Course Syllabus
Course summary:
This an upper-level course designed to introduce you to the principle biophysical methods used to characterize proteins and nucleic acids. This course will provide a survey of old-school and up-and-coming methods in biophysics. Additionally, you will learn to read, interpret, and discuss scientific literature related to the biophysical methods being presented.
Learning objectives:
After taking this course, you should be able to:
- Analyze, interpret, and discuss scientific literature.
- Design experiments to test biophysical properties of macromolecules.
- Critique biophysical methods (strengths/weaknesses).
- Interrogate structures and sequences of macromolecules.
- Write concise, critical reviews of assigned papers and present findings to your peers.
Course Design:
Science has actually demonstrated that we learn more when we are actively engaged in the learning process. That being said, I will lecture on physical methods in biochemistry. However, each of these lectures will include an activity, problem set, or question to work on in small groups. Additionally, we will discuss a paper in depth after every second lecture. We will have three midterm exams during the semester. These exams will require you to apply the logic and concepts we have discussed in class. We will also have several pop quizzes throughout the semester. The pop quizzes will be counted as bonus points. If you have been following along with the material in class, you should be well-prepared for both the exams and pop quizzes.
Download full syllabus here.
Course Summary:
Date | Details | Due |
---|---|---|
Thu Aug 27, 2020 | Calendar Event Fa20 - PHYSICAL METHODS OF BIOCHEM (54310) | 11am to 12:30pm |
Calendar Event Introduction to course: Why study biophysical methods? / Properties of proteins | 11am to 12:30pm | |
Assignment Pop quiz 2 | due by 11:59pm | |
Tue Sep 1, 2020 | Calendar Event Fa20 - PHYSICAL METHODS OF BIOCHEM (54310) | 11am to 12:30pm |
Calendar Event Properties of proteins II, nucleic acids, DNA sequencing, and microarrays | 11am to 12:30pm | |
Calendar Event Office Hours - Fa20 - PHYSICAL METHODS OF BIOCHEM (54310) | 3pm to 4pm | |
Thu Sep 3, 2020 | Calendar Event Caitie Office Hours Fa20 - PHYSICAL METHODS OF BIOCHEM (54310) | 10am to 11am |
Calendar Event Fa20 - PHYSICAL METHODS OF BIOCHEM (54310) | 11am to 12:30pm | |
Calendar Event Paper discussion: Quantitative monitoring of gene expression patterns with a complementary DNA microarray. | 11am to 12:30pm | |
Assignment Journal article summary 1 | due by 11am | |
Assignment Journal article presentation 1 | due by 12:20pm | |
Tue Sep 8, 2020 | Calendar Event DNA cloning, protein expression, and purification | 11am to 12:30pm |
Calendar Event Fa20 - PHYSICAL METHODS OF BIOCHEM (54310) | 11am to 12:30pm | |
Calendar Event Office Hours - Fa20 - PHYSICAL METHODS OF BIOCHEM (54310) | 3pm to 4pm | |
Thu Sep 10, 2020 | Calendar Event Caitie Office Hours Fa20 - PHYSICAL METHODS OF BIOCHEM (54310) | 10am to 11am |
Calendar Event Fa20 - PHYSICAL METHODS OF BIOCHEM (54310) | 11am to 12:30pm | |
