2) At physiological ph (7.0), what is the net charge of this peptide? (note this only requires knowing the R groups on each amino acid)

Transcription

1 page1 (of10) Proteins and peptides (9 points) Behold, a license plate! It is from a custom classic car (ca. 1940) on display at Simpson s Nursery in Jamul, which has many plants and a remarkable collection of vehicles (go figure ). 1; 4 pts) Write the sequence of the peptide spelled out in the plate, using the three letter code (eg. a tripeptide of tryptophan would be TrpTrpTrp). 2) At physiological ph (7.0), what is the net charge of this peptide? (note this only requires knowing the R groups on each amino acid) 3) Give a one sentence, general description of a prosthetic group 4) Write the name of the prosthetic group that contains iron 5; 2 pts) Write the name of the type of protein secondary structure that is depicted in the little pictures, using the space under each one

2 page2 (of10) Flipping M & M (8 points) You are analyzing three enzymes (A, B and C) that catalyze the same reaction. You determine the velocity (V) at various substrate concentrations (S), and plot the data using the Lineweaver-Burk method, excoriated by Eminem (see inset box). who re those jerks, lineweaver and burk? they took my curve and made a line that takes some nerve so I ll speak my mind those foolish nerds be wastin your time cause the hyperbola is still sublime Eminem: The Slim Substrate LP The resulting graph is shown on the right, with each enzyme s data indictated by letter. Answer the following questions. 6) What does the horizontal axis represent? 7) What does the vertical axis represent? 8) Which enzyme has the highest Vmax? 9) Which enzyme attains 50% Vmax at the lowest substrate concentration? 10) A fourth isozyme has a curved lineweaver burke plot. Sketch what the S vs V plot for that enzyme will look like in the space to the right.. 11) What can you say about the structure of this fourth enzyme? 12) (not Lineweaver-Burk related) Write the equation that defines kcat k cat = (Hint: this is not Km) 13) What is the definition of kcat in English? That is, use a sentence to describe its physical meaning, as opposed to an equation.

3 page3 (of10) Three residues for the Enzyme-Kings (8 points) The catalytic triad is a very common feature of many enzymes that hydrolyze chemical bonds. We focused on chymotrypsin in this class. Below are the three amino acids of the chymotrypsin catalytic triad. Name each amino acid, and in one sentence describe its function in the catalytic triad. 14) name: 15) function in catalytic triad: 1 16) name: 17) function in catalytic triad: 2 18) name: 19) function in catalytic triad: 3 20; 2 pts) Some catalytic triads have the amino acid cysteine in place of one of the amino acids above. Which amino acid above (you can say 1, 2, or 3 if you don t remember the name) would be the logical one to be substituted by cysteine in these alternate triads? Why? (one sentence).

4 page4 (of10) The last step (11 points) A recent article (Zanella et al. (2005) British Journal of Heamatology 130, 11-25) describes a genetic deficiency in red cell pyruvate kinase (PK). This is the most common defect in the glycolytic pathway, occurring in approximately 1 in 20,000 patients, and in the worse cases results in life-threatening neonatal anemia. Let s think about this enzyme and the effects of its loss in a cell 21; 4 pts) Write the reaction catalyzed by PK. Include the structures and names of the glycolytic pathway molecules; include any cofactors or other substrates used or produced in the reaction. In cells that have a PK deficiency, there is a buildup of the substrate of the PK reaction, and a build up of 2 phosphoglycerate (2-PG) and 3 phosphoglycerate (3-PG). Let s think about this. What are the two reactions that directly precede the PK reaction? Write each in the space provided. No need for structures, just names like 3-PG, etc. Include all reactants and products. 22) First (earlier) of the two reactions (here): 23) Second of the two reactions (here): 24) So why do the two molecules mentioned above build up in this syndrome? (one sentence) PK is allosterically regulated. Two regulators of PK are fructose 1,6 bisphosphate and ATP. Predict how each affects the enzyme s activity (inhibitor, activator) and say with one sentence why it makes sense. 25; 2 pts) Fr1,6bP is an allosteric of PK. This makes regulatory sense because: 26; 2 pts) ATP is an allosteric of PK. This makes regulator sense because:

5 page5 (of10) Thinking about drinking (8 points) Ingested ethanol is detoxified by the liver to harmless acetate. This occurs by a two reaction pathway, in which ethanol is converted into acetaldehye, and then acetaldehyde is converted into acetate. You have never seen this pathway, but your current knowledge will allow you think about ethanol detoxification in clear, chemical terms. Let s go! 27; 2 pts) First, draw the structures of the three molecules. I have included ethanol. That level of detail is fine ethanol acetaldehyde acetate The first step (ethanol to acetaldehyde) is catalyzed by alcohol dehydrogenase. The second step (acetaldehyde to acetate) is catalyzed by aldehyde dehydrogenase. Both use NAD+ as a substrate. Write the balanced reaction for the first step showing the two structures; and include NAD+ in the reactions. 28; 2 pts) Alcohol dehydrogenase reaction: Antabuse, is used clinically as a deterrent to drinking. It is an inhibitor of aldehyde dehydrogenase, and patients on Antabuse get very ill if they drink alcohol. 29) When a person on Antabuse drinks ethanol, what molecule do you expect to accumulate? 30; 2 pts) The E o for the acetaldehyde/ethanol half reaction is ev. Write the balanced half reaction, including electrons. 31) From the E o value, say which direction the half-reaction runs spontaneously, justifying your answer (one sentence).

