BCHS 3201 Biochemistry I Laboratory Prelab Quiz 1

Pre Lab: Quiz 1 1. The study of all of the proteins expressed in an organism at a particular time and/or set of conditions is called: genomics proteomics metabolomics omics 2. In a microarray, to see what genes hav ...

Pre Lab: Quiz 1 1. The study of all of the proteins expressed in an organism at a particular time and/or set of conditions is called: genomics proteomics metabolomics omics 2. In a microarray, to see what genes have been expressed (transcribed) by the cell under our set of experimental conditions, we will purify from the organism: DNA cDNA mRNA Protein 3. For our microarray project, the model organism under study is Eschericia coli Shewanella oneidensis Drosophila melangastor Arabidopsis thaliana4. How is the protective group removed to allow the addition of nucleotides to the probe on the DNA chip? addition of silane rinse with water UV light exposure capping agent 5. What is in a probe pair on an Affymetrix chip? two different probes for the same gene one probe to the specified gene and one blank cell for calibration one probe to the specified gene and one probe with a mismatch in the center of the probe to the specified gene to gauge non-specific hybridization levels one probe for the control cRNA to bind and one probe for the experimental condition cRNA to bind6. In the yeast microarray example shown below, which genes (probe arrays are in yellow brackets) are downregulated when the yeast are grown on minimal media instead of rich media? a, b, e, f c, d, e c, d a, f 7. Why are side groups on a nucleotide capped when building probes on a microarray? to prevent mismatches during hybridization with the sample To prevent creation of branched probes on the chip To create the mismatches for a probe pair on the chip To prevent elongation of probes that have incorporated a nucleotide in the wrong place8. What plant phytohormone inhibits seed germination to prevent premature sprouting? abscisic acid giberrelin ethylene Auxin 9. In which process(es) below is sugar signaling involved? Choose all that apply. Starch metabolism Flowering Heat senescence Seed germination 10. If sugar levels in a plant are high, you would expect expression of genes involved in photosynthesis to be downregulated. upregulated.PreLab Quiz 2 Which of the following represents a properly balanced centrifuge (check all that apply): Group of answer choices d b a c Flag question: Question 2Question 3 1 pts How will the plasmid DNA be separated from chromosomal DNA in this plasmid purification lab? Group of answer choices ethidium bromide intercalation salting out gel electrophoresis differential centrifugation Flag question: Question 3 What happens to plasmid DNA if you leave it in Solution II, lysis buffer, for too long? Question 2 1 ptsQuestion 4 1 pts Group of answer choices Plasmid rings can no longer renature or re-base pair Plasmid DNA strands renature with themselves Plasmid DNA renatures with chromosomal DNA DNA degrades Flag question: Question 4 After lysing your E.coli cells and neutralizing the reaction, you will spin down the solution. Do you keep the supernatant or pellet to use in the next step? Group of answer choices pellet supernatantQuestion 5 1 pts Question 6 1 pts Flag question: Question 5 Which has more resolving power? Group of answer choices 1% agarose gel 4% agarose gel Flag question: Question 6 What should you do with the liquid waste from this lab? Group of answer choicesQuestion 7 1 pts Put it in the jug in the fume hood Pour it in the biohazard fliptop trash can Bleach it for 20 minutes Pour it down the sink Flag question: Question 7 Why must you wait 10 minutes after adding TE/RNase to the dry DNA pellet? Group of answer choices To neutralize the lysis buffer To allow time for the plasmid to precipitate To allow time for the RNA to be hydrolyzed or degraded To chelate any divalent cations that might allow DNase to degrade the plasmidQuestion 8 1 pts Question 9 1 pts Flag question: Question 8 How will you mix the contents of the microcentrifuge tube after adding Solution II and Solution III to the cell culture? Group of answer choices Vortex Invert Shake Pipet gently Flag question: Question 9Question 10 1 pts Where should you expect to the see plasmid DNA after you spin it down out of solution? Group of answer choices impossible to see smeared up one side of the tube at the bottom of the tube Flag question: Question 10 What is agarose? Group of answer choices Seaweed Gelatin TapiocaQuestion 1 1 pts Soy-based gel Jell-O PRELAB QUIZ 2 How do bacteria prevent their own DNA from being cleaved by restriction enzymes? Group of answer choices by phosphorylating their own bacterial DNA by phosphorylating the restriction enzyme by methylating their own bacterial DNA by methylating the restriction enzymeQuestion 2 1 pts Flag question: Question 2 Which of these could be a functional restriction site (think palindromes)? Group of answer choices a b c dQuestion 3 1 pts Question 4 Flag