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Originally posted by UltimaOnline:
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
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Originally posted by Flying grenade:
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. -
Originally posted by Flying grenade:
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.
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In an earlier post, I mentioned that the sterics do not allow significant tertiary interactions between adjacent amino acid residues (as wrongly taught by your school teacher, and therefore unsurprisingly, probably many other Singapore JC teachers as well).
To understand this more clearly, use google images to check out alpha helices and beta-pleaded sheets (ie. the 2 most common secondary structures).
Alpha helix : https://www.google.com.sg/search?q=alpha+helix&tbm=isch
Beta-pleated sheet : https://www.google.com.sg/search?q=%CE%B2-pleated+sheet&tbm=isch
Notice that in both secondary structures (for different sterical reasons), the R groups of adjacent amino acids are oriented in 3D space (ie. sterics) away from each other, making R group interactions between adjacent amino acids difficult, minimal or downright impossible.
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Originally posted by UltimaOnline:
In an earlier post, I mentioned that the sterics do not allow significant tertiary interactions between adjacent amino acid residues (as wrongly taught by your school teacher, and therefore unsurprisingly, probably many other Singapore JC teachers as well).
To understand this more clearly, use google images to check out alpha helices and beta-pleaded sheets (ie. the 2 most common secondary structures).
Alpha helix : https://www.google.com.sg/search?q=alpha+helix&tbm=isch
Beta-pleated sheet : https://www.google.com.sg/search?q=%CE%B2-pleated+sheet&tbm=isch
Notice that in both secondary structures (for different sterical reasons), the R groups of adjacent amino acids are oriented in 3D space (ie. sterics) away from each other, making R group interactions between adjacent amino acids difficult, minimal or downright impossible.
i see !!!
yes, i was thinking of that yesterday
Thank You Ultima, for the clarification, information, details, explanation, and elaboration !
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tcher taught this
https://www.dropbox.com/s/5x9xi380i5pahph/20160715_110434-1.jpg?dl=0
comments?
My qn : NH3+ and OH group have interaction? maybe H-bonding, pd-pd, id-id, pd-id ?
no ion dipole interaction cuz OH not charged right?
amino acids (residues) have ion dipole interactions with water cos all charged, have '+' or '-' charge on atoms e.g. H+ and OH- of water, '+' on N atom of NH3+ group
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page 148 cs toh advanced guide
example 6, at bottom of page
PCl5 (g)《》PCl3(g) +Cl2 (g)
yes i understand cstoh's explanation, and understand less PCl5(g) would dissociate
noted that Kp is not affected by changes in pressure (because partial pressure or in other cases, concentration, the partialP/conc , of both reactants and products increases/decreases by same amount right? )
but i thought of what I've learnt ,read , and done questions before,
when P decrease, eqm position shift left as predicted by LCP, wouldn't conc PCl5 increase?
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Originally posted by Flying grenade:
tcher taught this
https://www.dropbox.com/s/5x9xi380i5pahph/20160715_110434-1.jpg?dl=0
comments?
My qn : NH3+ and OH group have interaction? maybe H-bonding, pd-pd, id-id, pd-id ?
no ion dipole interaction cuz OH not charged right?
amino acids (residues) have ion dipole interactions water cos all charged, have '+' or '-' charge on atoms e.g. H+ and OH- of water, '+' on N atom of NH3+ group
If the previous H bonding, the NH2 behaved as H bond acceptor, upon protonation, that particular H bond would be broken, and since the new R group interaction (eg. new ionic bond formed another amino acid R group, or new H bond formed with another amino acid R group with NH3+ as H bond donor) differs from the previous R group interaction, the tertiary structure has changed, and we say the protein has been denatured. -
Originally posted by UltimaOnline:
If the previous H bonding, the NH2 behaved as H bond acceptor, upon protonation, that particular H bond would be broken, and since the new R group interaction (eg. new ionic bond formed another amino acid R group, or new H bond formed with another amino acid R group with NH3+ as H bond donor) differs from the previous R group interaction, the tertiary structure has changed, and we say the protein has been denatured.OOOOHH OK I SEE !! understood. thanks ultima
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Originally posted by UltimaOnline:
If the previous H bonding, the NH2 behaved as H bond acceptor, upon protonation, that particular H bond would be broken, and since the new R group interaction (eg. new ionic bond formed another amino acid R group, or new H bond formed with another amino acid R group with NH3+ as H bond donor) differs from the previous R group interaction, the tertiary structure has changed, and we say the protein has been denatured.if during previous H bonding, NH2 behaved as H bond donor, upon protonation, H bond not broken?
or it is affected?
if it is affected, then
that particular H bond would be broken, and since the new R group interaction (eg. new ionic bond formed with another amino acid R group, or new H bond formed with another amino acid R group with NH3+ as H bond donor) differs from the previous R group interaction, the tertiary structure has changed, and we say the protein has been denatured.
