorations with Research Organisms for Experiential Science
How is broth different from agar? Why would you make one over the other?
Broth is a growth media that remains in a liquid state whereas agar is a gelatinous growth media that is a solid. agar plates allow organisms to grow in colonies or be isolated from other organisms, liquid cultures allow cells to grow rapidly and in large amounts.
Calculating concentrations: C1V1 = C2V2
C1V1=C2V2 is used to calculate an unknown quantity where two solutions/mixtures are proportional ... C1V1 = Concentration (start) and Volume (start) C2V2 = Concentration (final) and Volume (final) Concentration can be in cells/ml, g/L, %, mg/ml, mM, M and so on. Volume can be in µl, ml, or L. In both cases, you need to make sure that the units are the same on both sides of the equation. For example: If you have a culture of Tetrahymena and you calculate that it has 50 cells/ml, how could you make a 10 ml culture with a concentration of a 5 cells/ml? C1 = 50 cells/ml V1 = X C2 = 5 cells/ml V2 = 10 ml 50 cells/ml V1 = 5 cells/ml x 10ml V1= 50/50 = 1 ml 1 ml of stock culture added to 9 ml of media (This is a 1:10 dilution.)
How can we use yeast to to study human genes and molecular pathways?
Due to the similarities between the genes/DNA in yeast and how they react to mutations and the responses we observe, we can
Describe the cell structure of yeast cells. Are yeast eukaryotic or prokaryotic? Are they single cellular or multicellular?
Eukaryotic, single cellular
Do you know your team members names and have their contact information?
Gia Fernandez, Gracie Hobson, contact via email
How does the coronavirus that causes COVID-19 enter into the cell?
Scientists made connections between the SARS-CoV-2 of 2019 and the SARS-CoV of 2002. Previously, it was discovered that the SARS-CoV of 2002 infected humans using the Angiotensin Converting Enzyme Receptor (ACE2), and that SARS-CoV-2 that causes COVID-19 did so as well. As shown in the figure below, a portion of the spike protein on the virus, binds to a portion of the ACE2 receptor that is found on a variety of cells in the body, but the ACE2 receptor in mice did not bind the virus!
Explain the role of DNA Repair enzymes.
Some proteins "sense" the DNA damage and activate the repair pathways. Others are activators or inhibitors of the cell cycle checkpoints. These checkpoints are required to allow the DNA to be replicated and "proofed" before cell division. Other proteins are involved in repairing errors in DNA replication by cutting out mismatches and fixing breaks. Remarkably, many of these genes and the DNA repair pathways that they are responsible for, are conserved(share an evolutionary history)between humans and yeast and can be identified bioinformatical
What role did the hACE2 mice play in COVID-19 research?
The SARS virus enter through the humans ACE2 receptor, mice have a different receptor which did not allow for the SARS virus to be accepted by the mice however with genetic engineering of the mice's DNA, we were able to embed human ACE2 receptors within the mice. This allows the virus to gain access within the mouse and connect with these receptors causing the mice to become susceptible. After developing a viable sample of mice, we are then able to breed these modified mice using invitro fertilization alongside traditional breeding to breed these mice at cost to send to other labs for research into potential therapeutics and vaccines
What is the difference between a serological pipette and a micropipette? When would you use one over the other?
a serological pipette is a glass syringe that can hold and transfer volumes ranging between 0.1-50ml, a micropipette can hold and transfer volumes between 0.2 microliters - 5m. You would use the serological pipette when the chemicals might be damaging to the plastic tips of the micropipette
You have 5 ml of a stock solution that has 100 mg/ml of ethidium bromide and you want to make 1 ml of 10 mg/ml. What volumes will you use and what instruments will you use to transfer the liquids?
c1v1=c2v2, 100mg/ml X 5ml = 10mg/ml X ?ml -> 500mg = 10mg/ml X ?ml -> 500mg/10(mg/ml) = 50ml = ?ml. You could possibly use the serological pipette to transfer the 5ml stock as well as the 10mg/ml concentration even the newly formed 50ml stock but for this as well as the 100 mg/ml concentration the micropipette would also be appropriate
What did Leland, Hartwell, and Nurse win the Nobel Prize for?
establishing the role of different genes in controlling the cell cycle and investigating the link between the cell cycle in yeast and that in humans.
10x concentration and serial dilution
one unit of buffer is diluted into nine units of water in order to achieve a 10x buffer. For micro buffers, this is what serial solutions which is having a standard solution diluted into three unknown samples.
Containers and equipment for mixing solutions
things such as beakers and erlenmeyer flasks are generally used for mixing and storing solutions, the graduation marks on the sides of these containers represent approximations. Volumetric containers/graduated cylinders use exact volumes of liquid substances. TC = to contain, TD = to deliver, Serological pipettes TD = 0.1-50mL, Micropipettors = 0.2 microliters - 5ml, Graduated cylinders = >50ml, Hamilton glass syringes - microliter ranges.
Explain how to make NGM agar plates.