question: Question 3 Which of the following pairs of enzymes is an example of a neoschizomer? Group of answer choices a b c b,c, and d Flag question: Question 4Question 5 1 pts Which type of scenario is preferred when designing a cloning experiment so that the desired DNA insert gets inserted in the correct orientation in the plasmid? Group of answer choices 1 enzyme that leaves blunt ends 2 enzymes that leave blunt ends 1 enzyme that leaves sticky ends 2 enzymes that leave different sticky ends Flag question: Question 5 Cleavage of sequences by a restriction endonuclease at sites slightly different than the defined recognition sequence is called Group of answer choices 1 ptsQuestion 6 1 pts glycolytic activity methylation neoschizomer activity star activity exonuclease activity Seeing more or fewer bands of DNA on your gel than you expect after a restriction digest reaction of a plasmid with known sequence can be the result of Group of answer choices failure to digest all of the target DNA in the sample no digestion star activity all of the aboveQuestion 7 1 pts Question 8 1 pts Flag question: Question 7 You should vortex your restriction digest reaction for thorough mixing. Group of answer choices True False No answer text provided. No answer text provided. Flag question: Question 8Question 9 1 pts When you set up your restriction digest reaction, you should add the restriction enzyme to the tube first, before adding any other reagent after adding everything except the DNA and mixing gently last, after adding all other reagents and mixing gently No answer text provided. Flag question: Question 9 If you are short on time and don’t run the gel long enough, Group of answer choices the bands will be squashed at the top of the gel and may not separate completely the bands will be smeared.Question 10 1 pts the bands will be wavy. the buffer will precipitate, leaving speckles on the gel. Flag question: Question 10 The charge on DNA is . The wire is the positive electrode on the gel electrophoresis apparatus. positive/black positive/red negative/black negative/red 09/18 Todats lab and last weeks lab will be one report together - plasmid purification and digestAll the post lab questions from last week and this week will be Microarray literature work due next week Maybe prelab Will finish the himewirj plasmid digest next monday when class ends Next week will start microarray workshop 09/25 Picking one gene, down regulated and up regulated’ - Looking at the gene how it affects the cell, the role to the cell Look at sugar signaling or hormone signaling That gene is needed for the literature search, if cant find a good gene in the search choose the ext gene In the title write the gene name, and organism name Aradiosis Thaliana Your name comes first, at the end is the corresponding author( group members?)In the introduction: Introduce the species, why are we doing microarray importance, hypothesis? In the discussion : bring up the results again, tables etc No figures from google even if cite it U can draw charts, figures etc - We can use our own pie charts, because we made that Instead of higher say there was a 1.5 increase etc. etc 20-25 % is okay in similarity After submitted the final draft, use the chatgpt made paper and your own written paper. - Write a 2 page paper separating the differences from both those papers When looking at papers *publications* see if itt talk about signaling. At5g35735 only three signaling AT5G52300 AT5G52310 At5g28770Question 1 1 pts Question 2 1 pts Vi - > 51760 PRElab quiz 4 hill reactions Where do the carbon fixation reactions which synthesize sugar occur? thalakoids stomata stroma epidermis What is the source of the electrons in the electron transport chain for photosynthesis?Question 3 1 pts Question 4 Group of answer choices sunlight photons carbon dioxide water If a chemical species GAINS an electron, it is oxidized reduced Flag question: Question 4Question 5 1 pts The artificial electron acceptor we will be using as the Hill reagent in the Hill reaction experiment in this lab is 2,6-dichloroindophenol (DCPIP or DPIP)) ferrocyanide oxygen water In this experiment, we will be looking for a change in the color of the reaction from clear to blue 1 ptsQuestion 6 1 pts Question 7 1 pts blue to clear red to clear clear to red Where do plants get the carbon they need to synthesize sugar? soil fertilizers or composting matter air (CO2) Light energy How do electrons travel from Photosystem II to Photosystem I?Question 8 2 pts Group of answer choices diffusion through the lipid bilayer shuttled via plastocyanin 1ST ATTEMPT - shuttled via plastoquinone pumped by ATP synthase Flag question: Question 8 What are the product(s) of the "light" reactions of photosynthesis? Choose all that apply. NADPH NAD SugarQuestion 9 1 pts ATP 1ST ATTEMPT - ADP Flag question: Question 9 What is another name for the part of photosynthesis that can occur without the presence of light? Group of answer choices Calvin Cycle Citric Acid