Biochemistry II
FCH 532
Spring 2011
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 19-Jan 28
1: Introduction to genetics, 2: bacterial genetics, intro to
nucleic acids, 3: DNA, 4, 5: Molecular biology
Jan 28- Feb 9
6: Molecular biology , 7: Molecular biology, PCR, gene
expression, genome sequencing, 8: Genomes and protein
evolution, 9: Needleman-Wunsch algorithm, DNA chips,
10: DNA structure
Feb 11
EXAM 1
Feb 12 – Feb 16
11, 12, 13: DNA structure, DNA replication,
Topoisomerases
Feb 21 – Feb 25
14: DNA replication, 15:DNA repair, 16: recombination
repair
Feb 28 – Mar 4
17: DNA repair, 18, 19 : RNA transcription,
Mar 3 – Mar 9
20: processing, splicing, introns , 21: Translation
Mar 11
EXAM 2
Mar 14 – Mar 28
Spring Break
Mar 21 – Mar 25
22: Translation, 23: Nitrogen cycle, amino acid metabolism,
24: urea cycle
Mar 28 – Apr 1
25-27: amino acid metabolism
Ch 1-4, 5
Ch 6, 7
Ch 29, 30
Ch 31
Ch 31, 32
Ch 26
Apr 4 – Apr 6
28, 29: amino acid metabolism
April 8
Apr 11-18
Apr 20
April 22
Apr 25 – May 1
To be determined
EXAM 3
Purine and pyrimidine metabolism
ACS EXAM
No class, Easter Break
Photosynthesis
FINAL EXAM
Ch 28
Ch 24
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