The official course website will be with e-learning. Use the following to login with Microsoft Explorer:

http://lss.at.ufl.edu/services/respondus/respondus.shtml

NOTE: The elearning website is now functional. Open the section that is active for Spring Semester, 2008.

You will need to use Microsoft Explorer as your browser.

Announcement: You can purchase clickers at the campus book store. The brand is not important. If you already have a clicker for another course, you can use it for PCB4522 also. However, you need to specifically register it for PCB4522. The bad news is that due to a glitch in the software campus-wide, the clickers can not be used until after Jan 21, 2008. I understand that the information regarding how to register your clicker is on the box it came in.

Spring 2008 Exam Schedule

Requested exams:

Exam 1    Jan 24 2:00-3:00    approved

Exam 2    Feb 21 2:00-3:00    approved

Exam 3    Mar 27 7:00-8:00    approved

Exam 4    Apr 22 7:00-8:00    approved

Final        May 01 3:00-5:00    approved

Note: Exams 3 and 4 will be held at night.

Required Text: Genes IX by Benjamin Lewin

INDEX spring 2007

• Instructor information
• Contact instructor  and office hours (Gurley)
• Graduate School Programs at UF
• Department of Microbiology & Cell Science home page

Midterm Semester Evaluation Form

• Exam Schedule
•  
• Exam Test Results  Enter Test Code for each exam. Click on the question number (QN) on the left to see your answer and the correct answer. Note: test codes are listed below.

Exam 1 Test Codes

Exam 2 Test Codes

Exam 3 Grades

Exam 4 Grades

Exam 5 (Cumulative Final)

• Grade Book 2007   (Final posting; May 2, 2007; 5:30 PM)
  • exam 1 = 16.66 pts.
  • exam 2 = 27.78 pts.
  • exam 3 = 27.78 pts.
  • exam 4 = 27.78 pts.
  • max genome project = 2 pts.
  • max attendance (checked 5 times) = 1 pt.
  • Final Grade = ((ex1 x 16.66)+(ex2 x 27.78)+(ex3 x 27.78)+(ex4 x 27.78)+genome+atten) x 0.01
  • The Cumulative Final will substitute for the lowest exam grade. If it is lower than all others, there is no penalty. If exam 1 is the lowest grade, the final grade will be calculated two ways: 1) substitute the cumulative final for exam 1, and 2) substitute the cumulative final for the second lowest grade. The higher grade of these two possibilities will be the final grade.

   

  • Grade Scale:
  • 89.50-103.00 = A
  • 84.50-89.49 = B+
  • 79.50-84.49 = B
  • 74.50-79.49 = C+
  • 69.50-74.49 = C
  • 64.50-69.49 = D+
  • 59.50-64.49 = D
  • 00.00-59.49 = E

  Major Topics to Study for the Cumulative Final

•  
• Weekly Reviews are held Thursday afternoons from 5-7 in the main seminar room of the Microbiology and Cell Science building.  
• Genomics Project (unknown cDNAs & instructions) 2007
• Advanced Genomics Project 2007 Cancelled

Seminar

 

Dr. Eva Czarnecka-Verner

 

__________________________________________________

• Textbook

The text is "Genes IX" by Benjamin Lewin. The newer the
edition, the better.  The text is required. We  recommend it because our lectures are largely drawn from its material. Our exams will be from the lecture notes and the textbook.

• Lecture Notes 2006 and 2007
• Note: These lectures are subject to update at any time. Make sure that you have the most current version. Updates are indicated and announced in class.

Spring 2007 (note: a PowerPoint file is listed as well as the same file in PDF form. For large files, the PDFs are broken down into smaller files to aid downloading.)

                    First day of class: Genetics and early man-Gurley PowerPoint    (updated; 1:00 PM, Mon. Jan 8, 2007)

                                                Genetics and early man-PDF-6/page

                                                Genetics and early man-PDF-3/page

• Review questions for "Genetics of early man"

Life & Exodus PowerPoint

                    Lectures based on the TEXT (Genes VIII) below:

Part I-DNA Replication, Repair, Recombination, Transfer and Chromatin Structure:

   1) Wed Jan 10 Lecture 1-2 The Replicon; PowerPoint file (updated 10:10 AM; Sat Jan 13, 2007)

                                        Lecture 1-2 The Replicon 6p PDF (updated 10:10 AM, Sat Jan 13, 2007)

                                        Lecture 1-2 The Replicon 3p PDF updated 10:10 AM, Sat Jan 13, 2007)

                  2) Fri Jan 12 Lecture 1-2 (continued)- The Replicon (updated 10:10 AM, Sat, Jan 13, 2007)

• Review questions for Lectures 1-2 "The Replicon".

