Protein: Polymers made up of difference sequences of 20 standard amino acids. Functions: Enzymes, defensive proteins, hormonal and regulatory proteins Function is dependent on structure of the protein! Structure of Amino Acid: Amine Carboxylic acid Side Chain (R)-- varies; this variation determines which amino acid it is! Alpha (α) Carbon: Stereocenter 18 are S, 1 is R, and 1 is achiral How can structure influence function? Amino acids have different side chain properties 1. Hydrophobic nonacidic side chains: Low polarity. 2. Hydrophobic acidic side chains: High polarity. 3. Hydrophilic nonacidic side chains: They like water, but not readily deprotonated. 4. Hydrophilic acidic side chains: They like water AND readily deprotonated. Look for carboxylic acid in the side chain. 5. Hydrophilic basic side chains: Look for nitrogen lone pairs that accept a proton in the side chains! How do amino acids form chains? They form peptide (amide) bonds The -OH from carboxylic group of one atom combines with the one of the H's from the nitrogen group to form H20. Can have two conformations: cis and trans o Each C-C and C-N bond on the α-carbon has three staggered conformations as well (2 gauche and 1 anti) ---> This leads to A LOT of conformations
This amide bond bond has partial pi character due to resonance between the nitrogen lone pair and carbonyl group. o This partial pi character increases the barrier to rotation around the C-N bond o Important for the amide bond to remain rigid to maintain shape of the protein Peptide bonds formation between the amino acids Ala, Ser, and Val Peptide linkages How to tell where N-terminus or C-terminus is? Locate the a-carbon on the most left amino acid Is the nitrogen on the left of the carbon? Yes No This is the N-terminus This is the C-terminus If one amino acid is drawn with nitrogen on left, that means all amino acids within the structure have the nitrogens on the left, and the last amino acid with have the nitrogen on the left, meaning it is N-
Summary of Primary, Secondary, Tertiary, and Quarternary Structure Primary Structure A chain made up of amino acids Type of bonds: pep5de bond (covalent bonds) Can be cis/trans Secondary Structure α-helix, β-sheet, random coil α-helix is more elastic, like a coil β-sheet is more rigid than α-helix Type of bonds: H bonding which reduces floppyness H bonding between the H acached to the nitrogen and the carbonyl Oxygen Proline can't par5cipate in this H bonding because it only has one N H to begin with and it used when forming the pep5de bond Ter1ary Structure Polypep5de chain bent at specific sites depending on the environment If it's in a polar environment: hydrophilic side chains point out, hydrophobic side chains point in Type of bonds: Disulfide bridges links between sulfurs that help hold chains together (formed between two cysteine side chains) Also H bonding between side chains, London forces Quarternary Structure Combina5on of two or more subunits Subunits can be proteins, carbohydrates, coenzymes, etc. Type of Bonds: Noncovalent bonding (H bonding, London forces, ion dipole, etc)
Practice Problems: 1. Determine how many conformations exist in a decapeptide containing only glycine. 2. What type of bonds are significant for keeping the secondary structure together? 3. What makes an amino acid's side chain basic? 4. Sketch the structure of the amino acid aspartic acid given that the side chain is CH 2 COOH. Is the side chain hydrophilic or hydrophobic, and acidic or basic? Solutions: 1. The peptide bond has two conformations: cis and trans. The C-C and C-N bonds also each have three staggered conformations. Thus each amino acid in the decapeptide can have 2x3x3=18 conformations. Since there are 10 amino acids in this chain, 10 10 = 1.0 x 10 10 conformations. 2. H-bonding maintains the 3D shape of the secondary protein structures. 3. If there's a nitrogen lone pair to accept a proton on the side chain, then the side chain will exhibit basic properties. 4. Hydrophilic Acidic side chain
Sources: Dr. Hardinger's Lecture Supplement Dr. Hardinger's Thinkbook http://homepages.ius.edu/dspurloc/c122/images/aminostrc.gif http://homepages.ius.edu/dspurloc/c122/images/aminostrc.gif http://www.chemistry.wustl.edu/~courses/genchem/tutorials/hemoglobin/images/alphahelix.jpg http://w3.hwdsb.on.ca/hillpark/departments/science/watts/sbi3u/class_summary/protein_- _Primary_Structure.jpg