Calendar Event Gel electrophoresis | 11am to 12:30pm | |
Assignment Pop quiz 3 | due by 11:15am | |
Tue Sep 15, 2020 | Calendar Event Fa20 - PHYSICAL METHODS OF BIOCHEM (54310) | 11am to 12:30pm |
Calendar Event Paper discussion: ATP-dependent recognition of eukaryotic origins of DNA replication by a multiprotein complex. | 11am to 12:30pm | |
Assignment Journal article summary 2 | due by 11am | |
Assignment Journal article presentation 2 | due by 12:25pm | |
Calendar Event Office Hours - Fa20 - PHYSICAL METHODS OF BIOCHEM (54310) | 3pm to 4pm | |
Thu Sep 17, 2020 | Calendar Event Caitie Office Hours Fa20 - PHYSICAL METHODS OF BIOCHEM (54310) | 10am to 11am |
Calendar Event Chromatography | 11am to 12:30pm | |
Calendar Event Fa20 - PHYSICAL METHODS OF BIOCHEM (54310) | 11am to 12:30pm | |
Tue Sep 22, 2020 | Calendar Event Fa20 - PHYSICAL METHODS OF BIOCHEM (54310) | 11am to 12:30pm |
Calendar Event Mass spectrometry | 11am to 12:30pm | |
Calendar Event Office Hours - Fa20 - PHYSICAL METHODS OF BIOCHEM (54310) | 3pm to 4pm | |
Thu Sep 24, 2020 | Calendar Event Caitie Office Hours Fa20 - PHYSICAL METHODS OF BIOCHEM (54310) | 10am to 11am |
Calendar Event Fa20 - PHYSICAL METHODS OF BIOCHEM (54310) | 11am to 12:30pm | |
Calendar Event Paper discussion: Separation and characterization of factors mediating accurate transcription by RNA polymerase Il. | 11am to 12:30pm | |
Assignment Journal article summary 3 | due by 11am | |
Assignment Journal article presentation 3 | due by 12:20pm | |
Tue Sep 29, 2020 | Calendar Event Fa20 - PHYSICAL METHODS OF BIOCHEM (54310) | 11am to 12:30pm |
Assignment Exam 1 | due by 12:20pm | |
Calendar Event Office Hours - Fa20 - PHYSICAL METHODS OF BIOCHEM (54310) | 3pm to 4pm | |
Thu Oct 1, 2020 | Calendar Event Caitie Office Hours Fa20 - PHYSICAL METHODS OF BIOCHEM (54310) | 10am to 11am |
Calendar Event Determining concentrations and folding of nucleic acids and proteins. | 11am to 12:30pm | |
Calendar Event Fa20 - PHYSICAL METHODS OF BIOCHEM (54310) | 11am to 12:30pm | |
Sun Oct 4, 2020 | Assignment Nobel prize nomination and defense | due by 11pm |
Tue Oct 6, 2020 | Calendar Event CD and fluorescence spectroscopy | 11am to 12:30pm |
Calendar Event Fa20 - PHYSICAL METHODS OF BIOCHEM (54310) | 11am to 12:30pm | |
Calendar Event Office Hours - Fa20 - PHYSICAL METHODS OF BIOCHEM (54310) | 3pm to 4pm | |
Thu Oct 8, 2020 | Calendar Event Caitie Office Hours Fa20 - PHYSICAL METHODS OF BIOCHEM (54310) | 10am to 11am |
Calendar Event Fa20 - PHYSICAL METHODS OF BIOCHEM (54310) | 11am to 12:30pm | |
Calendar Event Paper discussion: Panorama of ancient metazoan macromolecular complexes. | 11am to 12:30pm | |
Assignment Journal article summary 4 | due by 11am | |
Assignment Journal article presentation 4 | due by 12:20pm | |
Tue Oct 13, 2020 | Calendar Event Fa20 - PHYSICAL METHODS OF BIOCHEM (54310) | 11am to 12:30pm |
Calendar Event FRET and introduction to single molecule approaches | 11am to 12:30pm | |
Calendar Event Office Hours - Fa20 - PHYSICAL METHODS OF BIOCHEM (54310) | 3pm to 4pm | |
