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 PEPTIDE Fig 5-1 Essential Cell Biology, Alberts et al A.K.A Amide Bond

Protein Structure Backbone –amide nitrogen -  -carbon - carbonyl carbon Side chains –R-groups of each amino acid on  -carbon Peptide bond is planar giving rigidity to backbone Primary Structure Amino Acid Sequence Fig 3-4

Protein Structure Secondary Structure intramolecular folding of backbone  -helix  -sheet Fig 3-8

Alpha-helix Fig. 3-8 Copyright 2008 by Saunders/Elsevier. All rights reserved.

Coiled-coil of two parallel alpha-helices Fig Copyright 2008 by Saunders/Elsevier. All rights reserved.

Coiled-coil of two parallel alpha-helices Fig Copyright 2008 by Saunders/Elsevier. All rights reserved.

Beta-sheets Fig. 3-8 Copyright 2008 by Saunders/Elsevier. All rights reserved.

Protein Structure Tertiary structures –Proteins can have any combination of secondary structures Fig 3-9

Protein Structure Modeling protein structures X-ray crystallography Ribbon Space-filling Fig 2-9

Protein Structure Panel 5-2 Essential Cell Biology, Alberts et al Backbone Ribbon Wire Space-filling

Protein Structures Structural & Functional Domains FN – fibronectin Ig – immunoglobulin SH – src homology Fig 3-13

Nucleic Acids Nucleotides –Nitrogenous base Purine –Adenine –Guanine Pyrimidine –Cytosine –Thymine –Uracil –Pentose sugar 2’-deoxyribose Ribose –Phosphate 1-3 (mono, di, tri- phosphate)

Nucleic Acids Nitrogenous bases

Pentose sugar Nucleic Acids

Nucleoside Base + Sugar –Adenosine –Guanosine –Thymidine –Cytosine –Uridine

Phosphate –1-3 (mono, di, tri-phosphate) 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 rRNAPhe tRNA

Simple sugars –Monosaccharides Glucose Fructose Galactose Mannose Ribose Arabinose Carbohydrates 6-carbon 5-carbon

Carbohydrates Important modificationsGlycosidic bonds glcNAc glcUA

Carbohydrates Glycoconjugates (polysaccharides, complex carbos) –Starch (plants) –Glycogen (animals) Branched polymers of glucose –Cellulose Unbranched polymers

Carbohydrates Important attachments to amino acid residue side chains

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

Carbohydrates Proteoglycans –Proteins with attached glycosaminoglycans –Cell surface proteins –ECM