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.
if say, lys and ser is side by side joined by a peptide bond, is
there H bonds between the R groups?
Usually not, due to steric factors. R group interactions are
usually, and most importantly, between non-adjacent amino acid
residues. If the only R group interactions are between adjacent
amino acid residues, then there would be no meaningful tertiary
structure, which is what gives proteins its biological function. In
which case, proteins would be useless, and you would have died even
before you were born.
Now you understand why your drawing is misleading and incorrect?
And your school teacher didn't point out this error?!? Or worse,
your school teacher taught the entire class this wrong way?!?
you mean no H bonds between adjacent lys and ser due to steric
factors, not Lys and ser cannot exist side by side due to steric
factors right?
ultima, pls take a look at pg 38 of this thread to see 2 more
posts I've posted
Yes, obviously. Lys-Ser and Ser-Lys amino acid residues certain do
exist. But R group interactions do not usually exist between
adjacent amino acid residues, and are far more important and
meaningful (in terms of tertiary structure enabling biological
function) when they occur between non-adjacent amino acid residues,
as is mostly the case.
Yes Ultima, exactly. Whole class was taught wrongly.
Ultima, that's why i am very very thankful ,of you, helping us type
out, and more importantly, Elaborate out All(small and big,
important and the nitty gritty ) the Details, and Most Importantly,
teach and correct us to learn the correct and right
education.
my only regret is i didn't discover BFJC earlier.
I Feel Very Frustrated and sad that I've discovered so much that
I've learnt throughout my life, is wrong. Happy because at least i
discover it.
i am very thankful that i receive education from BFJC, one of
the only true educators and education.
Another important skill I've acquired from BFJC is to
learn to suspect and question and double check if something is
taught wrong, and i seek clarification via books, online, and
forums.
some people don't even know they're learning the wrong
things(like me in the past, receive without critically evaluating
and discerning what I've learnt ), and once they discover,they'll
be angry and happy.
for me, I haven't been doubting Chem stuffs I've learnt until
this year, it's late, i wished i was more inquisitive and a
critical thinker last time, but better late than never
Very good, but at the end of the day, you still need to bring home
to bacon. Being physically incarnate, the highest pinnacle of
success necessitates success in all aspects of your life.
This includes academia. Even if you've now grown to understand
Chemistry more deeply than your school mates, but at the end of the
day, if you still fail to perform under examination conditions, and
still fail to score an A grade (or whatever grade is to your
personal satisfaction, for whatever goal), it means you've failed
and disappointed yourself (not others), in that you've not lived up
to your maximum potential.
For your own sake, don't disappoint yourself. Get the grade you
know you can, for this year's upcoming A levels.