Chemistry and Biochemistry

College of Science and Engineering
Dean: Sheldon Axler

Department of Chemistry and Biochemistry
TH 806
415-338-1288
Chair: James B. Orenberg

Undergraduate Advising Coordinator: Peter T. Palmer
Graduate Coordinator: Jim R. Keeffe

Faculty

Professors—Aragón, Buttlaire, Erden, Gronert, Keeffe, Luckey, Macher, Orenberg, Simonis, Trautman, Zeile

Associate Professors—Berkman, DeWitt, Gerber, Manning, Palmer, Wu

Assistant Professors—Baird, Esquerra, Gassner, Ichimura, Komada

Research Assistant Professor—Yen

Adjunct Professors—Banin, Holmes, Roitman, Ross, Runquist

Programs

B.A. in Chemistry
B.S. in Biochemistry
B.S. in Chemistry
Minor in Chemistry
M.S. in Chemistry
M.S. in Chemistry: Concentration in Biochemistry


Program Scope and Career Outlook

The Department of Chemistry and Biochemistry offers an outstanding educational environment for undergraduate and graduate students. The department's degree programs are designed to prepare students for graduate study, health professions programs, and professional careers such as teaching and laboratory positions with biotechnology and pharmaceutical companies. An important objective is to educate versatile chemists and biochemists who understand the theoretical basis and practical applications of their discipline and are well prepared to succeed in graduate school and professional positions.

The Bachelor of Arts in Chemistry is particularly well-suited for those students whose career goals involve the integration of chemistry with other fields. This program provides excellent preparation for pre-medical students and high school science teachers, as well as those who will pursue further studies in the pharmaceutical sciences, veterinary medicine, and dentistry. Additionally, the B.A. in Chemistry may be combined with a minor in engineering, business, social sciences, the humanities, or the arts to provide the student with a unique synthesis of experience applicable to careers in patent law, management, sales, marketing, chemical engineering, regulatory affairs, technical writing, scientific journalism, library science, environmental protection, and art restoration. Students who are considering teaching chemistry should consult with a credential adviser in the Department of Chemistry and Biochemistry before planning the major. Specific courses in competency assessment are required for the credential program.

The Bachelor of Science in Chemistry, which is approved by the American Chemical Society, prepares students to pursue a career in chemically-oriented industry or to begin graduate study in chemistry and other molecular sciences. The degree provides a solid foundation in mathematics and physics, breadth in traditional chemical subdisciplines (analytical, inorganic, organic, and physical chemistry), and depth in one or more areas of chemistry. This program provides excellent training in instrumental analysis and emphasizes quantitative and analytical aspects of the discipline.

The Bachelor of Science in Biochemistry is designed for those students who wish to be particularly well qualified in the rapidly expanding fields between biology and chemistry. The extensive laboratory training program provides exceptional preparation for careers in biotechnology and enjoys a favorable reputation among biotechnology companies in the Bay Area. This degree provides a strong foundation for a graduate degree in biochemistry, and it is an excellent degree choice for entry into medical or dental college.

The Master of Science in Chemistry, which is approved by the American Chemical Society, is designed as a balanced program in analytical, inorganic, organic, and physical chemistry, and biochemistry. The department also offers the Master of Science in Chemistry with a Concentration in Biochemistry for students who want to specialize in the biochemical aspects of chemistry. The American Chemical Society placement examinations, while not greatly influencing the graduate status of the student, will determine where individual weaknesses exist so that corrective emphasis may be applied. The department also offers a cooperative M.S./Ph.D. program with the University of California, Davis for defined minority students and women from all ethnic groups (contact the department chair for further information). Work leading to the master's degree should provide for the best possible balance between theoretical course work and research. A student completing the program should be prepared to pursue a career in the field of chemical research and development at the technical level, teaching, or have the necessary foundation to continue studies toward the doctorate.

The Committee on Professional Training of the American Chemical Society enthusiastically commended the department for the excellence of its undergraduate program. High-quality teaching, one-on-one advising, and opportunities for students to participate in research under the direct supervision of active faculty members who are recognized authorities in their field are significant features of the department. Chemistry and Biochemistry faculty members are actively involved in research, and many undergraduate students work on research projects during their senior year, working closely with their faculty research adviser. Examples of research projects currently under investigation by our faculty members and their research students include:

Analytical Chemistry: Evaluation of Martian soil analog materials. Development of new methods for direct monitoring of pollutants via mass spectrometry. Novel analytical techniques for separation and detection of redox-sensitive trace species.

