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• Cell Chemistry and Biosynthesis Chemical Components of A Cell • • • • • Major Atoms Covalent bonds, Ionic bonds Four major families of small molecules Sugar, fatty acids, amino acids, nucleotides Three macromolecule families: polysaccharide, protein, nucleic acid • Non covalent bonds determine molecular shape and interactions Carbon and Hydrogen Chemical Elements for Live Organisms Covalent Bond and Ionic Bond Sodium Chloride: ionic bond formation The geometry of covalent bonds Important Energy Levels The Van der Waals forces Acid Donate a proton Base Absorb a proton or donate OHNH3+H2O->NH4++OHNaOH->Na++OH- Ionic bonds in Water Hydrogen bond Polar interaction: a elecgtropositive hydrogen is shared by two neighboring electornegative atoms Molecular Interaction in solution 1. H-bond (hydrogen bond), 2. Ionic bond, 3. Van der Waals 4. Hydrophobic “force” Four Major Small Organic Molecules Sugar [(CH2O)n, carbohydrates] Glucose Disaccharide Condensation and hydrolysis Fatty Acids Phospholipid (amphipathic) Amino Acid Amino Acid and pH values Peptides and proteins Nucleotides ATP (ribonucleotide adenosine triphosphate) Nucleotides and DNA, RNA DNA: deoxyribonucleic acids A(adenine) G(guanine) T(thymine) C (cytosine) RNA: ribonucleic acids A G U(Uracil) C Macromolecules Three families of macromolecules The assembly of macromolecules • Proteins • Protein Structures and Shapes • Protein Functions Protein Structures and Shapes • Amino acids • Peptide bonds a helix and b sheet • Domains and Modules • Classification of Families • Protein Assembly Amino Acids form polypeptide through peptide bond Structural Components of a protein The 20 Amino Acids 2 negative, 3 positive, 5 non-charged polar, 10 nonpolar Read Page 132-133, panel 3-1 Limitations on the bond angles Ramachandran plot Three major noncovalent bonds that help protein folding 1. Ionic bond 2. van der Waals 3. Hydrogen bond Hydrophobic “forces” The importance of hydrogen bond Folding and Refolding Secondary structures a helix and b sheet Coiled-coil structure a-keratin Two types of b sheet structures Src Kinase The combination of ahelix and b-sheets Green Fluorescence Protein Classification of protein families Two serine proteases Two homeodomains from different species (yeast a2, green; drosophila engrailed protein, red) Domains and Modules Domain shuffling Calcium binding domain Kringle domain Module Examples The combination of Modules Design Strategy ECFP(1-227) SH2(from c-Src) Linker Substrate EYFP 433 nm Weak FRET 433 nm Strong FRET 527 nm Src Activation Phosphatase 490 nm The Src reporter with CFP and YFP monomers Protein Subunits Hydrophobic forces Hemoglobin Protein assemblies Actin Filaments Disulfide bonds Extracellular matrix protein are covalently cross-linked by Disulfide bonds Hexagonally packed globular protein subunits can form flat sheets Self-Assembly Tobacco mosaic virus (TMV) Model Structure Electron Micrograph The formation of Virus shell X-Ray Crystallography of different virus (A) Tomato bushy stunt virus (B) poliovirus (C) simian virus 40 (SV40) (D) satellite tobacco necrosis virus Three mechanisms of length determination for self-assembly Protein assembly aided by assembly factors (insulin assembly) Protein Functions • • • • • • • • • Protein Binding Protein conformation Antibody Enzyme and substrate Catalytic Reaction Kinase and phosphatase GTPase, GEF, GAP Motor protein Membrane-bound protein Protein binding Protein binding sites Protein binding site Cyclic AMP Protein binding sites 1. Restriction of water entrance 2. Alteration of reactivity Sequence Comparison to find conserved binding sites Three ways for two proteins to bind Antibody Noncovalent bonds and protein interactions Binding Energy and Equilibrium constant Enzyme Kinetics Read Panel 3-3, page 165
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