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Biology 2107 Lab Final Exam Study Guide with Answers

by: dorsa Notetaker

Biology 2107 Lab Final Exam Study Guide with Answers BIOL 2107K Lab

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this is a study guide given to students by the lab TA, Doug Stone, and I typed the answers on it in blue. It also has a section with calculation problems that don't have the answers but still good ...
Honors Principles of Biology I
Dr. Brewer
Study Guide
Biology, lab, Studyguide, biology2107, GeorgiaState
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This 19 page Study Guide was uploaded by dorsa Notetaker on Friday April 22, 2016. The Study Guide belongs to BIOL 2107K Lab at Georgia State University taught by Dr. Brewer in Spring 2016. Since its upload, it has received 8 views. For similar materials see Honors Principles of Biology I in Biology at Georgia State University.


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Date Created: 04/22/16
BIOL 2107 Honors Lab Spring 2016 Final Study Guide Define resolution. Resolution measures the smallest distance two objects can be apart from each other, but still be distinguished as separate objects. You are using a microscope with an NA of 0.25 under blue light (450nm), what is the resolution of this objective? Resolution = 0.61λ/NA Resolution = (.61 x 450)/.25 = 1098 What was used as a color indicator in the protein assay experiment? Coomassie blue dye reagent In a spectrophotometer, cuvette is placed between the light source and the detector. What properties allow for separation of DNA fragments in DNA gel electrophoresis? DNA charge (negative) and size What is the working principle of gel electrophoresis? (Background Information): Gel electrophoresis is the standard lab procedure for separating DNA by size (e.g. length in base pairs) for visualization and purification. Electrophoresis uses an electrical field to move the negatively charged DNA toward a positive electrode through an agarose gel matrix. The gel matrix allows shorter DNA fragments to migrate more quickly than larger ones. Thus, you can accurately determine the length of a DNA segment by running it on an agarose gel alongside a DNA ladder (a collection of DNA fragments of known lengths). What is the function of loading dye in gel electrophoresis? 1) it provides a visible dye that helps with gel loading and will also allows you to gauge how far the gel has run while you are running your gel; and 2) it contains a high % glycerol, so after adding it your sample is heavier than water and will settle to the bottom of the gel well, instead of diffusing in the buffer. What is the net charge of a DNA molecule? Negative What is the function of the stain? Most of the components of cells are colorless. Stains are used to bind to and to make visible specific structures within the cell so that they are more easily visible in the microscope. Explain the function of each of the components of a standard PCR reaction: Polymerase- polymerase can efficiently synthesize DNA under the heat- intensive conditions of the PCR reaction. MgCl 2 The concentration of MgCl2 influences the stringency of the interaction between the primers and the template DNA. MgCl2 supplies the Mg++ divalent cations required as a cofactor for Type II enzymes, which include restriction endonucleases and the polymerases used in PCR. dNTPs- DNTPs are the nucleotide bases added to the growing DNA strand by the DNA polymerase. The purpose of the deoxynucleotide triphosphates (dNTPs) is to supply the “bricks.” Since the idea behind PCR is to synthesize a virtually unlimited amount of a specific stretch of double-stranded DNA, the individual DNA bases must be supplied to the polymerase enzyme. This much is obvious. What might not be as obvious is the fact that the PCR reaction requires energy. The only source of that energy is the β and γ phosphates of the individual dNTPs. Primers- PCR primers are short fragments of single stranded DNA (15-30 nucleotides in length) that are complementary to DNA sequences that flank the target region of interest. The purpose of PCR primers is to provide a “free” 3'-OH group to which the DNA polymerase can add dNTPs. Template- This is the DNA/gene that you wish to amplify. Buffer- The primary purpose of this component is to provide an optimal pH and monovalent salt environment for the final reaction volume. The salts will pass the electricity. Explain what occurs in each step of the PCR Reaction and the approximate temperature it occurs: Denaturation- (separating the target DNA) During the first step of PCR, called denaturation, the tube containing the sample DNA is heated to more than 90 degrees Celsius (194 degrees Fahrenheit), which separates the double-stranded DNA into two separate strands. The high temperature breaks the relatively weak bonds between the nucleotides that form the DNA code. Annealing- (Binding Primers to the DNA Sequence) The PCR will copy only the specific DNA sequences that are present in Chlamydia and absent from other bacterial species. To do this, PCR uses primers, man-made oligonucleotides (short