Principles of Biochemistry, 4th Ed or 5th Ed., Lehninger, Nelson, Cox, 2005 ...
The purpose of this course will be to explore the fields of biochemistry and ...
BIOC 4113, Molecular Biology FALL, 2010 Instructor:
Patricia Ayoubi, Ph.D. 246F Noble Research Center 405-744-6199
[email protected] http://biochemistry.okstate.edu/faculty-research-1/patricia-ayoubi
Office Hours:
MW 10AM-11AM Additional times by appointment and drop-ins are welcome!
Teaching Assistant:
Gloria Perez
[email protected] 352-516-2629 246A Noble Research Center Office hours: MWF 11:30-12:20, TR 4:00-5:00 and by appointment Lecture:
MWF 12:30-1:20PM, 348B NRC
Text:
Principles of Biochemistry, 4th Ed or 5th Ed., Lehninger, Nelson, Cox, 2005 (Required) Biochemistry, 6th Ed., Berg, Tymockzo, Stryer, 2007 (Recommended)
Prerequisites: BIOC 3653 and BIOL 3023 or equivalent. Purpose: BIOC 4113 provides a semester of a advanced biochemistry-molecular biology curriculum for students majoring in these and related sciences. Students must have completed one semester of general biochemistry covering the entire spectrum of topics contained a general textbook of Biochemistry and one semester of genetics. The purpose of this course will be to explore the fields of biochemistry and molecular biology in greater depth, integrating multiple topics and current state-of-the-art. Emphasis will include molecular biology and the methodologies applicable to contemporary biochemistry as it relates to research, medical or clinical fields. Attendance: Attendance is not required but strongly encouraged and class roll will be taken daily. Materials presented in class will generally be a supplementation to text materials while emphasizing the subtopics for exams thus failure to attend lectures may present a disadvantage to students. Exemplary attendance or excessive absence will be taken into consideration in assigning a final grade. It will be assumed that all students will read the pertinent sections of the text prior to lecture and that they will reread and study those sections being discussed in class following class. Students are encouraged to seek additional sources of information on topics they feel are not adequately covered in the assigned text or in class and will openly discuss with the instructor issues they find confusing. Online Course Website and Resource: https://oc.okstate.edu/ (OSU Desire2Learn, D2L) Course Podcast videos: Podcasts or videos of lecture will be viewable as streaming video (and downloadable) through the D2L course site or you can subscribe using iTunes. Apple’s QuickTime player (available for free at http://www.apple.com/quicktime/download/) will be required for playback of the MP4 videos. To subscribe to the “Advanced Biochemistry” Podcasts through iTunes, you must first download and install Apple iTunes from http://www.apple.com/itunes (Mac and PC versions are available free of charge) then subscribe to the Podcast as follows: (1) Open iTunes, (2) select the “Advanced” menu option (3) drop down to “Subscribe to Podcast…” then (4) enter the following URL (without quotes) “http://media-biochem.nrc.okstate.edu/ayoubi/4113/FA10/rss4113FA10.xml” into the dialog box and click “OK”. Once you have subscribed, you can then select which videos you would like to download and watch.
Online Resources : Course Website (D2L, Desire2Learn) http://oc.okstate.edu Lehninger textbook: http://bcs.whfreeman.com/lehninger OR http://bcs.whfreeman.com/lehninger5e Stryer textbook: http://www.whfreeman.com/biochem5 OR http://bcs.whfreeman.com/biochem6 OR http://www.ncbi.nlm.nih.gov/books/bv.fcgi?rid=stryer.TOC (5th edition only) Informatics (a few of my favorites) http://www.ncbi.nlm.nih.gov http://www.ncbi.nlm.nih.gov/books/bv.fcgi?rid=gnd.TOC&depth=2 http://www.rcsb.org/ http://www.hprd.org http://www.hgmd.cf.ac.uk (register or login using
[email protected] and 89ayt12UP42) http://www.ensembl.org
Exams: Three regular one-hour exams will be given during the semester. A comprehensive final exam will be administered Friday, December 17th, 2010 from 10:00PM to 11:50AM. Exams (regular exams and the final exam) will contain multiple choice and short answer questions and will include recognition, recall, describe, explain and problem-solving type questions. Homework: Homework will be administered at various times and will consist of thought provoking problems, paper (research journal articles) reviews, case studies, quantitative problems, in depth calculations and/or internet and computer exercises. Homework will emphasize lecture topics and may included methodologies applicable to contemporary biochemistry and molecular biology, have application to research or will have clinical and medical relevance. Homework problems will be posted on the OSU D2L website. Quizzes: Short quizzes consisting of one or a few questions will be given unannounced at any time. Quizzes may cover previous or current subject matter. Term Paper: Each student will be required to prepare a written term paper containing a minimum of 8 typed pages of text excluding the figures, tables and references (double spaced, maximum font size of 12 points). Identical printed and electronic versions of the completed paper will be required on the same day and must pass plagiarism analysis using TurnItIn (see below). Electronic submission can be on CD, by email, post to D2L or other electronic delivery method. The paper will consist of a review of a single human gene and resulting protein associated with a human disease (ie, the gene must encode for a protein and directly or indirectly cause a disease). The gene might include a single member of a gene family or the product might be a single component or subunit of a larger protein complex. Additional information on the paper content is provided below.
