1. Biomolecules Survey Part 3: Amino Acids, Peptides, and Proteins Lecture Supplement page 238

2. Why Bother With Protein Structure? Molecular structure controls function Repeating unit Enzyme selectivity Drug design Many others Fundamental protein structure = amide polymer

3. Amino Acids The Fundamental Building Block of Peptides and Proteins All amino acids have amine and carboxylic acid groups All are primary amines (R-NH 2 ) except proline Amine (base) + carboxylic acid = proton transfer possible: Neutral (unionized) formZwitterionic (ionized) form K eq > 1 at physiological pH  -carbon Side chains (R) vary 18 are S, 1 is R, 1 is achiral

4. Amino Acids The 20 standard amino acids categorized by side chain properties: Hydrophilic versus hydrophobic Hydrophobic nonacidic side chains Glycine (Gly) Achiral Alanine (Ala)Valine (Val)Leucine (Leu)Isoleucine (Ile) Proline (Pro) 2 o amine (HNR 2 ) Tryptophan (Trp)Phenylalanine (Phe)Methionine (Met) Acidic versus basic versus neither (nonacidic)

5. Amino Acids Hydrophobic acidic side chains Side chain more acidic than water Cysteine (Cys) Hydrophilic nonacidic side chains Tyrosine (Tyr) Serine (Ser)Threonine (Thr)Asparagine (Asp)Glutamine (Gln)

6. Amino Acids Hydrophilic acidic side chains Hydrophilic basic side chains Nitrogen lone pairs to accept a proton Do I have to memorize amino acid structures? Aspartic acid (Asp)Glutamic acid (Glu) Lysine (Lys)Arginine (Arg)Histidine (His)

7. Amino Acids Form Peptides Amino acids link via peptide bond (an amide); form chains Ala Ser Val Serine side chain configuration? Verify with model of complete tripeptide -2 H 2 O

8. Amino Acids Form Peptides A tripeptide (three amino acids) Naming: Val-Ser-Ala or Ala-Ser-Val? N-terminus  C-terminus N-terminusC-terminus AlaSerVal Amino acid sequence = primary structure of peptide or protein Like amino acids, peptides and proteins also have zwitterionic forms:

9. How Does Peptide Bond Influence Structure? Trans Amino acid chain opposite sides of C-N bond Cis Amino acid chain same side of C-N bond Torsional strain: Trans < cis; equilibrium favors trans isomer by ~ 2 kcal mol -1 Conjugation effects: Barrier to rotation around C-N bond ~16 kcal mol -1 is planar Amide is conjugated:

10. The Protein Conformation Problem Consider major conformational isomers of a glycine peptide: Each glycine has 2 x 3 x 3 = 18 major conformations Verify with models A small protein consisting of 14 glycine has 18 14 = 3.7 x 10 17 major conformations! Number of conformations  significantly if more amino acids, or side chains present Problem:Protein function requires well-organized and restricted structure Solutions: Local conformational restrictions: Cis/trans isomers and planarity Intramolecular hydrogen bonds Results: Reduced protein flexibility Reduced structure randomness trans or cis 3 staggered

11. Secondary Structure Structural randomness reduced by intramolecular hydrogen bonds  -Helix Clockwise spiral down H-bonds parallel to axis Side chains point out from center Elastic coil: Thinkbook binding Causes three basic motifs: The secondary structures of proteins There is an H-bond between C=O and N-H of residue 1 and residue 4 (residue 2 and residue 5) (… etc.)

12. Secondary Structure  -Sheet: Two or more aligned, H-bonded  -strands Parallel  N-termini same end) or antiparallel  N-termini opposite ends) The illustrated  -sheet is antiparallel  -Sheet more rigid/less elastic than  -helix Significant component of keratin (hair, wool) and silk Make your own silk: Thinkbook Appendix C N-terminus C-terminus N-terminus  -Strand: A “fully extended” polypeptide chain (as opposed to being in a helix)

13. Secondary Structure (Random) Coil: Not really random, just hard to describe Key point: Random coils do not have catalytic activity Denatured proteins adopt the shape of a random coil

14. Tertiary Structure Tertiary structure : Three-dimensional atomic positions Response to environment: Side chain orientation depends on environment Polar environment (water) Nonpolar environment (core of cell membrane) Hydrophilic side chainspoint outpoint in Hydrophobic side chainspoint inpoint out Disulfide bridges : Form loop within one chain, or bond two separate chains Cys Found in: Insulin (3) Keratin (hair) Others Aspects of protein structure determined by side chain composition

15. Quaternary Structure Quaternary structure : Association of two or more subunits by noncovalent bonds Subunits = proteins, carbohydrates, coenzymes, etc. Large surface areas  noncovalent forces can be significant magnitude Quaternary structure = four subunits

16. Four levels of protein structure Primary structure: amino acid sequence Secondary structure: alpha helix, beta strand / beta sheets Tertiary structure: spatial arrangement of amino acid residues and disulfide bonds Quaternary structure: spatial arrangement of subunits and nature of their interactions

17. Insulin – Primary Structure

18. Insulin – Secondary Structure and Tertiary Structure To play with an interactive 3D-Model of the insulin monomer: http://www.pdb.org/pdb/101/motm_disscussed_entry.do?id=4ins http://www.pdb.org/pdb/101/motm_disscussed_entry.do?id=4ins -3 alpha helices -1 beta strand

19. Insulin – Quaternary Structure Insulin hexamer (inactive form of insulin; long-term storage in the body)

20. Protein Structure Representations Myoglobin stores O 2 in muscle tissue via heme ~70%  -helix A globular protein (~spherical shape) Helix = fuchsia Sheet = yellow Coil = white Worldwide Protein Data Bank: http://www.wwpdb.org/

21. Protein Structure Representations Retinol Binding Protein Helix = fuchsia Sheet = yellow Coil = white Important for vision

22. Protein Structure Representations Lactate Dehydrogenase Helix = fuchsia Sheet = yellow Coil = white Quaternary structure = four identical protein subunits Released in bloodstream by damaged muscles Indicative of heart damage or failure Subject of Chem 153L experiments