Biochemistry: Enzyme reaction mechanisms. Synthesis of enzyme inhibitors, characterization of transition-state analogs, and measurement of enzyme-ligand interactions. Isolation and characterization of methyl transferase enzymes. Structure-function relationships in membrane transport proteins and mechanisms of membrane biogenesis, with emphasis on outer membrane proteins of Escherichia coli. Biosynthesis and regulation of the expression of complex carbohydrate cell surface antigens. Characterization of enzymes involved in the nitric oxide cellular signaling pathway.

Metalloprotein Biochemistry: Structural and functional studies of metalloproteins involved in redox reactions, oxygen activation, oxygen transport, and signal transduction.

Environmental Chemistry: Determination of structures and speciation of metals and trace elements adsorbed on environmental surfaces. Modeling speciation, precipitation, and adsorption reactions of trace elements in environmental systems. Mechanisms of heavy metal tolerance/accumulation in plants. Effects of heavy metals on gene expression in plants. Detection of trace levels of volatile organic compounds and heavy metals in urban air, water, and soil samples.

Inorganic/Bioinorganic Chemistry: Transition metal organometallic chemistry. Photochemistry and photophysics of organometallic compounds. Performance of thin-film polymer electrolytes. Development and applications of multi-dimensional NMR methodologies for the structural analysis of platinum complexes and paramagnetic molecules. Bioinorganic chemistry of paramagnetic Fe(III) porphyrins, chromium(III) complexes, and cobalt(II,III) complexes to model structure-function relationships of heme proteins, the glucose tolerance factor, and vitamin B12.

Organic/Bioorganic Chemistry: Reaction mechanisms and synthetic applications of organic peroxides. Small rings. Heterocyclic chemistry. Chemistry of singlet oxygen. Mechanisms of fundamental organic reactions: computational approaches to modeling the transition states of nucleophilic substitutions and elimination reactions. Conformations of small peptides. Structure-reactivity relationships in acid- and base-catalyzed organic reactions, including heterolytic cleavage of C-H and C-C bonds. Design and synthesis of substrate analogs to elucidate the catalytic mechanisms of enzymes. Design and synthesis of novel enzyme inhibitors for use in sensitizing tumor cells to common chemotherapeutic strategies.

Physical/Biophysical Chemistry: Characterization of structural features and dynamic behavior of natural and synthetic macromolecules in solution using physical methods and theoretical models. High precision computational modeling and electro-optic characterization of hydrodynamic transport properties of small, medium, and large molecules. Electrical and mechanical properties of nucleic acids, proteins, molecular motors, and protein-nucleic acid complexes. Biophysical applications of electron spin resonance spin labels. Diffusion and solubility of molecular oxygen in biomembranes and in other tissue. Biophysical spectroscopic methods, including nanosecond time-resolved polarized absorption spectroscopy, to characterize biological function and examine the molecular basis of disease.

Students obtain extensive hands-on training in the use of state-of-the-art research instruments and obtain valuable training in modern laboratory techniques and computational methods. These include, for example, nuclear magnetic resonance spectrometers, a state-of-the-art mass spectrometry facility, and numerous modern instruments. Computers are used extensively in chemistry classes, and the department's modern facilities include the Computational Chemistry and Visualization (CCV) laboratory. The CCV laboratory houses state-of-the-art computer workstations with 3D graphics capabilities and enables instructors to teach molecular modeling applications and computational chemistry in inorganic chemistry, physical chemistry, organic chemistry, and biochemistry lecture and laboratory courses.

UNDERGRADUATE PROGRAMS IN CHEMISTRY AND BIOCHEMISTRY

High school preparation for the chemistry and biochemistry degree programs should include two years of algebra, one year of geometry, one-half year of trigonometry, one year of chemistry, and one year of physics.

Mandatory Advising. To avoid unnecessary delays in the completion of the program, students are required to meet with their assigned major adviser to discuss their progress and to plan their course of study. Gator Reg Hold applies to spring class registration for all students admitted to the major for the first time in fall, and to fall registration for all chemistry and biochemistry majors. It is also suggested that students consult with a GE adviser before selecting courses to meet General Education requirements.

All courses used in the major program must be completed with letter grades.

