Biochemistry

Subject abbreviation: BCH College of Natural and Agricultural Sciences

Xuan Liu, M.D., Ph.D., Chair Graduate Program (951) 827-4116 Undergraduate Program (951) 827-7294 biochemistry.ucr.edu

Professors Richard J. Debus, Ph.D. Li Fan, Ph.D. Russ Hille, Ph.D. Paul B. Larsen, Ph.D. Xuan Liu, M.D., Ph.D. Ernest Martinez, Ph.D. Jikui Song, Ph.D.

Professors Emeriti Thomas O. Baldwin, Ph.D. Craig V. Byus, Ph.D. (Biochemistry/Biomedical Sciences) Michael F. Dunn, Ph.D. Darold D. Holten, Ph.D. Richard A. Luben, Ph.D. (Biochemistry/Biomedical Sciences) Justin K.M. Roberts, Ph.D. Stephen R. Spindler, Ph.D.

Associate Professors Gregor Blaha, Ph.D. Sihem Cheloufi, Ph.D. Jernej Murn, Ph.D. Sean O’Leary, Ph.D.

Assistant Professors Maria Ninova, Ph.D. Adam Norris, Ph.D. Megan Norris, Ph.D. Daniel Petras, Ph.D. Pei Su, Ph.D. Associate Professor of Teaching Stephanie Dingwall, Ph.D.

Assistant Professors of Teaching Selene Bobadilla, Ph.D. Sarah Radi, Ph.D.

Senior Lecturer Emerita Miriam Ziegler, Ph.D.

Cooperating Faculty Michael E. Adams, Ph.D. (Entomology/ Molecular, Cell and Systems Biology) Bahman Anvari, Ph.D. (Bioengineering) Julia Bailey-Serres, Ph.D. (Botany and Plant Sciences) Devin K. Binder, Ph.D. (Biomedical Sciences) Katherine A. Borkovich, Ph.D. (Microbiology and Plant Pathology) Richard Cardullo, Ph.D. (Evolution, Ecology, and Organismal Biology) Chia-En Chang, Ph.D. (Chemistry) Sonali Chaturvedi, Ph.D. (Microbiology and Plant Pathology) Juhong Chen, Ph.D. (Bioengineering) Meng Chen Ph.D. (Botany and Plant Sciences) Patrick Degnan, Ph.D. (Microbiology and Plant Pathology) Adler Dillman, Ph.D. (Nematology) Nicholas Dipatrizio, Ph.D. (Biomedical Sciences) Thomas Eulgem, Ph.D. (Botany and Plant Sciences) Kevin Freedman, Ph.D. (Bioengineering) Weifeng Gu, Ph.D. (Molecular, Cell and Systems Biology) Rong Hai, Ph.D. (Microbiology and Plant Pathology) Richard Hooley, Ph.D. (Chemistry) Ansel Hsiao, Ph.D. (Microbiology and Plant Pathology) Hailing Jin, Ph.D. (Microbiology and Plant Pathology) Ryan Julian, Ph.D. (Chemistry) Isgouhi Kaloshian, Ph.D. (Nematology) Fedor Karginov, Ph.D. (Molecular, Cell and Systems Biology) Thomas Kuhlman, Ph.D. (Physics and Astronomy) Yanran Li, Ph.D. (Chemical & Environmental Engineering) Jiayu Liao, Ph.D. (Bioengineering) David Lo, Ph.D. (Biomedical Sciences) Declan McCole Ph.D. (Biomedical Sciences) Leonard Mueller, Ph.D. (Chemistry) Meera Nair, Ph.D. (Biomedical Sciences) Carolyn Rasmussen, Ph.D. (Botany and Plant Sciences) Pegan Scott, Ph.D. (Biomedical Sciences) Frances Sladek, Ph.D. (Molecular, Cell and Systems Biology) Valentine Vullev, Ph.D. (Bioengineering) Ian Wheeldon, Ph.D. (Biomedical Science) Emma Wilson, Ph.D. (Biomedical Sciences) Huimin Zhang, Ph.D. (Molecular, Cell and Systems Biology) Jingsong Zhang, Ph.D. (Chemistry) Linlin Zhao, Ph.D. (Chemistry) Sika Zheng, Ph.D. (Biomedical Sciences) Changcheng Zhou, Ph.D. (Biomedical Sciences) Nicole Zur Nieden, Ph.D. (Molecular, Cell and Systems Biology)

The three emphases areas within the Biochemistry major are Chemistry, Biology, and Medical Sciences. The Biology and Chemistry emphases are for students interested in postgraduate education or employment in the basic areas of the discipline of Biochemistry. The goal of the Medical Sciences emphasis is to prepare students for admission to postbaccalaureate education in the health professions. The Biology, Chemistry, and Medical Sciences emphases focus on the development of laboratory and critical thinking skills, and hands- on laboratory experience. In addition, participation in an independent research project (BCH 197) or research tutorial (BCH 190), carried out under the supervision of a faculty member, is encouraged. Internships in industry (BCH 198I) are also available, and often lead to valuable job experience and employment opportunities.

