Syllabus 48000/A8005

City College of New York

Department of Chemistry and Biochemistry



Course:          Chem. 48005/A8005

Course title:  Biochemistry II

Designation: Required course


Catalog Description:

A8005: Biochemistry II. Molecular basis of enzyme action, membranes (transport and signal transduction), protein structure, signal transduction, virology, bioinformatics, genomics, proteomics, molecular basis of replication, transcription of genetic information, immunology. Prereq: a one semester undergraduate biochemistry course.              


Prerequisites:                       Chem. 32002; A grade of C or higher is required in the prerequisite course



Hours/Credits:          3 hours per week, 3 credits


Textbook:      Although no textbook is required, some course material (which will be posted) will come from the text, Principles of Biochemistry, 5th ed., by Nelson, Michael M. Cox and Lehninger, Albert  ISBN 0-71-674339-6, yr. 2005. Students may wish to obtain a copy of the book for reference.


Course objectives:


The first half of the course covers advanced topics in biochemistry that build upon the basic principles of biochemistry covered in Chemistry 32002 (Principles of Biochemistry) including photosynthesis, synthesis of complex carbohydrates, elements of the immune system, signaling pathways/hormone action that regulate metabolic reactions, biochemical principles of neuron function.


The second half of the course explores contemporary areas in modern biochemistry with a focus on gene function and expression in eukaryotic and prokaryotic systems (exemplified by bacteriophage lambda).  Students will also learn some of the basic concepts and practical applications of biotechnology including gene cloning and expression in engineered vector systems, artificial chromosome construction, site directed mutagenesis, approaches to gene therapy.  Southern blotting/RFLP analysis using pulsed field gel electrophoresis and chromosome walking will be discussed in the context of markers of genetic disease.  This part of the course will also examine the biochemical bases of various disease states resulting from alterations in metabolic processes with a focus on mitochondrial-based diseases.  Several lectures will be devoted to retroviral oncogenes and tumor suppressors and their relationship to signaling pathways involved in regulation of cell growth and cancer 


After completing this course, students should:                           


1.  know the basic steps and important intermediates in the light and dark reactions of


2.  know the basic steps and important intermediates in the synthesis of complex carbohydrates.

3.  be able to distinguish between the humoral and cellular immune systems and know the basic components

     and the function of the components of each system. 

4.  be able to outline the steps in the biotechnological approaches to genetic disease including the genetic basis

     of the cancers discussed in class.

5.  be able to detail the main steps and intermediates in the pathways by which hormones regulate metabolism

     via glycolysis and the Kreb’s cycle and carbohydrate transport.

6.  be able to describe the functions of the elements of lambda bacteriophage in the lytic cycle or lysogeny

7.  be able to describe the basic steps in the techniques of biotechnology described in class.  Students should be

     able to provide examples of how these techniques are applied to modern biomedicine, gene therapy and

     genetic engineering

8.  know the structure and function of the basic ion channel types involved in neural transmission and the

     experimental techniques used to analyze how they function in motor control, memory and sensory input.

9.  to be able to outline the steps and critical enzymes involved in the generation of reactive oxygen species

     (ROS) in mitochondria and how mitochondrial-derived ROS activate particular signaling pathways.

10. be able to describe the processes by which retroviral oncogenes are transduced and subsequently activated

      in the host.  Students should know how the human homologs of the oncogenes covered in class function in

      cell cycle control and cancer.


Attendance policy – The lectures distill the critical elements and concepts from the source materials (textbook and handouts) that will be presented in the exams.  Also, there may be some important information presented in lecture that is not covered in the source materials.  For these reasons it is necessary to attend lectures in order to gain the most from the course and to maximize performance on exams.      


Statement on Academic Integrity - The CCNY policy on academic integrity will be followed in this course. The policy statement can be found by logging onto the CCNY website: ( All students must read the details regarding plagiarism and cheating in order to be familiar with the rules of the college.  Cases in which there are violations of academic integrity will be prosecuted according to these rules.  The Policy of Academic Integrity can also be found in the Undergraduate Bulletin.


Grading - based on 3 lecture exams. Students will be given the option to take a cumulative final exam.  The final exam can be used to replace one regular exam grade or as a makeup for ONE missed exam


Policy on INC grades - Makeup exams for INC grades in Chemistry courses will be completed no later than two weeks after the end of classes. INC may be assigned to students who fail to take any one the 3 lecture exams and do not make up the deficiency by taking the comprehensive final examination but otherwise have a passing grade in the course.  A passing grade is computed by averaging all examinations/assignments which include a zero grade for missed examinations/assignments [or In calculating the passing grade, missed class examination/assignment is given a value of zero and included in the computation of the grade].  A student must have a very good reason (such as a conflict with another scheduled examination, death of spouse, injury sustained in a catastrophic incident and {proof is also required}) for missing the registrar-scheduled final exam and be given an INC grade.  If the reason is not forthcoming, then a letter grade of F should be assigned.  An Incomplete Grade Agreement form must be signed by the Instructor before the student is allowed to take the makeup exam.  Payment of a fee at the Bursar's office is required in order to take the makeup examination.  The Registrar may waive the fee if the reason for granting an INC grade is conflict with another scheduled examination.  Grades for a makeup exam will be submitted within one week of the administration of the exam.