Understanding Protein Structure: Secondary, Tertiary, and Quaternary Structures - Prof. Yo, Study notes of Biochemistry

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Proteins - I

DNA encodes the sequence of amino acids that constitute the protein. The amino acid sequence is called the primary structure. Functioning proteins , are not long polymers of amino acids. These polymers fold to form discrete three- dimensional structures with specific biochemical functions.

The three dimensional structure becomes more complex when the R groups of amino acids far apart in the primary structure bond with one another. this level of structure is called tertiary structure and is the higher level of structure that an individual polypeptide can attain.

• (^) Tertiary structure: spatial arrangement of amino acids that are far from each other in the primary structure (compacting of a polypeptide into domains); mediated by weak non-covalent interactions between R groups;

Many proteins require more than

one chain to function. Such proteins

display quaternary structure, which

can be as simple as a functional

protein consisting of two identical

polypeptide chains or complex as one

consisting of dozens of different

polypeptide chains.

Noncovalent interactions important for protein structure:

1. Hydrogen bonds
2. Electrostatic interactions (ionic interactions, salt bridges)
3. van der Waals forces – interactions between infinitesimal dipoles generated in atoms by the random movement of the negatively charged electrones
4. Hydrophobic interactions – association of relatively nonplolar molecules or groups in aqueous solution solution with other nonpolar molecules or groups rather than with water (“cage” effect)

The peptide bond (CO-N) has 40% character of a double bond, therefore it is planar; it is also polar

Amino acid sequences have directions. This illustration of the polypeptide try-gly-gly-phe-leu (YGGFL) shows the sequence from the amino terminus to the carboxyl terminus. This pentapeptide , leu-enkephalin , is an opioid peptide that modulates the perception of pain. The reverse sequence , leu-phe-gly-gly –try (LFGGY) , is different pentapeptide , with different chemical properties.

Main chain – backbone Residue- C= O - hydrogen bond accepter Exception proline N_H –good hydrogen bond donor These groups interact with each other and with functional groups from side chains to stabilize particular structures.

Proteins have unique amino acid sequences specified by genes

Insulin was the first protein

to be sequenced

In 1953 Frederick Sanger won the Nobel prize for protein sequencing. Land mark in biochemistry It took 10 years, many people, and it took 100 g of protein! Today it takes one person several days to sequence the same insulin. 1021 AA b-- glactosidase

Primary structure determine the three dimensional structure of a protein, and the three dimensional structure determine the protein function. What are the rules governing the relation between an amino acid sequence and the three dimensional structure of protein?

1. The polypeptide bond is essentially planar. Thus , for a pair of amino acids linked by a peptide bonds , six atoms lie in the same plane: alpha carbon atom and CO group of the first amino acid and the NH group and alpha carbon atom of the second amino acid.
2. The peptide bond has considerable double bond character owing two resonance structures: the electrons resonate between a pure single bond and a pure double bond.

Peptide bonds are planar. In a pair of

linked amino acids, six atoms lie in a

plane. Side chains are shown in green

balls