CHEM-647  BIOCHEMICAL EVOLUTION Syllabus Fall Semester 2000

Amino acid conservation  and replacement inCytochrome c R. E. Dickerson Sci. Am. 226(4):59 (1972)

This syllabus contains lots of information. Please read it carefully and refer to it during the semester.

Instructor:  Prof. Harold B. White
    Office:        123 Brown Lab
    Phone:        831-2908 (w), 737-7988 (h)
    E-mail:        halwhite@udel.edu
   Office Hours: Normally, the hour after class will be available for office hours; however, you should feel free to contact me by phone or e-mail or to stop by my office at other times. If I do not have pressing business, I will be happy to meet on the spur of the moment.

Meeting Time and Place: 8:00 - 9:15 A.M., TR in 108 Pearson Hall.

Prerequisite: CHEM-642 Biochemistry or CHEM-527 Introduction to Biochemistry

Text: There is no required text; however, any general text such as that by Voet and Voet; Lehninger; Zubay; or Stryer will be helpful. The money you save by not buying a text can be used to photocopy articles that create personal resource files on case study problems and your term paper/case study topic. If you would like to purchase a text, I would recommend Fundamentals of Molecular Evolution, Second Edition by Graur and Li (1999), Sinauer.

Grading: Because CHEM-647 is a graduate-level course with a small enrollment, personal initiative in the form of outside reading and class participation is expected. A fundamental general background in biochemistry at the level of CHEM-642 or CHEM-527 is assumed. Classes will be structured around interactive lectures, class and group discussion of problems, and student presentations. There will be no formal examinations per se. Evaluation of each student's performance will be based on homework assignments (40%), a term paper/case study problem (25%), seminar/case study presentation (15%), and a follow up interview based on your presentation topic (10%). "Appa" (attendance, preparation, participation, and attitude) constitute the remaining 10%.

While your grade will be based on your performance, there is no grading curve in this course. If everyone does "A" work, everyone will get an "A." It is in your best interest to help your classmates; however, do it as a teacher. If you know something, don't just give the information. Explain it. Practice effective communication. If you don't know something, seek understanding rather than "the answer." Develop the skill to recognize and define what you don't know and learn not to be satisfied with superficial answers.

Important General Information

Course Description: Biochemical Evolution is a vast and rapidly growing subject.  The recent literature displays a heavily emphasis on comparative analysis of both the primary and tertiary structures of proteins and the nucleotide sequences of genes and genomes.  With the completion of the Human Genome Project and the rapid accumulation of other genomes, it is impossible to analyze all of the information available and it is easy to expend lots of time on trival questions. Thus, it is absolutely essential that students learn to recognize and formulate interesting questions and become aware of the power and limitations of the methods. For that reason, the first two and a half months of this course (see schedule) will provide case study problems as examples of recently resolved issues and current controversy. Classes from mid-November into December will be devoted to student presentations of their term paper / case study problems and will provide the opportunity for students to explore interesting problems in biochmeical evolution.

Course Objectives: Education changes people. Thus students should be different as the result of taking this course.  As a result of completing CHEM-647, Biochemical Evolution, I expect students will:

1. Acquire a better sense of the unity of life on earth and the relationships among major groups of organisms including humans.

2. Be able to read and understand the significance of most articles published in the Journal of Molecular Evolution and Molecular Biology and Evolution.

3. Understand and be able to communicate Darwin's theory of evolution by natural selection.

4. Appreciate the relevance of biochemical evolution to understanding and treating infectious diseases.

5. Be able to construct phylogenetic hypotheses and test them by analyzing sequence information using standard tree-building software.