pieces of synthetic DNA) that bind, or anneal, only to sequences on either side of the target DNA region. Two primers are used in step two - one for each of the newly separated single DNA strands. The primers bind to the beginning of the sequence that will be copied, marking off the sequence for step three. During step two, the tube is cooled and primer binding occurs between 40 and 60 degrees Celsius (104 – 140 degrees Fahrenheit). Step two yields two separate strands of DNA, with sequences marked off by primers. The two strands are ready to be copied. Extension- In the third phase of the reaction, called extension, the temperature is increased to approximately 72 degrees Celsius (161.5 degrees Fahrenheit). Beginning at the regions marked by the primers, nucleotides in the solution are added to the annealed primers by the DNA polymerase to create a new strand of DNA complementary to each of the single template strands. After completing the extension, two identical copies of the original DNA have been made. Follow Questions to the Yogurt Experiment: 1. From your results, what can you conclude about what causes milk to turn into yogurt? Bacteria. One or more types of bacteria from yogurt causes “yogurtness.” 2. What evidence do you have to support your conclusions? Based on Koch’s 2  postulate, the pathogen can be isolated from the diseased host and grown in pure  culture. We infected the milk, which was our pure culture, with yogurt that had the bacteria. If we have successfully followed Koch’s postulates we have: 1) isolated a possible causative agent from  yogurt (the diseased individual); 2) grown that microbe in a pure culture on an agar plate; 3) reintroduced  that agent into a healthy individual (milk) and seen the symptoms of the disease (the milk turns into  yogurt) and; 4) again isolated the same bacteria from the newly infected individual. 3. Can any bacteria turn milk into yogurt? What evidence do you have to support your answer? No because there are already some bacteria existing in the milk and they can not turn the milk into  yogurt. No, the E. coli in tube 6 should not have turned the milk into yogurt”. 4. Can yogurt­making bacteria be prevented from making yogurt? What evidence do you have to support your answer? Yes, the ampicillin should have prevented the milk in tube 6 from turning into yogurt. However we can  only say this if the positive control (tube 2) does turn into yogurt. 5. If you had just added yogurt to the milk and found that it made yogurt, what would that show and what would that fail to show? It would show that something in yogurt causes yogurt to form.It would not show what the causative agent  was. It could be a bacteria, virus, fungus, prion, parasite, or even something else. 6. Why is it important to inoculate milk with bacteria from a single colony rather than from multiple bacterial colonies? Yogurt and diseased individuals may harbor more than one kind of bacteria. We would not know what  type of bacteria causes yogurt to form. 7. Some bacteria will only grow when they have access to specific types of nutrients. If some bacteria in the yogurt would only grow in milk, and would not grow on agar, how would this have affected your investigation?The causative bacteria would not grow on the plate and thus no bacterial colony that we found would cause the disease to appear in a healthy individual. We might try the experiment again with a different, perhaps more general nutrient media in the hope of being able to grow the right bacteria. Some disease -causing bacteria, such as tuberculosis, grow poorly if at all on any artificial medium and thus it is difficult to work with them. In an electrophoresis setup, no bands were observed when the gel was run. The possible reason could be: a) DNA is positively charged and the DNA sample was loaded on the side of positive electrode b) DNA is negatively charged and the sample was loaded on the side of the negative electrode c) DNA is negatively charged and the sample was loaded on the side of the positive electron Why is it important to use positive and negative controls in experiments? Give one example of a positive and negative control used in the macromolecule lab. Because a positive control allows us to know what a positive test truly looks like and minimizes the odds of a false positive result. And a negative control in an experiment would indicate a solution that will not yield a positive result. For example, for lipid identification, we use DI water for negative control and Sudan IV for positive, which makes the solution red. Which of the following will give a positive test for the Sudan IV test? a) Glucose b) Fats c) Halogens d) Polysaccharides A membrane bag of "dialysis tubing" is filled with water and NaCl and placed into a beaker which contains a starch solution. Explain what will happen to each of the following and why: a) the starch – it will remain in water because of the large size of starch molecules it can not pass through the membrane b) the NaCl – some of the NaCl will diffuse to the water outside of the bag until the concentrations get equal c) the water – the water will