BCHM 3010 Exam 1 Study Guide
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This 12 page Study Guide was uploaded by Morgan Dimery on Monday February 1, 2016. The Study Guide belongs to 3010 at a university taught by Dr. Cheryl Ingram-Smith in Spring 2016. Since its upload, it has received 49 views.
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Date Created: 02/01/16
Exam 1 Study Guide 1. What properties do all 20 standard amino acids share? What gives them different characteristics? 2. List the 20 standard amino acids; give their 3 letter code, their 1 letter code, and name the group of amino acids they are apart of. 3. True or false: Zwitterions can only act as acids. 4. Which groups of amino acid contribute to the overall peptide net charge? 5. When is an amino acid fully deprotonated? Which group (carboxyl or amino) loses their proton first? Explain 6. Using the following information draw out the amino acid glutamate at pH 1, 5, 8, & 13. Determine the charge of each. α carboxyl group pKa= 2 R-‐group carboxyl group pKa= 6 α amino group pKa= 11 7. What is wrong with the following table? pH NH3+ Arg Ala Glu Trp COOH 1 +1 +1 0 0 0 7 +1 +1 -‐1 -‐1 -‐1 14 0 0 -‐1 -‐1 -‐1 8. What dictates the final structure of the protein? Explain. 9. Explain the difference between configuration and conformation. 10.True or false: Hydrogen bonding greatly stabilizes tertiary structures. 11.What kinds of things form hydrophobic interactions? What is the purpose of doing this? 12.What causes the peptide bond to not have complete free rotation? 13.Explain the differences between alpha helices and beta sheets. 14.How do you tell the difference between the tertiary structure of a protein and the quaternary structure? Can these ever be the same? If so, how? 15.List some advantages of the quaternary structure. 16.In what two ways are proteins classified? 17.What is a fibrous protein’s “claim to fame”? A globular protein? 18.Alpha keratin and collagen are both fibrous proteins and are both composed of helices. What makes the helices so strong? 19.Fibrous proteins can be _______________________, or ___________________________, but never ______________________. 20.In class we talked specifically about how collagen and silk fibroin were able to pack tightly together with one another. How are they able to? 21.True or false: Globular proteins cannot contain both alpha helices and beta sheets in the same protein. 22.What forms as a globular protein folds? What is the purpose of the tight packing? 23.What causes metal-‐rich and disulfide-‐rich proteins to become unstable? 24.A ______________ is an area of a protein that folds on its on. They can also have separate ____________________ from each other. It is driven by the _________________ __________. They still must interact with one another to get to the final _______________ structure. 25.What is a motif? Are they larger or smaller than domains? 26.Explain the difference between protein families and protein superfamilies. 27.Intrinsically folded proteins contain large amounts of which amino acids? Why? 28.What do intrinsically folded proteins bind to that is thought to make them more stable? 29.Why is protein denaturation said to be cooperative? What are some things that cause protein denaturation? 30.Where are the unfolded structures found on a protein-‐folding funnel? What about the native structure? Why do different proteins have funnels that look different from one another? 31.Explain the difference between molecular chaperones and chaperonins. 32.How does protein misfolding cause disease? Name some examples of diseases caused by protein misfolding. 33.What is the main purpose of protein purification? 34.How does centrifugation separate proteins? What about salting out? 35.What is the difference between the stationary phase and the mobile phase in column chromatography? 36.Large proteins come out of a gel filtration faster than smaller proteins. Why? 37.True or false: Anion exchangers have positively charged beads that bind to proteins with a net negative charge. 38.When the salt concentration is ___________, the hydrophobic regions of proteins have a strong interaction with the beads in the column. When the salt concentration is __________, the interaction starts to become weaker and the proteins fall off the sides of beads. Proteins with more ___________________ _____________ will stay attached to the beads longer than those that have less. 39.Why can affinity for ligand binding be used for protein purification? 40.True or false: Ion exchange chromatography can usually purify a protein in one step. 41.What effect does SDS have on a protein? Why is this beneficial? 42.The purpose of a protein purification table is to see how well your process purification worked. What should you look at to check this? 43.What is the difference between specific activity and total activity? 44.Hemoglobin and myoglobin are in the same ______________________________. This means that they have the same _____________________ structure, but not the same ________________ structure. 45.True or false: Ligand binding can cause conformational changes that require a bond being broken. Explain if false!!! 46.What order is the association constant? The dissociation constant? 47.Two Kd values for a protein and its ligand were determined and found to be 2 and 7 (hypothetical values). Which value shows a stronger bond between the protein and ligand? 48.Describe the structure of heme. How many subunits of heme does myoglobin have? Hemoglobin? 49.Myoglobin may not be good for oxygen transport, but it is great for oxygen storage. What makes it so good at it? 50.Why would heme rather bind with CO than O ? What helps it so that the 2 O 2nds up having a better chance? 51.What about hemoglobin makes it good at both binding to and releasing oxygen? Explain how in the human body this is beneficial. 52.Which state has a higher affinity for oxygen, the R or T state? 53.What kind of curve does hemoglobin have on a graph? What does this represent? 54.Hemoglobin is an example of ________________ cooperativity. Meaning that the first binding event causes a ___________ affinity at other sites. 55.Why does part of the graph of hemoglobin have a slope of 1 and another part have a slope of 3? 56.How does the Bohr effect influence the binding of oxygen and carbon dioxide? 57.How could BPG help you in a real life situation? 58.What amino acid is changed in a person with sickle cell anemia? What is it changed to? What effect does this have on a red blood cell? 59.True or false: Enzymes can make reactions that would normally never happen occur. 60.How are enzymes categorized? 61.Enzymes affect __________ ________, but never affect the _________________. 62.ΔG = 0.4. Is the product or the substrate favored? Is the reaction spontaneous or nonspontaneous? 63.What is the main job of an enzyme? 64.What does the rate of the reaction depend on? 65.What is a characteristic of enzymes that makes them very economically friendly? 66.What would be wrong if the enzyme bound to the substrate with a perfect lock and key fit? 67.Which amino acids are involved with acid-‐base catalysis? Why? 68.What is the name of the bond that is formed in covalent catalysis? What does it do to help the reaction go faster? 69.Why is it so hard to measure the formation of the ES complex? 70.What is going on during the steady state region? 71.What is k and what does it mtell us? 72.What is the Michaelis-‐Menton Equation? 73.Why will the curve on a graph for the above equation eventually level off? 74.On a Lineweaver-‐Burk double reciprocal plot what is the y-‐intercept? The x-‐intercept? 75.Is it better to have a low k or a high k ? m m 76.What does k tell us? cat 77.True of false: k /k can be used to compare the efficiency of two cat m substrates. 78.Explain the difference between the sequential mechanism and the ping-‐ pong mechanism.
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