Biology I: 2011 Final Exam Diagram Bank Each diagram below is annotated as they will be on your Final Exam. You must identify the annotated features/concepts before the day of your exam. Plan ahead and carefully analyze and annotate one or two diagrams each night in preparation for the exam. Compare your analysis to your classmates and discuss. If you are unable to identify a feature on the diagram, you should use your available resources to do so. The Exam questions will not, in general, be asking what is the feature labeled 1? Make sure you understand the significance of each annotation to the overall diagram and the biological process/concept it represents. For each experimental type question predict the possible outcomes for each. 1. Protein folding and substrate binding The diagram below represents the interaction between a portion of a protein active site and its substrate. There are multiple interactions that bind the substrate to the active site. Significant structures extending from the protein backbone are highlighted and labeled. Label 3 points to the entire substrate. Protein folding and substrate binding a. Did you identify the different amino acids represented in the diagram? b. Did you look up the chemical property of these amino acids? c. Did you notice that one of the parts on the backbone being identified is not a sidechain? d. Did you identify the type of chemical interaction between the amino acids and the substrate? e. Do you know what the NH 3 + and COO- represent
2. Levels of protein structure The diagrams below are representations of the protein-hormone insulin. The protein insulin is made up of two polypeptides referred to as A chain and B chain. The two chains are clearly labeled on each of the three representations below. Levels of protein structure a. Did you identify the different levels of protein structure being represented in the diagrams? b. How many residues on Chain A? On Chain B? c. How many disulfide bonds in this protein? What type of interaction is this? d. You will be asked to analyze DNA sequences that could possible code of the region highlighted as 1 on the B chain or insulin. Do you know how to transcribe and translate from DNA sequence to amino acid sequence?
2.Gene/plasmid structure and transformation Below are diagrams for the three plasmids ppingry, pbiology, and ptsh. Each plasmid has three genes of interest: two antibiotic resistance genes and the GFP gene. All three genes are regulated by either the Lactose operator or the Arabinose operator. You may assume that all essential genes/proteins for proper functioning of the operon is available. Ampicillin (Amp), tetracycline (Tet), and Kanamycin (Kan) are all antibiotics. Amp R, Tet R, and Kan R are the corresponding resistance genes. You and your two lab partners each take one of the plasmids and transform it into E.coli. You plate transformed bacteria on six different types of plates (labeled and identified below). The close-up diagram of a gene shows the general organization of coding sequence and regulatory regions. Gene/plasmid structure and transformation a. Did you determine the type of growth you expect to see on each of the plates (1 through 6) if any one of the plasmids were used in a transformation experiment? b. Do you know what antibiotics do to bacterial growth? c. Are you clear about the difference between Amp R and Ampicillin? (they are not the same thing) d. Do you know the consequence of a gene under regulation of an operator?
3. Enzyme activity, diffusion, cellular respiration The following lab investigation shares characteristics to two experiments you might have done in class: the lab using dialysis tubing to observe the selective permeability of an artificial membrane and a respiration lab (either plants, crickets, or yeast) that allowed you to observe and measure rates of respiration. Each of the bags below are made of a selectively permeable membrane that does NOT allow anything larger than a monosaccharide to pass through. Each bag is labeled with its contents. For this investigation, the amylase in the fourth bag is capable of breaking down its substrate into its monomer units. You place each bag into a beaker containing a yeast culture (yeast suspended in water). Yeast are single-celled fungus (eukaryotes). Yeast has the ability to metabolize glucose and starch. It does NOT metabolize lactose. You place each bag into the beaker containing yeast culture and use your preferred method to measure rate of respiration by observing the amount of gas produced by the yeast (using either a respirometer or an airlock to count bubbles). There is enough dissolved oxygen in the culture so that the yeast will be metabolizing the carbohydrates through aerobic respiration during your investigation. Also assume that the carbohydrates will never be entirely consumed during your investigation (e.g. the yeast in beaker 1 will never completely metabolize all the glucose that becomes available to them). Enzyme activity, diffusion, cellular respiration a. Which of the five beakers will be producing carbon dioxide? b. What is the source of the carbon dioxide that can be produced in these beakers? c. Do you know the relationship between lactose and lactase? Starch and amylase? d. What is amylase?
4. UV damage to DNA, restriction digestion, gel electrophoresis You want to design a lab investigation based on what you learned in class about the molecular effect of UVc (short-wave UV radiation) damage on DNA You decide to investigate the effect of UVc exposure to DNA based on the ability for restriction enzymes to digest the UVc exposed DNA. You acquire a sample of linear DNA with the following sequence (just one strand shown): You also have three different restriction enzymes: HindIII, AseI, and EcoRI. The restriction sites for the enzymes are shown below. The arrow along the sequence represents the locations of the bond in the DNA backbone hydrolyzed by the restriction enzyme. Notice that the corresponding restriction sites are underlined in the sequence above. You set up three restriction digestions using your DNA sample and each of the three restriction enzymes. You then set up three more digestions, this time using the DNA sample after exposing it to UVc radiation. You separate the six restriction digestions using gel electrophoresis. You get the following results. The sample identity is labeled above each gel well. You are initially surprised with your results; you expected that all of the UV exposed DNA would not be digested by the restriction enzyme. You then take a closer look at the three restriction sites and notice that AseI cuts across two thymines. The bonds formed across the thymines as a result of UVc radiation, referred to as a thymine dimer, is directly interfering with the ability for AseI to cut DNA at its restriction site.
