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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
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