6. Identify and articulate personal knowledge gaps and efficiently locate the information needed to fill them.

7. Scientifically critique "intelligent design" and "irreducible complexity."

8. Be able to describe in their own words and discuss using examples concepts and ideas such as:

the molecular clock hypothesis homology, orthology, and paralogy molecular divergence and convergence neutral and selected mutations alleles in populations endosymbiotic theory the "RNA World" radioisotopic dating

"Selfish Gene" hypothesis gene duplication and the origin of new functions phylogeny fitness allopatric and sympatric speciation classification of major groups of organism maximum parsimony and neighbor joining methods

9. Recognize and be familiar with the contributions to biochemical evolution by some of the following scientists:
 

Avise, John Benner, Steven A. Cairns-Smith, Graham Cann, Rebecca Crick, Francis Dayhoff, Margaret DeDuve, Christian Dickerson, Richard Doolittle, Russell F. Doolittle, W. Ford Eigen, Manfred

Fitch, Walter Fox, Sidney Gilbert, Walter Joyce, Gerald Jukes, Thomas Kimura, Motoo Knowles, Jeremy Lake, James Margulis, Lynn Miller, Stanley Nei, Masatoshi

O'Brien, Stephen Orgel, Leslie Pääbo, Svante Palmer, Jeffrey Powers, Dennis Sibley, Charles Sogin, Michael Szostak, Jack W. Wächtershäuser, G. Wald, George Wilson, Allan Woese, Carl

Biochemical Evolution is not about memorization. This course is about understanding, thinking, pursuing knowledge, identifying resources, and communicating. It is about making evolution understandable at the molecular level, hopefully interesting, and possibly exciting enough that you will want to continue learning about it for the rest of your life. (Two former students have gone on to do graduate work with evolutionists on the list above.)

I enjoy teaching this course because I decide the content and can select topics that I find (and hopefully you will find) interesting. Biochemical Evolution is not a prerequisite for any other course. It is not structured around a particular text and it lacks a defined body of material "to cover." This allows me to include an eclectic mix of topics that range from natural history to geochronology along with evolution and biochemistry. This is a course that in broad view can provide a unifying perspective on life and the world around us.

Groups and Group Function:

Each student will be assigned to a group of about 4 students. These groups will function independently during class and outside of class for the whole semester.  The collective resources and efforts of the group will be used to deal with the case-study assignments.  For example, several learning issues may be identified in group discussion during class and group members will be assigned or volunteer to investigate particular issues and report back to the group.  The goal is to have everyone learn more than they would have working alone.  Nevertheless, individual work (often 8 - 12 hours/week) provide the foundation for productive and synergistic group work.

In order to promote effective group function, each group will discuss and agree upon a list of ground rules at the beginning of the semester.  All students will evaluate themselves and their fellow group members with respect to contributions to group function at least twice during the semester.  This evaluation will contribute to the "appa" (attendance, participation, preparation, and attitude) portion of the course grade and will be used  primarily in deciding borderline grades.

Assignments

Case Study Problems (40%):

There will be about seven case study problems during the first part of the course. Each deals with an important issue or controversy in biochemical evolution. The purpose of these exercises is to promote understanding of biochemical evolution by thinking about and analyzing real problems. In general, case studies reports will be due every week or two until Thanksgiving break.

Because my objective is your understanding, I encourage you to use the library and discuss these case study problems with other students in and outside of class. Consider diverse resources including faculty here and elsewhere (via e-mail) after you have spent some time analyzing the problems on your own.   While free exchange of information is expected both within and outside of groups, case study reports must be written individually as an opportunity for you to demonstrate to me and to yourself that you understand the concepts and issues involved.

Collaboration with other students does not include copying or paraphrasing of their answers.  Plagiarism will not be tolerated.  If you are uncertain about what this means, review the University's policy on academic dishonesty.  Write up your own answer in your own words. I look for well-thought-out answers that are clearly and neatly presented.  I expect acknowledgment of the resources you use (books, articles, web sites, and people). Also, assignments for this course cannot be submitted for credit in another course.