                  3) Wed Jan 17 Lecture 3 Conjugation (chapter 13 continued) (updated 1:36 PM, Mon, Jan 15, 2007)

                                        Lecture 3 Conjugation 6p PDF (updated 1:36 PM, Mon, Jan 15, 2007)

                                        Lecture 3 Conjugation 3p PDF (updated 1:36 PM, Mon, Jan 15, 2007)

• Review questions for Lecture 3 Conjugation (updated Thurs Jan 24; version 2 is the latest.)

                4) Fri Jan 19     Lecture 4 Plasmid replication & the eukaryotic ORC (updated 1:20 PM, Mon, Jan 22, 2007)

                                        Lecture 4 Plasmid replication & the eukaryotic ORC 6p PDF (updated 1:20 PM, Mon, Jan 22, 2007)

                                        Lecture 4 Plasmid replication & the eukaryotic ORC 3p PDF  (updated 1:20 PM, Mon, Jan 22, 2007)

• Review questions for Lecture 4 Plasmid replication & the eukaryotic ORC  (updated Thurs Jan 25; version 4 is the latest.)

                 5) Mon Jan 22     Lectures 5-6 DNA polymerase (updated 11:45 AM, Wed, Jan 24, 2007)

                                           Lectures 5-6 DNA polymerase 6p PDF (updated 11:45 AM, Wed, Jan 24, 2007)

                                           Lectures 5 DNA polymerase 3p PDF (updated 11:45 AM, Wed, Jan 24, 2007)

• Review questions for Lectures 5-6 DNA polymerase

                 6) Wed Jan 24     Lecture 5-6 (continued)

Wed Review Session 5-7 PM in the main seminar room of the Microbiology and Cell Science building.

Thurs Review Session 5-7 PM in the main seminar room of the Microbiology and Cell Science building. (same as the Wed session)

                 7) Fri Jan 26       Exam 1 (16.66% of course grade)

• Text Assignments for Exam 1:

Chapter 13 The Replicon

Required: sections 13.1 through 13.14

Skip: sections 13.15 through 13.20

Required (but not covered in lecture or handouts): section 13.21 (single copy partitioning system)

Required: 13.22 through 13.25 (only relevant parts of the Summary)

 

Chapter 14 DNA Replication

Required: section 14.1 through 14.4

Skip for now: 14.5 through 14.12

Required: section 14.13 through the middle of page 401 (Stop before "The role of RF-C and PCNA...)

Skip for now the rest of the chapter.

_________________________________________________________________________________________   

                8) Mon Jan 29        Lecture 7 The Enzymes of DNA Replication

                                             Lecture 7 The Enzymes of DNA Replication 6p PDF

                                             Lecture 7 The Enzymes of DNA Replication 3p PDF

• Review questions for Lecture 7-8 Enzymes of DNA Replication

       9) Wed Jan 31 Continuation of Lecture 7-8

Text assignment: from chapter 14, p. 391 section 14.5 (Structure) through section 14.19 (Origins sequestered) p. 411.

      10) Fri Feb 2     Lecture 9-10 Repair   

Lecture 9-10 Repair 6p PDF

                                        Lecture 9-10 Repair 3p PDF

      11) Mon Feb 5 Continuation of Lecture 9-10 Repair

•  Review questions for Lecture 9-10 Repair

Text assignment: from chapter 15, p. 447 section 15.20 (Repair systems...) through section 15.28, p. 460. Skip section 15.26, p. 456.

      12) Wed Feb 7   Lecture 11-12 Recombination

Lecture 11-12 Recombination 6p PDF

                                        Lecture 11-12 Recombination 3p PDF

     13) Fri  Feb 9     Lecture 11-12 Recombination   

•  Review questions for Lecture 11-12 Recombination

           14) Mon Feb 12 Lecture 13 Transposition (Dr. Eva Czarnecka-Verner)

Lecture 13 Transposition 6p PDF

Lecture 13 Transposition 3p PDF

         15) Wed Feb 14 Lecture 14 Transposition -continued (Dr. Eva Czarnecka-Verner)

• Review questions for lecture 13-14 Transposition (updated version 3; Tues)

         16) Fri Feb 16 Lecture 15 Chromatin (Drs. Czarnecka-Verner and Gurley) (Fri: 41% attendance)

Lecture 15 Chromatin-version 2 6p PDF

Lecture 15 Chromatin-version 2 3p PDF

        17) Mon Feb 19 Lecture 16 Chromatin & Nucleosomes-continued (This material will be included on Exam 2)

• Review questions for lecture 15-16 Chromatin & Nucleosomes  

Special review sessions Monday and Tuesday from 5-7:00 PM.

