Molecular Biophysics Biochemistry

Class of 2020Enrique De La Cruz, 336A Bass (432-5424) enrique.delacruz@yale.eduEnrique M. De La Cruz, Ph.D. is a Professor in the Department of Molecular Biophysics and Biochemistry atYale University. He is a first generation Cuban-American who was raised in Newark, NJ. Dr. De LaCruz earned his Ph.D. degree in Biochemistry, Cell & Molecular Biology (BCMB) with Dr. ThomasD. Pollard at Johns Hopkins University School of Medicine and received postdoctoral training in thelaboratories of Dr. H. Lee Sweeney and E. Michael Ostap at the University of Pennsylvania Schoolof Medicine. Dr. De La Cruz has published extensively in the areas of actin and myosin regulation,RNA helicases, and signaling enzymes, for which he has received a number of awards and honors.Click here to visit his lab web page.Patrick Sung, C130A SHM (785-4553) patrick.sung@yale.eduPatrick Sung studied Biochemistry at the University of Liverpool and earned his DPhil from OxfordUniversity. He received postdoctoral training in Biochemistry and Genetics at the University ofRochester, joined the University of Texas Medical Branch in Galveston as Assistant Professor in1993, and relocated to the University of Texas Health Science Center in San Antonio as AssociateProfessor in 1997. He was appointed Full Professor in Molecular Biophysics & Biochemistry at Yalein 2003, and served as Department Chair between 2009 and 2015. His research focuses on themechanism of DNA break repair in yeast and human cells. Click here to visit his lab webpage.To schedule an appointment with Professor Sung, please email him directly, and copy his administrativeassistant: Shanna.lavacca@yale.eduClass of 2021Wendy Gilbert, C127 SHM (785-4857) wendy.gilbert@yale.eduWendy Gilbert studied Molecular Biology at Princeton (AB 1994) and Biochemistry at UCSF (PhD 2004).After postdoctoral training at UC Berkeley, she joined the faculty at MIT (2008). In 2017 she movedto Yale as an Associate Professor of Molecular Biophysics and Biochemistry. Wendy is passionateabout RNA Biology and about increasing diversity and inclusiveness in STEM fields. Wendy’s labcombines systems approaches, molecular genetics, and biochemistry to understand posttranscriptional gene regulation in eukaryotic cells. Click here* to visit her lab webpage.Mark Solomon, 218 BASS (436-9053) mark.solomon@yale.eduMark Solomon is a Professor in the Department of Molecular Biophysics and Biochemistry at YaleUniversity. The long range goal of our lab is to understand biochemically how cell growth anddivision are regulated by checkpoints within the cell and by controls imposed from the surroundingtissues. The cyclin-dependent protein kinases (CDKs), whose activities are required for cell cycletransitions, are regulated via multiple mechanisms including specific association with a cyclin,multiple phosphorylations (both positive- and negative-acting), sensing of a threshold, and at leasttwo feedback loops that combine to produce the precise and abrupt activation of protein kinaseactivity necessary for accurate cell cycle transitions. We study the protein kinases, phosphatases, andregulatory proteins that control CDKs. We also study the ubiquitin-mediated degradation of cyclinsand other mitotic proteins and how this degradation is blocked by the Spindle-Assembly Checkpoint.To schedule an appointment please email mark.solomon@yale.edu.Majors Accepted to the B.S./M.S. ProgramKarla Neugebauer, C123 SHM (785-3322) MBBUndergrad@yale.eduSpring 2018 Michael Koelle will advise.3