The department offers both B.A. and B.S. degrees. The major and emphasis requirements are the same for both, and most students choose the B.S. degree. The B.A. degree requires 12 additional units of Humanities and Social Sciences courses, and 16 units or a course 4 equivalency level of a foreign language (see College Breadth Requirements).

Note: A maximum of 12 units of 190-199 courses may be counted toward the 180 unit graduation requirement. All courses used towards the Biochemistry major requirements must be taken for letter grades.

Transfer students desiring to major in Biochemistry must have completed:

• 1. Two quarters of calculus, equivalent to

MATH 009A and MATH 009B

• 2. A year of general chemistry, equivalent to

CHEM 001A, CHEM 01LA, CHEM 001B, CHEM 01LB, CHEM 001C, CHEM 01LC

• 3. A year of organic chemistry, equivalent to

CHEM 008A, CHEM 08LA, CHEM 008B, CHEM 08LB, CHEM 008C, CHEM 08LC

• 4. A course in general biology, equivalent to

BIOL 005A and BIOL 05LA

Strongly recommended but not required for admission to the major are:

• 1. General Biology, equivalent to BIOL 005B

and BIOL 005C

2 One quarter of Ordinary Differential Equations, equivalent to MATH 046

• 3. General physics (calculus-based) equiva-

lent to PHYS 002A, PHYS 002B, PHYS 002C or PHYS 040A, PHYS 040B, PHYS 040C

Students must have a minimum grade point average of 2.70 in transferable college courses.

See Undergraduate Studies section.

See College of Natural and Agricultural Sciences, Colleges and Programs section.

Some of the following requirements for the major may also fulfill some of the college’s breadth requirements. Consult with a department advisor for course planning.

The major requirements and the emphasis requirements are the same for the B.A. and the B.S. degree in Biochemistry. Choose one emphasis.

Continuation in the major requires that the stu- dent maintains cumulative and upper division/ science GPAs of 2.00 or higher, a GPA of 2.00 or higher in each academic quarter, and makes ad- equate progress in the major with no more than 16 units of repeated courses. Adequate progress in the major is defined as (a) earning no grade lower than a “C-” in any required lower division mathematics or science course, STAT 010, CHEM 008A, CHEM 08LA, CHEM 008B, CHEM 08LB, CHEM 008C, CHEM 08LC, or any upper division BCH course, and (b) completing MATH 007B or MATH 009B and CHEM 001A by the end of the Fall Quarter of the second year of residence and BCH 110A or BCH 110HA, and BCH 110B or BCH 110HB, by the end of the third year of residence. Fresh- men must also complete BCH 095 with a grade of “S” during their first year of residence. BCH 095 may be waived for transfer students and students who change their major after their first year. Freshmen in the Medical Science Emphasis must also complete BCH 096 with a grade of “S” during their first year of residence. BCH 096 may be waived for transfer students and students who change their major after their first year. A student who does not meet these adequate progress standards will be discontinued from the major. In addition, a student who receives a grade of “D+” or lower in any two of the courses in (A) on the first attempt, or in any one of these courses in each of two attempts, will be discontinued from the major. Students who receive a grade lower than “B-” in BIOL 005A or CHEM 008A are strongly encouraged to complete BCH 100 during their second year of residence to better prepare themselves for BCH 110A or BCH 110HA, BCH 110B or BCH 110HB, and BCH 110C or BCH 110HC.