• Text Assignments for Exam 2: (completed)

Chapter 14 The Replicon

Required: sections 14.4 through 14.13 (DNA polymerases control fidelity of replication through Separate eukaryotic DNA polymerases undertake initiation and elongation)

Skip: section 14.14 (Phage T4)

Required: 14.15 (Common events in priming replication at the origin)

Skip: section 14.16 (...mainly lambda origins)

Required: section 14.17 through 14.19  and the relevant parts of the Summary (The primosome is needed to restart replication through Origins may be sequestered after replication)

Chapter 15 Recombination and Repair

Required: sections 15.1 through 15.10  (Introduction through The Ruv system resolves Holliday junctions)

Skip: section 15.11 through 15.19 (Gene conversion through Lambda recombination)

Required: sections 15.20 through 15.28 and the relevant parts of the Summary (Repair systems correct damage to DNA through Eukaryotic cells have conserved repair systems)

Skip: section 15.29 (A common system repairs double-stranded breaks)

Chapter 16 Transposons

Required: sections 16.1 through 16.8 (Introduction through Nonreplicative transposition proceeds by breakage and reunion)

Skip: the rest of the chapter

Chapter 19 Chromosomes

Required: section 19.1 (Introduction)

Skip: section 19.2 (Viral genomes are packaged...)

Required: 19.3 through 19.7 (The bacterial genome is a nucleoid through chromatin is divided into euchromatin and heterochromatin)

Skip: section 19.8 (Chromosomes have banding patterns)

Required: sections 19.9 through 19.20 (Lampbrush chromosomes are extended through Summary)

Chapter 20 Nucleosomes

Required: section 20.1 through 20.2

Skip: section 20.3 (DNA is coiled in arrays of nucleosomes)

Required: section 20.4 (Nucleosomes have a common structure)

Skip: sections 20.5 through 20.6

Required: sections 20.7 through 20.20.10 (The path of nucleosomes in the chromatin fiber through Reproduction of chromatin requires assembly of nucleosomes)

Skip: section 20.11 (Do nucleosomes lie at specific positions?)

Required: sections 20.12 through 20.13 ("Are transcribed genes organized in nucleosomes?" through "Histone octamers are displaced by transcription")

Skip: sections 20.14 through 20.16 (DNA hypersensitive sites change chromatin structure through An LCR may control a domain)

Required: relevant parts of the Summary

 

        18) Wed Feb 21       Exam 2 (27.78% of course grade)

Part II-Transcriptional Regulation of Gene Expression:

        19) Fri Feb 23 Lecture 17 Bacterial Transcription-Part I   (Version 3 is current.)

Lecture 17 Bacterial Transcription-Part 1 6p PDF

Lecture 17 Bacterial Transcription-Part 1 3p PDF

Optional Articles:

1. Structure of a Transcribing T7 RNA polymerase Complex, (1999) Cheetham, M. T. & Steitz, T. A., Science 286: 2305-2309.
2. Structure of a T7 RNA polymerase elongation complex at 2.9 A resolution, (2002) Tahirov et al., Nature 420: 43-50.

        20) Mon Feb 26 Lecture 18 Bacterial Transcription-Part I-continued

• Review questions for Bacterial Transcription (total) Version 6 is current. Version 6 differs from version 5 by the addition of questions regarding Archaea only (You don't have to print the entire list again.).

Text Assignment: Chapter 9 Transcription; sections 9.1-9.17 (pp. 241-263)

      21) Wed Feb 28 Lecture 19 Bacterial Transcription-Part I-continued

      22) Fri Mar 2 Lecture 20 Bacterial Transcription-Part 2

Lecture 20 Bacterial Transcription-Part 2 6p PDF (3 new slides; p. 6)

Lecture 20 Bacterial Transcription-Part 2 3p PDF (3 new slides; p. 11)

23) Mon Mar 5 Lecture 21 Bacterial Transcription-Part 2-continued

23) Wed Mar 7 Bacterial Transcription-Part2-continued and start Lecture 22 CAP catabolite protein

Lecture 22 CAP catabolite activator protein 6p PDF

Lecture 22 CAP catabolite activator protein 3p PDF

NOTE: Have you checked your exam 2 answers against the Key? If not, use the Exam Test Results feature above.

 24) Fri Mar 9 Lecture 23 CAP catabolite protein-continued; we may start Termination of Transcription, depending on the time.

Spring Break Week!