diffuse out of the bag because the concentration of water is low in compare to starch d) the size of the bag – gets smaller because it loses water Which of the following are positive test results? a) Potassium permanganate-colorless b) Iodine-black c) Sudan IV-colorless d) Biuret-bluish/purplish e) Silver nitrate-precipitation There is an unknown solution which has been checked by macromolecule tests. The result is : Biuret test—bluish color, Pottassium permanganate test—pink, Iodine test —black, Sudan IV test—colorless. What is the component of this unknown solution? Starch What is in a solution that gives following results: Potassium permanganate- pink no glucose Sudan IV- pink lipid Iodine- black starch Biuret’s-bluish protein (if dark blue) Carbohydrates are composed of carbon, hydrogen and oxygen Peptide bonds can be found in this macromolecule : Protein What direction does water move in an isotonic solution? Water does not move to any direction because the concentration of water is equal on both sides Define hypertonic, hypotonic, and isotonic mediums. What occurs to a plant cell placed into each type of solution? Hypertonic: if the concentration of water in the medium surrounding a cell is less than that of the cytosol, the medium is hypertonic. Water laves the cell by osmosis and the cell will shrink. If a plant cell is placed in this solution it will shrink. Hypotonic: if the concentration of water in the medium surrounding a cell is greater than that of the cytosol, the medium is hypotonic and if a plant cell is placed in this solution it will swell. Isotonic: if the concentration of water in the medium surrounding a cell is equal to that of the cytosol, the medium is isotonic. If a plant cell is placed In this solution, water will neither leaves or enters the cell. The cell’s appearance will remain unchanged. If you place a dialysis tubing with 5M glucose solution in a beaker of water, what do you expect to happen? Why? The concentration of water inside the bag is very low so the water from the beaker would diffuse into the bag to make the concentrations equal. As a result, the bag will swell. Circle the best term: The cytosol of a cell is hypertonic/hypotonic to distilled water. Elodea normally lives in fresh water. What changes would you observe in the cells of an Elodea plant that was suddenly moved from fresh water to salt water? Why? The cell will shrink because the concentration of water in the salt water that the plant cell is placed into is very low as a result water exits the cell to adjust the concentration of water on both sides and make them equal. -You know that this cell is in a(n) Hypotonic solution because the cell swells. Suppose that you have an osmosis apparatus. In one side of the apparatus, there are a 100 mL of solution composed of distilled water and iodine. In the other side, there is a 10% starch solution. The liquid levels in both sides are initially the same. Answer the following questions in complete sentences. a. What will happen to the level of the water and iodine solution (Side A)? water level goes down because the water travels over to the starch solution b. What will happen to the level of the starch solution (Side B)? it will go up because the water travels from A to B c. In which direction across the semipermeable membrane will the water molecules move when the system reaches equilibrium? It will move in both directions and the net movement would be zero The picture shows a glass chamber separated into two parts by a semi- permeable membrane. Compartment A has 60% sugar solution and compartment B has water in it. In which direction will the water flow? State the reason and the name of the process? The water would move from solution B to A because in solution A, the concentration of water is low. As a result, water moves down the concentration gradient to make its concentration equal on both sides. What connects two amino acids when forming a protein? Peptide bonds (the covalent bonds) What substance diffuses in osmosis? a. water b. protein c. ions You are performing a gram stain on a gram negative sample of bacteria. Describe what color you would expect to see if you left out the components listed: Crystal violet: purple Iodine: purple Decolorizer: clear Safranin: pink You are performing a gram stain on a gram positive sample of bacteria. Describe what color you would expect to see if you left out the: Crystal violet: purple Iodine: Purple Decolorizer: purple Safranin: purple Gram positive has a thick peptidoglycan layer while Gram negative have a thin peptidogylcan layer. List 3 examples of how humans use microorganisms in industry, and the products they produce. Lactic acid bacteria are used to make yogurt, cheese, sour cream, buttermilk and other fermented milk products. Yeast is used in the manufacture of beer and wine and for the leavening of breads. It is also involved in fermentations to convert corn and other vegetable carbohydrates into ethanol to make beer, wine, or gasohol; but bacteria are the agents of most other food fermentations. Antibiotics are substances produced by microorganisms that kill or inhibit