CMB 311 Study Guide - Midterm Guide: Ramachandran Plot, Beta Sheet, Pancreatic Ribonuclease

• School: URI
• Department: Cell and Molecular Biology
• Course: CMB 311
• Professor: Steven Gregory

Document Summary

Review: functional groups, hydroxyl, methyl, methylene, amino, aldehyde, ketone, carboxyl groups are acidic , give up protons, henderson-hasselbalch equation, when ph = pka the the value is 1. Peptide and 2 bonds on either side of alpha carbon: 2 bonds phi and si, ramachandran plot, plotting phi vs si angle. Light green favorable: dark green most favorable, secondary structures of proteins, all residue clusters. A-helix and beta sheet: know their structure, entirely hydrogen bonds(structure, phi and si different for both, right handed helix. Antiparallel and parallel beta sheets equally favorable: ribonuclease a, treated with urea. Proteins unfold/denature in urea: remove urea; protein will refold in native conformation, protein denaturation and refolding, as certain parts of protein fold, likelihood of interactions happening. Protein folding is cooperative : myoglobin and hemoglobin, myoglobin is a monomer and binds oxygens, binding of o2 is not cooperative ( cant communicate with other myoglobin cause its a monomer, hyperbolic curve, small kd, binds tightly.