Crystal structure of yeast general transcription factor complex containing TATA-binding protein (TBP), TFIIA and DNA.  Ref:  Tan, Hunziker, Sargent and Richmond, Nature, 381:127-134, 1996.  See page 3 for a more detailed description.

 What good are laboratory courses, anyway?
 
Any of you like to read or watch mystery, romance, fantasy or science fiction stories?  Do you like to figure out the ending or know the ending and then figure out how to get there?  The instructional laboratory has much in common with a good mystery.  Like a detective, you can experience the thrill of trying to discover new information and/or setting out to prove something.

Though equipped with five senses, you typically rely on sight for most information- gathering.  After all...seeing is believing!  In the lab, you gain hands-on experience with techniques typical of that field and (hopefully) see that the textbook does correlate with reality.  However, the laboratory environment is more than what meets the eye.  It's not enough to just go through the motions.  While in lab, you need to think about that mystery, to think about what you are doing, and to understand why you are doing it.  Comprehension and scientific appreciation also develop when you reason through data.  What do the data mean?  What are they telling you?  Do the data make sense?  Why or why not?  What can you conclude?

Mistakes may happen while doing experiments.  But, you can turn even these situations into positive experiences.  The ability to successfully troubleshoot (recognizing the problem, arriving at a strategy to fix it, and devising a course of action to avoid it again) is a valuable commodity in the workforce.  It is beneficial to come to lab well rested (okay, at least with a few hours of sleep) and well fed.  Not only will you get the most out your lab day, but also the risk of going to Ritenour is lowered.

Besides learning a lot, interpersonal skills can be strengthened.  Be it direct or indirect, connections are established among your labmates.  You share reagents, offer suggestions, ask for assistance, and design experimental tactics with each other.  Lab is more fun when you learn to work constructively with those whose personalities and interests differ from yours.  Common to academic, government, and industrial laboratories is the fact that space and equipment are often limited and you are all in that lab together.

As you take laboratory courses, consider this combination of two popular television advertisements -- Think differently and enjoy the ride.
 

Crystal Structure of Yeast - Dr. Song Tan

The figure on the cover shows how the yeast general transcription factors TBP (TATA-binding protein) and TFIIA bind  promoter DNA.  Although TBP makes the most extensive contact with DNA, each of the three components makes interactions with the other two (for example, TFIIA directly contacts with both TBP and DNA).  The three dimensional structure of the complex explains many previously unanswered questions and also directs future research by suggesting regions that are available for interaction with other transcription factors.

X-ray crystallography was used to determine the positions of each of the 3600 atoms in the complex.  Each of the four polypeptides shown was overexpressed in E. coli, purified by chromatography and then reconstituted with DNA, which was prepared by chemical synthesis. Crystallization of the resulting ternary complex, X-ray diffraction data collection from such crystals, and processing of the diffraction data led to determination of the three-dimensional structure.
 
 

Kudos to our undergraduates --

Christopher Vakoc (BMB ’01) has been selected as a Beckman Scholar.  The scholarship provides $5,500 to support students during each of two summers plus $1800/semester for FA 99 and SP 00.  In addition, $3000 is available to each awardee for travel and research supplies.  Christopher will travel to the Annual Research Symposium at the end of his research experience to present his findings to Beckman scientists and other winners at either the Beckman Center of the National Academies of Sciences and Engineering or at one of the five Beckman Research Institutes in California and Illinois.  The selection process was arduous and included an oral presentation and defense of the research each applicant intended to undertake.  Congratulations Christopher!!
 

David Dudzinski (BMB/Chem ’99) received three honors at Spring graduation.  First, at the University Scholars ceremony on Friday afternoon, May 15, David, along with other Schreyer Scholars, received the Scholars medal in recognition of completion of the honors program and senior thesis.  Second, and to his surprise, David was also selected as the recipient of the Paul Axt Prize.  Named in honor of the Scholars’ program first director, the Paul Axt Prize is awarded annually to a graduating University Scholar who exemplifies those attributes which Professor Axt sought to foster through the University Scholars Program:  the passionate commitment to inquiry that promotes high scholarly achievement and the intellectual curiosity and daring that lead to the development and pursuit of wide-ranging interests.  The recipient should be a student who has seized the opportunities offered by the University and the Scholars Program to create an undergraduate education notable for both its breadth and its depth.  The prize honors both the recipient and Professor Axt, whose vision and perspicacity shaped the University Scholars Program and under whose dedicated leadership from 1980 through 1986 the program prospered.  In the words of the presenter, the Paul Axt Prize represents "the best of the best".  Then at the Eberly College of Science commencement ceremony on Saturday morning, May 16, David shared the honor of being one of three College student marshals.  Normally, there is only one College student marshal, but this year, three students earned the honor by having reached graduation with perfect 4.0 cumulative averages.  The BMB Department is truly honored to have a student of David’s ability and accomplishments counted among its graduates.  Congratulations to an exceptional student!
 