BACHELOR OF ARTS IN CHEMISTRY

See the Undergraduate Programs in Chemistry and Biochemistry section above for general information for all chemistry students. Courses that are required for the major must be completed with a minimum grade point average of 2.0 and a grade of C- or better, with only one exception.

Lower Division Requirements Units
CHEM 115 General Chemistry I: Essential Concepts of Chemistry 5
CHEM 215/216 General Chemistry II: Quantitative Applications of Chemistry Concepts/ Laboratory (3/2) 5
MATH 226 Calculus I 4
MATH 227 Calculus II 4
One of the following sets: 8-12
PHYS 111/112 General Physics I/Laboratory (3/1) and  
  PHYS 121/122   General Physics II/Laboratory (3/1) or
PHYS 220/222 General Physics with Calculus I/Laboratory (3/1) and
  PHYS 230/232   General Physics with Calculus II/Laboratory (3/1) and
  PHYS 240/242   General Physics with Calculus III/Laboratory (3/1)
Total lower division requirements 26-30
Upper Division Requirements
CHEM 300 General Physical Chemistry I 1 3
CHEM 301 General Physical Chemistry II 1 3
CHEM 320 Quantitative Chemical Analysis 4
CHEM 333 Organic Chemistry I 3
CHEM 334 Organic Chemistry I Laboratory 2
CHEM 335 Organic Chemistry II 3
CHEM 336 Organic Chemistry II Laboratory 2 3
CHEM 422 Instrumental Analysis 4
CHEM 340 Biochemistry I or 3
  CHEM 349   General Biochemistry
Units of upper division electives chosen from the following list. Consult with an adviser regarding selection of elective courses and check course co- and prerequisites before enrolling. 2-3
  CHEM 341 Biochemistry II  
  CHEM 343 Biochemistry I Laboratory  
  CHEM 348 Clinical Biochemistry Laboratory (2)  
  CHEM 370 Computer Applications in Chemistry  
  CHEM 380 The Chemistry Behind Environmental Pollution  
  CHEM 425 Inorganic Chemistry  
  CHEM 433 Advanced Organic Chemistry  
  CHEM 470 Research  
  CHEM 699 Special Study in Chemistry (1-3)  
Total upper division requirements 30-31
Total for major 56-61

BACHELOR OF SCIENCE IN CHEMISTRY

See the Undergraduate Programs in Chemistry and Biochemistry section above for general information for all chemistry students. Students are required to complete 120 units to meet the requirements for the B.S. in Chemistry. Courses that are required for the major must be completed with a minimum grade point average of 2.0 and a grade of C- or better, with only one exception.

Lower Division Requirements Units
CHEM 115 General Chemistry I: Essential Concepts of Chemistry 5
CHEM 215/216 General Chemistry II: Quantitative Applications of Chemistry Concepts/Laboratory (3/2) 5
MATH 226 Calculus I 4
MATH 227 Calculus II 4
PHYS 220/222 General Physics with Calculus I/Laboratory (3/1) 4
PHYS 230/232 General Physics with Calculus II/Laboratory (3/1) 4
One of the following sets: 3-7
  CHEM 251 Mathematics and Physics for Chemistry or  
  MATH 228 Calculus III (4) and
  PHYS 240 General Physics with Calculus III
Total lower division requirements 29-33
Upper Division Requirements
CHEM 320 Quantitative Chemical Analysis 4
CHEM 333 Organic Chemistry I 3
CHEM 334 Organic Chemistry I Laboratory 2
CHEM 335 Organic Chemistry II 3
CHEM 336 Organic Chemistry II Laboratory 2 3
CHEM 340 Biochemistry I 3
CHEM 351 Physical Chemistry I 3
CHEM 353 Physical Chemistry II 3
CHEM 422 Instrumental Analysis 4
CHEM 425 Inorganic Chemistry 3
CHEM 426 Inorganic Chemistry Laboratory 2
CHEM 451 Physical Chemistry Laboratory I 2
Elective units which may include any of the courses listed below. These courses are organized via emphases which students can use to customize their degree program. Consult an adviser regarding selection of upper division elective courses and check course co- and prerequisites before enrolling. Graduate-level courses in chemistry or appropriate courses in biology, physics, geosciences, and computer science may be substituted upon prior approval of adviser. 6
Research and Special Topics Courses
CHEM 470 Research (3-6)  
CHEM 699 Special Study in Chemistry (1-3)
CHEM 640 Advanced Topics in Biochemistry (1-3)
CHEM 641 Advanced Topics in Chemistry (1-3)
CHEM 800 Special Topics in Chemistry (1-3)
Emphasis in Environmental Chemistry
CHEM 420 Environmental Analysis  
CHEM 821 Mass Spectometry
Emphasis in Materials Chemistry
CHEM 825 Theoretical Inorganic Chemistry  
PHYS 450 Introduction to Solid State Physics
Emphasis in Biochemistry
CHEM 341 Biochemistry II  
CHEM 343 Biochemistry I Laboratory
Emphasis in Bioorganic Chemistry
CHEM 640 Introduction to Medicinal Chemistry  
CHEM 433 Advanced Organic Chemistry
CHEM 832 Organic Synthesis
CHEM 842 Bioorganic and Medicinal Chemistry
Emphasis in Computational Chemistry
CHEM 370 Computer Applications in Chemistry and Biochemistry  
MATH 309 Computation in Mathematics
CSC 210 Introduction to Computer Programming
CHEM 850 Valency and Spectroscopy
BIOL 835 Computer Simulations in Biology (4)
Emphasis in Chemical Physics
CHEM 850 Valency and Spectroscopy  
CHEM 852 Statistical Mechanics
CHEM 820 NMR Applications and Techniques
MATH 374 Advanced Calculus
MATH 376 Ordinary Differential Equations I
PHYS 320 Modern Physics I
PHYS 370 Thermodynamics and Statistical Mechanics
Total upper division requirements 41
Total for major 70-74

