1. Protein: MONOMER – AMINO ACID

2. What is protein? Proteins are polymers of amino acids. Primary Structure Secondary Structure Tertiary Structure Quaternary Structure

3. What is amino acid? Amino acid: Amino acid: a compound that contains both an amino group and a carboxyl group attach to  -carbon  -carbon also bound to side chain group, R R gives identity to amino acid

4. Terminology  - carbon = the carbon that attach next to the carboxyl group  - amino group = amino group that attach to  -carbon Other type of amino group – eg. in Lysine, has  -amino group Lysine

5. Amino acid 1.All 20 are  -amino acids 2. For 19 of the 20, the  -amino group is primary; for proline, it is secondary amino acid  -Amino acid has an amino group attached to the carbon (  -carbon) adjacent to the carboxyl group

8. Generic amino acid at physiological pH amino acids exist as dipolar ionic species (have positive and negative charge on the same molecule) - zwitterion form Amino acid is an amphoteric molecule – act either as an acid or a base  - carboxyl group  carboxylate ion  - amino group  protonated amino acid Physiological pH Amino acids as dipolar ions

9. The amino acids can exist in two enantiomeric forms (nonsuperimposable mirror image) forms – exceptional for glycine Mirror plane  carbon Enantiomer Two steroisomers of amino acids are designated L- or D-. L – amino acid: abundant in nature, found in proteins, amino group on the left

10. Amino acid Only the L - form of amino acids is commonly found in proteins. Depending on the nature of the R group, amino acids are classified into four groups. 1. nonpolar 2. polar – neutral/uncharged side chain 3. acidic 4. basic Polar, charged Vs monosaccharide : D - form

11. Classification of amino acid Nonpolar (9 amino acids) Polar neutral/uncharged (6 amino acids) charged basic (3 amino acids) acidic (2 amino acids)

12. Classification of amino acids Simplest amino acid due to the R group = H No stereoisomer because the is achiral Nonpolar

13. Aliphatic cyclic structure – N is bonded to C2 atoms Amino group of become secondary amine – often called an imino acid Amino acids with nonpolar side chains - hydrophobic

14. Polar uncharged Amide bond – highly polar Thiol / sulfhydryl group – polar – under oxidizing condition, with other thiol groups to form disulfide bridges (-S-S-) – important in 3 o structure Phenol

15. Polar charged Basic Acidic Aspartate Glutamate

16. Essential Amino acid An essential amino acid or indispensable amino acid is an amino acid that cannot be synthesized de novo by the organism (usually referring to humans), and therefore must be supplied in the diet. vs non-essential amino acid

17. Ionization of Amino Acids Remember, amino acids without charged groups on side chain exist in neutral solution as zwitterions with no net charge In acidic solution – as base (protonation) In basic solution – as acid (deprotonation)

18. Ionization of amino acids At physiological pH, the carboxyl group of the amino acid is negatively charged and the amino group is positively charged. Amino acids without charged side chains (Group 1 and 2) are zwitterions and have no net charge. (H 3 + N-HCR-COO - ). A titration curve shows how the amine and carboxyl groups react with hydrogen ion.

19. Titration of amino acid At low pH a nonacidic/nonbasic amino acid is protonated and has the structure H 3 N + HCRCOOH (amino acid in cationic form) Increase of pH, dissociation of proton (H + ) from –COOH group form H 3 N + HCRCOO - (amino acid in zwitterionic form) At pK 1, amount of cationic form = amount of zwitterionic form Beyond pK 1, additional base ions will results in all amino acids in cationic forms deprotonated to zwitterionic forms – all amino acids have no net charge pI = isoelectric point = pH at which the amino acid has no net charge/all amino acids are in zwitterionic form Increase of pH beyond pI, will cause the dissociation of H + / deprotonation from H 3 N + resulting in formation of H 2 NHCRCOO - (anionic form) Increase of pH, more dissociation of proton (H + ) from –H 3 N + group, more amino acids in anionic form At pK 2, amount of zwitterionic form = amount of anionic form

20. Titration of Alanine When an amino acid is titrated, the titration curve represents the reaction of each functional group with the hydroxide ion Cationic form All amino acids are in the zwitterion form – at isoelectric point (pI) Anionic form pI (isoelectric point) = pH at which the amino acid has no net charge/ all amino acids are in zwitterionic form

