Structure, Function and Origin of Biopolymers
Chem 8853/4803, Spring, 2016
Dr. Loren Williams
School of Chemistry and Biochemistry
Georgia Tech

Links:
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 and protein. 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. In addition, the course will teach techniques for analysis, visualization and representation of biological macromolecules. Students will learn to make publication quality figures of DNA/RNA/protein. 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

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)

tRNA Project
pdb student 1 student 2 student 3
2ZUE Crisan, Cristian - -
1J1U Tjen, Kelsey - -
4RDX Meers, Chance Penev, Petar -
5CCB Mestre Fos, Santi Colinas, Adriana -
1U0B Pang, Han Lin, Chris -
4ARC Wagner, Samuel Eichstedt, Dedra -
4YYE Ledford, Keri Sha, Ying -
4YCO Hu, Rebecca - -
1FFY Madani, Nima Ku, Hsinying Davis, Kevin

Polymerase Project

Nakamura, T., Zhao, Y., Yamagata, Y., Hua, Y.-j., and Yang, W. (2012) Watching DNA polymerase [eegr] make a phosphodiester bond, Nature 487, 196-201 [PDF] [Supplementary Materials].

pdb scene # student 1 student 2
4ECQ 1 Crisan, Cristian Eichstedt, Dedra
4ECR 2 Hu, Rebecca Colinas, Adriana
4ECS 3 Lin, Chris Madani, Nima
4ECT 4 Meers, Chance Mestre Fos, Santi
4ECU 5 Pang, Han Penev, Petar
4ECV 6 Tjen, Kelsey Wagner, Samuel
4ECW 7 Davis, Kevin Sha, Ying
4ECX 8 Ledford, Keri Ku, Hsinying

Students in the Class
Crisan, Cristian
Davis, Kevin
Eichstedt, Dedr
Hu, Rebecca
Ku, Hsinying
Ledford, Keri
Lin, Chris
Madani, Nima
Meers, Chance
Mestre Fos, Santi
Pang, Han
Penev, Petar
Sha, Ying
Tjen, Kelsey
Wagner, Samuel
Colinas, Adriana