Uploaded November 2021 | Updated September 2026, 1 hour ago
Dr. KP takes you through the arrow pushing for the final 5 steps of glycolysis. These reactions are part of the energy-yielding payoff phase of the pathway!
00:00 Intro
00:24 Glyceraldehyde-3-phosphate dehydrogenase
04:47 Phosphoglycerate kinase
05:46 Phosphoglycerate mutase
07:14 Enolase
08:45 Pyruvate kinase
REFERENCES:
• Appling, D. R., Anthony-Cahill, S. J., & Mathews, C. K. (2016). Biochemistry: Concepts and connections. Pearson Education.
• McMurry, J., Begley, T. P., & Begley, T. (2005). The organic chemistry of biological pathways. Roberts and Company Publishers.
Dr. KP takes you through the arrow pushing for the final 5 steps of glycolysis. These reactions are part of the energy-yielding payoff phase of the pathway!
00:00 Intro
00:24 Glyceraldehyde-3-phosphate dehydrogenase
04:47 Phosphoglycerate kinase
05:46 Phosphoglycerate mutase
07:14 Enolase
08:45 Pyruvate kinase
REFERENCES:
• Appling, D. R., Anthony-Cahill, S. J., & Mathews, C. K. (2016). Biochemistry: Concepts and connections. Pearson Education.
• McMurry, J., Begley, T. P., & Begley, T. (2005). The organic chemistry of biological pathways. Roberts and Company Publishers.






![PyMOL 101, Lesson 3: File Types and Saving – Publication Quality Figures & Scenes
In this lesson, KP takes you through the input and output PyMOL files, how to save your session, how to export a high-quality PNG image. Finally, we’ll learn to save scenes, preserving the different renderings and views as you work through this tutorial.
00:00 Intro
00:21 PDB and CIF files
01:41 Publication quality image guidelines and saving
04:41 Saving scenes in a PyMOL session
REFERENCES
• Rachel Kramer Green, Beginner’s Guide to PDB Structures and the PDBx/mmCIF Format https://pdb101.rcsb.org/learn/guide-to-understanding-pdb-data/beginner%E2%80%99s-guide-to-pdb-structures-and-the-pdbx-mmcif-format
• PDB ID: 3uyn
• Elder, I., Fisher, Z., Laipis, P. J., Tu, C., McKenna, R., & Silverman, D. N. (2007). Structural and kinetic analysis of proton shuttle residues in the active site of human carbonic anhydrase III. PROTEINS: Structure, Function, and Bioinformatics, 68(1), 337-343.
***COMMAND LINE CODE to recreate the Lesson 2 structure***
fetch 3UYN, type=pdb1, multiplex=1
select zn, resn zinc
sele active, resi 5+7+62+64+67+94+96+119+199+200]
show sticks, active
zoom active
select active_water, ((resi 5+7+62+64+67+94+96+119+199+200, resn Zn)around 3.3) and(resn HOH)
hide nonbonded
show spheres, active_water
alter active_water, vdw=0.5
rebuild
hide sticks, name c+o+n PyMOL 101, Lesson 3: File Types and Saving – Publication Quality Figures & Scenes](https://i.ytimg.com/vi/ymkw7UMUnBw/mqdefault.jpg)

