BI/CH421 & BI/CH621 – Section A2 Fall 2016

1 biochemistry I Syllabus BI/CH421 & BI/CH621 Section A2 fall 2016 Faculty: Lecture: Dr. Deborah Perlstein Phone: (617) 358-6180 Office: Rm 382, 590 Comm. Ave. (SCI) Email: Dr. James Carolan (617) 358-8589 Rm 390B, 590 Comm. Ave. (SCI) Email: Laboratory: Dr. Didem Vardar-Ulu (617) 353-2500 Rm 358A, 590 Comm. Ave. (SCI) Email: Lecture: TR 2:00-3:30 CAS 224 Exams: M 5:00-7:00 Oct 3, Oct 24, Nov14, Dec 12 Location TBD Office Hours T 1-2; W10:30-11:30; R3:30-4:30 Review for exam Fridays 5-6, the friday before each exam Location TBD These review sessions will not contain a prepared lecture but is an opportunity to come and ask questions Lecture # Date Topic Reading in Voet, Voet and Pratt Related Problems (problems in text, then companion in bold) 1 T Sept 6 Introduction Ch 1, Section 1-1, 1-2 2 R - Sept 8 Thermodynamics Ch 1, Section 1-3; Companion: pg 5-6 Ch 1: 1-3; 6-15; 20.

2 5, 6, 12-15, 17, 21 3 T Sept 13 Water and hydrogen bonds Molecular Forces, pH Ch 2 Companion: pg 12-17, 20 Ch 2: 1,2, 5, 9, 12-21; 25, 26, 1-4, 8-16, 19, 21 4 R Sept 15 Finish pH; Amino acids I structure and stereochemistry Ch 4, intro, 4-1, 4-2, Companion 31-35 Ch 4: 1-3, 6-7, 12, 13, 15, 27, 28, 30, 1-4, 21-23 5 T Sept 20 Amino Acids II pI, peptide bond, amino acid derivatives; start proteins Ch 4, sections: 4-1D, 4-3 Ch 5, sections: intro, 5-1 Ch 6, sections: intro, 6-1A Ch 4: 5, 9, 14, 16-18, 20, 23, 25, 31, 5-16, 20, 24, 25 Ch 5: 1, 3 6 R- Sept 22 Proteins I primary structure and purification Ch 5, Section 5-2, Ch 5: 2, 4, 7-12, 21, 23-25, 1, 2, 4, 6, 8, 9, 11, 12, WileyPlus Exercise 5-2 7 T Sept 27 Proteins II protein sequencing Ch 5, sections 5-3 Ch5: 13-16, 27-33, 13-18 8 R Sept 29 Proteins III protein evolution, secondary structure Ch 5, Section 5-4 Ch 6, Section 6-1 Ch 5: 17-18; 19, 20, 22, 23, WileyPlus: Exercise 5-1.

3 5-3 Ch 6: 1, 2, 1, 2, 4, 5 EXAM 1 M Oct 3 Lectures 1-7 (amino acids) 9 T Oct 4 Proteins IV finish secondary structure, tertiary and quaternary structure Ch 6, sections: 6-1, 6-2, 6-3 Ch 6: 3, 7, 9, 10, 12, 21-24, 31, 6-8, 10-13 10 R Oct 6 Proteins IV Protein structure determination Ch 6, sections: 6-2 Ch 6: 11, 13, 14-17, 20 T Oct 11 NO CLASS (BU Monday) 11 R Oct 13 Proteins V- protein folding and stability Ch 6, sections: 6-4, 6-5 Ch 6: 16, 18, 28, 29, 32, 38, 18, 23-25, 28, 29 12 T Oct 18 Enzymes I enzymatic strategies Ch 11, sections: intro, 11-1, 11-2, 11-3 Ch 11: 1-3, 5-11, 14, 21, 22, 24, 30, 2-17 13 R Oct 20 Enzymes II steady state kinetics Ch 12, sections: intro, 12-1, Companion 112-118 Ch 12: 1, 5, 7-15, 22-25, 1, 2, 4-8, EXAM 2 M Oct 24 Lectures 8-12 (proteins) 14 T Oct 25 Enymes III inhibition Ch 12, Section 12-2 Ch 12: 19, 20, 27-30, 11-12 15 R Oct 27 Enzymes IV mechanism Ch 11, Section 11-4, 11-5 Companion 98-103 Ch 11: 17-20, 28, 30, 23-29 ** F Oct 28 T Nov 1 5-6:30 Lecture.

4 Overview of the nucleic acid structure and central dogma (DNA->RNA->Protein) and quiz you MUST attend one of these two lectures to take the required quiz that counts for 10% of your Exam 4 grade 16 T Nov 1 Enzymes V regulation Ch 7: Section 7-1 Ch12: Section 12-3 Ch 14: Section 14-1 D&E Companion 65-68 Ch 7: 1-4, 2, 11-13 Ch 12: 26, 15, 16 17 R Nov 3 Finish enzymes ** F Nov 4 T Nov 8 Nucleic acid structure and central dogma problem solving session attendance is optional. Students who chose to attend will earn bonus points on their quiz taken on Oct 28 or Nov 1 18 T Nov 8 Nucleic acids I structure and analysis Ch3, sections: intro, 3-1, 3-2, Ch24, sections, intro, 24-1, 24-2, 24-3, 24-5 Ch25, Section 25-4 Ch 24: 1-4, 7, 10-14, 29, 33, 35, 2-4, 12 19 R Nov 10 Nucleic acids II DNA replication and repair Ch3, Section 3-3.