Biology Emphasis

• 1. Lower-division requirements (76 units)

• a) BCH 095 or equivalent, BCH 015

• b) BIOL 005A, BIOL 05LA or BIOL 020, BIOL 005B, BIOL 005C

• c) CHEM 001A, CHEM 01LA, CHEM 001B,

CHEM 01LB, CHEM 001C, CHEM 01LC

• d) CHEM 008A and CHEM 08LA or CHEM 08HA and CHEM 08HLA, CHEM 008B

and CHEM 08LB or CHEM 08HB and CHEM 08HLB, CHEM 008C and CHEM 08LC or CHEM 08HC and CHEM 08HLC

• e) MATH 007A or MATH 009A, MATH 007B

or MATH 009B, MATH 046

• f) PHYS 002A, PHYS 02LA, PHYS 002B,

PHYS 02LB, PHYS 002C, PHYS 02LC

• g) STAT 010

• 2. Upper-division requirements (40-41 units)

• a) BCH 110A or BCH 110HA, BCH 110B or

BCH 110HB, BCH 110C or BCH 110HC, BCH 162, BCH 184

• b) At least 3 units from BCH 111, BCH 120,

BCH 153/BIOL 153/BPSC 153, BCH 180 (E-Z), BCH 183/BPSC 183, BCH 185, BCH 186, BCH 187, BCH 188, BCH 210, BCH 211, BCH 212

• c) BIOL 102

• d) CHEM 109 or CHEM 110A

• e) Choose two biological science courses

from the following:

• (1) BCH 111, BCH 120, BCH 153/BIOL 153/

BPSC 153, BCH 180 (E-Z), BCH 183/ BPSC 183, BCH 185, BCH 186, BCH 187, BCH 188, BCH 210, BCH 211, BCH 212

• (2) BIOL 105, BIOL 108, BIOL 114, BIOL 117,

BIOL 119, BIOL 121/MCBL 121, BIOL 121L/ MCBL 121L, BIOL 123/MCBL 123/PLPA 123, BIOL 124/MCBL 124, BIOL 128/CBNS 128, BIOL 151, BIOL 155/BPSC 155, BIOL 157, BIOL 159/NEM 159, BIOL 160, BIOL 161A, BIOL 161B, BIOL 171A, BIOL 171B, BIOL 171C, BIOL 171L, BIOL 173/ENTM 173, BIOL 175

• (3) BIOL 104/BPSC 104, BPSC 109/CBNS 109, BIOL 132/ BPSC 132, BIOL 143/

BPSC 143, BIOL 148/BPSC 148, BIOL 155/BPSC 155, BPSC 135, BPSC 149

• (4) BIOL 100/ENTM 100, BIOL 173/ENTM 173, ENTM 128

• (5) CBNS 101, CBNS 106, CBNS 116, CBNS 120/PSYC 120, CBNS 120L/PSYC 120L,

CBNS 124/PSYC 124, CBNS 125/PSYC 125, CBNS 150/ ENTX 150, CBNS 165, CBNS 169

• (6) ENSC 100

• (7) ENTX 101, CBNS 150/ENTX 150
• 3. BCH 190 or BCH 197 are available as

elective courses. Enrollment requires upper division standing and written permission of the supervising faculty member. No more than 9 units of courses numbered 190-199 may be counted towards the major.

Chemistry Emphasis

• 1. Lower-division requirements (81 units)

• a) BCH 095 or equivalent, BCH 015

• b) BIOL 005A, BIOL 05LA or BIOL 020, BIOL 005B, BIOL 005C

• c) CHEM 001A, CHEM 01LA, CHEM 001B,

CHEM 01LB, CHEM 001C, CHEM 01LC

• d) CHEM 005

• e) CHEM 008A and CHEM 08LA or CHEM-

08HA and CHEM 08HLA, CHEM 008B and CHEM 08LB or CHEM 08HB and CHEM 08HLB, CHEM 008C and CHEM 08LC or CHEM 08HC and CHEM 08HLC

• f) MATH 007A or MATH 009A, MATH 007B or

MATH 009B, MATH 046

• g) PHYS 002A, PHYS 02LA, PHYS 002B,

PHYS 02LB, PHYS 002C, PHYS 02LC

• h) STAT 010

• 2. Upper-division requirements (40-41 units)

• a) BCH 110A or BCH 110HA, BCH 110B or

BCH 110HB, BCH 110C or BCH 110HC, BCH 162, BCH 184

• b) At least 3 units from BCH 111, BCH 120,

BCH 153/BIOL 153/BPSC 153, BCH 180 (E-Z), BCH 183/BPSC 183, BCH 185, BCH 186, BCH 187, BCH 188, BCH 210, BCH 211, BCH 212, BIOL 119, BPSC 109/CBNS 109, BPSC 149

• c) BIOL 102

• d) CHEM 109 or CHEM 110A

• e) Two courses from CHEM 110B, CHEM 113, CHEM 125, CHEM 150A, CHEM 150B,

CHEM 166 (Other graduate courses may be substituted by students with a GPA of 3.00 or better with permission of the instructor and the faculty advisor.)