1.Use a graduated cylinder to add 50 ml of diH2O to the bottle. It is best practice to add some water first to help prevents the solids from getting clumped together and stuck on the bottom of the bottle. 2.Weigh out 1.2g agar and add to the water.3.Weigh out 0.2 g Tryptone and add to water.4.Swirl to mix. (Agar will not go in solution until it is heated.)5.Use a p1000 to add 1090 ml of 3MNaCl. (Remember not to go over the 1000. Divide by 2 and add 545 μl 2 times.)Dispose of the tip in the waste container.6.Use a serological pipette to add the 3.2 ml of 0.5 M KH2PO4.7.Use a graduated cylinder to measure and add the remaining 26mlwater.Preparing the bottles for the autoclave1.Label the bottles using the labeling tape and a permanent black marker. (Section, Team # and initials, Date, Contents)Make sure the tape is above the "80ml" mark so it does not come off in the autoclave or the water bath.2.Add a piece of autoclave tape to the lid of the bottle and label it with the day the section meets, section number and team number. (Example: TUE-01 TLA Team 1)3.Screw the cap on the bottle. (The cap will be loosened during autoclaving to allow the steam to penetrate the liquid. The bottles will be placed in an autoclave tray with a small amount of water in the bottom to prevent the solution inside the bottle from boiling over. After autoclaving, the bottles will be placed in a 60C water bath so the agar will remain liquid. Your instructors will autoclave this solution and store it in a water bath until next week.) Once the bath is ready to use pour into petri dishes
How many µl in a ml? How many ml in a liter? Hom many mM in a M? How many µM in a mM?
1000 µl in a ml(x1000 or /1000), 1000ml in a l (x1000 or /1000), 1000mM in a M (x1000 or /1000), 1000µM in a mM (x1000 or /1000)
The recipe of NGM agar calls for 15 g of agar for 1 Liter of media. How much agar will you need for a total of 75 ml of media?
15g/1L x 0.075L (75mlx1l/1000ml) = 1.13g needed
Explain how to make 100 ml of a 3M solution of NaCl.
3mol/1l, 100ml x 1l/1000ml = 0.1L, 3mol/1l x 0.1l = 0.3 mol NaCl needed to be added to the 100ml/0.1l solvent or 0.3mol NaCl x 58.44g/1mol = 17.53g needed
Why is yeast a good model organism?
In the lab it is easy to manipulate, can cope with a wide range of environmental conditions and controls cell division in a similar way to our cells. In 1996, it was the first eukaryotic organism to have its genome? sequenced. Fission yeast (Schizosaccharomyces pombe) has become a popular system for studying cell growth and division. It is useful partly because it is easy and inexpensive to grow in the lab, but also because its cells have a regular size and grow only in length, making it very simple to record cell growth. Fission yeast chromosomes share a number of important features with human chromosomes making the organism a very useful model in human genetics An important feature of these yeasts that makes them such useful organisms for studying biological processes in humans, is that their cells, like ours, have a nucleus containing DNA? packaged into chromosomes. Most metabolic and cellular pathways thought to occur in humans, can be studied in yeast. For example, studying signaling proteins in yeast has advanced our understanding of brain and nervous system development. Yeast cells divide in a similar manner to our own cells. In fact, it has been found that many of the genes? that work to regulate cell division in yeast, have equivalents that control cell division in higher organisms, including humans. KEY FACT The S. cerevisiae and S. pombe yeast genomes have just over 12 million base pairs. Both the S. cerevisiae and S. pombe yeast genomes have just over 12 million base pairs?. S. cerevisiae has around 6,000 genes while S. pombe has just over 5,000. At least 20 per cent of human genes known to have a role in disease have functional equivalents in yeast.
What characteristics are important to consider when choosing a model organism?
Is the organism easily obtainable, The main idea with this approach is to select an organism that is easy to maintain in the lab and can serves as an indirect means to understanding humans or other more complex systems. Model organisms vary depending on the type of questions that are being explored. For example, all cells use DNA and RNA, so molecular mechanisms, such as DNA replication, have been discovered in bacteria and virus, as well as single cell eukaryotic models, such as yeast. Yeast are the simplest eukaryotic cell, but we will see how they can be used to study cancer and types of infertility. These discoveries have been used to propose new hypotheses that can be tested in mammals and later applied to human health.
Have you contributed to the group's success by doing your part and by including all members? Describe the Collegiality Check performed each week.
