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Unformatted text preview: max [ ] [ ] [ ] 1 M I V S V I S K K = + + BIBC 102 2006 MIDTERM EXAM NOTES The midterm exam will cover the material presented in the first 10 lectures and problem sets 1 through 5. 1. Problem sets #1-5 : any question or slight variations on these problems, may be on the exam. 2. The 20 Amino Acids (aas): Be able to identify each of the 20 common amino acids if you are given the correctly drawn structure. Know the three and one letter abbreviations for each amino acid. 3. Protein Structure- Know definitions of the 4 levels: primary, secondary, tertiary, and quaternary. Primary = the amino acid sequence by peptipe N-C bonds aas with non-polar side chains Gly, Ala, Val, Leu, Ile, Met, Pro, Phe, Trp aas with uncharged polar side chains Asn, Gln, Ser, Thr, Tyr, Cys aas charged polar side chains. Asp, Glu, Lys, Arg, His Secondary = ordered H-bonded structures: -helix, -pleated parallel, -pleated anti-parallel sheets helix- Right handed coil- All N-H groups h- bond with C =O groups 4 residues apart.- All R groups project outward from helix core define the character of helix surface. pleated sheet- Know difference between parallel and anti-parallel pleated sheet structures- All N-H groups and C =O groups in an interior strand form h-bonds with adjacent strands.- R groups project alternately above/below the sheet plane define the surfaces of the sheet. Tertiary = 3-D globular folding Quaternary = bonding of subunits by non-polar connections/interactions Pure helices (hair) and pure sheets (silk) are found in some fibrous structures. In typical globular proteins, helices are 15 residues long, strands are 10 residues long. ( short because easier to form a globule, not a linear molec) All amino acids with hydrophobic side chains try to escape contact with water and are in the INTERIOR of globular proteins. Aas with polar/charged side chains are found on the protein SURFACE. The tendency of oil and water to separate into phases = the same driving force that causes the hydrophobic amino acid side chains to associate on the protein interior (to escape contact with water). This hydrophobic association drives the formation and stability of the 3D protein structure. Interior peptide bonds involve purely in N-H::O=C H-bonds by R groups no space in between. The structure is de-stabilized by 15 - 30kJ/mole for each hydrogen bond that isnt formed. Protein interiors are solidly packed, with a density = organic crystal. There is no water in the interior. Information needed to fold a protein correctly (to its tertiary/quaternary structure) lies in its primary sequence. Many denatured proteins will refold spontaneously with complete regain of protein activity....
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This note was uploaded on 04/17/2008 for the course BIBC 102 taught by Professor Price during the Spring '02 term at UCSD.
- Spring '02