Peptides and Proteins

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 AGSD CN-terminal aa C-terminal aa

M A

D – C – M

C – M – AS – G – A

A – S

L – D

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 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

Secondary Structure

• the 3-D arrangement (conformation) of segments of a peptide/protein chain due to rotation around C-C and C-N bonds

NH

C O

R

HC

O CHN

Secondary Structure

• There are several named conformations due to common typical combinations of rotation angles around C-N () and C-C () bonds:

– -helix -58º -47º

– -pleated sheet ( -140º 135º

– hairpin turns are sharp curves in the peptide chain, often due to proline residues

)

Problem w/ flat sheet and = 180º)

pleated sheet

7.0 Å

( = -140º; = 135º)

-pleated sheet can be stabilized by H-bonding between adjacent peptide chains

-helix( = -58º; = -47º)

-helix is stabilized by H-bondingwithin 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