Structure, Function and Origin of Biopolymers
Chem 8853/4803, Spring, 2020
Dr. Loren Williams
School of Chemistry and Biochemistry
Georgia Tech
12:00 pm - 1:15 pm
Molecular Sciences and Engr G021
Office Hours: Pretty much always.
Office: 1309 IBB

email: loren.williams@chemistry.gatech.edu
When sending e-mail to Dr. Williams, please put the following information in the subject line:
CHEM 8853, firstname lastname, subject
Example: CHEM 8853, Tom Brady, chronic traumatic encephalopathy

Links:
building block flash cards / Elements of Loren's Style / Pymol Scripts / Download Pymol Windows / Download Pymol Mac / Pymol Commands / PDB / PDB Instructions / DNA-Dart / 3DNA / Web of Science / NCBI / Tm Calculator / Reverse Complement / Molecular weights / ApE Blast/ClustalW Instructions using Enolase / Blast Example: Ribosomal Protein L2 fasta files / ClustalW Example: Ribosomal Protein L2 ClustalW Alignment / Muscle Example: Ribosomal Protein L2 Muscle Alignment / Homology Modelling with Swiss-Model / Vienna

Course Description
This course will focus on DNA, RNA, protein and carbohydrate. One goal is to for students to learn the biochemistry and structural biology underlying laboratory control and manipulation of nucleic acids. Another goal is to understand the molecular structure of biopolymers. We will try to understand the origins of the Central Dogma and of the Molecular Symbiosis at the core of biology. A third goal of the course will teach techniques for analysis, visualization, representation and presentation of biological macromolecules. Students will learn to interpret and describe biological macromolecules and to make publication quality figures. The course is appropriate for graduate students and advanced undergraduates who have background in biochemistry and macromolecular structure. Source material is the primary literature; there is no textbook.

Grades will be determined by quizzes, presentations, projects and class participation. It is expected that students will fully participate in class discussions, read papers in advance, and become highly proficient with molecular visualization and video editing software.

Students will be required to make several presentations as individuals and in groups. In addition students must present, and submit for a grade, one or more pymol scripts that produces a series of publication quality images of a nucleic acid structure and videos that represent molecular interactions.

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Topics [in progress]

Amino Acids
Bases, sugars nucleosides and nucleotides
DNA structure
RNA Folding
RNA - Protein Interactions
DNA Polymerase
Ribozymes
PYMOL: Molecular Visualization and Analysis in 3D
Illustrator: Publication Quality Images
PYMOL, Photoshop & iMovie: Molecular Videos (Williams Draft 1 Video)

Updates

• Monday 1/7/2020
Please download and install Endnote, Pymol and the Adobe Creative Suite.
• Tuesday 1/8/2020
To do: (i) Find a relevant paper to deconstruct, send the title/authors to Dr. Williams (see email instructions above), (ii) memorize amino acid and nucleotide building blocks (see the flash card link, above), (iii) set up firefox or chrome for automatic import into endnote, download the ro pymol script and try to get it running.