• 3. BCH 190 or BCH 197 are available as

elective courses. Enrollment requires written permission of the supervising faculty member. No more than 9 units of courses numbered 190-199 may be count- ed towards the major.

Medical Sciences Emphasis

• 1. Lower-division requirements (74 units)

• a) BCH 095 or equivalent, BCH 015

• b) BCH 096, BCH 098I

• c) BIOL 005A, BIOL 05LA or BIOL 020,

BIOL 005B, BIOL 005C

• d) CHEM 001A, CHEM 01LA, CHEM 001B,

CHEM 01LB, CHEM 001C, CHEM 01LC

• e) CHEM 008A and CHEM 08LA or CHEM 08HA and CHEM 08HLA, CHEM 008B

and CHEM 08LB or CHEM 08HB and CHEM 08HLB, CHEM 008C and CHEM 08LC or CHEM 08HC and CHEM 08HLC

• f) MATH 007A or MATH 009A,

MATH 007B or MATH 009B

• g) PHYS 002A, PHYS 02LA, PHYS 002B,

PHYS 02LB, PHYS 002C, PHYS 02LC

• h) STAT 010

• 2. Upper-division requirements (40-41 units)

• a) BCH 110A or BCH 110HA, BCH 110B or

BCH 110HB, BCH 110C or BCH 110HC, BCH 120, BCH 162, BCH 184

• b) BIOL 102

• c) CHEM 109 or CHEM 110A

• d) CBNS 101

• e) At least 3 units from BCH 183/BPSC 183, BCH 185, BCH 188, BIOL 119, BIOL 121, BIOL 128/CBNS 128, BIOL 161A, BIOL 161B, BIOL 171A, BIOL 171B, BIOL 171C,

BIOL 171L, BPSC 109/CBNS 109, BPSC 149, CBNS 106, CBNS 120/PSYC 120, CBNS 150/ENTX 150, CBNS 165, CBNS 169

Graduate and upper-division courses can be substituted with permission of the instructor and the faculty advisor. Graduate courses re- quire a GPA of 3.0 or greater in the sciences.

Students should be aware that CHEM 005 is often a requirement for admission to profes- sional schools.

The Department of Biochemistry offers a graduate program leading to the M.S. or Ph.D. degree in Biochemistry and Molecular Biology. This program emphasizes basic biochemistry with research specializations in the areas of molecular biology, physical biochemistry, molecular endocrinology, plant biochemistry and molecular biology, signal transduction, and biomedical research. It is designed for students who are planning a career of research and teaching in biochemistry at col- leges and universities or who wish to engage in biochemical investigations of fundamental or applied nature in private, governmental or commercial laboratories.

Admission Students who have completed a bachelor’s degree in physical, biological, chemical, or agricultural sciences are invited to apply to the program. Regardless of the area of their major for the baccalaureate degree, students should have taken the following courses prior to be- ginning graduate study in biochemistry or plan to make up deficiencies soon after entering graduate school:

• 1. One year of calculus

• 2. One year of general physics

• 3. One year of organic chemistry

• 4. An introductory course in physical chemistry

• 5. At least two courses in biology at the

upper-division level, including genetics

The Department of Biochemistry offers the Ph.D. degree in Biochemistry and Molecular Biology.

Course Work The following courses are required. Credit for upper division courses listed below will be given at the discretion of the graduate advisor if equiv- alent coursework has been taken previously. Students’ course requirements are determined in consultation with the graduate advisor for them upon their arrival. The graduate advisor suggests an individualized course program involving classes in biochemistry and subsidiary fields of study, chosen from any of the physical, biological, or agricultural sciences. Although an adequate course preparation is a requisite part of the training program, the department encourages early involvement of the students in research directed toward their dissertations.

BCH 110A-110B-110C: General Biochemistry

BCH 162; or equivalent research experience

BCH 184: Topics in Physical Biochemistry

BCH 210; Biochemistry of Macromolecules

BCH 211; Molecular Biology

BCH 212; Signal Transduction.

BCH 230 series: at least one course

BCH 240 Special topics in Biochemistry; required each quarter from the time the student finds a permanent major professor. The course consists of the laboratory group meeting of the student’s Major Professor

BCH 250 Oral Presentation in Biochemistry; this course must be taken prior to Advance- ment to Candidacy.

