8 23 2015 Proteins are composed of chains of amino acids linked together by peptide bonds General structure of an amino acid Proteins I R N C O C O Amino acids can be grouped by their side chains Amino acids can be grouped by their side chains Amino acids can be grouped by their side chains Peptide bonds are covalent bonds covalent bonds 90 kcal mol in water or vacuum electrons are shared electron sharing is unequal in a polar covalent bond 1 8 23 2015 Peptide bonds form via condensation reactions The conformation of a protein is specified by its amino acid sequence 3D shape is inherent 4 levels of protein structural organization primary amino acid sequence secondary tertiary quaternary 4 types of non covalent bonds forces act in cells properly folded proteins Types of non covalent bonds forces 1 Electrostatic attractions 3 kcal mol in water forces that attract oppositely charged atoms 2 Hydrogen bonds 1 kcal mol in water a weak bond between an electronegative atom and a hydrogen bound to another electronegative atom 3 Van der Waals interactions 0 1 kcal mol in water fluctuations in the electron cloud surrounding an atom creates a transient dipole this dipole induces an opposing dipole in a nearby atom generating an attraction 4 Hydrophobic forces not really a bond exclusion of non polar surfaces from the hydrogen bonded water network These non covalent bonds forces stabilize the 3D conformations of proteins Chaperones are proteins that improve the efficiency of protein folding in cells 2 8 23 2015 Hydrogen bonds between polypeptide backbone groups create secondary structures helix often found in proteins that span membranes helix 2 or 3 helices wrapped around each other form a stable coiled coil Hydrogen bonds between polypeptide backbone groups create secondary structures sheet can be parallel or antiparallel often form the core of stable proteins Quaternary structure is the binding of two or more polypeptides to form a single complex held together mostly by non covalent bonds forces Hydrogen bonds between polypeptide backbone groups create secondary structures sheet stabilized by H bonds between the C O and N H groups on adjacent lengths of a polypeptide chain alternate R groups extend in opposite directions The final 3D conformation of single polypeptide is the tertiary structure The overall folding of a single protein subunit held together mostly by non covalent bonds forces Protein domains are regions of a polypeptide chain that fold independently into a stable structure Cytochrome b562 NAD binding domain from lactic dehydrogenase Immunoglobin domain from an antibody 3 8 23 2015 Protein domains can be combined to create proteins with new functions Proteins have a variety of shapes X ray crystallography is used to determine the 3D structures of proteins Disulfide bonds are covalent bonds between cysteines that act as atomic staples to stabilize extracellular proteins Members of protein families have similar 3D structures and often similar aa sequences Nuclear magnetic resonance NMR spectroscopy is used to determine the 3D structure of small proteins Drawback Must be able to crystalize the protein no crystal needed 4
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