25) Mon Mar 19 Lecture 24 Termination of Transcription

Lecture 24 Termination of Transcription 6p PDF

Lecture 24 Termination of Transcription 3p PDF

26) Wed Mar 21 Lecture 25 Tryptophan Operon and Attenuation

Lecture 25 Tryptophan Operon and Attenuation 6p PDF

Lecture 25 Tryptophan Operon and Attenuation 3p PDF

27) Fri Mar 23 Lecture 26 Archaeal Transcription

Lecture 26 Archaeal Transcription 6p PDF

Lecture 26 Archaeal Transcription 3p PDF

 

• Text Assignments for Exam 3:

Chapter 9 Transcription

Required: sections 9.1 through 9.15

Skip: last part of section 9.16 (skip the part dealing with heat shock sigmas)

Required: section 9.17 (Sigma factors directly contact DNA)

Skip: sections 9.18 through 9.19 (sigma cascades and sporulation)

Required: sections 9.20 through 9.22

Skip: sections 9.23 through 9.25 (Anti-termination through Termination and anti-termination factors interact with RNA pol)

Required: all relevant parts of the Summary (section 9.26)

Chapter 10 The Operon

Required: sections 10.1 through 10.6

Skip: sections 10.7 through 10.9 (cis and trans mutations through Multimeric proteins)

Required: 10.10 through 10.14

Skip: section 10.15 (Mutant phenotypes...)

Required: sections 10.16 through 10.20

Chapter 11 Regulatory Circuits

Skip: section 11.1

Required: sections 11.2 through 11.6

Skip: sections 11.7 through 11.13 (the Stringent Response through Autogenous regulation...)

Required: sections 11.14

Skip: 11.15 (Termination in B. subtilis)

Required: sections 11.16 through 11.17

Skip: the remaining sections

 

28) Mon Mar 26 Exam 3  (27.78% of course grade)

---

 

29) Wed Mar 28 Lecture 27 Introduction to Eukaryotic Transcription

Lecture 27a Introduction to Eukaryotic Transcription 6p PDF

Lecture 27b Eukaryotic Transcription-1 (PowerPoint)

Lecture 27b Eukaryotic Transcription-1 6p PDF

Lecture 27b Eukaryotic Transcription-1 3p PDF

29) Fri Mar 30 Lecture 28 Eukaryotic Transcription-1 continued and Eukaryotic Transcription-2

Lecture 28 Eukaryotic Transcription-2 6p PDF

Lecture 28 Eukaryotic Transcription-2 3p PDF

30) Mon Apr 2  ---------ZZZZZZzzzzzzzzzzzzzzzz---------

31) Wed Apr 4 Lecture 30 Eukaryotic Transcription-1 continued and Eukaryotic Transcription-2

Optional Articles:

Review article: The RNA Polymerase II Machinery:

Structure Illuminates Function (2002), Nancy A. Woychik1 and Michael Hampsey, Cell, Vol. 108, 453–463.

Additional articles:

1) Conserved structure of Mediator and RNA polymerase holoenzyme, Francisco J. Asturias,* Yi Wei Jiang, Lawrence C. Myers, Claes M. Gustafsson,† Roger D. Kornberg‡, (1999) Science 283: 985-987.

2) Transcriptional coactivator complexes, Anders M. Naar, Bryan D. Lemon, and Robert Tjian, Annu. Rev. Biochem. (2001) 70:475–501.

3) The mediator coactivator complex: functional and physical roles in transcriptional regulation, Brian A. Lewis2 and Danny Reinberg, (2003) Journal of Cell Science 116, 3667-3675.

4) A high resolution protein interaction map of the yeast Mediator complex, Benjamin Guglielmi, Nynke L. van Berkum1, Benjamin Klapholz2, Theo Bijma1, Muriel Boube2, Claire Boschiero, Henri-Marc Bourbon2, Frank C. P. Holstege, and Michel Werner, (2004) Nucleic Acids Research, 2004, Vol. 32, No. 18 5379–5391.

5)  Mapping the location of TFIIB within the RNA Polymerase II transcription preinitiation complex: a model for the structure of the PIC, Chen, H.-T. and Hahn, S. (2004) Cell 119: 169-180.

6) Structural basis of transcription: an RNA polymerase II-TFIIB cocrystal at 4.5 Angstroms, Bushnell, D. A., Westover, K. D., Davis, R. E. and Kornberg, R. D. (2004) Science 303: 983-988.

31) Fri Apr 6 Lecture 31 Eukaryotic Transcription-2 (continued) and Eukaryotic transcription-3 Mediator

Lecture 31 Eukaryotic transcription-3 Mediator (6 p). PDF

Lecture 31 Eukaryotic transcription-3 Mediator (3 p). PDF

 

• Eukaryotic Transcription Review Questions Part A-version 3

31) Mon Apr 9 Lecture 32 Eukaryotic transcription-3 Mediator (continued) and  Eukaryotic transcription-4 TFIIE-H & transcription cycle

Lecture 32 Eukaryotic transcription-4 TFIIE-H & transcription cycle (6 p). PDF

Lecture 32 Eukaryotic transcription-4 TFIIE-H & transcription cycle (3 p). PDF

 

31) Wed Apr 11 Lecture 33 Eukaryotic transcription-4 TFIIE-H & transcription cycle (continued) and Transcription factors (Transactivators) PowerPoint

