CHEM 156 Physical Biochemistry

Fall quarter, 2017

Lecture room: YH CS76 Lecture time: MWF (except where noted) 1:00 - 1:50 PM
Lecture recordings available through UCLA BruinCast
Website: https://ccle.ucla.edu/course/view/17F-CHEM156-1

Instructor: John Colicelli, Biological Chemistry Dept., David Geffen School of Medicine at UCLA
Office: 350C BSRB email: colicelli@mednet.ucla.edu
Office Hours: Wednesdays 4:30 6:00 PM (and by appointment)

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:
1st midterm (30%) + 2nd 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 2nd 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
st
F 9/29 Chapter 6. 1 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. 2nd 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 (Keq)
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 (KD) 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: KM, Vmax, kcat
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)