Chapter 5: Amino Acids, Peptides and Proteins
• Page 133 textbook
• You must memorize the structures, names, three-letter abbreviations,
and one-letter abbreviations for the 20 natural L-amino acids used in
ribosome directed protein synthesis.
D-glyceraldehyde and
L-glyceraldehyde are the
reference compounds for
determining if an alpha
amino acid is the L- or Denantiomer.
Comparison of L-Glyceraldehyde to Amino Acids
The hydroxyl group of L-glyceraldehyde and the amino group of an L amino acid are
on the left side of the alpha carbon in this depiction.
Perspective Drawings and Fischer Projections for L- and
D- Glyceraldehyde.
Perspective drawings of D- and L-glyceraldehyde.
Main portions of amino acids.
α
L-Amino Acids
• Nature has a “handedness”. All ribosome directed protein synthesis
involves L-amino acids only. For L-alanine it is the S-enantiomer.
Glycine is the simplest alpha amino acid.
Glycine is not chiral
and therefore, it
does not have an
enantiomer.
Non-polar Amino Acids
Methionine
Isoleucine
Leucine
Aromatic Amino Acids
Acidic Amino Acids
For both aspartic acid and glutamic acid the side chain involves a carboxylic acid group.
At pH values greater than the pKa , these carboxyl groups would be unprotonated and
bear a negative charge.
Basic Amino Acids
These side chains have amino
groups that will bear a +1
charge when the pH is lower
that the pKa values for these
groups. The pKa for Histidine
(His) is near 6.0 which is quite
low for an amine type side
chain.
Proline is a cyclic amino acid
Due to restricted rotation
about single bonds, proline
tends to disrupt certain
motifs of secondary
structure. It is known as a
“helix disrupter.”
Serine and Threonine
Serine
Threonine
Glutamine and Asparagine
Both glutamine and asparagine have amide side chain groups.
Sulfur containing amino acids
Methionine
Cysteine
Table 5.1 (p. 134)
• Amino Acid Name
• Alanine
• Arginine
• Asparagine
• Aspartate
• Cysteine
• Glutamate
• Glutamine
• Glycine
3 letter abbrev.
Ala
Arg
Asn
Asp
Cys
Glu
Gln
Gly
1 letter abbrev.
A
R
N
D
C
E
Q
G
Table 5.1 (continued)
• Amino Acid Name
• Histidine
• Isoleucine
• Leucine
• Lysine
• Methionine
• Phenylalanine
• Proline
• Serine
3 letter abbrev.
His
Ile
Leu
Lys
Met
Phe
Pro
Ser
1 letter abbrev.
H
I
L
K
M
F
P
S
Table 5.1 (continued)
• Amino Acid Name
• Threonine
• Tryptophan
• Tyrosine
• Valine
3 letter abbrev.
Thr
Trp
Tyr
Val
1 letter abbrev.
T
W
Y
V
Memorize the names, 3-letter abbreviations and 1-letter abbreviations.
Biologically Active Amino Acids
•
The peptide bond
Formation of a peptide bond involves removal of H2O.
Planarity of the peptide bond.
Phi and Psi peptide torsion angles and free rotation.
There is free rotation about the bonds defined by the angles phi and psi. Remember
that the bond defined by angle omega has partial double bond character and
therefore has restricted orientation.
Peptide secondary structure.
• Two common structural motifs.
• Alpha helix
• Beta-pleated sheet
• Parallel and anti-parallel beta-sheet structures.
Alpha (α) helix structure is stabilized by hydrogen bonding between turns of helix.
Parallel and Anti-parallel β-Sheet Structures
β-barrel is a complex structure
based on anti-parallel strands
β – meander is also based on anti-parallel strands.
β α β unit – an α-helix is between two parallel β-strands.
Greek Key – another structure based on anti-parallel
strands.
Glutathione – An important anti-oxidant
Notice the sulfhydryl
(-S-H) group in this short
Peptide.
EF hand – a zinc ion, Zn2+ is coordinated in the
palm of the hand.
Leucine Zipper Structure – often involved in proteins
that bind to DNA.
Zinc Finger motif
These motifs are common
in proteins that bind other proteins,
DNA and/or RNA.
ATP Binding Domain
These motifs are present in enzymes
that catalyze reactions that use ATP
as a reactant. The ATP Binding
pockets are where ATP is hydrolyzed
into ADP or AMP.
Amino Acid interactions that stabilize protein structures.
Formation of Glutathione dimer
2 GSH + H2O2 → GSSG + 2H2O
Reduced form
Oxidized form
Oxidation of two cysteine residues to form cystine.
Reduced Form
Oxidized form
Functions of Proteins
• 1. Catalysis – Enzymes accelerate the rates of many reactions.
• 2. Structure – collagen (connective tissue), fibroin (silkworm protein)
• 3. Movement – actin, tubulin and associated proteins
• 4. Defense – keratin (protein in skin cells)
• 5. Regulation – protein-based hormones (insulin)
• 6. Transport – proteins function as carriers or transporters
• 7. Storage – reservoir of essential nutrients
• 8. Stress Response – heat shock proteins (hsps)
• 9. Toxins – Clostridium botulinum secretes botulism toxin, scorpions produce
tetrodotoxin
Prosthetic Group for Myoglobin - Heme
Tertiary Structure of Myoglobin with Heme present
Heme Group with Oxygen molecule bound.