Term Paper Option (25%):

Term Paper Option: If you write a term paper rather than a case study problem, it should have an informative title and present an original synthesis of information. Creating an original synthesis presents formidable challenges for most students. What is an original synthesis? A term paper that thoughtfully reviews the primary literature rather than relying heavily on secondary sources is more likely to provoke creative thinking and lead to an original synthesis. Such papers show a clear understanding of the topic and define the important unanswered questions in the field. Frequently original syntheses will be organized around a theme and include original tables and figures that summarize information from diverse sources. Original syntheses often play with ideas, provide an overview of the subject, critique and evaluate research results, and generally display personal input. In other words, the voice of the author is evident throughout. A beautifully written, thoroughly referenced paper can get no more than a "B⁺" if it is not an original synthesis with a well analyzed problem.

You should select a topic from those listed and hand it in on the "Request for Term Paper/Case StudyTopic" form by Tuesday, September 19. Other topics are acceptable but must be approved by the instructor. Remember, CHEM-647 is a biochemistry course. A term paper should include a thorough, up-to-date review of the literature and critical analysis of some unsolved problem in biochemical evolution. In this latter section, a restricted problem from the broader review topic will be defined, hypotheses presented, and possibly tested. In some respects the term paper will resemble a grant proposal. A check list of things I consider in grading term papers may help in organizing and writing your paper.

A paper should be well-organized, clearly written, and about 10 to 15 pages of single-spaced text. Relevant compounds, pathways, and mechanisms need to be illustrated. References should be cited in the format of Biochemistry or the Journal of Biological Chemistry. A guide to "Writing a Scientific Manuscript" by Thomas Spector should be consulted for issues of form and style [J. Chem. Ed. 71, 47-50 (1994)]. Your paper will be due on the day of your seminar presentation. You are responsible for having it typed, duplicated, and distributed to all the students in the class on or before the day of your seminar. It is important that this timing be observed. Late papers will preclude an "A" in the course!

Familiarize yourself with the meaning of plagiarism and the University's policies on academic dishonesty. A term paper should be your synthesis rather than a paraphrased version of others' work. Don't rely heavily on one or two secondary sources. Read the original sources. You may use the Writing Center or have a friend critique your paper; however, writing and revision are your responsibilities.

Case Study Option (25%):

Case Study Option: If you have an interest in teaching or would like to do something creative other than a term paper, you may like to write and present a case-study problem based on your topic. A case study should be about five pages long with an appendix of similar length that provides and explains the kind of response expected including references. As with a term paper, this should be a scholarly document. Case studies can take many forms, but good ones have intrinsic general interest, tell a story, and often involve a current controversy or dilemma that requires a decision based on incomplete information. Pedagogically, they should involve higher order thinking skills (analysis, evaluation, and judgement), stimulate group discussion, and require collaborative effort.

Perhaps the best way to construct a case study problem is to consider what you have learned about your topic, decide what is most important and interesting to know, and then think about ways you could get your peers to discover, experience, and learn that information without being told. Creative approaches may include chemical demonstrations, illustrative objects, or in class activities as part of the presentation.

You should select a topic from those listed and hand it in on the "Request for Term Paper/Case StudyTopic" form by Tuesday, September 19. Other topics are acceptable but must be approved by the instructor.

Selection of Term-Paper or Case Study/Seminar Topics and Presentation Dates:

Term paper/case-study topics and presentation dates must be selected and approved by me by Tuesday, September 19. You should not decide whether you want to develop your topic as a term paper or a case study until later. While you may want to schedule your presentation for as late as possible, consider that an early presentation will give you more time to spend on other courses at the end of the semester and will give you priority on topics. Your term paper/case study and class presentation are essentially your final examination. Because you will become an expert on your topic by the end of the semester and because a considerable part of your grade will be related to how well you develop your topic, pick something of interest to you. Some subjects you might consider are listed below; however, please feel free to request other topics. A good place to start is to search Medline via PubMed, a search engine provided by NIH. The links to article abstracts in the table below were obtain easily in one afternoon using Medline.