 

BMB WELCOMES NEWEST FACULTY MEMBER

Attention Junior CLS Students

JUST FOR FUN....(crossword puzzle borrowed from Palomar web site:  daphne.palomar.edu/wayne/crosword.htm)

ACROSS CLUES:

1. One member of a chromosome doublet.
6. Dark-staining body (composed of 2 chromatids) inside a cell during M-phase.
7.  Chromosome number of sterile animal such as a mule.
9. Body part with definite physiological function (made of more than one tissue).
10. Shrinkage of the cell contents (within cell membrane) due to water loss.
12. Prominent intracellular plant organelle that contains mostly water.
14. World's smallest flowering plant that produces the world's smallest fruit.
17. Phase of mitosis when conjoined sister chromatids separate from each other.
18. Number of haploid sets in a hexaploid cell.
20. Diameter of field of view in millimeters when using the 4X objective.
21. Purple, grape-like bodies inside cells of a potato tuber.
22. Phase of mitosis when chromosomes become visibly shortened and thickened.
23. Organelle site of cellular respiration and ATP production.
26. Number of haploid sets of chromosomes in a decaploid cell.
28. Aggregation of the same type of cells all performing a similar function.
29. Exactly 1000 of these metric units equals one millimeter.
30. Color of dye used to stain cheek epithelial cells in Biology 100 lab.
31. A female chicken (domestic fowl). [The opposite of a rooster!]
32. Acronym for Palomar Community College.
35. Movement of water molecules through a selectively-permeable cell membrane.
39. Phase of mitosis when chromosome doublets line up along equatorial plate.
40. Primary molecular composition of chromatids--in addition to protein.
41. Site of synthesis of ribosomal RNA within the nucleus of a cell.
43. A haploid female reproductive cell.
44. Minute, membrane-bound structure in cytoplasm with a specific function.
 
 

DOWN CLUES:

1. Occurs in the cytoplasm of animal cells during M-phase (typically in pairs).
2. Approximately 25 of these metric units makes one inch.
3. Stain used to test for the presence of starch molecules.
4. How many cubical grains of ordinary table salt (NaCl) equals one millimeter?
5. Number of Barr bodies inside the cheek cell of a human male.
6. Photosynthetic organelle inside plant cells.
8. Cell with two sets of chromosomes.
11. Mitosis actually refers to the division of this organelle into duplicates.
13. Region where 2 chromatids of a chromosome doublet are attached.
14. Plant cell structure composed of cellulose and lignin.
15. Radiating protein strands at poles of an animal cell during M-phase.
16. Number of sets of chromosomes in a diploid cell.
19. Phase of cell cycle when the organelles and chromosomes replicate.
20. Number of cells in field of view with 4X objective (each cell is 0.8 mm).
24. Number of Barr bodies inside cheek cell of male with Klinefelter's Syndrome.
25. Movement of water molecules into porous material causing swelling.
27. Number of haploid sets of chromosomes in a nonaploid cell.
28. Phase of plant mitosis when the cell plate forms.
29. One set of chromosomes from the mother.
32. One set of chromosomes from the father.
33.  ntracellular (intravacuolar) plant structure composed of calcium oxalate.
34. Cell with only one set of chromosomes.
36. Season of the year when smallest, most dense oak wood cells are produced.
37. Season of the year when largest stem (xylem) cells of an oak are produced.
38. Protein strands that attach to centromere region during M-phase of cell cycle.
42. Smallest subunit of a living system--containing cytoplasm and organelles.

SENIOR SCHREYER SCHOLARS RECEIVE MEDALS

Alvarez, James V., B M B, Dr. Gilmour,  Test System for  InVivo Analysis of Transactivator Function
Armen, Todd A., B M B, Dr. Gay,  Non-Genomic Effects of Testosterone and Estradiol on Bone-Forming Cells
Askari, Morad, P M, Dr. Tu,  Assessing Suspected Glutathione S-Transferase in Sacharomyces cerevisiae for Enzymatic Activity
Benson, David E., KINES,  Dr. Hymer,  Effect of Resistance Exercise Training in the Human Female on Bioactive Growth Hormone in the Circulation
Bianco, Nicole R., B M B, Dr. Bryant, Insertional Inactivation of the hofD Gene of Synechocystis sp. Stain PCC6803 Leads to a Bald and Lame Phenotype
Dixon, Aaron, B M B, Dr. Pugh, The TBA/TFIIA Interaction and the Role of the Amino Terminal Domain of TBP in Its Dimerization
Dougherty, Michael J., MICRB, Dr. Tien,  Site-Directed Mutagenesis of the Heme Pocket of Manganese Peroxidase
Dudzinski, David M., B M B / CHEM, Dr. Farber, Studies on the Structure of Proteins:  a/b Barrel Proteins, Histidine Ammonia-Lyase, and Expansins
Fisher, Carla S., B M B, Dr. Babitzke, Genetic Characterization of Bacillus subtilis csrA
Fuchs, Stephen M., CHEM, Dr. Tien, Heterologous Expression of Fungal Lignin Peroxidase Isozyme H8 and Characterization of the Veratryl Alchohol Binding Site
Gage, Robert M., B M B, Dr. Tu, Differential Gene Expression in Drosophila melangaster Following Pentobarbital Treatment
Kelch, Brian A., B M B, Dr. Bollinger, Chemical Rescue of Electron Transfer in the R2 Subunit of Ribonucleotide Reductase
McCardell, Amy K., BIOL, Dr. Reese, Selection and Analysis of TAF90 Mutants in Yeast
Nguyen, Christopher, B M B, Dr. Brenchley Characterization of a b-Galactosidase from a Psychrophilic Isolate
Ravindra, Anish K., P M, Dr. Simpson, High Resolutin Structural Analysis of Chromatin at Specific Loci:  Saccharomyces cerevisiae Silent Mating Type Locus HMRa
Schmiedekamp, Lumelle, B M B, Dr. Pugh / Dr. Schlegel, Interaction Analysis of Macromolecular Assemblies:  I. Solution Interactions of Yeast General Transcription Factor IIA, Yeast TATA-Binding Protein and TATA Containing DNA.  II.  Surface Interactions of Soluble CD14 and Annexin V with Phospholipid Surfaces
 