6 page6 (of10) Dr. Krebs, I presume (16 points) 32; 2 pts) What is the main catabolic function of the Krebs cycle in oxygen-using cells (one sentence)? 33; 2 pts.) What is the carrier for acetyl groups that delivers them to the Krebs cycle? Write the common abbreviation for the carrier both with and without an attached acetyl group and 34; 3 pts.) Write out Krebs cycle reaction catalyzed by citrate synthase, showing all substrates and products, and include the structures and names of the pathway molecules. 35; 3 pts) The Krebs cycle results in the production of 3 distinct energy-rich molecules. What are they? 36; 2 pts.) Pyruvate dehydrogenase (PDH) is a critical enzyme for producing substrate for the Krebs cycle. Write the balanced, net reaction catalyzed by PDH, including all reactants and products. No need for structures. Two critical PDH cofactors are TPP and lipoic acid. Describe briefly the function each in the PDH reaction. No need for pictures. 37) TPP: 38) Lipoic acid: 39; 2 pts.) We have discussed other dyhydrogenases, such as glyceraldehyde-3-phosphate dehydrogenase, alpha-ketogluarate dehydydrogenase, and succinate dehydrogenase. Which is most like PDH, and why (one sentence)

7 page7 (of10) Carbon in, carbon out (10 points) 40) In the Krebs cycle, two carbons are lost with each turn of the cycle. What is the form of the carbon that is lost? 41) If an acetyl group enters the Krebs cycle, and the cycle is allowed to go just one turn, how many of the added acetyl group s carbon atoms remain? (0, 1, 2): 42) There is an alternate cycle we discussed in class that avoids the loss of carbon, thus allowing use of acetyl groups for anabolism. What is the name of this cycle? 43; 2 points) In this alternate cycle, two reactions involve covalent addition of acetyl groups to cycle molecules. One of these molecules is also found in the Krebs cycle, and the other is unique to the alternate cycle. What are theses two molecules (just names)? and 44) Because there is no loss of carbon in this alternate cycle, acetyl groups that enter metabolism can be used for anabolism, such as the production of glucose. Can we use this cycle to convert acetyl groups into bigger molecules? Yes or no, and why (1 sentence). 45) When pathway intermediates are lost from the Krebs cycle, they can be replaced by four different reactions we have covered in class. What is the general name for these reactions? 46; 2 pts) One of these reactions is catalyzed by pyruvate carboxylase. Write the balanced reaction, including all substrates and products. No structures needed. 47) What role does biotin play in the pyruvate carboxylase reaction (one sentence)?

8 page8 (of10) It's Fructillyicious!!! (9 points) 48) Fructose is one of the most ingested sugars in the modern diet. What common dietary sugar contains fructose in its structure? 49; 2 pts) There are two ways that fructose enters glycolysis. One involves phosphorylation at the 6 carbon, and the other involves phosphorylation at the 1 carbon. What type of enzymes phosphorylate things, and what is the source of the phosphate that is transferred by such enzymes? type of enzyme source of phosphate Let s now explore how Fr-1-P, which isn t a glycolytic interemediate, enters glycolysis. 50; 2 pts) Write the reaction in which fructose is phosphorylated at the 1 position. Include the structure of the fructose and Fr-1-P; include all substrates and products. Draw the fructose in the linear (hint: ketone) configuration. Carbons with OH groups can be written -CHOH- or - CH 2 OH. Fr-1-P is processed to enter glycolysis by the action of fructose-1-phosphate aldolase (F1PA). This aldolase works in an identical manner to the aldolase of the glycolytic pathway. 51; 2 pts) Knowing this, draw the two products that result when F1PA acts on Fr-1-P, and write their names under them. 52; 2 pts) One of the products of F1PA is a glycolytic intermediate. The other molecule (an aldehyde) is almost a glycolytic intermediate. Write a plausible, energetically favorable biochemical reaction that would convert this molecule into a glycolytic intermediate. Include the structures and names of the substrate and product. Hint: remember question #49 above

9 page9 (of10) Whoa, dude where am I? (11 points) Here are 4 cellular locations A B C D mitochondrial outer membrane mitochondrial inner membrane mitochondrial matrix the cytosol For each phrase below, write the one letter that is best associated with the phrase 53) location of cytochromes 54) in contact with the cytosol 55) highly permeable to small ions and molecules 56) location of Krebs cycle enzymes 57) site of bacterial-type ribosomes 58) where ATP synthase is located 59) site of pentose phosphate pathway 60) contains porins 61) highly impermeable to small molecules and ions 62) where the PDH complex is found 63) location of glycolytic enzymes

10 page10 (of10) Truth is Truer than Fiction (T or F; 10 points) 64) No biochemical reactions in the cell have a positive delta G. 65) Glycogen is mobilized for metabolism by hydrolysis into monomers of free glucose. 66) A Michalelis-Menton enzyme is 80 % saturated when S equals 4 times the Km. 67) An enzyme decreases the forward activation energy more than the reverse activation energy. 68) Phosphate groups on proteins are removed by phosphatases. 69) ATP is a product of the reaction catalyzed by glyceraldehyde-3-phosphate dehydrogenase. 70) The Krebs cycle can not occur in the absence of oxygen. 71) A lactone is an intermediate of the pentose phosphate pathway. 72) In fermentation, both lactate and ethanol are formed to restore NAD +. 73) A reaction with a negative delta G must have a positive delta S,