Biochemistry/Genetics 431, Sections 202, 502

Spring Semester 2011

Room 108 Biochemistry, MWF 10:20-11:10AM

 

 

 

Instructor: Gary R. Kunkel, Associate Professor of Biochemistry

            office: 406A Biochemistry Building

            phone: 845-6257

            e-mail: g-kunkel@tamu.edu

            webpage URL: http://www.tamu.edu/classes/bich/kunkel/hp.html

 

Office hours: Mondays and Wednesdays 9-10AM.  Alternatively, arrange a time by contacting me via email.

 

Administrative contact: Ms. Tillie Rausch, 410 Biochemistry Building, trausch@tamu.edu

All exams and quizzes can be picked up from Tillie throughout the semester.

 

Class website: You will be able to access exam and quiz keys, a list of knowledge objectives, and any class handouts through a link on my webpage (listed above), and on the TAMU eLearning site.  In addition to the above information, you can use the eLearning site to view your exam/quiz scores as they are posted, and final grades in the course at the end of the semester.

 

Course coverage: BICH/GENE 431 is one course of a triumvirate of upper division biochemistry and molecular genetics courses (BICH440 + BICH441 + BICH/GENE431). This is a “stand-alone” molecular biology/genetics course designed for students who have already learned classical Mendelian genetics AND have completed a course in biochemistry that covers protein and nucleic acid structure, biochemical thermodynamics and enzymology. I expect that you know the material covered in Chapters 1-6 of our textbook, and recommend that you review those chapters on your own.

 

In BICH/GENE431 we will cover basic molecular biological techniques, the molecular basis of inheritance, gene structure and function, chromosomal organization, replication, repair, recombination, and transcription of DNA, translation and processing of RNA, regulation of gene expression, structure and functions of regulatory RNAs, gene expression in development, and systems biology.  This is A LOT to cover, and we will move quickly.  In outline, we will cover the entire textbook. However, because of time constraints, some material from the book will not be discussed in lecture.  For exams, I recommend that you concentrate on the subjects presented in lecture and listed in the “knowledge objectives” file(s) posted on the websites.

 

Prerequisites: One genetics course (GENE302*, or GENE301, or GENE320) PLUS the first semester of a biochemistry course (BICH440*, or BICH410, or MEPS313, or BIOL351). The courses marked with asterisks are the desired prerequisite courses. I assume that you have good background knowledge in classical genetics, and biochemistry of nucleic acids and proteins.

 

Textbook: Molecular Biology of the Gene, 6th edition, by Watson, Baker, Bell, Gann, Levine, and Losick

 

Examinations and Quizzes:

            Three “hour” exams during regular class time

                        Exam #1                    Wednesday, February 16               100 pts

                        Exam #2                    Wednesday, March 23                    100 pts

                        Exam #3                    Wednesday, April 20                       100 pts

 

            Final exam:                           Tuesday, May 10, 8:00AM              150 pts

                        The final exam is required of all students

 

            Six quizzes at the end of lecture period (10 pts each, drop the lowest score, so

50 pts total)

Friday, Feb. 4; Friday, Feb. 25; Friday, March 11; Friday, April 8; Friday, April 15; Friday, April 29

 

You should bring a calculator to all the exams.  The memory bank on all calculators must be emptied before the exam begins.

                       

Make-up exams for any of the hour exams will be offered to students only in the cases of officially recognized absences (see University Student Rules, section 7), or by special request in advance of the exam. The make-up exam must be scheduled within one week of the regularly scheduled exam that was missed, and except under extenuating circumstances, must be completed by then too.  Therefore, you must notify me as soon as possible regarding such excused absences.  If you miss your rescheduled make-up exam, you will receive a zero for that exam.

 

If you want any exam answers re-graded, requests must be submitted to me in writing along with the entire exam.  The deadline for submitting exams for regrading is one week after the graded exam is ready to be picked up.

 

Q/A sessions before exams: I have scheduled a question/answer session the evening before each midterm exam. These are optional, and no new information will be presented.  Strictly speaking, these are not “review” sessions, as I will be there to answer your questions.  These sessions are scheduled as follows: All in 106A Biochemistry, 6:00-7:00PM, Tuesday, Feb. 15; Tuesday, March 22; Tuesday, April 19.

 

Grading:

Section 502: The course grade will be determined based only on the total points accumulated from the exams and quizzes (total possible points = 500).  There will be no opportunity to earn extra credit by doing extra work.

The exams are likely to be challenging, so grades will probably be adjusted to following scale after each exam: 90-100% = A; 80-89% = B; 70-79% = C; 60-69% = D; less than 60% = F.