Lecture 33 Transcription factors (transactivators) (6p.PDF)

Lecture 33 Transcription factors (transactivators) (3p.PDF)

32) Fri Apr 13 Lecture 34  Transcription factors (Transactivators) -continued

• Eukaryotic Transcription Review Questions Part B

33) Mon Apr 16 Lecture 35  Transcription factors (Transactivators) -continued

34) Wed Apr 18 Lecture 36  Heat Shock Transcription Factors (HSFs)

Lecture 36 Heat Shock Transcription Factors (6p.PDF)

Lecture 36 Heat Shock Transcription Factors (3p.PDF)

• Heat Shock Review Questions

__________________________________

Lectures below this line have not been updated and reorganized.

Spring 2006 below:

                 2) Lecture 2 Replication PowerPoint-Czarnecka-Verner

                                      Lecture 2 Replication PDF (6/page)-Czarnecka-Verner

                         Lecture 2 Replication PDF (3/page)-Czarnecka-Verner

                  3) Lecture 3_Replication _B PowerPoint-Czarnecka-Verner

                                   Lecture 3_Replication_B (6/page) PDF-Czarnecka-Verner

                         Lecture 3_Replication_B (3/page) PDF-Czarnecka-Verner

                   4)  Lecture 4_Replication_C PowerPoint-Czarnecka-Verner

                                   Lecture 4_Replication_C (6/page) PDF-Czarnecka-Verner

                         Lecture 4_Replication_C (3/page) PDF-Czarnecka-Verner

                  5) Lecture 5_Replication_D PowerPoint-Czarnecka-Verner

                                   Lecture 5_Replication_D(6/page) PDF-Czarnecka-Verner

                         Lecture 5_Replication_D(3/page) PDF-Czarnecka-Verner

Lecture Material below included on Exam 2:          

                   1)  Lectures 6 & 7 Recombination PowerPoint-Gurley

                                                        Recombination (total) PDF-Czarnecka-Verner

                                 Recombination (part A) PDF-Czarnecka-Verner

                                 Recombination (part B) PDF-Czarnecka-Verner

                                 Recombination (part C) PDF-Czarnecka-Verner

                                 Recombination (part D) PDF-Czarnecka-Verner

                    2) Lectures 8 & 9 Repair (total) PowerPoint file -Czarnecka-Verner

                                 Repair (total) PDF(6/page) -Czarnecka-Verner

                                 Repair (total) PDF(3/page) -Czarnecka-Verner

                    3)  Lecture 10 Conjugation PowerPoint-Czarnecka-Verner

                            Lecture 10 Conjugation_(6/page) PDF-Czarnecka-Verner

                            Lecture 10 Conjugation_(3/page) PDF-Czarnecka-Verner                   

                    The text assignment is given in the last slide in Lecture 10 (pp. 370-371 [section 13.15 Septum formation] and pp. 377-379 [section 13.21 Single copy partitioning system)

                    4) Lecture 11 Transposition PowerPoint-Czarnecka-Verner

                            Lecture 11 Transposition (6/page) PDF-Czarnecka-Verner

                     Lecture 11 Transposition (3/page) PDF-Czarnecka-Verner

 

                     5) Lecture 12 & 13 Chromosomes & Nucleosomes (total) PowerPoint-Czarnecka-Verner  

                            Lecture 12 & 13 Chromosomes & Nucleosomes (total) (6/page) PDF-Czarnecka-Verner  

                            Lecture 12 & 13 Chromosomes & Nucleosomes (total) (3/page) PDF-Czarnecka-Verner  

    Updated lecture 13 (nucleosomes) to include information on the Histone Code (slides 70-72)

Exam 3 lectures below (subject to update in 2007):

                         1)  Bacterial Transcription-Part 1 PowerPoint  (last updated 4:15pm, Feb 24, 2006)
                            

                             Bacterial Transcription-Part 1 (6/page) PDF (last updated 4:15pm, Feb 24, 2006)

                             Bacterial Transcription-Part 1 (3/page) PDF (last updated 4:15pm, Feb 24, 2006)

 Articles:

    1) Structure of a Transcribing T7 RNA polymerase Complex, (1999) Cheetham, M. T. & Steitz, T. A., Science 286: 2305-2309.

    2) Structure of a T7 RNA polymerase elongation complex at 2.9 A resolution, (2002) Tahirov et al., Nature 420: 43-50.