Gel A 5. More restriction digestion and gel electrophoresis; follow up to diagram 5. *There are three similar diagrams here. Your test will have one of these three gel images. You decide to follow up your first experiment (results from good experiments should be reproducible). You obtain a sample of linear DNA with the following sequence. Rather than digesting the DNA using a single enzyme, you decide to run a few double-digestions (digesting the same sample of DNA with two different restriction enzymes). You also repeat the set of digestions on UV-exposed DNA. The following is the four digestions you set up: Non-exposed DNA, EcoRI Non-exposed DNA, AseI/HindIII UV-exposed DNA, EcoRI UV-exposed DNA, AseI/HindIII You are all excited about observing the results by separating the reactions by gel electrophoresis. You then realize that you did not label your individual reactions and have no idea what is inside each of the four tubes you have in your hand! But you are confident that you can tell apart the reactions once you run them in a gel. You proceed and get the following results. You are pleased with your results and rush out of the laboratory to share your results with your friends. UV damage to DNA, restriction digestion, gel electrophoresis a. Did you determine the approximate sizes of each DNA band visible in the gel? b. Can you explain the difference in band pattern in the two digestions using AseI?
Gel B You decide to follow up your first experiment (results from good experiments should be reproducible). You obtain a sample of linear DNA with the following sequence. Rather than digesting the DNA using a single enzyme, you decide to run a few double-digestions (digesting the same sample of DNA with two different restriction enzymes). You also repeat the set of digestions on UV-exposed DNA. The following is the four digestions you set up: Non-exposed DNA, EcoRI Non-exposed DNA, AseI/HindIII UV-exposed DNA, EcoRI UV-exposed DNA, AseI/HindIII You are all excited about observing the results by separating the reactions by gel electrophoresis. You then realize that you did not label your individual reactions and have no idea what is inside each of the four tubes you have in your hand! But you are confident that you can tell apart the reactions once you run them in a gel. You proceed and get the following results. You are pleased with your results and rush out of the laboratory to share your results with your friends.
Gel C You decide to follow up your first experiment (results from good experiments should be reproducible). You obtain a sample of linear DNA with the following sequence. Rather than digesting the DNA using a single enzyme, you decide to run a few double-digestions (digesting the same sample of DNA with two different restriction enzymes). You also repeat the set of digestions on UV-exposed DNA. The following is the four digestions you set up: Non-exposed DNA, EcoRI Non-exposed DNA, AseI/HindIII UV-exposed DNA, EcoRI UV-exposed DNA, AseI/HindIII You are all excited about observing the results by separating the reactions by gel electrophoresis. You then realize that you did not label your individual reactions and have no idea what is inside each of the four tubes you have in your hand! But you are confident that you can tell apart the reactions once you run them in a gel. You proceed and get the following results. You are pleased with your results and rush out of the laboratory to share your results with your friends. More restriction digestion and gel electrophoresis; follow up to diagram 5. a. Did you identify all EcoRI, AseI, and HindIII restriction sites in each of the provided DNA sequences? b. Based on the locations of the restriction sites, did you identify the four unknown digestions in each of the gels?
6. Energetics: Cellular Respiration and Photosynthesis The following diagrams highlight characteristics from two organelles in a cell. Answer the following questions based on your understanding of these organelles and the reactions that are dependent on them. Energetics; Cellular Respiration and Photosynthesis a. Did you identify all of the labeled molecules/processes? b. Are you familiar with the purposes of the two processes represented in these diagrams? c. Do you know what organelle these two are?
7. Phospholipids and membranes Observe the following diagram carefully. Based on the orientation of the phospholipids, you should be able to predict the chemical nature of the liquids shown in the diagram. Phospholipids and membranes a. Did you identify the chemical property of the spaces highlighted in the diagram? b. Do you understand how these two structures represented here form? c. How do these two structures differ in function in regards to the molecules they can potentially carry inside?
8. More phospholipids and membrane structure The labels (numbers 1 through 5) for the two diagrams correspond to the same part of the two diagrams. a. Did you identify all of the labeled molecules/parts of molecules? b. What structure are we looking at here?
9. The Endomembrane System The Endomembrane System a. Did you identify all of the labeled organelles/processes/structures? b. There are two distinct processes represented here that involve the endomembrane system. What are they? What is the purpose of these two processes? c. What type of macromolecule is are the cylinders represented by 4 and 5? How do their properties differ? d. What which process(es) involves the use of energy?