Cycle Circle of Life Water cycleQuestion 1 1 pts Question 2 1 pts 10.08 The acronym PAGE stands for Group of answer choices Protein Agarose Gel Electrophoresis Protein Acrylamide Gel Electrophoresis Polyagarose Gel Electrophoresis Perfectly Awesome Gel Electrophoresis Polyacrylamide Gel Electrophoresis Flag question: Question 2Question 3 1 pts Which has more resolving power? Group of answer choices agarose gel polyacrylamide gel Flag question: Question 3 In lab, we will give you pre-cast polyacrylamide gels to use. If you had to cast it yourself, however, the reagents you would use to catalyze the polymerization of the polyacrylamide matrix would be Group of answer choices ammonium persulfate and TEMED TEMED and sulfoxide bis-acrylamide and acrylamideQuestion 4 1 pts Question 5 1 pts SDS and tris-glycine buffer Flag question: Question 4 Which type of gel would you use if you wanted the protein to remain folded as it moves through the gel? Group of answer choices Native SDS Flag question: Question 5 Acrylamide is aQuestion 6 1 pts Group of answer choices lung irritant Mutagen Neurotoxin Harmless substance Flag question: Question 6 In PAGE, what is used to coat the protein with a negative charge? Group of answer choices Loading buffer Ethidium bromide SDSQuestion 7 1 pts Question 8 Coomassie blue Flag question: Question 7 What is the most abundant protein in the blood sera of mammals? Group of answer choices hemoglobin erythrocytes albumin lysozyme Flag question: Question 8Question 9 1 pts In the protocol, what do you have to remove from the gel cassette before placing it in the electrode assembly or the electric flow through the gel will be blocked? Group of answer choices comb buffer protein sample tape paper Flag question: Question 9 To remove the gel from the cassette without tearing it, what should you use in a squirt bottle to loosen the gel from the plastic? 1 ptsQuestion 10 1 pts Group of answer choices Tris-glycine buffer Coomassie blue Water Ethanol Bleach Flag question: Question 10 What is the purpose of treating samples with beta-mercaptoethanol when running an SDS-polyacrylamide gel? Group of answer choices denature the proteincoat the protein with a negative charge break the disulfide bonds contributing to quarternary structure break the peptide bonds between subunits disrupt hydrogen bonding in a subunitFunctional Categorization by annotation for : GO Molecular Function J Charts for Functional Categorization (Help) [#of annotations to terms in this GOslim category x 100] = % [ # of total annotations to terms in this ontology Functional Categorization by annotation for : GO Cellular Component Functional Categorization by annotation for : GO Biological ProcessQuestion 1 2 pts Question 2 2 pts Prelab quiz 6 10.22.23 crystallization What is the function of PEG in this lab? Group of answer choices It serves as a crowding agent to aid the assembly of proteins into the lattice It dissolves the lysozyme It stabilizes the charges on the outer surface of the protein It has no apparent function Flag question: Question 2Question 3 2 pts Izit is a solution Group of answer choices violet red blue pink clear/colorless Flag question: Question 3 What does the 'd' in the equation above stand for?Question 4 2 pts Group of answer choices The distance between the layers of the lattice The angle between the incident ray and the lattice plane The wavelength of the X-ray An integer describing the order of the reflection Flag question: Question 4 What are the steps required to create a 3-dimensional model of a protein structure? Group of answer choices The diffraction data must be transformed to yield the model of the protein The crystal must be subjected to an X-ray beam and the diffraction pattern captured on X-ray filmQuestion 5 2 pts Protein crystal must be dissolved in water A suitable crystal of the purified protein of interest must be grown Flag question: Question 5 What solution are we using as a diluting buffer for this experiment? Group of answer choices Sodium Potassium Phosphate Saline Phosphate Buffer Sodium Acetate TRIS11.05 Turnip kinetics lab 1. What reaction does peroxidase catalyze? Group of answer choices Conversion of water to hydrogen peroxide Conversion of hydrogen peroxide to water Conversion of guiacol to hydrogen peroxide Conversion of guiacol to water 2. What is the hydrogen donor in the kinetics lab? Guaicol Hydrogen peroxide Peroxidase Water Tetraguiacol 3. Data is linearized and used to construct a double-reciprocal or Lineweaver-Burk plot in this lab. Why? To more accurately determine Vmax To determine the type of inhibition occurring Both a and b 4. What should the total volume of each reaction in the experiment be? 60 µl30 µl 3 ml Variable 5. Which of the following is true? Hydroxylamine and guaicol should be disposed of in the appropriate waste container (not down the sink). Hydroxylamine is a known mutagen Hydroxylamine may cause burns on the skin Goggles and gloves are required for this lab All of the above