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).
D – C – M
A – S
C – M – A
S – G – A
L – D L D C M A S G A
N-terminal aa
C-terminal aa

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

7. Secondary Structure
There are several named conformations due to common typical combinations of rotation angles around C-N (f) and C-C (y) bonds:
f y
a-helix º º
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 y = 180º)

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

10. a-helix (F = -58º; y = -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