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Four Levels of Protein Structure Biological activity of protein is determined by these levels Primary structure is the sequence of amino acids in a polypeptide (Usually read N-C) Secondary structures are localized folds or helices that form within a region of a polypeptide Tertiary structures are larger folding events that are stabilized by interactions between R groups Quaternary structure is the interaction of multiple polypeptides within one active proteins Primary Structure Sequence of amino acids within a single polypeptide Are often similar among proteins of similar function Usually written from amino terminus to carboxy terminus Can also provide some insight into additional structures by the position of particular groups of amino acids Secondary Structure Localized within regions of polypeptide Stabilized by hydrogen bonding a helix-stabilized by frequent polar groups Right handed helices b-pleated sheets are formed by consecutive polar groups on two regions of polypeptide Tertiary Structure Large folding events that are stabilized by interactions between amino acids Hydrophobic interactions Disulfide bridge Very stable bond formed between two distant cysteine residues Ionic interactions -Hydrogen bonds form between polar groups Nonpolar regions generally internalize in structure Strong bond between oppositely charged side groups Quaternary Structure Only seen in compound proteins Interactions are maintained between polypeptide chains by bonds similar to tertiary structure Function is often unique to quaternary structure Individual components are unable to accomplish task alone Protein Structure Revisited Fig. 5-23 Denaturation Normal protein Renaturation Denatured protein Protein Conformation The 3D structure in which the protein is biologically active is called the active conformation Denatured protein has lost its active conformation Shape of a protein is consistent under identical conditions Proteins will attempt to find the lowest energy form under conditions Conditions that affect conformation Solvent (polar versus non-polar),pH, temperature and chemical agents (2-mercaptoethanol) Protein summary Very important biological macromolecules that perform a wide array of functions Polymers of amino acids 20 natural amino acids that have distinct R side groups The side groups determines the shape and function of a polypeptide There are four levels of structural organization of proteins Nucleic Acids Deoxyribonucleic acid (DNA) and ribonucleic acid (RNA) Polymer of nucleotides Store cellular information Molecules of inherited information Basis for genetics Often large, very complex molecules Serve as templates for proteins Help control regulation of cellular functions Nucleotides Comprises: A pentose sugar A nitrogen containing base An organic phosphate group Bases Two kinds of bases Pyrimidines are single ring structures Purines are double ring structures cytosine, thymine and uracil adenine and guanine In DNA G-C and A-T interactionss Pentoses Deoxyribose in DNA and Ribose in RNA Only difference is the lack of an Oxygen at carbon 2 in deoxyribose Ring structures Nucleic Acid Structure Phosphate group is attached to carbon 5 of pentose Oxygen of Phosphate forms a phosphodiester bond with the OH group on carbon 3 of the pentose Strands have a 5’ end and a 3’ end Fig. 5-27ab 5' end 5'C 3'C Nucleoside Nitrogenous base 5'C Phosphate group 5'C 3'C (b) Nucleotide 3' end (a) Polynucleotide, or nucleic acid 3'C Sugar (pentose) DNA vs RNA Both are important for cell function DNA is double stranded and longer-lived Both can serve as a template for the synthesis of the other RNA is single stranded and has shorter life DNA to RNA is very common (transcription) RNA to DNA occurs only with retroviruses (reverse transcription) Both have 5’-3’ orientations DNA Double Helix Structure elucidated by Watson and Crick Two strands are anti-parallel From work of Wilkens and Franklin 5’end of each strand aligns with 3’ end of complementary strand Bases pair by hydrogen bonding A-T (2 bonds)and G-C (3 bonds) Since strands are complementary they serve as a template for opposite strand Strands make Double Helix structure (twisted ladder)