Thu Oct 15, 2020 | Calendar Event Caitie Office Hours Fa20 - PHYSICAL METHODS OF BIOCHEM (54310) | 10am to 11am |
Calendar Event Fa20 - PHYSICAL METHODS OF BIOCHEM (54310) | 11am to 12:30pm | |
Calendar Event Optical tweezers | 11am to 12:30pm | |
Assignment Pop quiz 4 | due by 11:12am | |
Sat Oct 17, 2020 | Calendar Event Fa20 - PHYSICAL METHODS OF BIOCHEM (54310) | 10am to 11am |
Sun Oct 18, 2020 | Calendar Event Fa20 - PHYSICAL METHODS OF BIOCHEM (54310) | 10am to 11am |
Tue Oct 20, 2020 | Calendar Event Fa20 - PHYSICAL METHODS OF BIOCHEM (54310) | 11am to 12:30pm |
Calendar Event Paper discussion: Kinesin Walks Hand- Over-Hand. | 11am to 12:30pm | |
Assignment HW 1 | due by 11am | |
Assignment Journal article summary 5 | due by 11am | |
Assignment Journal article presentation 5 | due by 12:25pm | |
Calendar Event Office Hours - Fa20 - PHYSICAL METHODS OF BIOCHEM (54310) | 3pm to 4pm | |
Thu Oct 22, 2020 | Calendar Event Caitie Office Hours Fa20 - PHYSICAL METHODS OF BIOCHEM (54310) | 10am to 11am |
Calendar Event Fa20 - PHYSICAL METHODS OF BIOCHEM (54310) | 11am to 12:30pm | |
Calendar Event Ligand binding I: surface plasmon resonance and anisotropy | 11am to 12:30pm | |
Sat Oct 24, 2020 | Calendar Event Fa20 - PHYSICAL METHODS OF BIOCHEM (54310) | 10am to 11am |
Sun Oct 25, 2020 | Calendar Event Fa20 - PHYSICAL METHODS OF BIOCHEM (54310) | 10am to 11am |
Tue Oct 27, 2020 | Calendar Event Fa20 - PHYSICAL METHODS OF BIOCHEM (54310) | 11am to 12:30pm |
Calendar Event Ligand binding II: isothermal titration calorimetry and anisotropy | 11am to 12:30pm | |
Assignment Pop quiz 5 | due by 11:13am | |
Calendar Event Office Hours - Fa20 - PHYSICAL METHODS OF BIOCHEM (54310) | 3pm to 4pm | |
Thu Oct 29, 2020 | Calendar Event Caitie Office Hours Fa20 - PHYSICAL METHODS OF BIOCHEM (54310) | 10am to 11am |
Calendar Event Fa20 - PHYSICAL METHODS OF BIOCHEM (54310) | 11am to 12:30pm | |
Calendar Event Paper discussion: In vitro selection of RNA molecules that bind specific ligands | 11am to 12:30pm | |
Assignment Journal article summary 6 | due by 11am | |
Assignment Journal article presentation 6 | due by 12:25pm | |
Sat Oct 31, 2020 | Calendar Event Fa20 - PHYSICAL METHODS OF BIOCHEM (54310) | 10am to 11am |
Sun Nov 1, 2020 | Calendar Event Fa20 - PHYSICAL METHODS OF BIOCHEM (54310) | 10am to 11am |
Tue Nov 3, 2020 | Calendar Event 11/03/20 X-ray crystallography: theory | 11am to 12:30pm |
Calendar Event Fa20 - PHYSICAL METHODS OF BIOCHEM (54310) | 11am to 12:30pm | |
Assignment HW 2 | due by 11am | |
Calendar Event Office Hours - Fa20 - PHYSICAL METHODS OF BIOCHEM (54310) | 3pm to 4pm | |
Thu Nov 5, 2020 | Calendar Event Caitie Office Hours Fa20 - PHYSICAL METHODS OF BIOCHEM (54310) | 10am to 11am |
Calendar Event Fa20 - PHYSICAL METHODS OF BIOCHEM (54310) | 11am to 12:30pm | |
Assignment Exam 2 | due by 12:20pm | |
Sat Nov 7, 2020 | Calendar Event Fa20 - PHYSICAL METHODS OF BIOCHEM (54310) | 10am to 11am |
Sun Nov 8, 2020 | Calendar Event Fa20 - PHYSICAL METHODS OF BIOCHEM (54310) | 10am to 11am |
Tue Nov 10, 2020 | Calendar Event Fa20 - PHYSICAL METHODS OF BIOCHEM (54310) | 11am to 12:30pm |