2) Bacterial Transcription-Part 2-Regulation of Promoter activity PowerPoint (updated March 8, 2005)

Bacterial Transcription-Part 2 (6/page) PDF (updated March 9, 2005)

Bacterial Transcription-Part 2 (3/page) PDF (updated March 9, 2005)

 

3) Bacterial Transcription-Part3  PowerPoint (updated March 9, 2005)

Bacterial Transcription-Part 3 PDF (6/page) (updated March 9, 2005)
Bacterial Transcription-Part 3 PDF (3/page) (updated March 9, 2005)

 

4) CAP catabolite activator protein.PowerPoint
     CAP catabolite activator protein.PDF

 

5) Termination.PowerPoint
    Termination.PDF

 

6) Tryptophan Operon.PowerPoint
     Tryptophan Operon.PDF

 

7) Archaeal Transcription PowerPoint
    Archaeal Transcription PDF

Archaeal Transcription PDF subfile A (pp. 1-2)
Archaeal Transcription PDF subfile B (pp. 3-4)
Archaeal Transcription PDF subfile C (pp. 5-6)

Exam 3 study questions (updated after each lecture):

Exam 3 Text readings (Genes VIII):

•     Chapter 9 Transcription

    9.1 Introduction - 9.13 Promoter efficiencies increased or decreased by mutation

    9.16 Substitution of sigma factors may control initiation - 9.18 Sigma factors may be organized in cascades

    9.20 Bacterial RNA polymerase terminates at discrete sites - 9.22 How does Rho factor work?

    9.26 Summary (except the last two paragraphs about antitermination)

•     Chapter 10 The Operon

    10.1 Introduction - 10.6 Repressor is controlled by a small molecule

    10.9 Multimeric proteins have special genetic properties - 10.14 DNA-binding is regulated...

    10.16 Repressor binds three operators... - 10.20 Summary

•     Chapter 11 Regulatory circuits

    11.1 Introduction - 11.6 CRP (CAP) bends DNA

    11.14 Alternative secondary structures control attenuation

    11.16 E. coli tryptophan operon controlled by attenuation - 11.17 Attenuation controlled by translation

    11.23 Summary (applicable paragraphs)

Exam 4 lectures below (2005):

                    1) Introduction to eukaryotic transcription-PowerPoint

Introduction to eukaryotic transcription-PDF (6 per page)

                        Topics: Building the preinitiation complex; TFIID/TAFs; Mediator; transactivators; DNA binding domains; steroid receptors, repression.

                    2) Eukaryotic transcription1 PowerPoint (updated April 4, 2006)

Eukaryotic transcription1 (3 slides/page).PDF (updated April 4, 2006)

 

Articles:

1) Review The RNA Polymerase II Machinery:

Structure Illuminates Function (2002), Nancy A. Woychik1 and Michael Hampsey, Cell, Vol. 108, 453–463.

 

                 3)  Eukaryotic transcription2a: TFIID and TFIIB. PowerPoint  (updated 5:00 pm, Apr 4, 2006)

Eukaryotic transcription 2a : TFIID and TFIIB (3 slides/page).PDF (updated 5:00 pm, Apr 4, 2006)

 

4) Eukaryotic transcription 2b: Mediator. PowerPoint (updated 5:00 pm, Apr 4, 2006)

Eukaryotic transcription 2b: Mediator (3 slides/page). PDF (updated 5:00 pm, Apr 4, 2006)

Articles (optional):

1) Conserved structure of Mediator and RNA polymerase holoenzyme, Francisco J. Asturias,* Yi Wei Jiang, Lawrence C. Myers, Claes M. Gustafsson,† Roger D. Kornberg‡, (1999) Science 283: 985-987.

2) Transcriptional coactivator complexes, Anders M. Naar, Bryan D. Lemon, and Robert Tjian, Annu. Rev. Biochem. (2001) 70:475–501.

3) The mediator coactivator complex: functional and physical roles in transcriptional regulation, Brian A. Lewis2 and Danny Reinberg, (2003) Journal of Cell Science 116, 3667-3675.

4) A high resolution protein interaction map of the yeast Mediator complex, Benjamin Guglielmi, Nynke L. van Berkum1, Benjamin Klapholz2, Theo Bijma1, Muriel Boube2, Claire Boschiero, Henri-Marc Bourbon2, Frank C. P. Holstege, and Michel Werner, (2004) Nucleic Acids Research, 2004, Vol. 32, No. 18 5379–5391.

5)  Mapping the location of TFIIB within the RNA Polymerase II transcription preinitiation complex: a model for the structure of the PIC, Chen, H.-T. and Hahn, S. (2004) Cell 119: 169-180.

6) Structural basis of trarnscription: an RNA polymerase II-TFIIB cocrystal at 4.5 Angstroms, Bushnell, D. A., Westover, K. D., Davis, R. E. and Kornberg, R. D. (2004) Science 303: 983-988.

