BBS501 Section 1
Lecturers: Yie-Hwa Chang
DRC Room 515
Phone: #79263
E-mail:
Tomasz Heyduk
DRC Room 425
Phone: #79238
E-mail:
Rachel Hickey
DRC Room 435
Phone: #79237
E-mail:
Section director: Tomasz Heyduk
Lectures 1: Review of thermodynamics (I)
Lecturer: Tomasz Heyduk Date: 08/24/15 9-10 AM
Suggested reading: Biochemistry, Goeffrey L. Zubay (4th edition), chapter 2.
Biochemistry, Donald and Judith Voet (2nd edition), chapter 3.
Molecular Biology of the Cell, Alberts et al (4th ed.)., chapter 2.
OUTLINE
1. Criteria for spontaneity:
· both energy and entropy are important for determining the direction of the process
· free energy
2. Applications of free energy calculations in biochemistry:
· calculation of free energy change of the reaction from known standard free energies of formation
· driving the unfavorable reactions by coupling to favorable processes
3. Examples of entropy changes in some biologically important processes:
· entropy changes of mixing
· entropy changes of solvation
· entropy changes of ionization
· entropy changes of protein-ligand complex formation
4. Example of entropy-driven biologically important effects
· hydrophobic effect
· polyanion effect
Lecture 2: Review of thermodynamics (II).
Lecturer: Tomasz Heyduk Date: 08/25/15 9-10 AM
Suggested reading: Biochemistry, Goeffrey L. Zubay (4th edition), chapter 8.
Biochemistry, Donald and Judith Voet (2nd edition), chapter 3.
Molecular Biology of the Cell, Alberts et al (4th ed.)., chapter 2.
OUTLINE
1. Temperature dependence of free energy.
· heat capacity
· enthalpy-entropy compensation
2. Concentration-dependence of free energy
· free energy change of dilution
3. Free energy and equilibrium constant
· -temperature dependence of equilibrium constant
· -how thermodynamic parameters are determined
Lecture 3: Chemical equilibrium (I)
Lecturer: Rachel Hickey Date: 08/26/15 9-10 AM
Suggested reading: Physical Biochemistry, D. Freifelder, chapter 18.
OUTLINE
1. Basic properties of the equilibrium constant.
2. Bimolecular binding reaction
3. Determining equilibrium constant for bimolecular binding reaction.
4. Equilibrium vs kinetics.
5. Transition-state theory of chemical reactions in solution.
6. Basic laws of chemical kinetics.
Lecture 4: Chemical equilibrium (II).
Lecturer: Rachel Hickey Date: 08/27/15 9-10 AM
Suggested reading: Physical Biochemistry, D. Freifelder, chapter 18.
OUTLINE
1. Positive and negative cooperativity:
· biological significance of cooperativity
2. Molecular interpretations of cooperativity:
· direct interaction between bound ligands
· indirect effects - allostery
3. Models of allosteric protein:
· Monod-Wyman-Changeux (MWC) model
· Koshalnd-Nemethy-Filmer (KNF) model
· allosteric inhibitors and allosteric activators
4. Macromolecular interactions: test tube vs cell
· macromolecular crowding
Lecture 5: Hydrodynamic properties of macromolecules
Lecturer: Tomasz Heyduk Date: 08/28/15 9-10 AM
Assigned reading: Physical Biochemistry, D. Freifelder, chapter 9 and 11.
OUTLINE
1. Diffusion of macromolecules in solution:
· concentration gradient dependence
· viscosity dependence
· size and shape dependence
· rotational diffusion
2. Determination of hydrodynamic properties of macromolecules
· movement of macromolecules in solution under external force
· analytical centrifuge
· concentration dependence of sedimentation coefficient
· light scattering and correlation spectroscopies
3. Effect of cellular environment on hydrodynamic properties of macromolecules.
Lecture 6: Structure and biophysics of nucleic acids.
Lecturer: Tomasz Heyduk Date: 08/31/15 9-10 AM
Suggested reading: Biochemistry, Goeffrey L. Zubay (4th edition), chapter 30.
Biochemistry, Donald and Judith Voet (2nd edition), chapter 28.
DNA: Structure and Function@, R.R. Sinden, chapter 1 and 2.
Molecular Biology of the Cell, Alberts et al (4th ed.)., chapter 4.
