The octapeptide contains the amino acids A, C, D, G, L, M, S. Enzyme digestion and mass spectrometry identify the fragments D-C-M, A-S, C-M-A, S-G-A, and L-D. This information determines the primary structure is L-A-G-S-D-C-M-A. Secondary structure is based on bond rotations forming elements like alpha helices and beta pleated sheets. Tertiary structure describes the overall shape from peptide chain folding while quaternary structure involves interactions of multiple protein subunits.

1. Peptides and Proteins

2. Peptide primary structure problem
• 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).
L A
G
S
D C
N-terminal aa C-terminal aa
M A
D – C – M
C – M – A
S – G – A
A – S
L – D

3. 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

4. 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)

5. Primary Structure
• the amino acid sequence, written from the N-
terminal (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

6. 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
C O
R
H
C
O C
H
N

7. 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
)

8. Problem w/ flat sheet
(F and  = 180º)

9. b-pleated sheet
7.0 Å
(F = -140º;  = 135º)
b-pleated sheet can be stabilized by H-bonding
between adjacent peptide chains

10. a-helix
(F = -58º;  = -47º)
a-helix is stabilized by H-bonding
within a peptide chain

11. 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)

12. 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