Biochemistry II
FCH 532
Spring 2012
Instructor: Dr. Christopher T. Nomura
Office: 318 Jahn
email: ctnomura@esf.edu
SYLLABUS
REQUIRED TEXTBOOK: “Biochemistry” 3rd ed., Voet and Voet, 2004.
Room and Time: FCH532 will meet from 10:35 AM -11:30 AM MWF in room 111 Marshall.
Website: http://www.esf.edu/chemistry/nomura/fch532/
General course outline: The first half of the course will be examining nucleic acids, DNA and RNA structure
and molecular biology. The second half of the course will be on amino acid, pyrimidine and purine metabolism
followed by photosynthesis.
Grading and Exams: NO MAKEUPS and NO LATE ASSIGNMENTS!
The course will consist of at least three 100-point midterm exams and a 150-point final. All exams are
cumulative and consist of multiple-choice, short answer, matching, and other types of questions. Your final
exam time will be announced later on in the course. You will also have an ACS exam on the last day of class
covering all topics in biochemistry. In addition, you will have several in-class quizzes during the course of the
semester. Grading will be on a curve average. Graduate students scores do not affect the curve but rather their
grade is simply determined by where they fall on the undergraduate average.
Office Hours: Office hours will be on Wednesday, immediately after class 11:35 AM – 12:30 PM or by
appointment.
Schedule: A tentative schedule is included with this syllabus. It is meant to guide you in your readings. We
will have some guest lectures throughout the semester to cover for days that I am out of town. Material covered
in these lectures is based on my lecture notes and will be included in the exams.
TENTATIVE SCHEDULE;
Jan 17-Jan 27
1: Introduction to genetics, 2: bacterial genetics, intro to
Ch 1-4, 5
nucleic acids, 3: DNA, 4, 5: Molecular biology
Jan 27- Feb 8
6: Molecular biology , 7: Molecular biology, PCR, gene
Ch 6, 7
expression, genome sequencing, 8: Genomes and protein
evolution, 9: Needleman-Wunsch algorithm, DNA chips,
10: DNA structure
Feb 10
EXAM 1
Feb 13 – Feb 17
11, 12, 13: DNA structure, DNA replication,
Ch 29, 30
Topoisomerases
Feb 20 – Feb 24
14: DNA replication, 15:DNA repair, 16: recombination
repair
Feb 27 – Mar 2
17: DNA repair, 18, 19 : RNA transcription,
Ch 31
Mar 5 – Mar 7
20: processing, splicing, introns , 21: Translation
Ch 31, 32
Mar 9
EXAM 2
Mar 12 – Mar 16
Spring Break
Mar 19 – Mar 26
22: Translation, 23: Nitrogen cycle, amino acid metabolism, Ch 26
24: urea cycle
Mar 26 – Apr 2
25-27: amino acid metabolism
Apr 4 – Apr 6
28, 29: amino acid metabolism
April 9
Apr 11-18
April 20-27
April 30
To be determined
EXAM 3
Purine and pyrimidine metabolism
Photosynthesis
ACS EXAM
FINAL EXAM
Ch 28
Ch 24
Biochemistry II
FCH 532
Spring 2012
Instructor: Dr. Christopher T. Nomura
Office: 318 Jahn
email: ctnomura@esf.edu
What I expect you to have learned in FCH 530:
1.
Core Pathways
 Glycolysis
 Gluconeogensis and glycogen biosynthesis
 Pentose phosphate pathway
 TCA cycle
 Fatty acid biosynthesis and breakdown
By learning I mean all structures, names of all reactants (not just abbreviations), and the names
of the enzymes catalyzing the different steps. You should also have a basic understanding of
how things are regulated.
 Feed back inhibition
 Allosteric control
 Hormonal control
2.
Basic Protein structure including;
 Name and structure of the 20 protein amino acids
 3 and 1 letter abbreviations
 Chemistry of the peptide bond
 Basic physical chemistry controlling primary, secondary, tertiary and Quaternary structure
3.
Mechanistic biochemistry including
 Acid-base chemistry and how it applies to enzyme mechanisms
 Michalis-Menten Enzyme kinetics and its permeations
 Coenzyme structure and function
 Thiamine Pyrophosphate
 Niacin
 Riboflavin
 Biotin
 Coenzyme A
 Lipoic acid
4.
Basic organic chemistry as it applies to biochemistry
 Aldol condensation
 Enol-keto tautamerism
 Enolate attack on a activated ketone
 Others ?
Start to understand the “why” of biochemistry
Biochemistry II
FCH 532
Spring 2012
Instructor: Dr. Christopher T. Nomura
Office: 318 Jahn
email: ctnomura@esf.edu