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Originally posted by UltimaOnline:
If the previous H bonding, the NH2 behaved as H bond acceptor, upon protonation, that particular H bond would be broken, and since the new R group interaction (eg. new ionic bond formed another amino acid R group, or new H bond formed with another amino acid R group with NH3+ as H bond donor) differs from the previous R group interaction, the tertiary structure has changed, and we say the protein has been denatured.i see.
i think despite NH3+ grp have 3 H , possible to form H bonds but it will be more thermodynamically favourable to form ion dipole interactions rather than H bonds
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Originally posted by Flying grenade:
page 148 cs toh advanced guide
example 6, at bottom of page
PCl5 (g)《》PCl3(g) +Cl2 (g)
yes i understand cstoh's explanation, and understand less PCl5(g) would dissociate
noted that Kp is not affected by changes in pressure (because partial pressure or in other cases, concentration, the partialP/conc , of both reactants and products increases/decreases by same amount right? )
but i thought of what I've learnt ,read , and done questions before,
when P decrease, eqm position shift left as predicted by LCP, wouldn't conc PCl5 increase?
See see see?!? Again, I bet your school didn't teach you properly. This is one of the all too common misconceptions suffered by Singapore JC students.When pressure is changed (by changing the volume of the container), the molarities and partial pressures of the reactants and products change, hence because Kc & Kp doesn't change (since temperature doesn't change), and Qc & Qp now changes, hence position of equilibrium shifts, so as to allow Qc & Qp to equalize with Kc & Kp, to re-establish equilibrium.
In other words, position of equilibrium shifts BECAUSE Kc & Kp doesn't change. Geddit? U think ur school mates truly understand this concept / topic, when even u urself are confused?
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Originally posted by Flying grenade:
i see.
i think despite NH3+ grp have 3 H , possible to form H bonds but it will be more thermodynamically favourable to form ion dipole interactions rather than H bonds
Do you realize (no you don't, and neither do 99.9% of Singapore JC students), that depending on the exact ion and molecule (ie. case by case), the so-called ion - permanent dipole interaction (don't be lazy, there are 2 types of ion - dipole interactions) may actually be a hydrogen bond (enhanced by the formal charge present)?Positive formal charge = electron-withdrawing by induction, enhancing strength of H bond donated. Negative formal charge = more electron-rich, enhancing strength of H bond accepted.
True ion - permanent dipole interactions are inorganic (eg. Na+ and Cl- with H2O solvent) rather than organic (eg. amino acids), because you also need to consider the geometry (eg. tetrahedral) of the molecule. So understandably, Singapore JCs don't teach all these coz they (fairly enough) know Singapore JC students will be confused by all these.
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Originally posted by Flying grenade:
page 148 cs toh advanced guide
example 6, at bottom of page
PCl5 (g)《》PCl3(g) +Cl2 (g)
yes i understand cstoh's explanation, and understand less PCl5(g) would dissociate
noted that Kp is not affected by changes in pressure (because partial pressure or in other cases, concentration, the partialP/conc , of both reactants and products increases/decreases by same amount right? )
but i thought of what I've learnt ,read , and done questions before,
when P decrease, eqm position shift left as predicted by LCP, wouldn't conc PCl5 increase?
You COCONADEN!!! (more pleasant, organic vegan/vegetarian version of cockanaden)Becoz [PCl5] increases (as you mentally worked out), *THATS WHY* CS Toh wrote "less PCl5 dissociates (at equilibrium)"!!! Again, as posted earlier, this shifting of position of equilibrium is because Kc & Kp value did NOT change (since temperature didn't change).
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what are the 2 types of ion dipole interactions? ??
ion permanent dipole interactions, what's the other one??
tried to research online but can't find any meaningful results !
Ultima, help make this world a better place
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Originally posted by UltimaOnline:
Do you realize (no you don't, and neither do 99.9% of Singapore JC students), that depending on the exact ion and molecule (ie. case by case), the so-called ion - permanent dipole interaction (don't be lazy, there are 2 types of ion - dipole interactions) may actually be a hydrogen bond (enhanced by the formal charge present)?Positive formal charge = electron-withdrawing by induction, enhancing strength of H bond donated. Negative formal charge = more electron-rich, enhancing strength of H bond accepted.
