Biological Macromolecules
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1 Introduction for Chem 493 Chemistry of Biological Macromolecules Dr. L. Luyt January 2008 Dr. L. Luyt Chem
2 Biological macromolecules are the molecules of life allow for organization serve a functional purpose structural complementarity allows for chemical interactions Biological macromolecules are carbon based compounds consist of building blocks many are polymeric with repeating subunits sequence of the subunits determines structure and function Dr. L. Luyt Chem
3 Summary of biological macromolecules relevant to Chem 493 Amino Acids Monosaccharides Nucleotides Peptide/Protein Polysaccharide Nucleic Acid enzymes hormones receptors membrane channels cell structure energy storage structure DNA, storage of information RNA, protein synthesis Dr. L. Luyt Chem
4 Properties of biomolecules: 1. Have a directionality Structural polarity Consists of a head and tail, direction to structure H 2 N R 1 C 2 H + H 2 N R 2 C 2 H -H 2 H 2 N R 1 H N C2 H R 2 N-terminus C-terminus Dr. L. Luyt Chem
5 Properties of biomolecules: 1. Have a directionality Structural polarity Consists of a head and tail, direction to structure Dr. L. Luyt Chem
6 Properties of biomolecules: 1. Have a directionality Structural polarity Consists of a head and tail, direction to structure Dr. L. Luyt Chem
7 Properties of biomolecules: 2. Contains information Sequence of monomers contains information Especially for peptides and nucleic acids Side-chain functional groups give unique properties Unique Sequence = Unique Recognition Dr. L. Luyt Chem
8 Properties of biomolecules: 3. Consist of a 3-dimensional architecture Linear sequences, but can turn, fold, coil R HN NH H N R Adapt unique 3-dimensional structures NH R R Number 88 CRYSTAL STRUCTURE F HUMAN APLIPPRTEIN A-I (PDB code: 1av1) Dr. L. Luyt Chem
9 Structure of Peptides and Proteins Primary Structure: amino acid sequence protein of n residues = possibility of 20 n sequences Neuromedin B Gly-Asn-Leu-Trp-Ala-Thr-Gly-His-Phe-Met-NH 2 Dr. L. Luyt Chem
10 Secondary Structure: spatial arrangement of peptide backbone α-helix, β-sheet, random coil, reverse turns Dr. L. Luyt Chem
11 Tertiary structure: folding of secondary structures to create the three dimensional structure of a single polypeptide chain TERTIARY STRUCTURE F AP-D-ALANYL CARRIER PRTEIN Quaternary structure: the arrangement of subunits where more than one peptide chain creates the protein Crystal structure of hemoglobin 4 subunits = tetramer Dr. L. Luyt Chem
12 Properties of biomolecules: 4. Interact through structural complementarity Biological function of a biomolecule is achieved through structural complementarity Weak chemical interactions Ionic bonds, ion/dipole, dipole/dipole Hydrogen bonding Hydrophobic interactions Van der waals interactions Dr. L. Luyt Chem
13 Properties of biomolecules: 4. Interact through structural complementarity Weak chemical interactions Ionic bonds 5-10 kcal/mol - attractive forces between oppositely charged polar functions Ion/dipole 2-8 kcal/mol, dipole/dipole 1-3 kcal/mol Eg. Acetylcholine interaction with muscarinic receptor NH 3 H 3 C H CH 3CH3 N CH 3 Dr. L. Luyt Chem
14 Properties of biomolecules: 4. Interact through structural complementarity Weak chemical interactions Hydrogen bonding 2-5 kcal/mol - between a hydrogen atom (covalently bonded to N,, S) and a second electronegative atom (H bond acceptor) Donors Acceptors H N H H P H N H H Dr. L. Luyt Chem
15 Properties of biomolecules: 4. Interact through structural complementarity Weak chemical interactions Hydrophobic interactions, very weak kcal/mol - between nonpolar molecules in close proximity - this minimizes the hydrophobic surfaces available to water Van der waals interactions, very weak 0.5 kcal/mol - induced dipole interactions between closely approaching atoms/molecules Dr. L. Luyt Chem
16 Properties of biomolecules: 4. Interact through structural complementarity Lock and Key Dr. L. Luyt Chem
17 Chemistry of Biological Macromolecules Purposes for doing this? structural elucidation chemical synthesis of biologics As organic chemists, we want to synthesize and modify biological macromolecules. modifying the properties of biomolecules - prevent enzymatic degradation - improve bioavailability, pharmacokinetics, potency - conjugate to dyes, radionuclides, cytotoxic agents DRUGS Imaging Agents Dr. L. Luyt Chem
18 Chemistry of Biological Macromolecules As organic chemists, we want to synthesize and modify biological macromolecules. This course will demonstrate: protecting groups required for biomolecule synthesis and derivatization solid-phase (polymer supported) synthesis and automation preparation and reactivity of monomers (amino acids, monosaccahrides, nucleotides) synthesis of polymeric biomolecules (peptides, oligosaccharides, nucleic acids) approaches used to design drugs from biological macromolecule leads recent literature for applications Dr. L. Luyt Chem
19 Chemistry of Biological Macromolecules Examples of biomolecules peptide hormones and analogues Gonadotropin-releasing hormone (GnRH) agonists H Glu His Trp Ser Tyr Gly Leu Arg Pro Gly NH 2 - gonadorelin acetate (Lutrepulse) used to treat infertility - pump delivers peptide via IV every 90 min pglu His Trp Ser Tyr Gly Leu Arg Pro Gly NH 2 - Leuprolide acetate - 15X potency, daily injection or implant pglu His Trp Ser Tyr Gly DLeu Arg Pro NH N H H N pglu = pyroglutamate = 5-oxoproline Dr. L. Luyt Chem
20 Chemistry of Biological Macromolecules Examples of biomolecules oligosaccharides Disaccharides - sucrose H H H H H H H H Gentamicin - antibiotic Dr. L. Luyt Chem
21 Chemistry of Biological Macromolecules Examples of biomolecules nucleoside analogues 5-Fluorodeoxyuridine (Floxuridine) - A pyrimidine based antimetabolite NH F NH H N H N H H H Dr. L. Luyt Chem
22 Chemistry of Biological Macromolecules SUMMARY Properties of biomolecules: 1. Have a directionality 2. Contains information 3. Consist of a 3-dimensional architecture 4. Interact through structural complementarity As organic chemists, we want to synthesize and modify biological macromolecules. Dr. L. Luyt Chem
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Model Worksheet Teacher Key
Introduction Despite the complexity of life on Earth, the most important large molecules found in all living things (biomolecules) can be classified into only four main categories: carbohydrates, lipids,