Dates
BIOC 4113 Tentative Lecture Schedule, Molecular Biology, Fall 2010 Patricia Ayoubi, Ph.D.,
[email protected] 246F Noble Research Center, 405-744-6199 Tentative Topics and Exam Schedule Reading
Nucleic Acids and Genomics Aug 23-25 Nucleotides and Nucleic Acids Aug 27Gene Expression, RNA Synthesis, and Protein Synthesis Sep 13 Sep 6 Labor Day (no classes) Sep 15 Informatics and Resources for Genomics Sep 17
DNA-Based Techniques and Technologies
Sep 20
In class paper review
Sep 22
Ch 8 Ch. 24-28 (not all sections will be covered) www Ch. 9 and/or Journal Article(s) Journal Article(s)
Exam #1 (Ch 8, Ch 24-28, excludes techniques informatics and www)
Proteins and Proteomics Sep 24-27 Amino Acids, Peptides and Proteins Sep 293D Structure and Function of Proteins Oct 4 Oct 6-8 Enzymes and Kinetics Oct 11-18 Antibodies
Ch 3 Ch 4-5, 34 (Stryer), www Ch 6 Ch 33 (Stryer)
Oct 15 Oct 20
Fall Break (no classes) Informatics and Resources for Proteomics
www
Oct 27 Nov 1
Exam #2 (Ch 3-6, Stryer Ch 33, 34, excludes informatics and www) Topic for written report due
Cell-to-cell Communication and Signal Transduction Oct 22 Biological Membranes and Transport Ch 11 Oct 25Sensory Systems Ch 32 (Stryer) Nov 1 Nov 3 Navigating the NCBI site www Nov 5-12 Biosignaling (Signal Transduction Pathways) Ch 12 Nov 15 Written Report Due (three forms required: printout, Turnitin.com and electronic copy) Nov 15-Dec 8 Student Oral Presentations (note: two exams given during this time) Nov 19 Nov 22 Nov 24-26 Dec 10
Exam #3 (Ch 11, 12, and Stryer Ch 32, excludes informatics and www) Standardized Exam (such as ACS Biochemistry or GRE Biochemistry) Thanksgiving Break (no classes) No Class (Makeup day for Seminar Attendance)
Dec 17
Comprehensive Final Exam (10:00-11:50AM)
Good Luck!!
The above schedule is an approximation of the topics that will be discussed in class. Changes in the topics or order may occur in response to interest or difficult. If necessary, exam dates may change by ±1-2 days at the instructor’s discretion. Any changes in exam dates will be announced in class and posted on the OSU 2DL website.