The Bachelor of Arts DegreeThe B.A. program provides the intellectual discipline of biophysics and biochemistry for students who wantto have sufficient time for in-depth studies outside the major or who are interested in molecular biology aspart of a liberal education and may not want to go on to graduate work in any of the natural sciences. B.A.program majors have an opportunity to carry out research in faculty laboratories after they have completedtheir required MB&B laboratory course. In the absence of Advanced Placement (AP) in any of the naturalsciences or mathematics, completion of at least 19.5 science credits is required for the B.A. major.Requirements for the B.A. program in the MB&B MajorThe table shows the MB&B course requirements in the Basic Sciences (Part A) and in the AdvancedSciences (Part B) for the B.A. degree. Courses prefixed with a star (*) may be waived by receiving scores onAP tests or placement exams sufficient to earn acceleration credits in the particular subjects, even if thestudent does not choose to accelerate. Note that you can find a complete list of MB&B courses, includingelectives, at the end of this handbook.Bold letters after the number of credits indicate footnotes.Part A. Basic Sciences CreditsIntroductory Biology:*BIOL 101, 102, 103, and 104Chemistry:*General: CHEM 161, 165, or 163, 167; and 134L, 136LOrganic: CHEM 174, 175, or 220, 221, and 222L, 223LPhysical: CHEM 328 (may substitute CHEM 332)Physics:*PHYS 170, 171, or 180, 181, or 200, 201Mathematics:*Calculus: MATH 112 and either MATH 115 or 11623a3b1c22dTotal Course Credits in Basic Science (Maximum)13Part B. Advanced Sciences and Senior RequirementMB&B:Biochemistry: MB&B 300, 301, and 251L (0.5 credit)Biophysics: MB&B 302 (may substitute CHEM 333)MB&B Elective: One additional MB&B courseMB&B 490b (Senior requirement)Quantitative reasoning (QR) elective2.5f111g1eTotal Course Credits in Advanced ScienceTotal Credits Required for B.A. Degree6.519.54

a: (For class of 2018 and earlier, the previously offered general chem. courses will be accepted: 112, 113, or114, 115, & 116L, 117L; or 118 & 119L)b: Only students having AP for CHEM 113 are eligible for CHEM 174. By taking freshman organicchemistry (CHEM 174, 175) in the fall followed by organic chemistry (CHEM 221b) in the spring of thefreshman year, a student is able to take MB&B 300a/301b in the sophomore rather than the junior year.c: CHEM 328a is the standard one-term physical chemistry course that should be taken by most MB&Bmajors. A small number of students with especial interest in physical chemistry may want to take CHEM332a instead of CHEM 328a. Taking CHEM 332a gives students the option to take a second term of physicalchemistry, CHEM 333b, as a substitute for the biophysics course MB&B 302b. Aside from the morefundamental treatment given in Chem 332 (viz., trying to explain basic concepts and to demonstrate fromwhere the venerable tenants/equations of thermodynamics actually originate), the primary difference betweenthese two courses resides in the focus of applications (with Chem 328 obviously being more oriented towardsbiochemical applications).d: MATH 115 and 116 are essentially equivalent in terms of calculus level. MATH 116 is a more intimateclass, with readings grounded in biology and more use of differential equations to solve problems. Even ifyou place out of MATH 115, you may consider MATH 116 because of the unique topics presented. Pleaseconsult the instructors (e.g. John Hall) if you wish to discuss this further.e: Several courses that fulfill this requirement and fit nicely with the interests of MB&B majors are asfollows: MB&B strongly encourages all majors to strengthen their skills in statistics and data analysis. Inparticular, S&DS 110 (Introduction to R) and S&DS 220 (Intensive Intro Stats) include instruction in the Rpackage for statistical computing, which is useful for all biologists. Some MB&B majors may be interestedin S&DS 105 or 230, CPSC 100, 112, 201 or above. For those interested in computational or structuralbiology, multivariable calculus is advantageous (MATH 120 or ENAS 151). Linear algebra (Math 222 or225) is highly recommended for computational biologists. Others with permission from academic advisor orDUS. AP credit cannot be applied toward the quantitative reasoning elective.f: MB&B 251L is cross listed as MCDB 301L. This means that students could sign up for the class as“MB&B 251” if they need an additional chemistry lab for premed purposes. On the other hand, studentswho have already take at least three chemistry labs could instead register for “MCDB 301L” and thuscomplete both their MB&B biochemistry lab course requirement AND a premed “biology lab” courserequirement at the same time.g: The MB&B senior requirement for both B.S. and B.A. degrees is fulfilled by participation in MB&B 490bduring the second semester of the senior year. This course will confer course credit for completion of thesenior project in the department. Students prepare a written report and make an oral presentation on recentadvances in research on a topic of their choice within biochemistry and biophysics. Students will meet withthe faculty during the first two weeks of the spring term to agree upon a topic and approach.Written presentation: The paper is expected to be 15–25 pages in length, and should critically review theliterature on a scientific topic within biochemistry and biophysics. A first draft of the paper is due twoweeks prior to the date of the oral presentation. It is inappropriate for students to resubmit a paperprepared for another course in fulfillment of the senior requirement. The literature project must beoriginal new work approved by the faculty member overseeing the senior project. It is recommendedthat students who took research for credit earlier in their training write a new 15–25 page literaturereview on the topic of their research, and append to it the research report they previously completed forthe research course. Faculty in charge of the program will provide suggestions for the paper and returnit to the student. A final draft of the paper is due the first day of the reading period of the student’s finalterm.Oral presentation: Students will make a 15-minute oral presentation during the last three weeks of thestudent’s final term in a general scientific format open to the public. Other students in the senior projectcourse are expected to attend the presentations.5

