Question

A fun little brain teaser all can join! :)
TOPIC: Protein chemistry for biologists.

Answer 1

Two molecules of N‐methyl acetamide can associate to form a dimer. (structure of N‐methyl acetamide can be found in attachment as this is biology!)

1) Sketch the dimer structure, and label and name the interactions that can
stabilize it.

2) The dimerization reaction is thermodynamically much more favourable in apolar solvents than in water. Explain why that is the case, and discuss the implications for the stability of proteins.

Answer 2

https://www.twiddla.com/2471901 come ill try to draw

Answer 3

does it have something to do with not stable C-N bonds?

Answer 4

Hmmmm nope. :)

Answer 5

I'd say there are two reasons to 2) one is more intuitive the other one requires a little knowledge about the nature of hydrogen bonding

Answer 6

hydrophobic interactions are weaker than H bonds
does it have to do with that?

Answer 7

are we trying to form a pure dimer? in the sense that you dont want any interaction with solvent and u want to enclose the charged areas of this compound inside and the CH3 regions outside

Answer 8

i might be imagining too much

Answer 9

Now you are getting to something yes.

Answer 10

so the fact that we are enclosing O and N region to inner part of the forming dimer means that we are physically bringing them closer to H region that was bound to N on each compound

Answer 11

Hmmm sorta... You know a little of thermodynamics right, like Gibbs free energy?

Answer 12

yeah

Answer 13

Good; try argue in terms thermodynamics, eg. the contribution to the gibbs free energy:
\[\large \Delta G = \Delta H - T \Delta S\]

Answer 14

What happens to the enthalpy \(\Delta H\) and the entropy \(\Delta S\)?

Answer 15

entropy positive and enthalpy negative value?

Answer 16

And why? :)

Answer 17

because release of energy gotta be more than input

Answer 18

Hmmm yeah sorta. Oh well here is the solution :)

Answer 19

if gibbs free energy is negative or less than 0
u'd need less energy to create a disorder

Answer 20

thats what we want to do right?

Answer 21

negative or 0*

Answer 22

and from the looks of it we want to limit that disorder?

Answer 23

1) picture attached, note the molecule is acetamide, but the principle is the same!

2) Inside of a protein or in apolar solvent there are no competing water interactions, and the dimerization will be stronger. Also, the electrostatic nature of hydrogen bonds will be enhanced by the apolar surroundings as for example seen from Coulomb's law, where the energy is inversely proportional to the dielectric constant.

This means (and is the take home message of this brain teaser): buried hydrogen bonds will contribute substantially more to protein stability compared solvent exposed hydrogen bonds. Similarly, having buried hydrogen-bond donor or acceptors that is not involved in hydrogen bonding are destabilizing.

Answer 24

i see it does make sense

Answer 25

It does right? :D

Answer 26

yeah
i did think of this
but i didnt know how to word it lol well i tried to but i failed kinda

Answer 27

i suck at o chem hhh

Answer 28

Not always easy to phrase it no.

I got this little table actually that kinda also show the effect of the solvent:
\(
\begin{array}{|l|}
\hline
\ Solvent& \Delta H (kJ/mol)&\Delta S (J/mol*K)& \Delta G (kJ/mol)\\
\hline
Carbon~tetrachloride&-17&-45&-3.8\\
\hline
Dioxane&-3.3&-16&1.6&\\
\hline
Water &0.0&-41&12.8\\
\hline
\end{array}
\)
At 25 degrees and standard conditions.

Answer 29

yeah i see the difference now

Answer 30

And this is the reason why one of my articles are so hard :P cause I need to consider this stuff when doing electrostatics :)

Answer 31

i see it, i feel like physiology is so much easier lol