BIO HELPPP

1. Shown Below. When the amino acids are linked by peptide bonds, the alpha amino N and the carboxyl C are in an amide link and they possess no charge. What makes the amino acid polar is its R group. If the R group is charged (i.e. has a positive or negative charge, it is basic or acidic, receptively). If it contains a polar group in its R side (i.e. OH), it will be hydrophilic.

2. The energetics of protein folding determine the 3D structure of a folded protein. Folded proteins usually have a hydrophobic core in which side chain packing stabilizes the folded state, and charged or polar side chains occupy the solvent-exposed surface where they interact with surrounding water. Minimizing the number of hydrophobic side-chains exposed to water is an important driving force behind the folding process. Formation of intramolecular hydrogen bonds provides another important contribution to protein stability. The strength of hydrogen bonds depends on their environment, thus H-bonds enveloped in a hydrophobic core contribute more than H-bonds exposed to the aqueous environment to the stability of the native state. Fibrous proteins are quite rigid due to their phi and psi angles that make the amino acid side chains point outward which prevents outside sources from disrupting the secondary strucutre, which is the structure held together by the amino acid polymer backbone via hydrogen bonds. If the secondary structure is disrupted, the forces that hold the protein together in rigid, fibrous form is lost.

3. A common motif in the secondary structure of proteins, the alpha helix (?-helix) is a right-handed coiled or spiral conformation, in which every backbone N-H group donates a hydrogen bond to the backbone C=O group of the amino acid four residues earlier. In alpha helices, the side chains are on the outside while the other protion of the peptide such as the alpha carbon and nitrogen are on the inside. This property is what makes a-helices fibrous, that is because their back bone (the inner part) is protected, making it a common structure. Similarly, alpha-helices are also the most common protein structure element that crosses biological membranes, it is presumed because the helical structure can satisfy all backbone hydrogen-bonds internally, leaving no polar groups exposed to the membrane if the sidechains are hydrophobic.

4. The beta sheet (also beta-pleated sheet) is the second form of regular secondary structure in proteins, only somewhat less common than alpha helix. Beta sheets consist of beta strands connected laterally by at least two or three backbone hydrogen bonds, forming a generally twisted, pleated sheet. A beta strand (also beta strand) is a stretch of polypeptide chain typically 3 to 10 amino acids long with backbone in an almost fully extended conformation. A beta turn will have 5 residues or 4 residues (where glycine is the third residue) allowing for abrupt 180 degree turns. The structure is stabalized by hydrophic hydrogen bonding forming parellel and antiparellel (antiparellel being more stable) interactions.

If I missed anything, let me know.

Bio_man 8)