Seminar/Case Study Presentation (15%):

Student presentations will be limited to 40 minutes (including class discussion) and will be presented in class during November and December. For those presenting a seminar, the seminar should be on some interesting aspect of biochemical evolution covered in your term paper. Consider your audience and try to develop a single significant point well rather than try to cover everything. Student seminars are often poorly organized or poorly presented because too much time was spent on gathering information and not enough time on its synthesis. When you are a speaker, you must decide what is most important and consider how those points can be communicated best. Consider what you want to put on overheads or on the blackboard. Focus on communication of significant information and ideas rather than total coverage. Remember that CHEM-647 is a chemistry course and therefore one should use biological and human interest aspects of the topic, but not to the exclusion of the important biochemical aspects.

For those presenting a case study problem, the class format will be different and may involve demonstrations, leading the class in discussion, or long periods of observation and supervision. In order to emphasize the tremendous value of effective communication, part of the grade for the presentation (and the term paper) will be based on effective communication. You may discuss your topic and its presentation with me at any time. You are encouraged to rehearse your presentation with a friend so that you know how long it will be and so that the presentation of difficult points can be polished. Suggested reading: "The Art of Talking about Science," Science 154, 1613-1616 (1966) by Sir Lawrence Bragg.

Each of your classmates will fill out a questionnaire about your presentation. These will be handed to me after your presentation and given to you during the following week when we meet to discuss your term paper/case study and your class presentation. The philosophy of these evaluations and a sample questionnaire are available.

Interview (10%):

Each student must schedule a one-hour meeting with me to be held during the week following his or her seminar presentation. At that meeting, your graded term paper or case study problem will be returned and we will discuss issues related to your topic and your presentation. You will be expected to be able to discuss your topic in chemical terms and know the structures of common metabolites such as amino acids, TCA and glycolytic intermediates, common fatty acids and sugars, and common cofactors and how they work.

Appa (10%):

Each person has distinctive knowledge, experiences, learning styles, and communication skills. The person who knows the most may not be the person who explains things best. Success in life often depends on the ability to work together and tap the different strengths of coworkers. In order to contribute to the learning of your classmates and to learn from them, you should attend class regularly and be on time, arrive prepared, participate in discussions, and generally have a constructive attitude. To encourage these traits, 10% of your grade will depend on them.

Some Possible Term Paper/Case Study Topics:

a)    Where do enzymes with new activities come from?  There is abundant evidence that many enzymes that catalyze a particular type of reaction are homologous, i.e., one was derived from the other or from a common ancestor enzyme.  Taxonomic characters such as substrate specificity, inhibitors, mechanism, stereospecificity, molecular weight, subunit structure, crystal structure, amino acid sequence, phylogenetic distribution, etc., can be brought to bear on this problem.  Much of this literature is not written in an evolutionary context, so pertinent data must be ferreted out and organized into a coherent picture.  Papers in the European Journal of Biochemistry 214, 549-561 (1993) and 215, 687-696 (1993) are good examples of original syntheses for PLP-dependent enzymes and biotin-dependent enzymes, respectively.  The evolution of P-450 enzymes is discussed in FEBS Letters 332, 1-8 (1993).

b)     Are nuclear genes encoding mitochondrial and chloroplast enzymes really derived from the genome an ancient endosymbiont?  Mitochondria and chloroplasts are considered to be derived from endosymbiotic bacteria.  Such a relationship could explain the many cases of enzyme duplication.  For instance, the citric acid (TCA) cycle operates inside the mitochondria; however, most of the TCA enzymes occur as mitochondrial and cytoplasmic isoenzyme pairs.  Are there any features of the mitochondrial or chloroplast enzymes which make them more similar to their bacterial counterparts than to their cytoplasmic neighbors?  Some possible points of departure can be found in Cell 47, 73-80 (1986), Biochem. J. 270, 651-657 (1990), and Eur J Biochem 228(3):551-61 (1995).