                   4)   Eukaryotic transcription3 Power Point   (updated April 13th, 2006)

Eukaryotic transcription3 (3 slides/page).PDF (updated April 13th, 2006)

                   5) Transcription factors (Transactivators) PowerPoint (updated May 1, 2006)          

       Transcription factors (Transactivators) PDF (3 per page) (updated May 1, 2006)

                    6) Heat Shock-Dr. Czarnecka-Verner PowerPoint (updated April 17, 2006)

                            Heat Shock-Dr. Czarnecka-Verner PDF (3 per page) (Updated April 17, 2006)

_____________________________________________________________________________

                   Note: T-DNA is not on any exams in 2006

 7)  T-DNA & Genetic Engineering- PowerPoint 
                               

                      T-DNA & Genetic Engineering- PDF-(3 per page)

Exam 4 Text assignment:

Genes VIII chapters 21-22 (Promoters and Enhancers; Activating Transcription)

    Skip sections 21.19-21.25

Genes VII chapter 20-21 (Initiation of Transcription; Regulation of Transcription)

---

Exam Study Questions:

Study questions for the Exam 1:

                   Exam 1 lecture 1 questions-Czarnecka-Verner

                            Exam 1 lecture 2 questions-Czarnecka-Verner

                            Exam 1 lecture 3 questions-Czarnecka-Verner

                            Exam 1 lecture 4 questions-Czarnecka-Verner

                            Exam 1 lecture 5 questions-Czarnecka-Verner

Study questions for the Exam 2:

      Exam 2 lectures 6 & 7-Czarnecka-Verner

                          Exam 2 lecture 10 questions-Czarnecka-Verner

                          Exam 2 lecture 11 questions-Czarnecka-Verner

                          Exam 2 lecture 13 questions-Czarnecka-Verner

Study questions for Exam 3:

    Exam3 question PowerPoint file (updated March 3, 2006)           

     Exam 3 questions PDF file (updated March 3, 2006)

Study questions for Exam 4:


                         A- Introduction to Eukaryotic Transcription & Basal Factors handouts (updated April 18th, 2005) Questions 65-69 have either been added or modified.
                       

                         B- Chapter 22: Transcriptional Regulation handout

                         C- Heat Shock

T-DNA is not on exam 4.                        

    D-  T-DNA
 

Text Assignments for Exam 4: MS Word document (Genes VII finished, others in progress)
Text Assignment for Exam 4 (MS Word)

• Exam Schedule Spring 2007

            Exam 1    26Jan             6 lectures    16.66%

            Dr. Martin L. King Day (Jan 15)

            Exam 2    21 Feb          10 lectures    27.78%

            Spring break  (March 10-17, 2006)

            Exam 3    26 Mar          10 lectures    27.78%
           

            Exam 4   20 Apr           10 lectures    27.78% 

                                                                 total=100.00%  

            
            The time of the cumulative final  Tues May 1^st, 2007 12:30-2:30 pm

            36 lectures total

            NOTE: cumulative final will substitute for lowest grade.

            Extra Credit: Genomics project (optional) can add 2.0 pts. to final grade

            Note: Genomics project reports due Friday, April 20, before 5:00 pm. Slide under Dr. Gurley's office door (Microbiology & Cell Science Building, room 1150).

• No excused absences permitted; however, you can substitute the cumulative final for your lowest grade (including a zero you may have from an absence).

Review Missed Exam Questions:

1) Select the following link: http://classcd.net/scripts/WebResults_CGI.exe/runquery?CourseID=PCB4522.

2) Select the course and exam.

3) You will see a histogram of the class scores on the last exam.

4) Enter your UF ID number where it asks for your "social". Be sure to add a zero (0) to the last digit of your UF ID number. You will only see the missed questions.

5) Select the questions that you want to view.  You will see a lot of useless font information preceding each question and answer. Try to see if you can sort through all the mess and read the questions and answers. Sorry that it is so much trouble, but the program is still in development and should be modified before the next exam.

    (Missed Questions)

• Review Sessions-Spring 2007

* http://campusmap.ufl.edu/. Campus Map

• LINKS for Genomic Project (Spring 2007)
•  Download your unknown cDNA (2007)

• Instructions for Genomic Project

            2007 Genomics Project Workshop/help sessions:

            (to be announced)

            Genomics Project due Apr 20 (slide under Dr. Gurley's office door; room 1150)

• ---

  Participation in the genomic project is an easy way to add up to 2 points to your final course grade. All the information that you need is in the "Instructions to Genomic Project". If you would like for the instructor to guide you through the entire process, attend one of the help sessions given in an IFAS computer lab according to the schedule below:

• ---

  RasMol Home page
• Go to RasMol homepage to download RasMol to your computer, then see "NOTE" below for how to view with RasMol. NOTE: these files have already been converted from HTML to "pdb" format (see note below) and can be directly viewed in RasMol. You can download help and instructions here.
•  
• or you can download RasMol directly here.
•  
• Directions for viewing molecular structures using RasMol:

  1) First Download these "pdb" files to your computer. These files will contain text that is converted into structure by the RasMol program in step 2.

