BCHS 3304 1st Edition Exam #2 Study GuideChapter 5: Modern Sequencing - Sequencing by Mass Spectrometry o Mass spectrum: are highly accurate scales  Electrospray Ionization (ESI) Calculate mass from Masspec data  Tandem Mass Spectrometry o Fragmentation  Peptide Fragmentation (CID)- It’s predictable - Difference in fragment masses=amino acidso Sequencing  Deriving Sequence Information - Database Search Methods- De novo Sequencing  Total Protein Sequencing - Cytochrome C: The Story of a Highly Conserved Protein - Applications of Sequence Information o Sequence Comparison  Protein and DNA Sequence Data Banks o Evolutionary Relationships Homology and Evolutionarily Related Proteins - Gene Duplication in Clotting ProteinsChapter 6: 3D- Structure of Proteins - Secondary Structure - 3-Dimensional Structure o Conformation - 4 Levels of Protein Structure o 1. Primary Structure  Amino acid sequence o 2. Secondary Structure  Alpha helix- Helix Types Beta strands/sheet- Examples of Twisted beta-sheet proteins- Connections between adjacent beta-sheets- Beta sheet facts  Beta turn Random coilo 3. Tertiary Structure Peptide Biological function Catalytic mechanism  X-ray Crystallography Side chain Locations in Proteins- Non-polar side chains- Charged polar residues - Uncharged polar residues  Selected Protein Structures  NMR Spectroscopy Protein Domains o 4. Quaternary Structure  Peptide chains  Protein Folding- Do not have to know besides proteins can be unfolded/denatured o Denatured proteins can be refolded, sometimes requiring helper proteins Spatial arrangements of subunits (folded chains)- Protein Isolation o Understand the basic physical and chemical properties of the protein o Know the considerations - Stability: Proteins Can Denature o Stabilization of Proteinso Purification Strategy  Protein Solubility  Salting Out- Chromatography o Types o Ion Exchange o Proteins are charged o Gel Filtration o Hydrophobic Interaction o Revered Phase Chromatography o Affinity Chromatography  His-tag Affinity Chromatography- Electrophoresis (PAGE)o SDS-PAGEo Isoelectric Focusing o 2D Gel Electrophoresis o Ultacentrifugation - Basics of Detection - Hemoglobin and Myoglobin o Function of Hemoglobin and Myoglobino The Heme Group o Function of the Globino Myoglobin: Oxygen Binding o The Hill Equation o Hill Ploto Contrast Mb Binding to Hemoglobin o The Bohr Effect  T and R state summary o Hemoglobin and Myoglobin in O2 & CO2 Transport- D-2,3-bisphorphoglyecerate (BPG) o BPG and High-Altitude Adaptation o Hemoglobin S-fibers o Hemoglobin S Mutant o S-Fibers Chapter 7: Muscle Contraction - Myosin and Actino Myofibrils  Contraction o Thick (Myosin) Filament o Thin (Actin) Filament with Myosin Heads o Antibodies  Structure o Diagram of IgGo Immunoglobulin Light Chaino Antigen Cross-Linking by Antibodies o Monoclonal Abs as