Flashcards in Amino Acids And Peptides Deck (21):
Protonic Equilibria of Amino Acids
Both the NH2 and the COOH groups in an amino acid undergo ionization in water.
At pH 7.4: a zwitterion forms, both + and - charges, neutral, amphoteric, amino group is protonated and carboxyl group is deprotonated.
Point at which the compound has no net charge, is average of pKa's
How can the protonation state of a functional group be determined?
By comparing the pKa of the functional group to the pH of the solution.
If pHpKa the group will be largely protonated
If pH is near the pKa the group will exist as a mixture of the two forms
Hydrophobic and Aliphatic AA's
Gly, Ala, Leu, Ile, Val
Hydrophobic and Aromatic AA's
Phe, Tyr, Trp, (His)
Hydrophilic and polar AA's
Hydrophilic and hydroxyl AA's
Ser, Thr, (Tyr)
Hydrophilic and charged AA's
Arg, Lys, Asp, Glu, (His)
Gly (no R), Pro (imino)
All amino acids (except glycine) are optically active.
Dextrorotatory - rotating the plane of polarization of light to the right, D-amino acids are often found in bacteria and used as antibiotics and drugs that inhibit AIDS virus HIV-1 from entering cells
Levorotatory - rotating the plane of polarization of light to the left, all amino acids are found in L
Does geometry of proteins affect reactivity?
What connects AA residues?
Peptide bond is neither acidic nor basic, charge determined by terminal groups and amino acid side chains.
What is the fundamental linkage in the structures of peptides and proteins?
Planar amide bond
-Ionic bonds or electrostatic interactions
-van der Waals forces
Tendency of non polar compounds to self- associate in an aqueous environment.
Driving force is increase in entropy of water structure which occurs when no polar molecules/groups coalesce.
Van der Waals forces
-attraction of 2 atoms due to charge distribution
-becomes repulsion at close distances
Name from the free amine
Use -yl endings for the names of AA's
The last AA with the free carboxyl group uses AA name