 

I may adjust this scale, but never in an upward manner to negatively affect your grade.

 

Quiz scores will not be adjusted, and will be interpreted by the same standard grading scale.

 

Section 202 (Honors): Exams and problem sets will be the same as for students enrolled in Section 502.  Honors students will be required to attend five additional sessions approximately every third week to discuss published research papers.  To calculate course points, cumulative points from exams + quizzes will be multiplied by a factor of 0.9 (max. possible = 450).  10% of the course grade (50 pts) will be assigned from work performed during the extra sessions. A supplemental syllabus will describe the distribution of these points.

 

The American with Disabilities Act (ADA) is a federal anti-discrimination statute that provides comprehensive civil rights protection for persons with disabilities.  Among other things, this legislation requires all students with disabilities be guaranteed a learning environment that provides for reasonable accommodation of their disabilities.  If you believe you have a disability requiring an accommodation, please contact the Department of Student Life for Students with Disabilities in Room 126 of the Koldus Building, or call 845-1637.

 

Aggie Honor Code: “An Aggie does not lie, cheat, or steal or tolerate those who do.” Academic integrity is paramount in all activities during this course.  On each exam and quiz, you will be required to sign a statement acknowledging that you have observed this honor code.  See the Honor Council Rules and Procedures at http://www.tamu.edu/aggiehonor.

 

 

Schedule of Lectures / Exams / Quizzes:


 

Date

Topic

Reading

W 1/19

Introduction

 

F 1/21

Methods of Molecular Biology

Chapter 21

M 1/24

Methods of Molecular Biology

Chapter 21

W 1/26

Methods of Molecular Biology

Chapter 21

F 1/28

Model Organisms

Chapter 22

M 1/31

Genome Structure, Cell Cycle

Chapter 7

W 2/2

Chromatin Structure

Chapter 7

F 2/4

Chromatin Structure and Regulation, QUIZ 1

Chapter 7

M 2/7

DNA Replication

Chapter 8

W 2/9

DNA Replication

Chapter 8

F 2/11

DNA Replication

Chapter 8

M 2/14

DNA Repair

Chapter 9

W 2/16

EXAM 1 (covers Chaps. 21, 22, 7, 8)

 

F 2/18

DNA Repair

Chapter 9

M 2/21

Homologous Recombination

Chapter 10

W 2/23

Homologous Recombination / Site-specific Recombination

Chaps. 10, 11

F 2/25

Transposition of DNA, QUIZ 2

Chapter 11

M 2/28

Mechanisms of Transcription in Prokaryotes

Chapter 12

W 3/2

Mechanisms of Transcription in Eukaryotes

Chapter 12

F 3/4

Mechanisms of Transcription in Eukaryotes

Chapter 12

M 3/7

RNA Splicing

Chapter 13

W 3/9

RNA Splicing

Chapter 13

F 3/11

RNA Splicing, QUIZ 3

Chapter 13

M 3/14

Spring Break

 

W 3/16

Spring Break

 

F 3/18

Spring Break

 

M 3/21

Translation

Chapter 14

W 3/23

EXAM 2 (covers Chaps. 9, 10, 11, 12, 13)

 

F 3/25

Translation

Chapter 14

M 3/28

Translation

Chapter 14

W 3/30

Genetic Code

Chapter 15

F 4/1

Transcriptional Regulation in Prokaryotes

Chapter 16

M 4/4

Transcriptional Regulation in Prokaryotes

Chapter 16

W 4/6

Transcriptional Regulation in Prokaryotes

Chapter 16

F 4/8

Transcriptional Regulation in Eukaryotes, QUIZ 4

Chapter 17

M 4/11

Transcriptional Regulation in Eukaryotes

Chapter 17

W 4/13

Transcriptional Regulation in Eukaryotes

Chapter 17

F 4/15

Regulatory RNAs, QUIZ 5

Chapter 18

M 4/18

Regulatory RNAs

Chapter 18

W 4/20

EXAM 3 (covers Chaps. 14, 15, 16, 17)

 

F 4/22

Reading Day – No classes

 

M 4/25

Gene Regulation in Development

Chapter 19

W 4/27

Gene Regulation in Development

Chapter 19

F 4/29

Genome Analysis and Systems Biology, QUIZ 6

Chapter 20

M 5/2

Genome Analysis and Systems Biology

Chapter 20

Tu 5/3

Genome Analysis and Systems Biology

Chapter 20

Tu 5/10

FINAL EXAM: 8:00-10:00AM