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Biochemistry Lecture No. 4.docx

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Biochemistry 3380G

Biochemistry Lecture No. 4: Protein Structure th Thursday September 13 , 2012 Secondary Structure Of Proteins: -The second level of protein structure describes the local pattern of the backbone or linear amino acid sequence. These structural elements are stabilized by hydrogen bonds between the backbone amino and carboxyl termini. Two major types of secondary structure include the alpha helix and the beta strand (also known as the beta-pleated sheets). There are other types of secondary structures, but these two are the most common. Hydrogen Bonds: -Hydrogen bonds are bonds between a hydrogen atom and an electronegative atom, such as nitrogen or oxygen, when the hydrogen itself is covalently bonded to another electronegative atom. This form of bonding occurs very frequently in many types of protein structures. Hydrogen bonds are strongest when the three atoms involved are in a straight line. For example, amino acids in polypeptide chains are often hydrogen bonded together. Hydrogen bonding is most recognized in water molecules. The Alpha Helix: -The alpha helix is a coiled spring arrangement of secondary structures found in proteins. It follows precise dimensions (3.6 residues per turn of the coil) and it is formed from the outward projections of the side chains of the amino acids involved (no interior space). It is stabilized by H-bonds. An example of this is in the enzyme aromatase, converter of testosterone into estradiol, which contains many alpha helices. Beta Sheets: -Hydrogen bonding occurs between the backbone of two or more polypeptide chains arranged adjacently and in parallel with each other. Amino acid side chains project alternately up and down. -There are two conformations of beta sheets: anti-parallel (where the N-terminus and C-terminus are not lined up) and parallel (where the N-terminus is lined up). Again this is all the product of hydrogen bonding. *The type and quantity of secondary structures formed will be based upon the primary sequence given. Tertiary Structure: -This level of protein structure concerns the 3-D arrangement of the polypeptide chain (native conformation). It is stabilized by bonds between side chains or between side chains and the backbone. Interactions occur between residues distant in the linear sequence, which gives the overall shape o
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