BACHELOR OF SCIENCE IN BIOCHEMISTRY

See the Undergraduate Programs in Chemistry and Biochemistry section above for general information for all chemistry students. Students are required to complete 120 units to meet the requirements for the B.S. in Biochemistry. Courses that are required for the major must be completed with a minimum grade point average of 2.0 and a grade of C- or better.

Lower Division Requirements Units
CHEM 115 General Chemistry I: Essential Concepts of Chemistry 5
CHEM 215/216 General Chemistry II: Quantitative Applications of Chemistry Concepts/ Laboratory (3/2) 5
MATH 226 Calculus I 4
MATH 227 Calculus II 4
BIOL 230 Introductory Biology I 5
One of the following sets: 8
PHYS 111/112 General Physics I (3/1) and  
  PHYS 121/122   General Physics II (3/1) or
PHYS 220/222 General Physics with Calculus I/Laboratory (3/1) and
  PHYS 240/242   General Physics with Calculus III/Laboratory (3/1)
Total lower division requirements 31
Upper Division Requirements
CHEM 300 General Physical Chemistry I 1 3
CHEM 301 General Physical Chemistry II 1 3
CHEM 320 Quantitative Chemical Analysis 4
CHEM 333 Organic Chemistry I 3
CHEM 334 Organic Chemistry I Laboratory 2
CHEM 335 Organic Chemistry II 3
CHEM 340 Biochemistry I 3
CHEM 341 Biochemistry II 3
CHEM 343 Biochemistry I Laboratory 3
Upper division chemistry and biology elective units which may include any of the courses listed below. At least 4 units must have a CHEM prefix and at least 4 units must be laboratory units (lab unit designations are in parentheses). Consult an adviser regarding selection of upper division elective courses and check course co- and prerequisites before enrolling. Graduate level courses in chemistry or appropriate courses in biology, physics, geosciences, and computer science may be substituted upon prior approval of adviser. 14
Upper Division Electives in Chemistry
CHEM 336 Organic Chemistry II Laboratory (lab, 2)  
CHEM 338 Organic Chemistry II: Special Projects Laboratory (lab, 2)
CHEM 370 Computer Applications in Chemistry and Biochemistry
CHEM 420 Environmental Analysis (lab, 1)
CHEM 422 Instrumental Analysis (4; lab, 2)
CHEM 425 Inorganic Chemistry
CHEM 426 Inorganic Chemistry Laboratory (2; lab, 1)
CHEM 433 Advanced Organic Chemistry
CHEM 443 Biophysical Chemistry Laboratory (4; lab, 2)
CHEM 451 Physical Chemistry Laboratory (2; lab, 1)
CHEM 470 Research (lab, 3) [must be biochemistry related topic]
CHEM 640 Advanced Topics in Biochemistry (1-3) [all topics]
Upper Division Electives in Biology
BIOL 350 Cell Biology  
BIOL 351 Experiments in Cell Biology and Genetics (4; lab, 2)
BIOL 355 Genetics
BIOL 357 Molecular Genetics
BIOL 358 Experiments in Molecular Biology (4; lab, 2)
BIOL 361 Human Genetics
BIOL 382 Developmental Biology
BIOL 401 General Microbiology
BIOL 402 General Microbiology Laboratory (2; lab 2)
BIOL 435 Immunology
BIOL 436 Immunology Laboratory (2; lab, 2)
BIOL 524 Plant Molecular Biology
BIOL 525 Plant Physiology
BIOL 526 Plant Physiology Laboratory (2; lab, 2)
BIOL 612 Human Physiology
BIOL 613 Human Physiology Laboratory (2; lab, 2)
BIOL 640 Cellular Neurosciences
Total upper division requirements 41
Total for major 72

