BIOL 3510 1st Edition Lecture 2 Outline of Last Lecture I Introduction to cells II Microscopy III Prokaryotes and Eukaryotes IV Model Organisms Outline of Current Lecture I Introduction to proteins II Types of Non Covalent Bonds Forces III Protein structures IV Measuring Protein Current Lecture Proteins are composed of chains of amino acids linked together by peptide bonds Amino acids can be grouped by their side chains Peptide bonds are covalent bonds 90 kcal mol in water or vacuum where electrons are shared shared unequally in a polar covalent bond Polar covalent bonds create dipoles within a molecule due to unequal electron distribution 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 secondary tertiary quaternary 4 Types of Non Covalent Bonds Forces in Cells 1 Electrostatic attractions 3kcal mol forces that attract oppositely charged atoms 2 Hydrogen bonds 1kcal mol a weak bond between an electronegative atom and a hydrogen bound to another electronegative atom 3 Van der Waals interactions 0 1 kcal mol 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 These notes represent a detailed interpretation of the professor s lecture GradeBuddy is best used as a supplement to your own notes not as a substitute Chaperones are proteins that improve the efficiency of protein folding in cells Hydrogen bonds between polypeptide backbone groups create secondary structures Alpha helix Polypeptide twists to form a cylinder Stabilized by H bonds between a C O n and a N H n 3 Often found in proteins that span membranes 2 or 3 of them wrapped around each other form a stable coiled coil Beta 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 Can be parallel or anti parallel Often form the core of stable proteins Intrinsically disordered sequences correspond to unstructured regions of some proteins The final 3D conformation of single polypeptide is the tertiary structure held together mostly by non covalent bonds Quaternary structure is the binding of two or more polypeptides to form a single complex held together mostly by non covalent bonds forces Protein domains are regions of a polypeptide chain that fold independently into a stable structure They can be combined to create proteins with new functions Disulfide bonds are covalent bonds between cysteines that act as atomic staples to stabilize extracellular proteins Proteins have a variety of shapes Members of protein families have similar 3D structures and often similar amino acid sequences X ray crystallography is used to determine the 3D structures of proteins Nuclear magnetic resonance NMR spectroscopy is used to determine the 3D structure of small protein
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