BCH 251 Graduate Seminar in Biochemistry; one formal oral presentation is required in the student’s first four years in the program.

BCH 252 General Seminar in Biochemistry; must be taken every quarter, when offered except when they present in the seminar, they must enroll in BCH 251 instead. Excep- tions to this rule may be made by petition to the Graduate Advisor in cases where the General Seminar in Biochemistry conflicts with the student’s Teaching Assistant re- sponsibilities

GDIV 403 Interdisciplinary Seminar: Research and Scholarship Ethics; must be taken once within one year of advancement to candidacy.

Elective Course Requirement: The elective courses consist of at least 9 units of graduate or upper division undergraduate course work in the sciences. Courses taken to satisfy deficien- cies at the time of admission cannot be count- ed toward the elective course requirements.

At the end of the second quarter, students se- lect major professors and are ready to initiate a research project. At the end of the first year, students submit a written report describing their research efforts and relating them to current biochemical work in related areas.

Written and Oral Qualifying Examinations At the end of the first year, and no later than the end of the second year, students take a comprehensive written qualifying examination consisting of material from BCH 210, BCH 211, and BCH 212.

Upon successful completion of this exam, the student will then submit and orally defend a research report in which they describe the research they have performed thus far and develop a plan for their complete dissertation research project. This fulfills the requirement for an oral qualifying examination. Students completing all necessary requirements are advanced to candidacy for the Ph.D. degree.

Students must sit the comprehensive written exam within the first two years in the pro- gram. Unless excused by either the graduate advisor or department chair, failure to sit the examination will be regarded as a failed exam. Students must sit every sequential offering of the exam and no student will be given more than two attempts to achieve a satisfactory grade on the comprehensive written exam.

The Oral Qualifying Exam can be taken in one of the following modes: In-Person or Hybrid. The student and their advisor will discuss which mode best suits the subject matter, with the advisor making the final determination. Students taking the exam In-Person are expected to present on campus with all committee members physically present. If Hybrid is chosen, the student is expected to present the exam on campus in a video enabled room that supports some members physically present and others remote.

Dissertation and Final Oral Examination Following completion of their research, students submit a written dissertation and conclude their studies with an oral defense of the dissertation.

The Final Defense can be taken in one of the following modes: In-Person or Hybrid. The student and their advisor will discuss which mode best suits the subject matter, with the advisor making the final determination. Stu- dents presenting the Final Defense In-Person are expected to present on campus with all committee members physically present. If Hybrid is chosen, the student is expected to present the Final Defense on campus in a video enabled room that supports some mem- bers physically present and others remote.

Teaching Requirement As part of the program,each student is required to serve at least two quarters as a teaching assistant.

Professional Development Training Ph.D. graduate students fulfill their profession- al training requirement through enrollment in BCH 250, BCH 252 and GDIV 403.

Normative Time to Degree 15 quarters. In the case that a student changes the degree aim from M.S. to Ph.D., normative time will be reset.

In addition to the Ph.D. program, the depart- ment offers two plans for the master’s degree (Plan I, Thesis; Plan II, Comprehensive Exam- ination). Both plans require completion of at least 36 course units; for Plan I, a maximum of 12 units may be for thesis research.

Course Work The following courses offered by the Biochem- istry Department, or acceptable substitutes (determined by the Graduate Advisor when the student joins the program), are required:

BCH 110A-110B-110C: General Biochemistry

BCH 162;or equivalent research experience

BCH 184: Topics in Physical Biochemistry

BCH 210; Biochemistry of Macromolecules

BCH 211; Molecular Biology

BCH 212; Signal Transduction.

BCH 230 series: at least one course BCH 252 General Seminar in Biochemistry; must be taken every quarter, when offered.

No more than 6 units of Biochemistry courses 240, 252, or 261 may be offered in fulfillment of the unit requirement at the 200 level.

In special cases, where it is otherwise impossible to obtain the required number of 200-level grad- ed courses, up to 4 units of Biochemistry 290 may be taken for graded credit. Approval of the Gradu- ate Advisor prior to enrollment is required. Also, a petition must be approved by the Graduate Dean.

Students pursuing Plan II must sit the first comprehensive written exam scheduled following the completion of the coursework. The exam will consist of material from BCH 210, BCH 211 and BCH 212. Unless excused by either the graduate advisor or department chair, failure to sit the examination will be regarded as a failed exam. Students must sit every sequential offering of the exam and no student will be given more than two attempts within one year following completion of the coursework to achieve a satisfactory grade on the comprehensive written exam.