Department of Chemistry
Description of Course
Spring 2016
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:
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:
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 071-674339-6, 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 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.
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:
(http://www1.ccny.cuny.edu/upload/academicintegrity.pdf). 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.
ADVANCED BIOCHEMISTRY
Lecture Schedule
Chemistry 48005/A8005
Spring 2016
Room MR1026
Mon, Wed 9:30-10:45
Professor Steinberg
============================================================================
Date
Topic
Text
Feb
1
3
Mon
Wed
8
10
Mon
Wed
15
Mon
17
22
24
29
Wed
Mon
Wed
Mon
2
Wed
7
9
14
16
21
Mon
Wed
Mon
Wed
Mon
23
Wed
28
30
Apr 4
6
Mon
Wed
Mon
Wed
11
Mon
13
18
20
Wed
Mon
Wed
Mar
Photosynthesis light reaction
Photosynthetic carbohydrate
biosynthesis
other carbohydrates, polyaccharides
Immune system
Lehninger pp. 742-758
Lehninger pp. 773-786
Lehninger pp. 791-796
Lehninger (4th ed) pp. 174-182
- no class Neurobiochemistry
Neurobiochemistry
Hormonal regulation of metabolism
Hormonal regulation of metabolism
handout
handout
Lehninger
Lehninger
pp. 923-940
pp. 923-940
Exam I
Biosignaling
Biosignaling
Regulation of gene expression
Regulation of gene expression
Bacteriophage Lambda – lytic cycle
Lehninger
Lehninger
Lehninger
Lehninger
handout
pp.
pp.
pp.
pp.
419-449
419-449
1136-1144
1136-1144
- no class Bacteriophage Lambda – lysogenic cycle
Recombinant DNA technology
Recombinant DNA technology
Recombinant DNA technology
handout
handout
handout
handout
Exam II
Oncogenes/retroviruses
Oncogenes/cell cycle regulation
Oncogenes and cancer
handout
handout
handout
- Spring Recess: April 22-April 30 May
2
Mon
4
Wed
9
11
16
Mon
Wed
Mon
Mitochondrial dysfunction
DNA damage/genomic deletions
Mitochondrial dysfunction
gene expression, aging and cancer
Genetic disease
Genetic disease
Genetic disease
handout
handout
handout
handout
handout
18 Wed
Exam III
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.
Office hours: Mon 1-3 PM, Wed 2-4 PM. Office: MR629; Tel: (212) 650-8560; Fax: (212)
650-6092; email: [email protected].
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.