Peptides and Proteins
Peptide primary structure problem
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An unknown octapeptide gives the following upon total hydrolysis:
A(2), C, D, G, L, M, S
Reaction of the octapeptide with Sanger’s reagent followed by total hydrolysis
gives “labeled” leucine (L).
Carboxypeptidase treatment of the octapeptide gives initially a high concentration
of alanine (A), followed by glycine (G) and then serine (S).
Leucineaminopeptidase treatment of the octapeptide gives initially a high
concentration of leucine (L), followed by aspartic acid (D) then cysteine (C).
Partial hydrolysis of the octapeptide gives the following identifiable fragments
D – C – M, A – S, C – M – A, S – G – A, and L – D
Write the correct primary structure (using one-letter abbreviations and following
the usual convention of listing the N-terminal amino acid on the left).
D–C–M
L– D
A–S
C–M– A
S– G–A
L
C
D
N-terminal aa
M
A
S
G A
C-terminal aa
Classification (vague)
• Peptides have fewer than 50 amino acids
– Oligopeptides (di, tri-, tetra-, etc.) up to about 10 aa
– Polypeptides (longer chain of aa than an oligopeptide)
• Proteins have more than 50 amino acids, and may
be combined with other structure classes, such as
carbohydrates, lipids, etc.
– Simple…yield only amino acids upon hydrolysis
– Conjugated…yield amino acids and other structure
types (carbohydrate, lipid, etc.) on hydrolysis
Levels of Protein Structure
• Primary structure: the amino acid sequence
• Secondary structure: the conformation due to
rotations around C-C and C-N single bonds
• Tertiary structure: the folding of the peptide chain
into its characteristic 3D-shape
• Quaternary structure: the aggregation of several
subunits held together by other than covalent bonds
(not all peptides have this feature)
Primary Structure
• the amino acid sequence, written from the Nterminal (on the left) to the C-terminal (on the
right). Formerly abbreviated using three-letter
abbreviations: Ala, Gly, Phe, Val, etc.; now we use
one-letter abbreviations: A, G, F, V.
Ala – Gly – Phe – Val
or
A-G-F-V
Secondary Structure
• the 3-D arrangement (conformation) of segments
of a peptide/protein chain due to rotation around
C-C and C-N bonds
N H
O C
H

C
H N  R
C O
Secondary Structure
• There are several named conformations due to
common typical combinations of rotation angles
around C-N () and C-C () bonds:


– a-helix
-58º
-47º
– b-pleated sheet ( )
-140º
135º
– hairpin turns are sharp curves in the peptide
chain, often due to proline residues
Problem w/ flat sheet
(F and  = 180º)
b-pleated sheet
(F = -140º;  = 135º)
7.0 Å
b-pleated sheet can be stabilized by H-bonding
between adjacent peptide chains
a-helix
(F = -58º;  = -47º)
a-helix is stabilized by H-bonding
within a peptide chain
Tertiary and Quaternary Structure
• Tertiary structure: the coiling or folding pattern of
single polypeptide chains
– Many individual shapes, but generally fall into one of
two categories:
• Fibrous (insoluble; generally function as structural component)
• Globular (soluble; coiled into compact, spherical shapes, with
hydrophobic groups oriented inward and hydrophilic groups
oriented outward toward the aqueous environment of the cell)
• Quaternary structure: non-covalent aggregation of
two or more protein molecules and possibly other
structures into functional units.
(examples will be shown in WebLab Viewer Lite)
Functions of Proteins
• Hemoglobin: the oxygen-carrying molecule in the
blood
• Insulin: regulates glucose metabolism
• HIV protease: cleaves peptide bonds of large protein
to allow activation of HIV virus within host cell
• Carboxypeptidase: digestive enzyme that hydrolyzes
peptides into their component amino acids
• Keratin: provides structure of wool, hair, fingernails,
and feathers