True ion - permanent dipole interactions are inorganic (eg. Na+ and Cl- with H2O solvent) rather than organic (eg. amino acids), because you also need to consider the geometry (eg. tetrahedral) of the molecule. So understandably, Singapore JCs don't teach all these coz they (fairly enough) know Singapore JC students will be confused by all these.
oh yea u mentioned and wrote before
ion dipole interactions may actually be a hydrogen bond (enhanced by the formal charge present
Thanks U.O.
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Originally posted by UltimaOnline:
You COCONADEN!!! (more pleasant, organic vegan/vegetarian version of cockanaden)Becoz [PCl5] increases (as you mentally worked out), *THATS WHY* CS Toh wrote "less PCl5 dissociates (at equilibrium)"!!! Again, as posted earlier, this shifting of position of equilibrium is because Kc & Kp value did NOT change (since temperature didn't change).
omg i understand liao thanks ultima you are the next best thing to god (using this expression metaphorically, as a comparison on how i perceive and revere u,
not god as philosophically or religiously, that's another topic, another debate, another school of thought/thought process)
thx for Helping us Think and figure stuffs out
glad that u can think and ur brain zai
thx u.o.
hahahaa "Do you realize (no you don't)" i lol-ed and chuckled
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Originally posted by Flying grenade:
what are the 2 types of ion dipole interactions? ??
ion permanent dipole interactions, what's the other one??
tried to research online but can't find any meaningful results !
Ultima, help make this world a better place
Write out the FULL names for the 3 types of van der Waals forces. Then if you understand the true nature of chemical bonding, the other type of ion - dipole interaction becomes obvious. -
Originally posted by Flying grenade:
omg i understand liao thanks ultima you are the next best thing to god (using this expression metaphorically, as a comparison on how i perceive and revere u,
not god as philosophically or religiously, that's another topic, another debate, another school of thought/thought process)
thx for Helping us Think and figure stuffs out
glad that u can think and ur brain zai
thx u.o.
hahahaa "Do you realize (no you don't)" i lol-ed and chuckled
God exists, it's just that religion (ie. all religions) got the definition of God wrong. Or if you prefer, whether God exists or not, depends on how you define God. -
Originally posted by UltimaOnline:
Write out the FULL names for the 3 types of van der Waals forces. Then if you understand the true nature of chemical bonding, the other type of ion - dipole interaction becomes obvious.ion (instantaneous) induced dipole interactions
thanks Ultima for guiding on how to think !!!!!!!!!
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Originally posted by Flying grenade:
ion (instantaneous) induced dipole interactions
thanks Ultima for guiding on how to think !!!!!!!!!
Eh no (instantaneous) lah. The following are the interactions between ion and ion, ion and polar molecule, ion and non-polar molecule, polar molecule and polar molecule, polar molecule and non-polar molecule, non-polar molecule and non-polar molecule, arranged from strongest to weakest, ceteris paribus.ion - ion (ie. ionic bonding)
ion - permanent dipole
ion - induced dipole
permanent dipole - permanent dipole
permanent dipole - induced dipole
instantaneous dipole - induced dipole
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Originally posted by UltimaOnline:
Eh no (instantaneous) lah. The following are the interactions between ion and ion, ion and polar molecule, ion and non-polar molecule, polar molecule and polar molecule, polar molecule and non-polar molecule, non-polar molecule and non-polar molecule, arranged from strongest to weakest, ceteris paribus.ion - ion (ie. ionic bonding)
ion - permanent dipole
ion - induced dipole
permanent dipole - permanent dipole
permanent dipole - induced dipole
instantaneous dipole - induced dipolegreat (best) summary !!!
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for the protonation of amines(no matter 1°, 2° , or 3°) ,
it's amine attack the H+ right?
not H+ attack amine right?
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Originally posted by Flying grenade:
for the protonation of amines(no matter 1°, 2° , or 3°) ,
it's amine attack the H+ right?
not H+ attack amine right?
The term "attack" is flexible, and can be used either way. But in terms of electron-flow mechanism, obviously you know only who can attack who. -
must unhybridised p orbital be an empty p orbital?
must an empty p orbital be unhybridised an p orbital?
lone pair resides in unhybridised p orbital
OBVIOUSLY THE ORBITAL IS NOT EMPTY