OUTLINE
1. Chemical structure of nucleic acids:
· purine and pyrimidine bases
2. Base-paring and higher order structure:
· Watson-Crick base pairs
· comparison of B-DNA and A-DNA helices
· accessibility of functional groups in DNA duplex
· alternative base pairing: formation of DNA triple helices
3. Stability of DNA duplex
4. Diversity of biological functions of nucleic acids.
Lecture 7: Analysis of nucleic acid sequence.
Lecturer: Tomasz Heyduk Date: 09/01/15 9-10 AM
Suggested reading: Metzker, M.L. Nature Rev. Genetics 11, 31, 2010.
OUTLINE
1. DNA sequencing technologies
2. Next Generation Sequencing
3. Microarrays
4. Examples of biological applications of modern techniques for the analysis of nucleic acid sequence:
· analysis of the transcriptome
· genome-wide analysis of protein binding to chromatin.
Lecture 8: Protein Folding
Lecturer: Yie-Hwa Chang Date: 09/02/15 9-10 AM
Suggested reading: Biochemistry, Jeremy Berg et al, sixth edition, chapter 2.
OUTLINE
1. Secondary Structure: The alpha-helix, the beta-sheet, turns and loops.
2. Tertiary Structure:
3. Quaternary Structure:
4. The amino acid sequence determines its three-dimensional structure
Lecture 9: Exploring Proteins and proteomes (I)
Lecturer: Yie-Hwa Chang Date: 09/03/15 9-10 AM
Suggested reading: Biochemistry, Jeremy Berg (6th edition), chapter 3.
OUTLINE
1. Purification of Proteins:
· The assay
· Total protein extract
· Protein purification
· Gel electrophoresis
· Protein quantification
2. Determination of amino acid sequence:
· Protein cleavage
· Edman degradation
3. Immunology and protein characterization
Lecture 10: Exploring Proteins and proteomes (II)
Lecturer: Yie-Hwa Chang Date: 09/04/15 9-10 AM
Suggested reading: Biochemistry, Jeremy Berg (6th edition), chapter 3.
OUTLINE
1. The basics of MALDI-TOF MS
2. The basics of ESI-MS
3. Liquid chromatography
4. Protein identification and quantification by MS
5. Protein modifications
6. Proteomics analysis of protein expression
Lecture 11: Exploring Proteins and proteomes (III)
Lecturer: Yie-Hwa Chang Date: : 09/08/15 9-10 AM
Suggested reading: Biochemistry, Jeremy Berg (6th edition), chapter 3.
OUTLINE
1. X-ray crystallography reveals three-dimensional structure in atomic detail
2. Nuclear Magnetic resonance spectroscopy can reveal the structures of proteins in solution
Lecture 12. Biophysical underpinning of protein function
Lecturer: Tomasz Heyduk Date 09/09/15 9-10 AM
Suggested reading: Hilser, V. J. Nature 498, 208, 2013.
Bullock et al. PNAS 94, 14338, 1997.
Dill, K.A. and Chan, H.S. Nature Structural Biology, 4, 10, 1997.
OUTLINE
1. Thermodynamic stability of native protein conformation.
2. Conformational flexibility of proteins.
3. Proteins as ensembles of conformational states:
· energy funnel view of protein folding
· alternative view of protein allostery
Lecture 13: Enzymes
Lecturer: Tomasz Heyduk Date: 09/10/15 9-10 AM
Suggested reading: Biochemistry, Goeffrey L. Zubay (4th edition), chapter 8-10.
Biochemistry, Jeremy Berg (6th edition), chapter 8.
OUTLINE
1. Chemical catalysis
2. Kinetics of enzymecatalyzed reactions
· The MichaelisMenten treatment of enzyme kinetics
· The steadystate model of enzyme kinetics
· Experimental measurements of Km and kcat
· Significance of Km and kcat constants
3. Enzyme Inhibition
· Reversible competitive, noncompetitive and uncompetitive inhibitors
· Irreversible inhibitors
Lecture 14: Investigation of macromolecule function one molecule at a time.
Lecturer: Tomasz Heyduk Date: 09/11/15 9-10 AM
Suggested reading: Single-molecule biophysics: at the interface of biology, physics and chemistry. J. R. Soc. Interface, 2008 5, doi: 10.1098/rsif.2007.1021.
OUTLINE
1. Why study the behavior of single molecules?
2. Overview of techniques for studying macromolecules at a single molecule level.
3. Examples of the insights into the behavior of macromolecules enabled by single molecule approaches.
· single molecule enzymology
· protein folding
Wednesday, September 16: EXAM