c)     Evolution of the genetic code. Using information on the x-ray structures of amino acid-activating enzymes and the base sequences of various tRNAs, can one deduce a phylogeny of tRNAs and tRNA synthetases?  Would this indicate the order in which different amino acids were incorporated into the code?  Or is the question of order meaningless for what may be a  "frozen accident" in which a sloppy, complex coding system got better and then became fixed?  See Trends in Biochemical Sciences 16, 1-3 (1991); 17, 159-164 (1992);  Proc. Natl. Acad. Sci. 88, 8121-8125 (1991); Cell 81, 983-986 (1995); and J. Mol. Evol. 40, 545-50 (1995).

d)     Why are there so few monomeric enzymes?  A large number of enzymes in intermediary metabolism are composed of identical subunits.  Such a general phenomenon would seem to imply an evolutionary significance to this sort of molecular organization.  How general is this phenomenon, and is there any evolutionary explanation?  Use Comp. Biochem. Physiol. 54B, 1-6 (1976) as a point of departure and relate it to the structures of the many enzymes now known.

e)     Selective advantage of isozymes and allozymes.  Why are isozymes and allozymes so common in multicellular organisms?  Their existence can be rationalized in part by tissue-specific regulation of differentiation and by heterosis, respectively.  Do these arguments apply to microorganisms (prokaryotes and unicellular eukaryotes)?

f)     Evolution of aerobic metabolism - How to deal with a poisonous gas.  Aerobic metabolism as exemplified by the TCA cycle coupled to the electron transport system in mitochondria is a relative latecomer as metabolic processes go.  Propose a rational sequence of evolutionary events that could have transformed an anaerobic process or system into an aerobic system.  The proposal should be documented by an analysis of existing systems in living anaerobic and aerobic organisms.

g)     Polymorphism, neutrality, and the rates of molecular evolution.  One might expect that a rapidly evolving protein (1 amino acid substitution/100 residues/10⁶ yr.) would show a relatively high amount of polymorphism in natural populations if nonselective evolution is important.  Can such a generalization be made based on information available?  See Proc. Natl. Acad. Sci. USA 90, 7475-7479 (1993) as a place to start.

h)     Evolutionary assembly of metabolic pathways.  It has been argued that metabolic pathways evolved in reverse order, i.e., the last enzyme in a biosynthetic sequence was the first to evolve [Proc. Natl. Acad. Sci. 31, 153 (1945)].  The coevolution of insect-plant relationships might predict that the biosynthesis of secondary plant substances (e.g., alkaloids), insect pheromones, etc., have evolved in the order they occur in a pathway, i.e., the last enzyme was the last to evolve.  Analyze and provide evidence for or against these proposals.

I)     Molecular opportunism and the rate of protein evolution.  Is there any evidence that a protein assuming a new function evolves very rapidly?  See J. Biol. Chem. 264, 11387-11393 (1989) and J. Mol. Evol. 28, 528-535 (1989) for lysozyme, and Mol. Biol. Evol. 10, 873-891 (1993) for cytochrome b.

j)     Convergent and parallel evolution of enzymes.  It is often assumed that enzymes catalyzing the same reaction are homologous having diverged from an ancestral enzyme with the same activity.  Yet, there are some indications that certain activities arose independently several times, e.g., alcohol dehydrogenase.  Is this true for alcohol dehydrogenase?  Are there other activities that display such a convergent pattern?  Does comparison of the tertiary structure of proteins unambiguously distinguish convergent from divergent evolution?  See J. Mol. Biol. 151, 179-197 (1981) and Proc. Natl. Acad. Sci. USA 92, 6793 (1995)

k)     Origin and evolution of introns.  The phenomenon of split genes is fairly general among eukaryotes.  It is not uncommon to have the coding region represent 10% of the total length of a gene and have up to 50 intervening noncoding regions.  It has been proposed that such an organization is of evolutionary significance.  How does the evolutionary argument compare with other suggestions for the function of intervening sequences?  Did the last common ancestor of life on earth have introns?  See Science 257, 1489-1490 (1992) and Proc. Natl. Acad. Sci. USA 94, 6820 - 6825 (1997) & 95, 5094 - 5099 (1998).

