Lecture3 Note

Lecture3 Note - Fri. 8.7.09 Lecture 3: Protein Structure...

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Fri. 8.7.09 Lecture 3: Protein Structure and Function I. Hierarchial Structure of Proteins Four levels of protein hierarchy o Primary Structure Sequence of polypeptide/ amino acid o Secondary Structure Consists of alpha-helix and beta-sheet. o Tertiary Structure More complex than the secondary structure. o Quaternary Structure Even more complicated. Amino Acids Amino Acids: The Building Blocks of Proteins. o All 20 amino acids have the same characteristic structure. o A central carbon atom covalently bonded to four partners: Amino group (NH2) Carboxyl group (COOH) Hydrogen atom (H) R-Group o R-group is variable among all 20 amino acids. In pH 7, amino acids exist in ionized form . o Zwitterion – when the net charge equals to 0. o There are 4 different groups attached to the alpha carbon o Therefore, all amino acids have stereo isomer except for one. Stereo isomer – same chemical property but different biological property. To change from one stereo isomer to the other isomer, bonds must be broken. o Glysine does not have a stereo isomer. Only L amino acids are found in proteins Primary Structure of Protein Primary Structure o A polypeptide is a polymer of amino acids o The primary structure of a protein is the specific linear sequence of amino acids. o The arrangement of amino acids makes each protein different.
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o Let’s say that we have 4 amino acids that make a polypeptide. How many possible sequences are there? 20^4 Abcd is different from dcba. Amino acids are linked by peptide bonds o The peptide bond is linked between a carbonyl group of one amino acid to amino group of another amino acid. o By dehydration reaction, (getting rid of water) peptide bond is formed. The backbone of a peptide chain has directionality. o Amino end is known as N-terminus (left end) o Carboxyl end is known as C-terminus (right end) o Alpha-carbon, nitrogen from the amino group, and carbon from the carboxyl group make up the backbone of a peptide. The side chains largely determine the properties of the protein. o Side chains determine the property of the amino acid. o Side chains stay away from the backbone structure. A single change in the primary sequence can cause devastating results in the structure and function of a protein. o Example: sickle cell. (#6 Glutamate changed to Valine) Secondary Structure of Protein The primary structure will determine how a protein will fold. o The secondary structure is determined by the peptide backbone interactions. o Where can H-bond be found? H-bond can be found where there is a electro negativity difference exist. The Alpha-helix o The spiral structure is held by hydrogen bonds between the O of the carboxyl group and the H of the amine group in the backbone. o
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Lecture3 Note - Fri. 8.7.09 Lecture 3: Protein Structure...

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