CONGRATULATIONS TO ALL ON THE ACCOMPLISHMENTS LEADING TO THESE AWARDS!!!

 TWO NEW INSTRUCTORS JOIN DEPARTMENT

Dr. Sypes will also be returning to Penn State where he received his Ph.D. in Biochemistry and Molecular Biology in 1994.  Since then, Dr. Sypes has served as an Adjunct Assistant Professor at Long Island University and at C.W. Post University where he has taught organic chemistry, biochemistry, and cell biology courses.  Dr. Sypes will also have an office located on the second floor of S. Frear.
 

FOCUS ON --- BMB 444 - Carbohydrates and Lipids

Have a "sweet" tooth?  Like to have free reign with expensive equipment?  Want to work with some "hot" stuff?  Then consider taking this one credit, twice-weekly, half semester elective.  Offered Spring semesters, BMB 444 introduces you to techniques and in-depth instrumentation not offered in any other BMB laboratory courses.

Here are some of the experiments you will conduct:
 

Having a sweet tooth can be life threatening to those at risk for diabetes.  Besides learning about this disease, you will use tests to diagnose whether a patient is "normal" or may have Type I or Type II diabetes.  (Do you know the difference between Type I and Type II diabetes?)

As part of a small group, your mission will be to identify two unknown commercial oils plus purify a fatty acid.  Part of your experiment is to figure out the proper high pressure liquid chromatograph (HPLC) parameters for sample detection and resolution.  Another aspect is running two different types of gas chromatograph setups, packed-TCD and capillary-FID, and comparing their sensitivity, accuracy, and ease of use.

Where's the "hot" stuff?  Using C14-glucose, you will learn how to safely handle and monitor radioactive material in addition to visualizing the initial reactions of glycolysis.

SPECIAL TOPICS COURSE FOR FALL 99 - MOLECULAR & CELLULAR TOXICOLOGY

Do YOU Qualify for Phi Beta Kappa??

• Must be in a non-professional major in the arts, humanities, social sciences or sciences.
• Must have a cumulative GPA of 3.6, if you have 90 or more credits completed, or a 3.8 if you have 60 to 89 credits completed
• Must have completed 60 credits at Penn State
• Must have completed one foreign language course to the second level, for example, Span 002, Fr 002, etc OR be certified as a native speaker of another language, OR have AP credit at that level
• Must have completed all General Education courses
• Must have 80% of total credits in liberal arts and science courses.

UPDATE ON COURSES...

As we reported in the Spring Newsletter, the department will begin offering several of our more heavily enrolled courses as multiple sections or in semesters in which they have not been previously offered.  You will want to be aware of these changes when you begin the registration process for Spring ’00.  The affected courses are as follows (additions are underlined):
 

Check the Schedule of Classes or CAAIS for times and locations.

University Scholars -- note you now have the opportunity to take Introductory Microbiology as an Honors course in Spring ’00.

This publication is available in alternative media on request.

The Pennsylvania State University is committed to the policy that all persons shall have equal access to programs, facilities, admission, and employment without regard to personal characteristics not related to ability, performance, or qualifications as determined by University policy or by state or federal authorities. The Pennsylvania State University does not discriminate against any person because of age, ancestry, color, disability or handicap, national origin, race, religious creed, sex, sexual orientation, or veteran status. Direct all inquiries regarding the nondiscrimination policy to the Affirmative Action Director, The Pennsylvania State University, 201 Willard Building, University Park, PA 16802-2801; Tel. (814) 863-0471; TDD (814) 865-3175.

BMB Undergraduate Newsletter is a publication of the Department of Biochemistry and Molecular Biology. Items for inclusion in the newsletter should be sent to BMB Undergraduate Newsletter, 108 Althouse Laboratory, University Park, PA 16802. Tel. (814) 865-5497; FAX. (814) 863-7024. U.Ed. SCI 00-17

Editors: - Philip W. Mohr, Ph.D., PWM1@PSU.EDU

                  - Mardi D. Hockenberry, MDH1@PSU.EDU