MINOR PROGRAM IN CHEMISTRY

Twenty-four units of chemistry are required, including CHEM 115 and CHEM 215/216, or their equivalents. Twelve of these units, including four upper-division units, must be taken at San Francisco State University. Twelve of the twenty-four units must be upper division. Eight of the twenty-four units must correspond to upper-division courses at San Francisco State University. Clinical Science majors who elect CHEM 334 usually meet all these requirements; they should consult a chemistry adviser regarding the Chemistry Minor.

All courses in the minor must be completed with letter grades (CR/NC is not acceptable). Only one course from each of the following pairs of courses can be counted towards the minor: either CHEM 130 or CHEM 333, not both; either CHEM 349 or CHEM 340, not both. The following courses, or their equivalents, cannot be counted toward the minor: CHEM 100, 101, 102, 105, 106, 361, 599, and 694.

GRADUATE PROGRAMS IN CHEMISTRY AND BIOCHEMISTRY

Admission to Program

Students must meet these criteria:

Written English Proficiency Requirement

Level One: newly admitted students are required to take the Graduate Essay Test (GET) (administered by the Testing Office) preferably before the first enrollment takes place, but no later than the end of the first semester of enrollment, to determine if writing deficiencies exist. If remedial work is necessary, the student shall be expected to complete prescribed course(s) in English. Level Two: later in the process of completing the master's degree, the student is expected to demonstrate an advanced level of proficiency in written and spoken English by successfully completing both CHEM 880 and a thesis.

Advancement to Candidacy

In order to be advanced to candidacy, students must:

NOTE: After initiating a research project, a graduate student must enroll each semester in CHEM 897 while actively engaged in research for the M.S. degree. A maximum of nine units of CHEM 897 may be included on the Graduate Approved Program.

MASTER OF SCIENCE IN CHEMISTRY

Program Units
CHEM 834 Organic Spectroscopic Methods 3
One of the following courses selected on advisement of adviser: 3
  CHEM 850 Valency and Spectroscopy  
  CHEM 851 Biochemical Spectroscopy
CHEM 880 Seminar 3
Other Requirements
CHEM 897 Research 6-9
CHEM 898 Master's Thesis 3
Related Study
Upper division/graduate courses in chemistry, physics, mathematics, or biology on advisement of graduate major adviser. 9-12
Minimum total 30
and Oral Defense of Thesis

MASTER OF SCIENCE IN CHEMISTRY: CONCENTRATION IN BIOCHEMISTRY

Program Units
CHEM 834 Organic Spectroscopic Methods 3
One of the following courses selected on advisement of adviser: 3
  CHEM 850 Valency and Spectroscopy  
  CHEM 851 Biochemical Spectroscopy
CHEM 880 Seminar 3
Other Requirements
Courses in biochemistry selected from the following: 6
  CHEM 841 Enzymology  
  CHEM 843 Membrane Biochemistry
  CHEM 844 Bioinorganic Chemistry
  CHEM 845 Glycoconjugate Biochemistry
  CHEM 846 Biology and Chemistry of Signaling Pathways
Upper division or graduate courses in chemistry, physics, mathematics, or biology on advisement of graduate major adviser. (May include courses listed above which have not been taken to satisfy either the core requirement or the 6-unit biochemistry requirement.) 3-6
CHEM 897 Research 6-9
CHEM 898 Master's Thesis 3
Minimum total 30
  and Oral Defense of Thesis


Footnotes

  1. CHEM 351 and 353 may be substituted for CHEM 300 and 301.
  2. CHEM 338 may be substituted for CHEM 336.


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