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IUPUI BIOC 800 - Exam 1 Study Guide

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Bioc 800 1st EditionExam # 1 Study Guide Lectures: 1 - 7Lecture 1Amino AcidsDescribe the main features of an amino acid.Each amino acid consists of a central carbon, an amino group, a carboxyl group and an R side chain. Differences in the R side chain distinguish the various amino acids.Draw all amino acids, know names, 3 and 1 letter abbreviations.Be able to correctly draw any peptide and the peptide bond.Be able to determine the net charge of any peptide.Describe what a cofactor, a conjugated protein, and a prosthetic group is.Cofactor: Many proteins (especially enzymes) require associated chemical constituents 9or cofactors) for functionConjugated protein: If the cofactor is attached covalently, the result is a conjugated protein. Conjugated proteins contain permanently associated chemical components,Prosthetic group: Non-amino acid part of conjugated protein.Describe why protein purification is important and what is the basic goal of all purifications.A pure preparation of a protein is crucial in determining its properties. The basic goals of purification include determine a protein’s properties, future structural studies, sequence analysis, and use for pharmaceuticals. Define specific analysisSpecific analysis: The number of enzyme units per milligram of total protein. This is a measure of purity of enzymes. Briefly describe the principles behind the different kinds of chromatography. Column chromatography takes advantage of differences in protein charge, size, and binding affinity. This is a powerful method of fractionation.Cation exchange chromatography is a separation of charge due to a solid matrix. This solid matrix has negatively charged groups which caused the net positive charge to move more slowlythrough the polar matrix.Size exclusion chromatography separates by size in which the larger proteins emerge sooner.Affinity chromatography separates proteins based on binding affinity.High-performance liquid chromatography (HPLC) consists of high pressure pumps that speed movement of protein molecules down column and improves resolution of protein.Understand the principles of electrophoresis and the advantage of SDS.Electrophoresis is the separation of proteins based on migration of charged proteins in electric field. SDS is a detergent that binds to proteins uniformly and allows separation based on length. Understand the basic principles behind protein sequencing and peptide synthesis. Lecture 2 (January 15) Identify the four levels of protein structure.Primary: amino acid sequenceSecondary: local conformation of some part of polypeptide (common folding patterns) a. α helix b. β sheetTertiary: polypeptide, overall 3-D structure Quaternary: multiple polypeptides ranging from simple dimers to large complexesDescribe the partial double bond character of peptide bonds and its implications for structureThe C-N has partial double bond character which makes the structure rigid and planar. This results in a weak dipole and rotation is only possible about the bonds connected to α carbon. This affects how bonds are formed within protein structures.Understand the two types of dihedral bonds.Φ (phi): angle around the α-carbon-amide nitrogen bond. Ψ (psi): angle around the α-carbon-carbonyl carbon bond.(In a fully extended polypeptide, both Ψ and Φ are 180°)Describe the important features of an alpha helix (pitch, aa per turn, bonding, dipole)The simplest structure polypeptide can adopt is the α helix. It is tightly wound (no hole in the middle) with the backbone on inside and R groups facing out (interactions between R groups stabilize protein. The twist is right-handed, pitch is 5.4 angstroms, and there are 3.6 amino acidsper turn of helix. Roughly every 3rd/4th turn, peptide residue will be on same face which means all peptide bonds take part in hydrogen bonding which stabilizes structure. All amide “N” points toward N-terminus of helix and all carbonyl “O” point towards C-terminus of helix which results in dipole. Identify which amino acids are/ are not found in helices. Alanine, Leucine frequently in helixes. Proline, Glycine are not found in helix (helix breakers)Describe features of β sheetThe β sheet is made up of series of strands that adopt the β conformation. Hydrogen bonds are formed between adjacent segments of polypeptide chains. These are more extended than helices. Several strands form sheets. Sheets are either parallel or anti-parallel (alternating amidegroup to carboxyl group) but R groups are always on the same side of sheet and alternate faces. These groups need to be small (Gly, Ala)Differentiate the two types of β turnsβ turns connect ends of 2 adjacent segments of anti-parallel β sheet. 180° turn is accomplished over four amino acids. Proline in position 2 or glycine in position 3 are common in β-turns and these are often found at protein surface.Briefly contrast fibrous and globular proteinsFibrous: having polypeptide chains arranged in long strands or sheets, insolubleGlobular: polypeptide chains folded into spherical or globular shape, water and lipid solubleDescribe key features of collagen responsible for its strengthCollagen is found in connective tissue, is a left-handed helix, and has 3 amino acids per turn. Strength is enhanced by covalent crosslinks between polypeptide chains. Collagen contains cross-linked triple-helixes and flexible linker (Lys-HyLys). Gly contributes to tight packing because of its small size.Compare motif versus domain in globular proteinMotif: fold recognizable folding pattern found in a number of proteins. Domain: entire sequence where independently stable, self-contained part of protein, folds autonomouslyIdentify four classes of proteinsAll αAll βα/βα+βDescribe what factors influence folding specifically be able to explain the hydrophobic effectBurial of hydrophobic residues in core (hydrophobic effect), maximization of H-bonds (especiallyin the core) and of stabilizing ion pairs. Briefly summarize the key findings of Anfinsen’s work1) All of the information needed to determine a protein’s tertiary structure is contained in the primary sequence.2) Correct disulfide bond formation occurs only after the protein achieves native tertiarystructure3) the native state is special because it is the lowest energy stateDefine molten globule-spontaneous collapse of polypeptide into collapsed state. Compact structure that contains some (or even all)


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