Oral group presentation: The oral presentations will be conducted in groups of four (4) students and review a single assigned research paper. The oral presentation must be prepared using PowerPoint, will last about 20 minutes each followed with 5 minutes of questions and discussion. Each group member must speak on a topic related to the paper. You will need to do additional review of additional research articles and review articles in order to fully grasp the paper you are assigned. I recommend that you utilize your textbooks listed above and PubMed http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?DB=pubmed to do additional research. Presentation format should include the following: (1) background and introduction, (2) results/data (possibly divided between two members of the group) (3) conclusions and implications. Nonpresenters: You are expected to attend every presentation. Pop quizzes will be given at this time to motivate attendance! You are expected to read EVERY paper before coming to class so be prepared to discuss it or even ask questions/answer. Attendance and participation during discussions will be part of your presentation grade so each should ask at least a few questions. Additional Term Paper Information: Term Papers will consist of a review containing a comprehensive discussion of the topics listed below. (1) Introduction (to explain the disease and why we should care about this gene) (2) Transcriptional regulation (both positive and negative, if known) (3) Post-translational modifications (if any) (4) Protein function, activity and regulation (5) Relationships between gene product and the disease (6) Summary or Conclusions including future direction of research, treatment or therapy Students must receive approval of their gene from the instructor prior to preparation of the report. However, do your research before deciding on a protein and if you are unable find to the required information then choose a different protein. The instructor will be available to assist students in making selections. Make your choices early as approval of genes/proteins is on a first-come basis and genes cannot be reviewed by more than one student. Grading: After dropping the lowest quiz grade; quiz scores will be totaled and assigned a weight equal to a single regular exam (ie, scaled to 100 total points). Homework grades will be totaled and assigned a weight equivalent to a single regular exam (also scaled to 100 points total). The term paper and oral group presentation are each equivalent to a single regular exam so take them seriously. The comprehensive final exam is worth more than a single regular exam. The breakdown is as follows: Four Regular Exams Quizzes various points total Homework Term Paper Oral Group Presentation Comprehensive Final Exam Course Total
100 points each various points each various points each 100 points 100 points 150 points
300 points 100 points 100 points 100 points 100 points 150 points 850 points
Grading will conform to this scale (however, the scale might be adjusted slightly to take into account exam difficulty and overall class performance). Final grades will be assigned according to a straight percentage
scale. The following percentage scale will serve as a guideline for letter grade assignment: 90 – 100% = A 80 – 89.9% = B 70 – 79.9% = C 60 – 69.9% = D 0 – 59.9% = F Text and other reading material: Most assigned readings will be in the main textbook: Principles of Biochemistry by Lehninger, Nelson, and Cox; Worth Publishers (Fourth Edition). Biochemistry by Stryer; Freeman and Company Publishers (2007) may be a secondary text however, students not owning the Stryer text book should not need to purchase it because the chapters we will use are posted at the web address given above. In
addition, students will be required to read various classic and current journal articles from assigned peer reviewed journals. Such articles needed for lectures will be posted on D2L as links or PDF files. It is the responsibility of each student to find additional articles required from the term paper and oral presentation but assistance will be provided if requested. Make-Up Exams and Quizzes: Make-Up exams and quizzes will be provided only for those missed for legitimate reasons. It is your responsibility to inform me as soon as possible and to provide official documentation (e.g., from your physician, academic advisor, or college Dean) stating that you could not take the exam due to this emergency or illness, in which case we will schedule a make-up exam.. Missed exams and quizzes will otherwise be assigned a grade of 0. Assistance from the Instructor: You should always feel free to contact Dr. Ayoubi outside of class, either during office hours, by appointment or simply drop-in. I have an open door policy. Feel free to call and stop by the office at any time. Please do not hesitate to seek any appropriate out-of-class assistance in your efforts to master the subject matter of this course. Plagiarism and TurnItIn: All written work will be submitted to TurnItIn.com for a plagiarism analysis. If any part of what you submit is found to be plagiarized the report will automatically receive a zero and be reported for academic dishonesty or misconduct. OSU provides details on the academic dishonesty policy posted at http://academicintegrity.okstate.edu/doc/2-0822-ai.pdf. You must to submit your written work to Turnitin.com prior to submitting it for grading. You must self enroll using a class ID and instructions and details will be provided. When you submit a document to TurnItIn for analysis, you will receive an originality report. You will need to address any potential plagiarism issues identified by TurnItIn before submission of your final report for a grade. Academic dishonesty or misconduct: Academic dishonesty or misconduct is defined in the Oklahoma State University Policy and Procedures Letter 2-0822. You should become familiar with this document as a matter of self-interest. There is a zero tolerance policy for academic dishonesty or misconduct. Disabilities: If any member of this class feels that he/she has a disability and needs special accommodations of any nature, we will work with you and the Office of Disabled Student Services, 326 Student Union, to provide reasonable accommodations to ensure that you have a fair opportunity to perform in this class. Please advise Dr. Ayoubi of such disability and the desired accommodations as early as possible to address your needs in a timely manner. Oklahoma State University Syllabus Attachment: We are very concerned about your success as a student at OSU. The information at the following link is provided to answer questions most often asked by students. http://osu.okstate.edu/acadaffr/aa/CurrentStudents.htm. A copy of this course syllabus and the OSU Syllabus Attachment are posted on the OSU D2L website for this course for your convenience. Drop and Add Dates: Monday, August 30 Monday, August 30 Friday, September 3 Monday, November 1 Friday, November 12 Friday, November 12 Friday, December 3
Last day to add a course (nonrestrictive) Last day to drop a course with no grade or fees Last day to add a course with permission of instructor (restrictive) Last day to file diploma application Last day to drop a course with automatic grade of W Last day to withdraw from all courses with automatic grades of “W” Last day to withdraw from all courses with an assigned "W" or "F"
HAVE A GREAT SEMESTER!! Additional or specific information about the course, term paper and oral presentation will be provided during the semester.
