BIOC 35400 - Biochemistry II: The Central Dogma - Molecular Biology of the Gene

Spring 2013

Lecture: MWF 10-10:50 AM, CNS 1C

Discussion and ‘dry lab’: F 12-12:50 PM Discussion and ‘dry lab’ in CNS 115

Maki Inada
CNS 156
Office Hours:
  • Tuesday: 2-3 PM
  • Thursday: 2-3 PM
  • or email anytime to make an appointment


Molecular Biology of the Gene (6th edition) by J. D. Watson et al.

Topic Schedule    

Course Description:

Biochemistry is the study of the molecular basis for life processes.  This course is an upper level undergraduate course for students primarily interested in, but not limited to, health professions or research careers.  In Biochemistry I, we cover structures of major biomolecules (proteins, sugars, fats, nucleic acids), enzymology, and work that enzymes do in living systems, otherwise known as metabolism.  In Biochemistry II, we will focus on fundamental processes of genetic flow of information from DNA to RNA to protein that govern gene expression in all living organisms.  We will examine the details (steps, machinery and regulatory mechanisms) of the Central Dogma of Molecular Biology – including DNA replication, DNA repair, RNA transcription, RNA processing and protein translation.  Modern molecular biological techniques used to study these areas will be discussed via primary literature.  We will have several guest speakers to expose us to their ongoing research.  Students will develop an understanding of how fundamental biochemical pathways relate to medicine and human disease through a group project presentation and a review paper. 

Course Goals:

 By the end of the course, you should be able to:

  1. Describe in detail the mechanisms of and macromolecules involved in genome maintenance, gene expression, and the regulation of gene expression.
  2. Describe several modern biochemistry and molecular biology techniques used in scientific research.
  3. Interpret data and solve biochemistry and molecular biology problems based on data from primary research articles.
  4. Understand and ask questions about current ongoing research. 
  5. Demonstrate self-directed learning in biochemistry by reading, understanding and presenting peer-reviewed articles from the primary literature.
  6. Effectively communicate current issues in biochemistry and molecular biology that relate to human health and disease in both written and oral forms.
  7. Recognize ways in which biochemistry and molecular biology influence daily life at the level of the organism.


The following are designed to test and ensure consistent progress on all of the stated learning goals:

  1. Discussion and Participation (10%) As this is an upper level course, you are expected to come prepared to class having read the reading and ready to participate and discuss.  In preparation, before each class, feel free to email me ( with any questions you have and I will address as many as I can.  Friday Discussion is also reserved for addressing any questions that may come up. 
  2. Assignments and Problem Sets (25%).  Daily assignments and problem sets will be assigned to help in your learning.  You are welcome and encouraged to work in groups on these. 
  3. Exams (40%) both in class and take home exams.  This will be your own work. 
  4. Final oral presentation and review paper (25%).  Instead of an in-class final, you will prepare a group oral presentation and write an individual review paper on a current area of your choosing in molecular biology.  Start thinking of your topic area NOW.  Further details will be provided soon.


Lectures and Discussions:  It is very important to be present at every lecture and discussion section, or you will miss information and key material.  Although I will make powerpoint presentations available on Sakai, not all material covered in class is always included.  The undergraduate handbook states the general policy that students are expected to attend classes and that they are responsible for all material when absent.  . 


Exams:  If for a valid reason you cannot attend a scheduled exam, you must contact me a week in advance.  If you are sick or it is an emergency, contact me by email or leave a message on my voicemail BEFORE the exam begins and provide written documentation with your excuse as soon as possible.  Failure to provide a valid reason for the absence can result in as little as a full letter grade off, or as much as a zero grade.  Please note that traveling early for a vacation is NOT a valid excuse for missing an exam.   

Course Evaluations:

Student input is highly valued and is important to maintain high quality instruction.  Course evaluations are requiredYou may get a ZERO for a homework assignment if not completed by the due date.  The evaluation will be submitted to the department Administrative Assistant online. .


Academic Honesty:

All work that you submit must be your own.  For many assignments you are encouraged to discuss and work in groups, but what you hand in is expected to be your own analyses and interpretation.  Please familiarize yourself with the definition of plagiarism.  All review papers submitted for this course will be reviewed by for detection of plagiarism.  You will have the opportunity to self monitor.  Academic dishonesty can lead to a zero grade on that assignment, a failing grade in the course, academic code probation, or suspension or expulsion from the College depending on the gravity of the violation and the decision of the judicial board. 


Students with Disabilities:

In compliance with Section 504 of the Rehabilitation Act of 1973 and the Americans with Disabilities Act, reasonable accommodation will be provided to students with documented disabilities on a case-by-case basis. Students must register with Student Disability Services with the Office of Academic Support Services (607-274-1005, TDD 607-274-7319, and provide appropriate documentation to Ithaca College before any academic adjustment will be provided. 

Biochemistry Topic Schedule:





Week of





Readings (Chapters in MBOG

Watson et al)



Jan. 21

Introduction – Central Dogma

1-2, 6


Jan. 28

Nucleic Acids, Chromatin structure



Feb. 4

DNA Replication



Feb. 11

DNA Mutation and Repair


Exam I

Feb. 18

DNA Recombination & Transposition


Take Home

Feb. 25




Mar. 4

RNA Splicing and Processing


Exam II/Take Home

Mar. 11

Spring Break!



Mar. 18




Mar. 25

Genetic Code



Apr. 1

Transcription regulation in prokaryotes



Apr. 8

Transcription regulation in eukaryotes


Take Home

Apr. 15

Regulatory RNAs


Exam III

Apr. 22

Regulation in Development



Apr. 29

Systems Biology


Exam IV

May 6



Take Home


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Page maintained and updated by Nancy Pierce.
Last updated 2/1/2013