  2) Open these files in RasMol (Open RasMol first, then open the files.) In Netscape click the right mouse button and "Save Link As". If you right click these files, you may open them directly, but you can not get the cartoon view.

Play around with the different views.  I like Display and Color settings of "cartoon" and "group". Try out the mouse to manipulate the orientation.

Mouse commands:

1) left click to rotate in various planes

2) left/shift to zoom

3) right click to move position

4) right/shift to clockwise or counterclockwise

Molecules (pdf files):

• lac repressor
• H-T-H of lac repressor
• sigma
• a-CTD
• Archaeal TBP/TFB/DNA
• Arabidopsis TBP with DNA
• Arabidopsis TBP
• human TFIIB
• Arabidopsis TBP with human TFIIB plus DNA
• T7 RNA polymerase
• CAP
• GCN4
• GCN4 DNA binding domain
• Gal4
• HSF (heat shock transcription factor)
• histones
• histone H1
• nucleosome
• glucocorticoid receptor
• myoD transcription factor
• Drosophila TAF42/62 complex
• Drosophila TAF230 N-terminal domain binding to TBP
• human estrogen receptor ligand binding domain
• AtTBP.text
• Brookhaven Protein Data Base (PDB)
• NOTE: retrieve protein files directly from PDB to your computer using "save as" in HTML format, then remove ".HTM" extension and replace with ".pdb" using the "rename" option. It is best to use "PDB Lite" and the extension will already be ".pdb."  To view, start RasMol on your computer and then open the protein file.

• Translate (select 6 frame translation)
• National Center for Biotechnology Information (NCBI)
• ORF Finder (at NCBI)
• Entrez (literature search)
• Pedro's Research Tools
• Human genome project information
• ExPASy (molecular tools)
• NCBI BLAST site
• CLUSTALW (best for printing; site in Great Britain)
• Sequence Editor (display CLUSTALW alignments)

V. UF Graduate School Opportunities in Molecular Biology:

Microbiology and Cell Science

Plant Molecular and Cellular Biology

Molecular Genetics & Microbiology

IPD Biochemistry & Molecular Biology

Index

VI. Instructor Information:

1.) William Gurley

Professor in Microbiology & Cell Science and the graduate program in Plant Molecular & Cellular Biology.

Research Area: transcriptional regulation of plant genes:

• heat shock transcription factors (HSFs) in plants,
• transcription factor IIB (TFIIB) from soybean and Arabidopsis,
• TFIID: functional characterization of TBP associated factors (TAFs) from Arabidopsis.
• Mediator in plants; discovery of plant-specific subunits in Arabidopsis.

Current research is focused on the characterization of the Mediator complex in plants. Experimental approaches include transient expression assays using particle bombardment and PEG transformation of plant cells. Protein-protein interactions are being studied using the yeast two-hybrid system, GST pull-down assays, gel mobility shift assays and chromatin immunoprecipitation (ChIP).

How to Contact: It is best to arrange an appointment.

Office hours: regular time; 3:00 to 5:00 pm, Fridays. Also, the day before an exam (during the week) all afternoon until 6:00 pm.

Office: Microbiology and Cell Science Building; room 1050; Lab: 1198

phone: (352) 392-1568 [office]; (352) 392-1177 [lab]

FAX: (352) 392-5922

email: wgurley@ufl.edu

 

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2.) Eva Czarnecka-Verner

Associate In Microbiology & Cell Science (Graduate Research Faculty). 

Research Area: transcriptional regulation of plant genes, heat shock transcription factors (HSFs) in plants, transcription factor IIB (TFIIB) from soybean and Arabidopsis, and the cloning and functional characterization of TBP associated factors (TAFs) from Arabidopsis. Current research is directed towards identifying the target proteins in the transcriptional preinitiation complex for interactions with heat shock transcription factors in plants. We are also characterizing protein-protein interactions between various transactivator proteins such as GF14 (Arabidopsis) and VP1 (maize) with transcription factor IIB from Arabidopsis. A more recent line of investigation seeks to assess the role of TAFs in the process of activated transcription in plants. Experimental approaches include transient expression assays using particle bombardment and PEG transformation of plant cells and HeLa. Protein-protein interactions are being studied using the yeast two-hybrid system, GST pull-down assays, gel mobility shift assays and fluorescence polarization spectroscopy.

How to Contact: It is best to arrange an appointment.

Office hours: regular time; 3:00 to 5:00 pm, Fridays. Day before exam (during the week) all afternoon until 6:00 pm.

phone: (352) 392-2400 [office]; (352) 392-1177 [lab]

FAX: (352) 392-5922

email: evaczar@ufl.edu