Amino Acids and Peptides
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Amino Acid Structure
D-alanine | L-alanine |
The
common R-groups -
the “alphabet of life”
(GAVLIPFWYMCSTHKRDENQ)
Polarity:
Nonpolar (aliphatic, aromatic);
Neutral - polar;
Acidic;
Basic
Aliphatic
( Ala, Val, Leu, Ile, Pro)
Aromatic
( Phe, Trp, Tyr)
Sulfur Containing
( Met,
Cys )
Alcohol Containing
( Ser, Thr )
Basic R Groups
( His, Lys, Arg )
Acidic R Groups
( Asp, Glu )
Amides
( Asn, Gln )
(You should know all amino acids by their 1 and 3 letter codes.)
Glycine (G) | Alanine (A) | Valine (V) |
Leucine (L) | Isoleucine (I) | Proline (P) |
Phenylalanine (F) | Trptophan (W) | Tyrosine (Y) |
Sulfur containing amino acids (Met, Cys)
Methionine (M) | Cysteine (C) |
Hydroxyl containing amino acids (Ser, Thr)
Serine (S) | Threonine (T) |
Basic Amino Acids (Lys, Arg, His)
Lysine (K) | Arginine (R) | Histidine (H) |
Acidic Amino Acids and Their Amides (Asp, Glu, Asn, Gln)
Aspartic Acid (D) | Glutamic Acid (E) |
Asparagine (N) | Glutamine (Q) |
Ionization / Titration properties of amino acids ; pKa ‘s
~10 ~2
+H3N -
CHR - COOH
R acidic (Glu, Asp )
~ 4
R basic (His ~ 6; Lys ~ 10; Arg ~ 12)
R other (Cys ~ 8 ; Tyr ~ 10)
Isoelectric point (pI)
pH
at which there is no net charge, electrically neutral
amino
acids with ionizable carboxyl side chains (+1
0 -1 -2)
pI= average of pKa’s of the two carboxyl groups ( pI = (pK1
+ pK2) / 2 )
amino
acids with N containing ionizable groups (+2
+1 0 -1)
pI = average of pKa’s of the N groups ( pI = (pK2 + pK3)
/ 2 )
(Another site for viewing AMINO ACIDS at OMM (Online Macromolecular Museum)
Peptide
Bonds - Proteins are linear polymers of a.a. residues
linked by “peptide bonds.”
Reaction:
a.a.R1 +
a.a.R2 =
dipeptide (R1-R2) +
water
DG of this reaction is +10
kJ/mol ; proteins are
metastable
(acid hydrolysis (6N HCl) / proteases
Resonance
structures result in planar amide group - trans form is favored
This image
was created by Dr. George Helmkamp, Jr. (UKMC)
Peptides
(dipeptide, tripeptide, etc. .....
polypeptide -
proteins)
Primary
Structure : +H3N - GVLAADEMLLKFYEE - COO-
N-terminus
C-terminus
Animo
acids --> amino acid residues (Glycyl-valyl-leucyl-alanyl-alanyl-aspartyl-
etc.)
Blocking groups: N-terminus (formyl- , acetyl- ); C-terminus (amide)
Conformation of polypeptides - rotational freedom limited to bonds on a-carbon
This image is from Dr. George Helmkamp, Jr. |