5 Ch25, sections 25-1, 25-2, 25-5 Ch26, intro Ch 24: 5, 7, 9 Ch 25: 1, 3-8, 10, 15-17, 19, 23, 25, 26, 35, 1-4, 6, 12, 14, EXAM 3 M Nov 14 Lectures 13-18 (enzymes) 20 T -Nov 15 Nucleic acids III the genetic code & transcription Ch26, Section 26-1, 26-3 (not entire Section , just topics covered in lecture). Ch27, sections: intro, 27-1 Ch 26: 1, 2, 4, 7, 13, 15, 25, 1 Ch 27: 1-4, 21 1, 2, 4-6 21 R Nov 17 Nucleic acids IV translation Ch 27, Section 27-4. Ch 27: 9-11, 15, 16, 25, 27, 33 7-14. 22 T Nov 22 Translation II 23 T Nov 29 Finish Nucleic Acids 24 R Dec 1 Carbohydrates Ch 8 Ch 8: 1, 3, 5, 6, 8, 9, 12, 13, 15, 23, 26, 29, 1-3, 5-9, 12 25 T Dec 6 Finish carbohydrades start lipids Ch 9 Ch 9:1, 3-5, 7, 12, 13, 15, 17, 19, 22, 25, 26 1-6, 8, 13-18, 21, 23 26 R - Dec 8 Membranes EXAM 4 M Dec 12 Lectures 19-25 (nucleic acids and carbohydrates.)

6 No lipids or membranes) Other important dates: last day to add a course September 19 last day to drop a course without a W grade Wednesday October 12 last day to drop a course with a W grade Friday November 10 Prerequisites: Students are REQUIRED to have passed ( C) 2 semesters of organic chemistry (CH204/212/214) Textbooks : There are 3 required texts for this class. All are available for purchase at the BU Bookstore and will be placed on reserve in the library. 1) fundamentals of biochemistry : Life at the Molecular Level, 5th edition by Voet, Voet & Pratt. 2) A Student Companion to fundamentals of biochemistry , 5th edition by Uzman, Eichberg, Widger, Voet, Voet, & Pratt.

7 3) biochemistry Laboratory Manual by Dean R. Tolan Students can also consider purchasing access to wileyplus though it is not required for the course but it does contain some additional resources students might find helpful throughout the semester Grading: BI/CH421 (undergraduate students): Lab 35%, midterm exams (best 3 of 4) 40%, Final 25% BI/CH621 (graduate students): Lab 30%, four exams 35%, Paper & Discussion 15%, Final 20% Suggested Problems: The syllabus lists some relevant problems associated with each lecture in both the textbook and the companion. Completion of these ungraded problem sets will enhance your understanding of the material and help you to identify concepts that you might need additional help mastering.

8 You are encouraged to work these problems independently or in small study groups. Any questions you have about these assigned problems should be addressed during Dr. Perlstein or Dr. Carolan s office hours. You can expect 10% of the points on each exam to come directly from these suggested problems. Exams: There will be four exams during the semester and a cumulative final exam. Your midterm exam component of your grade will be determined from your best three exam grades, dropping your lowest midterm exam grade. Exams will be on Monday evenings from 5-7. Students who are unable to attend an examination due to a serious illness, family emergency or religious observance should contact Dr.

9 Perlstein as soon as possible to make alternative arrangements BEFORE missing the exam. If you miss an exam, this will count as your low exam grade and be dropped. If you need any special accomodations for exams (extra time, specific room requirements, etc), you need to notify Prof. Perlstein about your needs ASAP and no later than Monday Sept 19th. We need time to plan for these requests and they cannot be accommodated last minute. Class participation: Throughout the semester, I will provide numerous opportunities to participate in lecture by working problems, writing questions for exam reviews, leading a portion of the discussion, etc. Your participation in these activities will be monitored and can result in a maximum of 15 pts to be added to your lowest exam grade (10% of points on one exam).

10 Students who attend lecture, volunteer to come up to the board to work problems for the class and actively participate in lecture, review sessions and office hours can expect to receive all 15 points. Laboratory: The laboratory course will also be accessed via its own Blackboard site separate from the lecture site as both A1 and A2 lectures are mixed in the laboratory Section . Completion of the lab will account for 40% of your final grade in the course. Additionally 10% of each midterm exam will contain questions about the laboratory material. biochemistry -A2 Website: This Section (A2)of the course will be using Blackboard. On this site you will find basic information about the course including the syllabus and introduction distributed on the first day of class which summarizes course policies and proceedures.