amino acid/peptide/protein Flashcards
structure of a.a.
NH2 + COOH + H + R group
alpha carbon
carbon bonded to all groups
alpha prefix
extinguish alpha functional groups from side chains
zwitter ionic form
NH2 - gain H+ (cations) and COOH lose H+ (anion)
Acidic a.a function and example
more hydrophilic in protein - polar
aspartic and glutamic acid
side chain exposed to aq media
basic a.a.
lysine - pKa=9 - normal amine for protonation
arginine - pKa=14 - resonance stabilised guanidinium group - v. basic
histidine - pKa=6.8 - aromatic imidazole side chain - protonates = conjugate acid
functionalised a.a
H bonds of side chains when protein bind to molecules
Asparagine, Glutamine, Serine, Methionine, Threonine
Cysteine - form disulphide bond = rigid structure
hydrophobic a.a.
lipophilic side chains - bind for HP groups and recognition and binding event
Glycerine, Alanine, Valine, Leucine, Isoleucine, Proline
Aromatic a.a.
bulky and HP - interior of protein
Phenylalanine, Tryptophan - HP
Tyrosine - form H bonds
stereochemistry nomenclature
D- and L- - all alpha a.a in protein has L-
D- a.a.
found in peptidoglycan components of bacterial cell wall
D/L - rotatioin
different from R/S
uses CORN rule
CORN rule
- H placed below plane
- priority - C=O then R group then NH2
clockwise - CORN rule
D a.a.
anti-clockwise CORN rule
L a.a.
stereochem 1 - implication of a.a.
one form of a.a. exist - asymmetric and chiral - recognised by one stereochemistry - has specificity and selectivity
stereochem 2 - implication of a.a.
E-catalysed reaction - stereoselective - chirality
alpha NH2 - electronic properties of a.a. pKa
its pKa < aliphatic amines
negativity of alpha-carbon effect acidity and basicity
N is highly electronegative - intensifies acidity of COOH
alpha COOH - electronic properties of a.a.
pKa < aliphatic COOH (4-5)
O2 in COOH - v. electronegative - weaken basicity of amine
2 O pull e- from amine - less available
conc of +ve and -ve charge
depend on pKa value at certain pH therefore amount of -ve and +ve charge
balance = net charge 0
isoelectric point (Pi)
at net change
standard chemical property
all a.a has own Pi means
each protein has certain pH value
net charge=0 - problem has unique pi value
Pi
measure by titration
or calculated by applying Henderson-Hasselbalch equation
planar bond
sp2 - because of resonance = bond v. stable and hard to hydrolyse
chemical synthesis
protecting group needed standardised
directionality
a.a. sequence
biological
DNA -> RNA -> peptide
occur in ribosome
primary protein structure
linear a.a. sequence
define down structure = similar properties
e.g. short hexapeptide
secondary protein structure
localised repeating rigid structure
various interaction - H bonding and HP interaction
alpha helix coiled and beta sheet - collection of multiple extended linear structure of H/HP interaction
tertiary protein structure
secondary peptide and flexible chains fold into 3D domain
similar primary = similar tertiary
quaternary protein structure
spatial arrangement of individual polypeptide chain subunit
collection of tertiary - large protein contain multiple domain
relationship of protein structure
primary - Lys act as B and Ser has OH on side chain therefore Nu-
Nu catalysed by B but are far apart at primary - can’t interact
alpha helix formed and folded to tertiary
therefore Lys and Ser - closer together - chemical reaction can be catalysed efficiently by groups
tertiary - not from same peptide chain - closer and interact between other a.a. side chains - quaternary
B in relationship of protein structure
base
