Department of Chemistry
Description of Course
Spring 2012
Course:
Chem. 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:
Co-requisites:
Chem. 45902; A grade of C or higher is required in the prerequisite course
Hours/Credits:
3 hours per week, 3 credits
Textbook:
Principles of Biochemistry, 5th ed., by Nelson, Michael M. Cox and Lehninger, Albert
ISBN 0-71-674339-6, yr. 2005
Course objectives:
The first half of the course covers advanced topics in biochemistry that build upon the basic principles of
biochemistry covered in Chemistry 45902 (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
photosynthesis.
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.
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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 and then following the links: Current
Students → Academic Services/Tutoring → Policy on Academic Integrity. 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 2009-2010.
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ADVANCED BIOCHEMISTRY
Lecture Schedule
Chemistry A8005
Spring 2012
Room MR1026
Mon, Wed 9:30-10:45
Professor Steinberg
============================================================================
Date
Topic
Text
Jan 30
Feb 1
Mon
Wed
6
8
Mon
Wed
13
15
20
21
Mon
Wed
Mon
Tues
22
Wed
27
29
Mar 5
7
12
14
Mon
Wed
Mon
Wed
Mon
Wed
19
Mon
21
26
28
Apr 2
4
Wed
Mon
Wed
Mon
Wed
16 Mon
18 Wed
23 Mon
25 Wed
May
30 Mon
2 Wed
7 Mon
9 Wed
Photosynthesis light reaction
Photosynthetic carbohydrate
biosynthesis
other carbohydrates, polyaccharides
Immune system
Complement system
-college closedThe blood clotting system
-college closedbiological products of amino acids
Lehninger pp. 742-758
Lehninger pp. 773-786
Lehninger pp. 786-788,791-796
Lehninger pp. 170-174,1014-1015
Handout
Handout
Lehninger pp. 873-882
Exam I
Biosignaling
Biosignaling
Biosignaling
Regulation of Glycogen metabolism
Hormonal regulation of metabolism
Hormonal regulation of metabolism
Lehninger
Lehninger
Lehninger
Lehninger
Lehninger
Lehninger
pp. 419-449
“
pp. 457-468
pp. 584-592, 604-608
pp. 923-940
pp. 923-940
Exam II
Neurobiochemistry
Neurobiochemistry
Phage lambda – lytic cycle
Phage lambda – lysogenic cycle
Recombinant DNA technology
-spring break April 6 - April 15
Recombinant DNA technology
Lehninger pp 449-455, Handout
Handout
Handout
Handout
Handout
Handout
Exam III
Regulation of gene expression
Mitochondrial dysfunction
in cancer
Oncogenes & retroviruses
Oncogenes, signaling pathways
and cell cycle regulation
Genetic disease
Genetic disease
Lehninger pp 1136-1144
Handout
Handout
Handout, Lehninger pp.469-479
Handout
Handout
14 Mon
Exam IV
Text: Lehninger Principles of Biochemistry: Nelson & Cox, 2008,
5th Ed. W.H. Freeman & Co., NY.
Office hours: Mon 1-3 PM, Wed 2-4 PM. Office: MR629; Tel: (212) 650-8560; Fax: (212)
650-6092; email: marste@sci.ccny.cuny.edu.
Grading: based on 4 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
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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 4 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.
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