3b Flashcards
what groups can be found in the side R chain
there can be ionisable groups in the side R chain
at pH 7,, what forms are the COOH and the NH2 in
the COOH is in the coo- state
the NH2 is in the NH3+ state
what amino acids are usually found in the protein surface aka near water
the amino acids with NH2//NH3 in their side chains
when does ph = pka
when the conc of a- and ha are the same
whats the ph and pka equation
ph = pka + log([a-]/[ha])
when is ph>pka
when theres u have [a-] > [ha]
high ph = more base = more nh3 become nh2 so u get more conjugate base of the acid
more conj base also bc u have nh2 and coo- whoch are both the conjugate bases
when is ph< pka
when u have more acid than conj base
[ha]>[a-]
bc at low ph the nh3 = nh3 and the coo- becomes cooh
so more cooh,, carb acid,, than the conjugate base.
when is smt a stronger base
when its hard to pull a H off it
when its positive charge can be shared between more things via resonance!!
so ignore if the nh3+ is only bonded to alkyl chains bc they cant offer any resonance stabilisation
describe the ph titration curves,, why is there a slow increase curve,, then a straight up line,, and then once again a slow increase.
y axis = ph
x axis = amount of OH-
bc at the beginning u have nh3 and cooh bc its very acidic to begin with
as u add more OH,, the ph increases but slowly,, bc the cooh aka the acid is reacting with the OH.
once the oh has reacted with all the cooh,, adding more oh will increase the ph insanely fast. bc theres nothing for it to react with
nothing to react with until we ge tto the pka of the ammonium ion. nh3+. adding more oh will then slowly increase the ph again bc the oh starts reacting with the nh3+ and removing a H+ to from NH2.
then theres another great increase of ph with oh addition due to it reacting with all the NH3+.
what is the middle part of the titration // ph graph
its the sharp increase in temp evem if we only add a small amount of the oh.
bc the compound is in its zwitterionic form.
ITS THE PI AKA ISOELECTRIC POINT
what part of the ph titration graph is the pi part
the sharp increase in the middle.
this is the pi // isoelectric point
this is where the compound is in its zwitterionic state
aka u have coo- and nh3+
what is the pi // isoelectric point between
its between the pka of the cooh and nh2
how do we find the pi value
pka1 + pka2 / 2
we take the average of the 2 pka points
what does the pi of 6.2 tell us
it tells us that at ph 6.2,, the complex is in its zwitterionic form,, aka the net charge will be 0.
a polar molecule and water relationship
a polar compound loves water and is hydrophilic bc it can form hydrogen bonds with it meaning its soluble in the water
a non polar compound and water relationship
cannot form hydrogen bonds with the water meanig its not soluble in the water which means its more likely to form a precipitate then to dissolve in it.
can the pka of 2 coo- in a compound differ
yes!! the one alpha to the nh3+ will have a lower pka
bc its more acidic bc its closer to the nh3+ which can stabilise the negative charge more
the group with the lowest pka will what
this will be the group that gets affected first,, normally its cooh which will turn into coo- once the pka is reached.
this is bc the lowest pka value is the most acidic one,, meaning it will release a H+ first
when theres 2 cooh moleucles in the compound,, explain how the titration ph curve changes
u have a slower increase in ph,, it takes more oh for the pi to be reached.
this is bc u need to reach both pka to make cooh turn into coo-.
how do we do the pi equation when we have more than 2 pkas
we look at what pkas the neutral form is between.
aka we find the net neutral compound then look to its left and to its right.
we take those pkas and divide them by 2.
this will be out pi,, aka our isoelectric point,, aka the ph at which the net charge of the compound is 0.
at the start of the graph,, the environment is super what
at the beginning the graph has a ph og like 0,, aka its really aicdic so obvs the cooh will be protonated and the nh3+ will be in its cationic form.
bc acidic = high H+ conc.so everything will be protonated.
OH isnt acidic bu what is
OH isnt acidic bc u cant stabilise the o- if its attached to an alkyl chain.
however phenol is acidic ,, bc the negative charge can be delocalised and stabilised by the aromatic ring via resonance!!
what are the 3 implications of ip for protein properties
- charge of protein affects its behaviour in ion exchange chromatography ( relies on the way positive and negative ions are attracted to wachother)
- important for separation of protein and aa in other analytic techniques.
- proteins are usually soluble when charged so when the pi is larger // smaller than the ph. aka when the ph is larger // smaller than the pi (the net charge being 0).
talk about ion exchange chromatography
u have positive resin and u have amino acids on the other side
the positive and negative will be attracted to eachother. this separates the anions but obvs wont move neutral compounds
