Structure and function of proteins and their constituent amino acids Flashcards
absolute configuration at the alpha position
All chiral amino acids in eukaryotes are L, and have their amino acid therefor drawn at left in Fischer Projections.
All chiral amino acids are S except cysteine.
All amino acids are chiral but glycine.
The alpha carbon is adjacent to the carbonyl.
Amino acids as dipolar ions
pKa of group is the pH at which, on average, half are protonated and half are not.
Above that pKa, the majority of the species is deprotonated.
pKa1 is the -COOH, pKa2 is the -NH2, pKa3 is the R group.
A whole amino acid is a zwitterion at its pI.
Titration curve is flat at the pKa’s and vertical at the pI.
Like Icharus, amino acids lose protons as they ascend.
Acidic amino acids
Glutamatic acid, Glu, E
Aspartatic acid, Asp, D
Negatively charged at phys pH (7.4)
Basic amino acids
Histidine, H, His
Arginine, R, Arg
Lysine, Lys, K
Positive at physiological pH
Hydrophobic
LIMPVAG (as well as W and F)
Hydrophilic
GSTAC (and Y)
oligopeptides
up to 20
resonance between amino nitrogen and carbonyl provides
rigidity
hydrolysis of amino acids
enzyme adds H to N and OH to C
secondary structure
alpha helix or beta sheet
helix breakers
glycine and proline
turns of beta sheets
glycine and proline
Denaturing
reduced to primary structure.
heat adds energy which overcomes hydrophobic interactions.
solutes can overcome cistine, H-bonds, and other side chain interactions.
Isoelectric point
average the two pKa’s flanking the pI.
No charged side chain, pI around 6.
positive side chain (basic), pI above 6.
Non-enzymatic protein function: binding
ex: hemoglobin, tscription factors, ca-binding.
transport or sequester.
transport affinity varies much with environment.
sequester affinity high across large range of conc.
Non-enzymatic protein function: cell adhesion
integral membrane proteins. surface of most cells. bind ECM and or other cells. three families: cadherins, integrins, selectins.
cadherins
group of glycoproteins. mediate ca-dependent cell adhesion. often hold similar cell types together: E-cadherin for epithelial, etc.