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Molecular Structures Classes of Biomolecules • Proteins – polymers of amino acids – alias: polypeptides, peptides, enzymes • Nucleic Acids – polymers of nucleotides – alias: DNA, RNA • Lipids – long chain hydrocarbons tails with carboxylic end – alias: fatty acids, triglycerides, phosphoglycerides, phospholipids, steroids • Carbohydrates – 3-6 carbon polyhydroxyl compounds – monosaccharides, disaccharides, polysaccharides, starches, glycogen Proteins & Amino Acids • Amino Acid Properties Proteins & Amino Acids • Common modifications to amino acids in proteins in cells – – – – – phosphorylation (kinasing) – signaling, activation/inactivation acetylation - histones disulfide bridges – protein folding hydroxylation – collagen polymerization glycosylation (see carbohydrates) Protein Structure • Peptide bond A.K.A Amide Bond Fig 5-1 Essential Cell Biology, Alberts et al Protein Structure Primary Structure Amino Acid Sequence • Backbone – amide nitrogen- -carbon-carbonyl carbon • Side chains – R-groups of each amino acid on -carbon • Peptide bond is planar giving rigidity to backbone Fig 2-6 Protein Structure Secondary Structure intramolecular folding of backbone -helix -sheet Fig 2-10 Protein Structure • Tertiary structures – Proteins can have any combination of secondary structures Fig 2-11 Fig 2-9 Protein Structure • Modeling protein structures • X-ray crystallography Space-filling Ribbon Protein Structure Backbone Wire Space-filling Ribbon Panel 5-2 Essential Cell Biology, Alberts et al Protein Structures • Structural & Functional Domains Fig 2-15 Nucleic Acids • Nitrogenous base Nucleic Acids • Pentose sugar Nucleic Acids • Nucleoside • Base + Sugar – Adenosine – Guanosine – Thymidine – Cytosine – Uridine Nucleic Acids • Phosphate – 1-3 (mono, di, tri-phosphate) Nucleic Acids • Nucleotides – Nitrogenous base • Purine – Adenine – Guanine • Pyrimidine – Cytosine – Thymine – Uracil – Pentose sugar • 2’-deoxyribose • Ribose – Phosphate • 1-3 (mono, di, triphosphate) Nucleic Acids • Polymerization of nucleotides – Phosphodiester bond • 3'-OH of added nucleotide SN2 attack on phosphate – DNA polymerase – RNA polymerase Nucleic Acid Structure • The Double Helix – Watson-Crick base pairs • A-T • G-C Nucleic Acid Structure • RNA secondary structure – Intermolecular base pairing – Stems & loops 16S rRNA Phe tRNA Carbohydrates • Simple sugars – Monosaccharides • • • • • • Glucose Fructose Galactose Mannose Ribose Arabinose 6-carbon 5-carbon Carbohydrates • Important modifications glcNAc glcUA • Glycosidic bonds Carbohydrates • Glycoconjugates (polysaccharides, complex carbos) – Starch (plants) – Glycogen (animals) • Branched polymers of glucose – Cellulose • Unbranched polymers Fig2-27 Carbohydrates • Important attachments to amino acid residue side chains Fig 2-28 Carbohydrates • Proteoglycans – Proteins with attached glycosaminoglycans – Cell surface proteins – ECM Fig 31-14 Carbohydrates • Glycosaminoglycans (GAGs, mucopolysaccharidse) – Polymer of disaccharide units – Sulfate common modification – Linked to protein by O- or N- linkage to S/T or N residues respectively Fig 31-13