4b Flashcards
how is an amide bond // amide formed from a carbonyl with a halogen on it and a nucleophile
the nucleophile attacks the c of the carbonyl and the e- get resonated onto the o to from o-
this is then used to kick off the halogen and reforms the carbonyl.
whats a good leaving group
Cl good so more reactive
CO2R
OR
NH2
O- bad so less reactive
carboxylic acid to amide,, what is the low energy version to make it
carboxylic acid + SOCl
to form acyl chloride
then u take an amine and react it via nucleophilic attack
from two amino acids to a dipeptide ,, what direction is favourable
the hydrolysis of the dipeptide is favoured!!
aka the formation of the 2 aa from a dipeptide is favoured
but we dont need to stress about it bc under normal confitions the half life for the hydrolysis is 300 years ish
how does a peptide // amide bond form in nature
the amino acid carboxylate attacks the P of triphosphate from atp.
the e- from the P-O move and basically u have ur amino acid with a PO4R on it
the other amino acids NH2 then uses its lone pair to attack the other amino acid complex’s carbonyl and forms an o-.
the o- is then used to kcik of the phosphate group to leave behind a dipeptide.
basically u attack the phophate with the forst amin oacid to activate it,, then u use the other amino acid to attack the first amin oacid and kick off the phosphate
describe the phosphate we attck using the amino acid when we form dipeptides
-o - P - o - but it has an o- at the top and =o at the bottom
dipeptides and polypeptides have what
they have directionality
how do dipeptides and polypeptides have directionality
they have directionality bc their ends are chemically different // chemically distinct from one another.
how do we normally draw dipeptides /// polypeptides
we draw N and then C
so the N terminus
and then the C terminus
so we start with the amine and end with the carboxylate.
for a protein to have the correct biological function,, what do we need to ensure
that the amino acids are in the correct order
describe the semi double bond that peptide bonds have
think of an amide.
the N: can be resonated up to the o to form an o-.
obvs the resonance structures show that the acc moleucle is between these two.
meaning amides have a semi double bond meaning its rotation is sort of restricted!!! bc it takes more energy for them to rotate bc obvs they have a semi double bond.
the N will also be less basic bc its using its lone pair to resonate onto the O instead of attacking a H.
what part of the amide does protonatonation normally occur at and why
normally occurs on the oxygen!!
bc the N is less basic bc it resonates onto the O instead of attacking H’s.
due to the double bond and restricted rotation on amides,, what does this mean
u can get cis and trans forms of stuff with an amide bond ,, the trans form is usually more stable tho.
can the cis and trans amide // dipeptides still interconvert
yesss
bc its a semi double bond the two things can still interconvert bc the bond can still rotate,,, the bond just rotates slower bc more energy is needed for the bond to rotate.
what evidence can we use when it comes to dipeptides and polypeptides to prove that there is infact a semi double bond
the C-N bond is slightly shorter than a normal signle bond,, and double bonds are normally shorter so calm.
the bond angle is larger,, the bond angle would be smaller at around 109 if the N was purely tetrahedral and didnt use its lone pairs to form a semi double bond,
although the amide bond has restricted rotation,, can the other bonds rotate
yes the other bonds can still rotate
the alpha carbon is usually the point of rotation
due to the restricted rotation of the peptide bond,, what does this due
- restricts the number of conformations a polypeptide chain can have
when were asked to draw a polypeptide chain of certain amino acids at physiological ph,, what do we need to make sure we do
make sure our first amino acid has NH3+ on the LHS,, draw the amide bonds,, for the furthest RHS aa,, make sure the carboxylate has only single bonds with the semi circle (-) in the middle.
bc its physiological ph its ph7,, so the COOH will be COO- but the amines will be NH3+ bc their pka hasnt been met yet.
SO SIDE CHAIN AMINES WILL ALSO BE NH3+ !!!!!!!
AND SIDE CHAIN COOH WILL BE COO- !!!
