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CHEM 156 Physical Biochemistry

Fall quarter, 2017

Lecture room: YH CS76

Lecture recordings available through UCLA BruinCast Website: https://ccle.ucla.edu/course/view/17F-CHEM156-1

Lecture time: MWF (except where noted) 1:00 - 1:50 PM

Instructor: John Colicelli, Biological Chemistry Dept., David Geffen School of Medicine at UCLA

Office: 350C BSRB

Office Hours: Wednesdays 4:30 – 6:00 PM (and by appointment)

email: colicelli@mednet.ucla.edu

Teaching Assistant: Wonhyeuk (Won) Jung Discussion group meeting times: Tuesday 1-2pm, Thursday 1-2pm Discussion group meeting room: CS76

Course objectives:

Students will learn to apply the concepts of thermodynamics, entropy, enthalpy, potential energy, free energy and kinetics to macromolecular structures and biochemical reactions.

Course material:

The course textbook is The Molecules of Life: physical and chemical principles by Kuriyan, Konforti and Wemmer. We will cover chapters 6-10, 12, 13, 15 and 16 (excluding material in gray “Box” sections). Copies of this book are on reserve in the Science and Engineering Library. Weekly discussions will review material covered in class and evaluate student understanding with quizzes.

Grading:

Letter grading based on performance in class and discussion groups using the following breakdown:

1 st midterm (30%) + 2 nd midterm (30%) + final (30%) + discussion group quizzes (10%).

Exams & Assignments:

Midterm and final exams will include problem-solving and short-answer questions. The final will focus on material covered after the 2 nd midterm, but will require an understanding of concepts discussed throughout the course.

Course description:

Lecture: three 50-minute classes per week. Discussion: one hour per week. Prerequisites: 110A, 153A. The biological world contains a seemly limitless variety of organisms, but all forms of life are constrained by the rules of physics and chemistry. This course examines how probability and energy distribution can explain biological systems. Areas of focus include the role of noncovalent bonds in macromolecular structures and the use of thermodynamics to predict equilibrium in reversible reactions.

NOTE:

Students needing academic accommodations based on a disability must contact the Center for Accessible Education (CAE) at (310) 825-1501, www.cae.ucla.edu or go to Murphy Hall A255. As the professionals with delegated authority from the campus to determine reasonable disability accommodations, CAE will assess all requested accommodations and communicate their recommendations to the course instructor. Students should contact CAE within the first two weeks of term to address the need for accommodations. If you have approval for proctoring arrangements during exams, please inform the instructor and TA well before the exam date.

Lecture Schedule:

 

Date

Topic

F

9/29

Chapter 6. 1 st law thermodynamics, types of energy, heat capacity, Boltzmann distribution

M

10/2

Noncovalent interactions, van der Waals force, denaturation of macromolecules

W

10/4

Dielectric constants, hydrogen bond, electrostatic bond, hydrophobic effect

F

10/6

Chapter 7. 2 nd law of thermodynamics, multiplicity, Gaussian distributions

M

10/9

Entropy and spontaneous changes in state, systems at equilibrium

W

10/11

Diffusion across semipermeable barriers

F

10/13

Chapter 8. Energy distribution, energy exchange within and between systems

M

10/16

Relationship between entropy and temperature

W

10/18

Chapter 9. Gibbs free energy, standard free energy (ATP hydrolysis)

F

10/20

Free energy of biomolecule formation (glucose formation)

M

10/23

EXAM I (Chs. 6, 7, 8 material)

W

10/25

Free energy and work in cells (movement of motor proteins, ATP synthase)

F

10/27

Chapter 10. Chemical potential, equilibrium constant (K eq )

M

10/30

Mass action ratio, acid-base equilibrium

W

11/1

Free energy changes drive protein folding, differential scanning calorimetry

F

11/3

In class discussion of research paper

M

11/6

Chapter 12. Ligand binding to proteins, dissociation constant (K D ) and affinity

W

11/8

Agonists, antagonists, competitive inhibition

F

11/10

Veterans Day

M

11/13

EXAM II (Chs. 9, 10, 12 material)

W

11/15

Chapter 13. Binding sensitivity versus selectivity, protein-small molecule interactions

F

11/17

Cooperative binding (calmodulin, myoglobin verses hemoglobin)

M

11/20

Protein-protein interactions, binding domains, symmetry (homo- and hetero-multimers)

T

11/21

Protein-DNA interactions (histones, transcription factors)

W

11/22

Thanksgiving

F

11/24

Thanksgiving

M

11/27

No class

T

11/28

Chapter 15. Reaction order, rate laws, kinetics

W

11/29

Reversibility, equilibrium and steady state

F

12/1

Catalysts, activation energy, transition states

M

12/4

Chapter 16. Enzyme kinetics: K M , V max , k cat

W

12/6

Enzyme mechanisms: hydrolases (NTPases), transferases, dehydrogenases

F

12/8

Evolved resistance to competitive inhibitors, allosteric inhibition

 

TBD

EXAM III (focus on Chs. 13, 15, 16, plus understanding of earlier material)