Hi Ultima, please take a look at above qn, from 2007 (can't edit
on same post cos can't find the cursor using phone hence cant type
on the post above with pic
part V)
i understand can illustrate using the pair of same amino acids,
but tcher instructed us to illustrate using pair of different amino
acids to make it more challenging
https://www.dropbox.com/s/md4v22dtowaymp1/20160714_100436-1.jpg?dl=0
Question :
https://www.dropbox.com/s/amfgl1ifmblcm99/20160714_101102-1.jpg?dl=0
drawn three lys-ser R group interactions
do we have to draw full displayed formula when showing R group
interactions?
need to show the linear H bonding between the R groups? is my
drawing of (3) acceptable?
from the Qn, HSA is a globular protein, and has a roughly
spherical shape in water, 67% of the amino acids are incorporated
into an α-helix
if need show linear H bonding , then lys and ser is one shorter
and one longer than the other,
if both R groups must originate from the same vertical starting
position, then showing linear H bonding is quite
difficult
Thanks, Ultima
You only need to fully display out the part of the R group which is
directly responsible for the R group interaction. The rest of the R
group can be condensed or skeletal.
As far as possible, always show linear H bonding. Yes, your
drawing of (3) is acceptable (except it can be improved, see next
sentence below).
Regarding originating from the same vertical starting position :
your drawing is actually misleading and incorrect.
Don't put a hypen between "lys" and "ser", it implies you
wrongly think these are 2 directly adjacent amino acid residues
(which would only be peptide bonded to each other, not H bonded by
R groups).
The way you drew it out, from the R groups from same 'starting
position', is incorrect and misleading. Because the amino acid
residues with the R group interactions will be many residues apart,
and because the polypeptide chain is non-linear (think of the
polypeptide chain as curving and twisting convolutedly all over the
place), hence you should have drawn the 2 amino acid residues as
originating from different 'starting positions' on paper, either
facing each other, or (more realistically) at an angle away from
each other. See CS Toh's diagram on the bottom of page 381
(Advanced Study Guide).
Lastly, don't forget you're attempting to translate a 3D
structure onto 2D paper. Each C-C bond is bent in 3D space, not
linear. On 2D paper, it may not always be possible to illustrate
perfect linearity (for all H bonds in all molecules), just do your
best to reflect this. Cambridge will be reasonable.
