BIOC 460, Spring 2008LEC 3, Amino Acid Structures andChemical Properties 1Lecture 3Introduction to Proteins;Amino Acids, the Building Blocksof ProteinsReading: Berg, Tymoczko & Stryer: Chapter 2, pp. 25-34Appendix to Chapter 2, pp. 60-61 (visualizing protein structures)See also posted General Chemistry Review notes for acid-base concepts,and online website on amino acids (linked in lecture notes directory)for excellent way to learn the amino acids’ structures and properties:http://www.biology.arizona.edu/biochemistry/problem_sets/aa/aa.htmlLecture may skip portions of these notes and use website,or go back and forth.Key Concepts• 4 levels of protein structure:1. Primary (1°)2. Secondary (2°)3. Tertiary (3°)4. Quaternary (4°)• Properties of the 20 amino acids that occur inpeptides and proteins are crucial to the structure andfunction of proteins– Stereochemistry– Relative hydrophobicity or polarity– Hydrogen bonding properties– Ionization properties– Other chemical propertiesBIOC 460, Spring 2008LEC 3, Amino Acid Structures andChemical Properties 2Learning Objectives• Explain the 4 levels of protein structure: primary,secondary, tertiary, and quaternary.• Draw the structure of a typical amino acid, indicating thefollowing features: α-carbon, α-carboxyl group, α-aminogroup, sidechain (“R group”), and ionic forms thatpredominate at acidic (say, pH 1), neutral (pH 7), and basic(pH 13) pH values.• Classify each of the 20 common amino acids found inproteins according to side chain type (aliphatic, aromatic,sulfur-containing, aliphatic hydroxyl, basic, acidic, amide,hydrophilic (polar), hydrophobic (nonpolar). (Thesecategories overlap extensively, e.g., glutamate is acidic andit’s very polar.)• Learn the structure of each of these 20 amino acids, withits full name and 3-letter abbreviation. DO THIS NOW –DON’T PUT IT OFF. You won't have to draw detailedstructures of arginine, histidine, or tryptophan, but youshould be able to recognize them, and draw the simplerstructures, with the ionization reactions of ionizable groups(see below).Learning Objectives, continued• Be very familiar with the approximate (“typical”) pKa valuesof the 7 ionizable R groups (side chains) and also the α-amino and α-carboxyl groups in peptides and proteins;note that numerical values of these "generic " pKa valuesfor the ionizable functional groups in peptides and proteinswill be on the cover sheet of Exam 1, but the pKa valuesare of little use if you don't know the chemical nature ofthe groups (see below). You do NOT need to know thepKa values for the ionizable groups on the free aminoacids.• Write out the ionization (protonation/deprotonation)reactions for the 9 ionizable functional groups (7 sidechains plus terminal α-amino and α-carboxyl groups), withappropriate structures; understand the charge propertiesof each form (conjugate acid and conjugate base) of eachgroup.BIOC 460, Spring 2008LEC 3, Amino Acid Structures andChemical Properties 3Protein Structure -- Overview• Primary structure: linear sequence of amino acids– polymer of amino acid residues (~50-1000)– linked by peptide bonds (covalent, amide linkages)• Terminology: amino acid residue, polypeptide (chain)• Building blocks: 20 amino acids (different side chains)• Protein function depends on correct 3-D folding ofpolypeptide– 3-D folded structure determined by AA sequence– Most proteins’ functions involve binding other molecules• Shape complementarity (steric, van der Waalsinteractions)• Chemical complementarity (hydrogen bonddonors/acceptors, charge complementarity, etc.)• Often the hydrophobic effect is important in binding.• Flexibility in structure (proteins are not rocks!)Structure of lactoferrin changes when it binds iron(common phenomenon, induced fit)Berg et al., Fig. 2-3ribbon diagram, just “backbone” atoms of polypeptide chain(easier to trace chain from one end to the other) Space-filling structure, all atoms of polypeptide chainBIOC 460, Spring 2008LEC 3, Amino Acid Structures andChemical Properties 4Biological Roles of Proteins (examples)1. Catalysis (enzymes) 2. Transport (e.g., hemoglobin - O2 transport in blood;transport of ions across cell membranes) 3. Storage (e.g., myoglobin - oxygen storage in muscle; seedproteins - storage of nutrients) 4. Coordinated motion (e.g., in muscle, cilia, flagella) 5. Mechanical support (e.g., collagen) 6. Protection (e.g., immune system - antibodies; bloodclotting proteins) 7. Regulation and communication (e.g., hormones,receptors, gene activation and repression, control ofenzyme activity) 8. Generation and transmission of nerve impulses 9. Toxins (bacterial, plant, snake, insect)Levels of Protein Structure1. Primary structure (1° structure): – sequence of AAs– linked by peptide bonds (amide linkages)2. Secondary structure (2° structure): – local, regular/recognizable conformations observedfor parts of peptide backbone of a protein– e.g, α-helix, β conformation, collagen helix 3. Tertiary structure (3° structure): – 3-dimensional conformation of whole foldedpolypeptide chain 4. Quaternary structure (4° structure): – 3-dimensional relationship of different polypeptidechains (subunits) – how the subunits fit together and their symmetryrelationships – only in proteins with more than 1 polypeptide chainBIOC 460, Spring 2008LEC 3, Amino Acid Structures andChemical Properties 5Levels of Protein StructureNelson & Cox, Lehninger Principles of Biochemistry, 4th ed., Fig. 3-16α-Amino Acids• carboxylic acids, so "α", "β" "γ", etc. designate order ofadditional C atoms on carboxyl group.• α carbon = central C atom, with 4 different substituents:1. α-carboxyl group2. α-amino group3. hydrogen atom4. R group = “side chain”(different structures for 20 different amino acids)• Stereochemistry: D vs. L– α carbon chiral (4 different substituents)– Enantiomers (non-superimposable complete mirrorimages)– All AAs in naturally occurring proteins are L-isomers.RBIOC 460, Spring 2008LEC 3, Amino Acid Structures andChemical Properties 6α-Amino Acids, StereochemistryBerg et al., Fig. 3-4UA’s BMB Biology Projectwebsite on amino acidsAs you "travel" ONward, from carbonyl C toward N of amino group, in L-amino acids R group is on left.Are there naturally-occurring D-aminoacids?α-Amino Acids, Ionizationα-carboxyl group α-amino groupBerg et al., Fig. 2-6BIOC 460, Spring 2008LEC 3, Amino Acid
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