Calendar Event X-ray crystallography: practical applications and workshop | 11am to 12:30pm | |
Calendar Event Office Hours - Fa20 - PHYSICAL METHODS OF BIOCHEM (54310) | 3pm to 4pm | |
Thu Nov 12, 2020 | Calendar Event Caitie Office Hours Fa20 - PHYSICAL METHODS OF BIOCHEM (54310) | 10am to 11am |
Calendar Event Fa20 - PHYSICAL METHODS OF BIOCHEM (54310) | 11am to 12:30pm | |
Calendar Event Paper discussion: The Structural Basis of Ribosome Activity in Peptide Bond Synthesis | 11am to 12:30pm | |
Assignment Journal article summary 7 | due by 11am | |
Assignment Journal article presentation 7 | due by 12:25pm | |
Sat Nov 14, 2020 | Calendar Event Fa20 - PHYSICAL METHODS OF BIOCHEM (54310) | 10am to 11am |
Sun Nov 15, 2020 | Calendar Event Fa20 - PHYSICAL METHODS OF BIOCHEM (54310) | 10am to 11am |
Tue Nov 17, 2020 | Calendar Event Electron microscopy: theory | 11am to 12:30pm |
Calendar Event Fa20 - PHYSICAL METHODS OF BIOCHEM (54310) | 11am to 12:30pm | |
Assignment Pop quiz 6 | due by 11:29am | |
Calendar Event Office Hours - Fa20 - PHYSICAL METHODS OF BIOCHEM (54310) | 3pm to 4pm | |
Thu Nov 19, 2020 | Calendar Event Caitie Office Hours Fa20 - PHYSICAL METHODS OF BIOCHEM (54310) | 10am to 11am |
Calendar Event Fa20 - PHYSICAL METHODS OF BIOCHEM (54310) | 11am to 12:30pm | |
Assignment Exam 3 practical | due by 12:20pm | |
Assignment Pop quiz 7 | due by 12:20pm | |
Sat Nov 21, 2020 | Calendar Event Fa20 - PHYSICAL METHODS OF BIOCHEM (54310) | 10am to 11am |
Sun Nov 22, 2020 | Calendar Event Fa20 - PHYSICAL METHODS OF BIOCHEM (54310) | 10am to 11am |
Tue Nov 24, 2020 | Calendar Event Computational approaches | 11am to 12:30pm |
Calendar Event Fa20 - PHYSICAL METHODS OF BIOCHEM (54310) | 11am to 12:30pm | |
Assignment Pop quiz 8 | due by 11:20am | |
Calendar Event Office Hours - Fa20 - PHYSICAL METHODS OF BIOCHEM (54310) | 3pm to 4pm | |
Thu Nov 26, 2020 | Calendar Event Caitie Office Hours Fa20 - PHYSICAL METHODS OF BIOCHEM (54310) | 10am to 11am |
Sat Nov 28, 2020 | Calendar Event Fa20 - PHYSICAL METHODS OF BIOCHEM (54310) | 10am to 11am |
Sun Nov 29, 2020 | Calendar Event Fa20 - PHYSICAL METHODS OF BIOCHEM (54310) | 10am to 11am |
Tue Dec 1, 2020 | Calendar Event Electron microscopy: workshop | 11am to 12:30pm |
Calendar Event Fa20 - PHYSICAL METHODS OF BIOCHEM (54310) | 11am to 12:30pm | |
Assignment Pop quiz 9 | due by 12:20pm | |
Calendar Event Office Hours - Fa20 - PHYSICAL METHODS OF BIOCHEM (54310) | 3pm to 4pm | |
Thu Dec 3, 2020 | Calendar Event Caitie Office Hours Fa20 - PHYSICAL METHODS OF BIOCHEM (54310) | 10am to 11am |
Calendar Event Fa20 - PHYSICAL METHODS OF BIOCHEM (54310) | 11am to 12:30pm | |
Calendar Event Paper discussion: Structural basis for the subunit assembly of the anaphase-promoting complex | 11am to 12:30pm | |
Assignment Pop quiz 10 | due by 12:20pm | |
Sat Dec 5, 2020 | Calendar Event Fa20 - PHYSICAL METHODS OF BIOCHEM (54310) | 10am to 11am |
Sun Dec 6, 2020 | Calendar Event Fa20 - PHYSICAL METHODS OF BIOCHEM (54310) | 10am to 11am |
Assignment Exam 2 bonus points (yay!) | ||
Assignment Pop quiz 1 |