NOTE: MB&B 470/471 are independent research courses for MB&B majors only that may be taken duringthe sophomore, junior, or senior years. Students receive letter grades. MB&B B.A. degree majors may takeup to two credits of these courses and count one of them as the “MB&B elective” toward their MB&BB.A. degree requirements. Students may take additional independent research for credit by registering forMB&B 472/473, which have identical requirements but are graded Pass/Fail. These additional credits do notcount towards the MB&B degree requirements. Ideally students will take MB&B 251L to receive agrounding in practical laboratory skills prior to taking an independent research course.Possible Course Programs for B.A. MB&B Majors Entering YaleWithout Any Advanced PlacementThis B.A. program provides the minimal number of science and non-science courses required of all MB&Bmajors. It earns a total of 36.5 course credits and assumes no AP credit. (Credits are indicated inparentheses). Students having AP in science are urged to replace introductory science courses by moreadvanced ones in their freshman year.FreshmanSophomoreBIOL 101-104(2)CHEM 161, 165(2)CHEM 134L, 136L(1)MATH 112a or bNon-scienceJuniorCHEM 220 and 221CHEM 222 and 223MATH 116 a or bQuantitativeReasoning(1) Non-science(3)MB&B requirements/Total6/9(2)(1)(1)MB&B 300aMB&B 301bMB&B 251L(1)PHYS 180a and 5/9.5TOTALCHEM 328aMB&B electiveMB&B 302bBiophysicsMB&B 490bSenior :1. Majors who must begin their study of a foreign language after entering Yale are urged to do so in theirfreshman year. The foreign language requirement should be completed by the end of the junior year.2. Half-credit courses such as BIOL 101-104 and MB&B 251L earn no course credit per se; one credit isawarded only after two such courses are completed. Additional half-credit courses include one-day-perweek lab courses offered by MCDB, Chemistry, Computer Science, Psychology, or Physics.6

