CHEM-642 Biochemistry                                     Name ______________________________
First Hourly Examination
10 AM to noon, Saturday, 17 March 2001
Dr. Hal White - Instructor

There are 10 pages to this examination. Write your name on each new page. Read every question so that you understand what is being asked. If you feel any question is unclear or ambiguous, clearly explain your answer or interpretation. Please call my attention to any errors you encounter.

You will be given a separate page which has many metabolic pathways written on it.

This examination will assess your learning, problem-solving skills, and ability to communicate clearly. It is intended to be challenging even to the best students in the class. Some of the questions will deal with material you have not seen before and is not in your text; however, they can be answered by applying basic principles discussed in the course.

Do not expose your answers to the scrutiny of your neighbors. Please fold under each page before you go on to the next.

Breakdown of the examination by sections:
 

Short Answer                  10 Points
Structure                        20 Points
Problems                        46 Points (+5 bonus)
Short Essays                  24 Points
Total                             100 Points (+5 bonus)

Exam Statistics:

N = 50            Range 22.5 – 83.5            Mean 56.25 ± 14.71


Part I - Short Answer Questions (1 point each)
____________ 1. Name for two or more proteins that catalyze the same reaction in a single cell
                            or organism.
____________ 2. Coenzyme used in reductive reactions in biosynthesis.
____________ 3. Ferredoxin is a protein containing an inorganic cluster of these two elements.
____________ 4. An end product of the shikimic acid pathway.
____________ 5. Enzymes activated by ATP are likely to regulate this class of pathways.
____________ 6. Within an order of magnitude, how long does the average ATP molecule exist
                            before it is used?
____________ 7. Inhibitor of prostaglandin synthesis.
____________ 8. The corrin ring of coenzyme B12 and the heme group of cytochromes belong
                            to this class of molecules.
____________ 9. The cellular location of ketone body formation.
____________ 10. The prosthetic group of fatty acid synthetase, 4-phospho-pantethiene, is also
                            part of this coenzyme.
Part II Structures: Identify each compound and below each provide a brief description of its function (2 points each).
 
1.
3.
 
2. 4.

Draw the indicated structures in the space above each name. (2 points each)
 
 
 
 
 

                                Oleic acid                                                         Guanosine
 
 
 
 
 

                                 Leucine                                                             Galactose
 
 
 
 
 

                                 Tryptophan                                                          CMP
 
 
 
 
 

Part III – Problems
1. Guaiol, a sesquiterpene found in the sap of certain trees, turns blue when it reacts with peroxides. This reaction was used as a test for peroxide in the 19th century. Guaiol is derived from farnesyl pyrophosphate (FPP). In the structure of guaiol below:

    A.    (3 points) Outline the three isoprene units that are imbedded in guaiol’s structure.
    B.    (2 points) Draw a circle around the carbon which is derived from the oxygen bearing carbon of FPP.
 
 

2.    (8 points) Waxes are common in nature. They provide the water-repellent surfaces to fruits, skin, and feathers among other things. Waxes are esters of formed from long-chain alcohols and a fatty acid. Starting with two molecules of palmitic acid, propose a biosynthetic pathway for the wax shown below.














3.    Consider the bacteria, Youdea hulliheni, that normally oxidizes glucose by the Embden-Meyerhof Glycolytic pathway, but, due to a mutation in the gene for phosphoglucose isomerase (the aldo-keto isomerase that interconverts G6P and F6P), must use the pentose phosphate pathway as a detour around the metabolic block as shown below. The cofactors for the individual enzymes are omitted but you will need to know them.


____ ATP
 
 

____ NAD(P)
  1. (4 points) In this modified pathway for glucose oxidation, five, rather than six, glyceraldehyde-3-Ps (GAP) are produced per three glucoses. Calculate the net production of ATP and NAD(P)H per glucose in going from glucose to pyruvate in this pathway. (Use the back of this page as a work sheet if necessary for this and subsequent questions.)
B. (6 points) If carbon 3 of glucose were labeled with 14C, how would the label be distributed in pyruvate?
C. (3 points) How would the 14C label be distributed in pyruvate, if the normal glycolytic pathway were operating alone, i. e. phosphoglucose isomerase is fully functional and the pentose phosphate pathway were not involved.

4.    The biosynthesis of phenylalanine requires erythrose-4-P (E4P) and two moles of phosphoenol pyruvate (PEP) as precursors as is shown below. Return to Question 3B and the metabolism of [3-14C] glucose in the bacteria lacking phosphoglucose isomerase.

  1. (8 points) Trace the labeled carbons and show which carbons of phenylalanine would be labeled. (Because the answer here is dependent on your answer on 3B, I will give up to 6 points for an answer that is consistent with an incorrect answer to 3B.)

    2.  

     
     
     
     

     
     
  1. Bonus Question (5 points) Do not do this until you have completed the rest of the examination. What would be the relative amounts of 14C in each of the labeled carbons of phenylalanine?


5. (12 points) Tryptophan degradation is a multi-step pathway which leads finally to AcCoA with a -ketoadipate (a KA) as an intermediate. Fragments of the last part of this pathway from a KA to AcCoA are shown below. Based on analogy to other metabolic pathways and your biochemical intuition, supply all the missing coenzymes, substrates, and reactants in the pathway.


Part IV - Essay Questions (8 Points each) Writing reflects how you think. Among the "right answers" I will read for the following questions, some will be better than others because they show greater depth of understanding, avoid extraneous or inaccurate information, provide a more logical structure, use appropriate examples, and select words with precision. Better quality answers will receive higher marks. Therefore, organize your thoughts before you write.
 

1.    Explain in words and show with clear examples (illustrated) the concept that despite the fact that NAD and NADP have similar reduction potentials and chemical properties, enzymes are specific for either NAD or NADP.

2.    By having two copies of genes encoding each enzyme, diploid organisms like ourselves are cushioned from the effects of a mutations that generate non-functional enzymes. Interestingly, genetic carriers for devastating metabolic diseases (persons heterozygous for a recessive detrimental mutation) produce about half the normal amount of the affected enzyme and yet rarely show any detrimental effects. Basically they are normal. In terms of metabolic flux in pathways, how can this be rationalized?
3.    Living organisms do not violate the laws of thermodynamics. Within terrestrial and shallow water ecosystems, the energy that maintains the living organisms can be directly attributed to photosynthetic organisms, the primary producers. It was a great surprise in the late 1970’s when a whole community of organisms was found in restricted regions of the ocean floor where no light penetrates [Natl. Geog. 156, 680 (1979)]. The energy input for these organisms apparently comes from H2S which comes out of nearby hydrothermal springs. One rather large organism there is Riftia pachyptila, a type of worm several inches in diameter and up to 10 feet long. These worms lack a mouth, digestive tract, and anus. Certain parts of their body contain high densities of endosymbiotic bacteria presumed to be capable of coupling the aerobic oxidation of sulfide to sulfate to the fixation of CO2 via the Calvin Cycle [Nature 293, 616 (1981), TIBS 7, 201 (1982), and Science 219, 297 (1983)].

Based on your knowledge of metabolism and the information above, suggest at least two specific pieces of biochemical information that you would want to know before you would accept the above hypothesis as possibly valid and not just a science fiction story. Indicate why this additional information would help your evaluation.


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Last updated 21 March 2001 by Hal White.
Copyright 2001, Harold B. White, Department of Chemistry and Biochemistry, University of Delaware, Newark, DE 19716