Lab Preparation Familiarize yourself with the locations and purpose of all of the lab's safety equipment, including fire extinguishers, eyewash stations, and emergency showers. Know what each lab entails before you enter the room, including any specific safety concerns. Wear appropriate safety gear, including long pants and closed-toed shoes! Your torso needs to be covered and you shirt should have sleeves. All long hair should be pulled back, roll up loose sleeves, and remove dangling jewelry. Notify your instructor of any allergies to latex or specific chemicals. You are not required to wear lab coats and safety glasses, but feel free to bring your own. Lab Behavior and Expectations No horseplay or "messing around" in the lab setting. No personal music, videos, or headphones. Keep your voice down and try to minimize the movement in the lab. Lab is more enjoyable and productive in a relaxed and calm atmosphere. Keep walkways, desktops, and countertops clear and as uncluttered as possible. Anything extraneous to the laboratory experiment should be stored safely away in the cubbies, including backpacks, etc. Know how to use the equipment in lab, and do not operate any equipment until you are instructed in its use! If you are uncertain about using a piece of equipment, please refer to your instruction manual or ask for instruction before trying to use it! A microscope will be assigned to your station. Take good care of your scope! Unless specifically told otherwise by your instructor, only work during regular, assigned lab hours and on the assigned experiments. Do not conduct any unauthorized experiments. Do not bring any food/drink into the lab, and never put anything in lab into your mouth! Never pipette by mouth. Do not apply makeup in the lab. Do not use chemicals from an unlabeled container, and do not return excess chemicals back to their container. Be careful around ethanol burners, hot plates, and heat blocks. Do not touch or place anything on the surface. Keep your area clean. Before you begin, use the cleaning solution and paper towels to clean your bench-top. Lab Cleanup and Reporting If you break any glassware, notify your lab instructor immediately! DO NOT pick up the glass pieces with your hands or throw them in the trash can. Your TA will clean up the broken glass and dispose of it in the broken glass box. Report all spills to your instructor immediately. Your TA will clean them up appropriately. Dispose of all solutions as instructed by your lab instructor, and do not put chemicals in the sink or trash unless instructed to do so. No soil in the sink! Any sample or solution that contains organisms needs to be disposed of in the autoclave bag. Used serological pipettes and tips that have been used with organisms also will go through the autoclave. Used glassware, concavity slides, and 24 well culture plates will be bleached and washed. Even basic lab equipment is expensive, and you may be required to pay all or part of its replacement cost if it is broken due to carelessness. Report malfunctioning equipment to your instructor immediately. At the end of each lab, thoroughly clean your lab area and return all equipment and supplies to their original locations. Do not remove any chemicals or equipment from the lab.
Do you know what is expected of you each week for pre-lab, lab, and post-lab?
Pre-Lab Activities: We will use Canvas to present all of the pre-and post-lab assignments for labs. To prepare for each lab, you should complete all items in the Canvas Module, including reading, watching videos, and answering questions. The Modules will include a series of reflective questions and/or calculations to make sure you understand the purpose and procedures introduced. You should take your own written notes and write the lab procedures in your own words in your lab notebook. Recording this information will better prepare you for lab and allow you to use your time efficiently. These notes will be checked randomly. The Pre-lab assignments will be due before you come to lab and will close at the start of your lab time. In-Class Meetings: Labs will meet each week face-to-face, with the exception of Week 1(synchronous Zoom meeting) and Week 11 (asynchronous online lab).There are no scheduled make-up labs. Please contact the Lab Coordinators if you have an emergency or any questions. Attendance and "lab quiz" questions will be recorded using Top Hat. TopHat "clicker" Questions(Lab): Each lab will begin with a "mini-lecture" which includes questions over the pre-lab material and biological concepts. Be sure and bring your phone or device so that you can join the session. Each question will be worth 2 points. One point for participation and 1 point for correctness. Post-Lab Assignments(15-20 points): The Post-lab assignments will include file uploads and/or Notebook-like posts. The Post-lab Assignments will be due within 24 hours of completing your in-class labs. Post-Lab Assignments: The Post-lab assignments will include file uploads and/or Notebook-like posts. The Post-lab Assignments will be due within 24 hours of completing your in-class labs.
What is the scientific name of baker's yeast?
Saccharomyces cerevisiae
What 4 "Heroes" are introduced in this course?
Saccharomyces cerevisiae, Caenorhabditis elegans, Tetrahymena thermophila, Rattus norvegicus
What are tryptone and peptone? Why are they added to media?
Tryptone is the assortment of peptides formed by the digestion of casein by the protease trypsin. Tryptone is commonly used in microbiology to produce lysogeny broth for the growth of E. coli and other microorganisms. It provides a source of amino acids for the growing bacteria Peptone is another complex mixture of nutrients. This is a source of carbon, nitrogen, vitamins and minerals. This is an enzymatic digest of animal proteins and provides the amino acids required for rapid growth. This mixture is used in many types of the media, including the media used to in the making of vaccines.
What does it mean "to transfer knowledge"? How does that relate to the philosophy of this course?
We are given the opportunity to learn about lab procedures and the important contributions that the laboratory has given to the world and the different researches that have been made. We are than able to learn about the techniques and equipment and procedures that were required to accomplish them. We are than allowed to practice these techniques ourselves, this can then allow us to grasp this information and knowledge and pass it on to others and therefore spreading the philosophy of the natural sciences.
What are homologs and orthologs?
We call these types of homologous genes which are found in different species but evolved from a common ancestral gene, orthologs.
How does the yeast genome compared to the human genome?
Yeast cells divide in a similar manner to our own cells. In fact, it has been found that many of the genes? that work to regulate cell division in yeast, have equivalents that control cell division in higher organisms, including humans.