MB&B Coursework Planning Sheet for the B.A. DegreeREQUIREMENTCOURSE NAMEIntroductory Courses(When alternative courses are listed on one line, circlethe name of the one taken)Introductory BiologyIntroductory BiologyIntroductory BiologyIntroductory BiologyBIOL 101BIOL 102BIOL 103BIOL 104General Chem 1TERM TAKENProposedEnrolledCompletedGradeCHEM 161 or 163(previously offered versions of general chem. and labswill be accepted for the classes of 2018 and earlier)General Chem Lab 1General Chem 2General Chem Lab 2CHEM 134LCHEM 165 or 167CHEM 136LCalculus 1Calculus 2Quantitative ReasoningMATH 112a/bMATH 116a/b or 115a/bSpecify course:Mid-level CoursesPhysics 1Physics 2PHYS 170a or 180a or 200aPHYS 171b or 181b or 201bOrganic Chem 1Organic Chem Lab 1Organic Chem 2Organic Chem Lab 2CHEM 174a or 220a/bCHEM 222La/bCHEM 175b or 221a/bCHEM 223La/bBiochemistry 1Biochemistry 2Biochemistry Lab BSMB&B 300aMB&B 301bMB&B 251LaUpper-level CoursesPhysical Chem 1BiophysicsMB&B Elective*Senior SeminarOther coursesOther coursesOther coursesCHEM 328a or 332aMB&B 302b or CHEM 333bMB&B 490*MB&B elective is any 200-level or above MB&B course, including any lecture, seminar, lab or research forcredit course.7

The Bachelor of Science DegreeThe B.S. program is designed especially for students with a strong commitment to research. B.S. programmajors have an opportunity to carry out research in faculty laboratories after they have completed theirrequired MB&B laboratory course. This program is readily adapted to permit qualified majors to enter thecombined B.S./M.S. program that leads to the simultaneous award of the two degrees at the end of four yearsin Yale College.In the absence of AP in any of the natural sciences or mathematics, and depending on the specific coursestaken, completion of 21.5 credits of science courses are required for the completion of the B.S. degree.Requirements for the B.S. Program in the MB&B MajorThe table shows the MB&B course requirements in the Basic Sciences (Part A) and in the AdvancedSciences (Part B) for the B.S. degree. Courses prefixed with a star (*) may be waived by receiving scores onAP tests sufficient to earn acceleration credits in the particular subjects, even if the student does not chooseto accelerate. Note that you can find a complete list of MB&B courses, including electives, at the end of thishandbook. Letters after the number of credits indicate footnotes. Courses in italics indicate those areas inwhich the B.S. degree differs from the B.A. degree.Part A. Basic Sciences CreditsIntroductory Biology:*BIOL 101, 102, 103, and 104Chemistry:*General: CHEM 161, 165, or 163, 167; and 134L, 136LOrganic: CHEM 174, 175, or 220, 221, and 222L, 223LPhysical: CHEM 328Physics:*General: PHYS 170, 171, or 180, 181, or 200, 201Mathematics:*Calculus: MATH 112 and either MATH 115 or 116Total Course Credits in Basic Science (Maximum)Part B. Advanced Sciences and Senior RequirementBiochemistry: MB&B 300a, 301b and 251 (.05)Biophysics: MB&B 302b (may substitute CHEM 333b)MB&B Electives: Two additional MB&B coursesAdditional science electiveMB&B 490b Senior ProjectQuantitative reasoning (QR) electiveTotal Course Credits in Advanced ScienceTotal Credits Required for B.S. Degree23a3b1c22d132.5f12g1h1i1e8.521.58