other microbes. They are used in the treatment of infectious disease. Antibiotics are produced in nature by molds such as Penicillium and bacteria such as Streptomyces and Bacillus. In your anti-microbial experiments, what were the negative and positive controls? Negative control: DI water Positive: tetracycline You are working with a chemical company that has created this new antimicrobial for carpets. The antimicrobial agent is silver, but it is bound to inert compounds. Design an experiment to show how you would test for its antimicrobial activity. Prepare a dish that is already filled with a lawn of bacteria into 3 sections. Place DI water treated filter, tetracycline treated filter disk to two section (place in the middle). In the thirst section, place a filter disk that has been treated with the new antimicrobial agent in the center. Compare bacterial growth of the new antimicrobial agent to the other two. Gram stain was performed on a pure E.coli culture. Upon observation under the microscope all the bacteria appeared purple in color instead of pink. Which step was not performed well in gram staining? Explain? Alcohol as a decolorizer was not added to it. alcohol makes holes in the cell wall and after safrain is added, it penetrates to the cell and makes it pink. Name 2 Gram + and 2 Gram – bacteria associated with normal microbiota. (normal flora: bacteria that live in your body without causing a disease state) Escherichia coli: a rod-shaped bacterium that lives in the human intestines (has gram negative cell wall) Staphylococcus aureus: a spherical bacterium that has a gram positive cell wall and lives in human nose and skin. Streptococcus mutans: a spherical bacterium with gram positive walls that lives in the mouth and causes tooth decay. Enterobacter: is a genus of common Gram-negative, facultatively anaerobic, rod- shaped, non-spore-forming bacteria of the family Enterobacteriaceae. Why did you add the following in gram staining technique? (Gram staining is based on the ability of bacteria cell wall to retaining the crystal violet dye during solvent treatment. The cell walls for Gram-positive microorganisms have a higher peptidoglycan and lower lipid content than gram-negative bacteria. Bacteria cell walls are stained by the crystal violet. Iodine is subsequently added as a mordant to form the crystal violet-iodine complex so that the dye cannot be removed easily. This step is commonly referred to as fixing the dye. However, subsequent treatment with a decolorizer, which is a mixed solvent of ethanol and acetone, dissolves the lipid layer from the gram-negative cells. The removal of the lipid layer enhances the leaching of the primary stain from the cells into the surrounding solvent. In contrast, the solvent dehydrates the thicker Gram-positive cell walls, closing the pores as the cell wall shrinks during dehydration. As a result, the diffusion of the violet-iodine complex is blocked, and the bacteria remain stained. is applied to the smear to give decolorized gram-negative bacteria a pink color) Iodine: to form the crystal violet-iodine complex so that the dye cannot be removed easily. This step is commonly referred to as fixing the dye. Safranin: making the gram negative pink Alcohol: dissolves the lipid layer from the gram-negative cells. And makes holes in the membrane so that safrain can diffuse Crystal Violet: Bacteria cell walls are stained by the crystal violet (dye) You are in the middle of performing a Gram staining when you realize that you ran out of safranin. You decide to replace it with a yellow dye that is known to work on bacteria. What do you expect the results to be? What color will gram positive bacteria be? purple And gram negative? Yellow How will you determine whether you have a Gram positive or Gram negative culture, if you are not provided with stains. Which media plates will you ask for and why? The EMB media plate would be se in this case. Gram 1 would appear blue or green and gram + would appear colorless. You have been given a sample and asked to determine its Gram stain. What will you do? Explain procedure in detail. Inculcate a colony of bacteria and add it to a drop of water on a microscope slide. Spread the bacteria around. Allow the water to dry. Heat fix the bacteria to the slide. Add crystal violet, iodine, decolorize and safarain in order and gently dab the water using Kim wipes. Place coverslip on top. Thanksgiving was just round the corner with great sales in restaurants and eateries. But with this, there have been a lot of food poisoning cases reported at the Fulton county area of Atlanta. You work in a lab in CDC. Preliminary reports suggest this could be possibly due to Gram-positive bacteria. What are the steps you would carry out to confirm if the agent is Gram positive or Gram Negative? Also, what type of bacteria would you see from a colony on EMB plate and what color would they exhibit under a microscope? After obtaining a sample of the bacteria responsible for the food poisoning, a gram stain can be done to determine whether it is gram – or +. An EMB plate could also be used. Bacteria that appears blue or