l)     Origin and evolution of new and complex biochemical functions.   Michael Behe, a biochemist from Lehigh University, recently published Darwin's Black Box — The Biochemical Challenge to Evolution (for and against).  In it he claims that biochemical systems such as blood clotting or flagella are too complex, "irreducibly complex," to have evolved and therefore must be the products of "intelligent design."  Pick some taxon-specific biochemical molecule, structure, or process that interests you and examine its origins and evolution, e.g., histones, antibodies, photosynthesis, embryonic development, insulin, electron transport chain, nuclear pores, chaparonins, methane production, keratin, visual pigments, a secondary metabolite, synthesis of certain amino acids or cofactors, etc. Try to postulate and justify reasonable intermediate stages.

m)     What selective forces drive codon usage patterns?  Examine codon utilization patterns for genes expressed in different tissue of the same organism or in response to different stimuli.  Evaluate the selective factors that might lead to differences where they are found.  See Proc. Natl. Acad. Sci. 83, 8132-8136 (1986).

n)     Identifying primitive molecular traits.  Cairns-Smith in his book, Seven Clues to the Origin of Life, concludes that the oldest components of biological systems are the least variable.  Is this a fundamental principle of biochemical evolution that can guide one in seeking the origins of any biochemical system? Can one determine the biochemical characteristic of the most recent common ancester of all life? Proc Natl Acad Sci  86:7054-8 (1989).

o)     Evolution of lipid membranes.  Archaebacterial membranes contain glygerolipids possessing ether-linked isoprenoid hydrocarbons.  Eukaryotes and other prokaryotes contain  glycerolipids with ester-linked fatty acids.  Both isoprenoids and fatty acids are  biosynthesized from acetyl-CoA.  Are the isoprenoid lipids a primitive or derived characteristic?  Are the biosynthetic pathways related by more than their precursor?  What circumstances/conditions would favor one pathway or end product over the other?

p)     Applying selection for in vitro evolution.  Until recently, biochemists had to be content  with laborious mutational approaches to modifying proteins and nucleic acids for medicinal or other commercial use if the natural products had some undesirable properties.  The recent  introduction of strategies to evolve (rather than design) useful molecules permits the  production of useful molecules that never before occurred in nature.  The limits are one's imagination.  What does the future hold?  See Science 249, 505-510 (1990), Science 265, 1032-1033 (1994) and Scientific American Dec. 1992 page 90 for a start.

q)     Looking backward in the future.  The first complete nucleotide sequence of the genome of a free-living organism, Hæmophilus influenzae, was published in 1995, all 1.8+Mbp [Science 269, 496-512 (1995)].  Many more genome sequences are know known and many others will appear in the next few years.  It has been said that an organism's evolutionary history is written in its genes.  How should this information be analyzed?   What are the important unresolved evolutionary questions that will soon be addressed?

r)     Phylogenetic nonsense generated by protein sequences. Relaxin, a peptide hormone homologous with insulin, appears to defy expected phylogenetic patterns [FASEB J  8, 1152-1160 (1994)].  How seriously does this challenge evolutionary theory?  Is this an isolated example?

s)    Molecular Mimicry. Mimicry is a well known phenomenon at the organismal level. Some spectacular examples among many include chemical mimicry by flowers that produce pheromones that attract male pollinators of a single insect species or visual mimicry by insects that look like leaves. Recently, two quite different crystal structures of translation factors (proteins) reveal an overall size and shape of tRNAs. Is this really an example of molecular mimicry as the authors think? If so, can the evolutionary forces at the molecular level be analogized to those that select for mimicry on the organismal level? [Science 270, 1464 - 1471 (1995); 286, 2349 - 2352 (1999)]