a: (For class of 2018 and earlier, the previously offered general chem. courses will be accepted: 112, 113, or114, 115, & 116L, 117L; or 118 & 119L)b: Only students having AP for CHEM 113 are eligible for CHEM 174. By taking freshman organicchemistry (CHEM 174, 175) in the fall followed by organic chemistry (CHEM 221b) in the spring of thefreshman year, a student is able to take MB&B 300a/301b in the sophomore rather than the junior year.c: CHEM 328a is the standard one-term physical chemistry course that should be taken by most MB&Bmajors. A small number of students with especial interest in physical chemistry may want to take CHEM332a instead of CHEM 328a. Taking CHEM 332a gives students the option to take a second term of physicalchemistry, CHEM 333b, as a substitute for the biophysics course MB&B 302b. Aside from the morefundamental treatment given in Chem 332 (viz., trying to explain basic concepts and to demonstrate fromwhere the venerable tenants/equations of thermodynamics actually originate), the primary difference betweenthese two courses resides in the focus of applications (with Chem 328 obviously being more oriented towardsbiochemical applications).d: MATH 115 and 116 are essentially equivalent in terms of calculus level. MATH 116 is a more intimateclass, with readings grounded in biology and more use of differential equations to solve problems. Even ifyou place out of MATH 115, you may consider MATH 116 because of the unique topics presented. Pleaseconsult the instructors (e.g. John Hall) if you wish to discuss this further.e: Several courses that fulfill this requirement and fit nicely with the interests of MB&B majors are asfollows: MB&B strongly encourages all majors to strengthen their skills in statistics and data analysis. Inparticular, S&DS 110 (Introduction to R) and S&DS 220 (Intensive Intro Stats) include instruction in the Rpackage for statistical computing, which is useful for all biologists. Some MB&B majors may be interestedin S&DS 105 or 230, CPSC 100, 112, 201 or above. For those interested in computational or structuralbiology, multivariable calculus is advantageous (MATH 120 or ENAS 151). Linear algebra (Math 222 or225) is highly recommended for computational biologists. Others with permission from academic advisor orDUS. AP credit cannot be applied toward the quantitative reasoning elective.f: MB&B 251L is cross-listed as MCDB 301L. This means that students could sign up for the class as“MB&B 251” if they need an additional chemistry lab for premed purposes. On the other hand, studentswho have already take at least three chemistry labs could instead register for “MCDB 301L” and thuscomplete both their MB&B biochemistry lab course requirement AND a premed “biology lab” courserequirement at the same time.g: One of the two must be an MB&B lecture or seminar course. The other can be another MB&B lecturecourse, research for credit, or the upper level lab course MB&B 460L. Only two course credits of MB&B470, 471 and 478, 479 may count towards the B.S. degree requirements – one as an “MB&B elective”and the other as the “additional science elective”.h: This elective is chosen, with the approval of the major’s MB&B Faculty Advisor, from among courseswith the Sc designation. Students may also use graduate courses offered by MB&B and other sciencedepartments, including Cell Biology, Human Genetics, Neuroanatomy, Pharmacology and Physiology.Courses must be at a higher level than those already required for the major. This elective can be anintroductory course if no other course in that field is required.i: The MB&B senior requirement for both B.S. and B.A. degrees is fulfilled by participation in MB&B 490bduring the second semester of the senior year. This course will confer course credit for completion of thesenior project in the department. Students prepare a written report and make an oral presentation on recentadvances in research on a topic of their choice within biochemistry and biophysics. Students will meet withthe faculty during the first two weeks of the spring term to agree upon a topic and approach.Written presentation: The paper is expected to be 15–25 pages in length, and should critically review theliterature on a scientific topic within biochemistry and biophysics. A first draft of the paper is due twoweeks prior to the date of the oral presentation. It is inappropriate for students to resubmit a paperprepared for another course in fulfillment of the senior requirement. The literature project must beoriginal new work approved by the faculty member overseeing the senior project. It is recommended9

that students who took research for credit earlier in their training write a new 15–25 page literaturereview on the topic of their research, and append to it the research report they previously completed forthe research course. Faculty in charge of the program will provide suggestions for the paper and returnit to the student. A final draft of the paper is due the first day of the reading period of the student’s finalterm.Oral presentation: Students will make a 15-minute oral presentation during the last three weeks of thestudent’s final term in a general scientific format open to the public. Other students in the senior projectcourse are expected to attend the presentations.NOTE: MB&B 470/471 are independent research courses for MB&B majors only that may be taken duringthe sophomore, junior, or

Department of Molecular Biophysics & Biochemistry. 1 . Biochemistry and biophysics are rapidly advancing areas of science that underlie the current dramatic progress in medicine. Our undergraduate degree programs are well suited for students planning to attend medical and/or graduate school in biochemistry, molecular biology, genetics .