green is gram – and if it’s colorless it’s +. Aseptic Technique is a set of specific practices and procedures performed under carefully controlled conditions with the goal of minimizing contamination by pathogens. A student was performing a microbiology experiment to isolate microorganisms from the soil. His instructor asks him isolate the gram negative bacteria from the lot. Which media should he use? a EMB b TSA c LB Label the following on the gram-positive drawing: cytoplasmic membrane, outer membrane, peptidoglycan layer. A. peptidoglyca n layer cytoplasmic membrane gram positive does not have an outer membrane. Only gram negative has it Outer peptidoglycan layer B. cytoplasmic membrane The part of the microscope that allows you to let more or less light through, is called? Diaphragm This page is printed out and turned in in class: You are looking under the microscope and see a stringy multicellular organism. The eye piece is 10X, and the objective length is 40X. What’s the magnification? You are using a microscope with an NA of 0.25 under blue light (450nm), what is the resolution of this objective? Given a scope with a 4x ocular and a 15x objective what is the total specimen magnification? Calculate the resolution of an objective lens with a magnification of 20X, wavelength 500 nm, and NA 0.25. Calculate the total magnification of an objective lens 40X, eyepiece 20X, and resolution 1098nm. Calculate the wavelength of light used if the resolution is 1000 nm with a magnification of 30x and NA 0.40. d) DNA is positively charged and the DNA sample was loaded on the side of the negative electrode After a long day of studying and testing at GSU, you get in your car and start driving towards home. The only thing on your mind is to eat that last hot pocket you have been craving for all day to satisfy your hunger. When you arrive home, you open the fridge and scream in anguish because the hot pocket disappeared. You look over to the dinner table and notice two things: the used plate with the hot pocket wrapper and a piece of hair belonging to the culprit. An idea suddenly crossed your mind: “I can do the DNA testing involving Gel Electrophoresis to find out who did this!” You notice three possible suspects: your mom, sister, and brother. Next, you grab a hair sample from the brushes and combs they each use and label them accordingly. Finally, you call your former Biology Lab TA, and explain your scenario. Laughing, he agreed to co-conduct this experiment with you and asks you to meet him in his lab at GSU. Who do you determine the culprit to be from the gel image below? (2 points) Mother Sister Brothe Culprit   r Calculation problems are printed out and turned in in class A disinfectant solution of hydrogen peroxide, H O , cont2in2 3.0 g in 100.0 mL. What is the molarity of H O ? 2 2 What is the molarity of a 15.0% by weight solution of K CrO ? 2 4 2+ A solution containing Mn is prepared by dissolving 274.5 g of pure manganese in nitric acid and diluting to 1.00 L. A 10.00 mL aliquot is then diluted to 500.0 mL. What is the molarity of the final solution? How many grams of C H O ar6 r12ui6ed to prepare 250.0 mL of a 0.250 M solution? Given a 25% solution of NaCl how many mLs of this solution would be used to prepare 350mL of a 10% NaCl solution? How would you make a 10 ml 1:10 serial dilution? You have a 5M solution and need 150ml of a 3M solution. Which variable in CiVi=CfVf is your unknown? You have a 1.55M NaCl solution. What is the concentration of this solution expressed as a percent solution? Would this solution be hypertonic, hypotonic, or isotonic to Elodea? How would one make 50ml of a 25% KCl solution? 15 ml of 3M MgCl solution is added to 45 ml of water. Determine the concentration 2 of this diluted MgCl 2olution. What is the percentage (%) of 2.5 M KCl? A solution is prepared by placing 50.0 g of KBr into a 100.0 mL volumetric flask that is then filled and mixed correctly. What is the molarity of the solution? How many grams of Na SO should be weighed out to make 500.0 mL of 0.500 M 2 4 solution? Using a stock solution of 5M, how much of this solution is required to make a 20mL solution of 2.5M? Using a stock solution of 5%, how much of this solution is required to make a 40mL solution of 2%? Describe how to make a 10 ml of 15% NaCl solution. What is the molarity of a 15% NaCl solution? How much of a 3% stock solution is needed to make a 500 ml 1% solution? You are provided with an Antibody solution that has a concentration of 6M. How would you make an 80 mL of a 1:20 dilution of this solution? What would the final concentration of the Antibody solution be? At your lab bench you have 500ml of an 8% NaCl solution. What is the molarity of this solution? The lab needs 250 ml of a 2% KCl solution, how much (ml) of the stock 10M solution would you need to use to make this dilution? When physiological saline solution is sterilized it has a concentration of 0.15 M. How many moles of NaCl are in 68 mL of this concentration? How would you make 25 mL of a 0.05 M saline solution using the sterilized saline solution?


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