Introduction to Biochemistry - End of session 2.1, 2.2 assessment

The interaction strength varies from ionic bond - hydrogen bond - Van der Waal's force, so hydrogen bond does not act over a longer or shorter distance, and it is not the weakest. The only difference is that because hydrogen bond is caused by a polar bond, so it is a directional force, unlike the others.

The answer is: "Hydrogen bonds are directional, both other types of noncovalent bond are not directional".

I did a similar problem before and got tricked, so I am not going to be tricked again. In this case, Arginine has a long side chain with a lot of bonds that can be rotated, none of the others can compare to.

The answer is "Arginine"

It is negatively charged, so the last two options are gone, it does not have a benzene ring, so it is not aromatic, therefore the answer is "Negatively charged, small, polar"

This is simply using the editor to create the structure again :)

There are no consecutive sequence of alpha region and beta region, therefore it is a loop.

The dotted lines are hydrogen bonds between the amide group and the carboxlate group. N is relatively electronegative than hydrogen is, so it pull the electrons to the N side and leave a partial charge on hydrogen, on the other hand, the oxygen to relatively electronegative than carbon so it leaves a partial negative charge on oxygen. So these partial charges attracts each other to form the hydrogen bond.

The hydrogen bond are useful to stabilize the structure of the alpha helix.

cis or trans conformation make sense only when we talk about double bond. The peptide bond participate in a resonance structure so that it is "sometimes " double. The sometimes double characteristics make it planar. And only on such planar structure we say cis or trans.

The bonds are mostly trans (with the exception of proline) is because of steric clashes.

The answer are: "The peptide bond has trigonal geometry" and "To prevent steric clash between adjacent R groups".

We started with the Unfolded protein, because of "Hydrophobic Effect", we dropped 140 KJ/mol. The Enthalpy change bring us another 150 KJ/mol down. However, the "Chain Conformational Entropy" drop causes us to gain 220 KJ/mol, the end state is its "Native Fold".

In step "A", Anfinsen added 8M urea ...
In step "E", Anfinsen added a small amount ...
In step "B", Anfinsen re-oxidized

In step "C" and "D", Anfinsen dialyze the protein.

The hydrophobic interaction in the protein core and the hydrogen bonding network in secondary structures are the main cooperative interactions.

The nucleation condensation model states that the hydrophobic core forms first while the diffusion collapse model states that the secondary structures forms first.

HSP70 transiently bind to nascently translated protein to avoid it binding to others.
HSP70 bind to it through interactions with hydrophobic peptides.