CH2 Key Concepts

AAs commonly found in nature are in what form?

L form (S isomer)

Peptide bonds are commonly found in what form? Trans or cis?

Trans

Which quadrant can Beta-sheet be found in Ramachandran Plot?

1st quadrant (top L)

Which quadrant can R handed alpha-helix be found in Ramachandran Plot?

3rd quadrant (bottom L)

Which quadrant can L handed alpha-helix be found in Ramachandran Plot?

2nd quadrant (top R)

Ea residue on an alpha helix has a rise of how many Å relative to previous helix?

1.5Å

Ea residue has rotation of how many degrees/amino acids per turn of helix?

100 degrees; 3.6 AA

What at the Beta carbon destabilizes helix due to steric clashes?

Branching

Beta sheets can be ______ and _________.

parallel; antiparallel

Sequence of AA linked by peptide bonds

primary structure

Local repeating folds of the peptide backbone (eg alpha helix, beta sheet)

secondary structure

3D relationship between different polypeptide chains

quaternary structure

What is the free energy difference between folded and unfolded proteins?

~42 kJ/mol

What are the 2 steps for the Anfinsen Experiment?

1. Denature ribonuclease (enzyme) w/ urea & B-mercaptoethanol

2. Dialysis to renature

In the Anfinsen Experiment, what happens if urea is removed first?

high protein activity

In the Anfinsen Experiment, what happens when the B-mercaptoethanol is removed first?

misfolded protein and low activity