21. Titration of amino acid pK 1 and pK 2 are proton dissociation constant from carboxyl group and amino group From titration of amino acid, the pI can be calculated The charge behavior of acidic and basic amino acids is more complex. – Group Polar/charged amino acid

23. Terminology peptide peptide: the name given to a short polymer of amino acids joined by peptide bonds; they are classified by the number of amino acids in the chain dipeptide dipeptide: a molecule containing two amino acids joined by a peptide bond tripeptide tripeptide: a molecule containing three amino acids joined by peptide bonds polypeptide polypeptide: a macromolecule containing many amino acids joined by peptide bonds protein protein: a biological macromolecule of molecular weight 5000 g/mol or greater, consisting of one or more polypeptide chains Primary structure = one polypeptide

25. Protein: 1 o, 2 o and 3 o structure

26. Peptide ***** Amino acid residue: a monomeric unit of amino acids

27. PROTEIN STRUCTURE :OVERVIEW

28. Primary structure Primary (1 o ) Structure = sequence of a chain of amino acids. Determines the final structure, eventually the properties of proteins

29. Peptide bond The amino acids are linked through peptide bond Peptide bond: Peptide bond: the special name given to the amide bond between the  -carboxyl group of one amino acid and the  - amino group of another amino acid peptide bond – covalent bond

30. Peptide bond: Feature Peptide bond – in trans configuration, acts as a rigid and planar unit. Has limited rotation around the peptide bond (C-N). COO - NH 3 + 1234 5 Free rotation

31. Secondary structure The planar peptide group and free rotating bonds between C  -N and C  -C are important Two types:  -helix and  -pleated sheet 2 o structure: involves the hydrogen-bonded arrangement of the backbone of the protein N O

32. Secondary structure:  -helix Structural features: 1.One polypeptide chain 2.Hydrogen bonds between the -CO and the –NH in the same polypeptide chain (intrachain) 3.The hydrogen bonds are parallel to the helix axis 4.Winding can be right- or left- handed (L- amino acid favor right-handed) N O   H bond

33. Secondary structure:  -pleated sheet Structural features: 1.More than one polypeptide chain 2.Two types: antiparallel and parallel pleated sheet 3.Hydrogen bonds between the -CO and the –NH in the same polypeptide chain or with other polypeptide chain (interchain) 4.The hydrogen bonds are perpendicular to the direction of chain    

34. Secondary structure:  -pleated sheet antiparallel pleated sheet = peptide chains are in the opposite directions parallel pleated sheet = chains are in the same direction, the N- and C- terminal ends are aligned

35. Tertiary structure Is the three-dimensional arrangement of all atoms in protein molecule Results from folding and packing of secondary structure Bring together amino acid residues far apart, permitting interactions among their side chains

36. Tertiary structure Is the three-dimensional arrangement of all atoms in protein molecule Involves non-covalent interaction and covalent bonds 1.Hydrogen bonds between the side chain 2.Hydrophobic interaction 3.Electrostatic interactions/attractions 4.Disulfide bonds – between the R group 5.Complexation with metal ions

37. Forces in 3˚ Structure Noncovalent interactions, including – hydrogen bonding between polar side chains, e.g., Ser and Thr – hydrophobic interaction between nonpolar side chains, e.g., Val and Ile – electrostatic attraction between side chains of opposite charge, e.g., Lys and Glu – electrostatic repulsion between side chains of like charge, e.g., Lys and Arg, Glu and Asp Covalent interactions: Disulfide (-S-S-) bonds between side chains of cysteines

38. Native conformation: three-dimensional shape of a protein with biological activity Tertiary or quaternary structures

39. Quaternary structure Final level of protein structure Association of more than one polypeptide chain to form a complex Subunit = individual parts of a large protein molecule = polypeptide chain Quaternary structure is the result of noncovalent interactions between two or more protein chains. Noncovalent interactions electrostatics, hydrogen bonds, hydrophobic 1 2 3 4

40. Quaternary Structure Oligomers are multisubunit proteins with all or some identical subunits. The subunits are called protomers. 1.two subunits are called dimers 2.four subunits are called tetramers

41. Quaternary structure If a change in structure on one chain causes changes in structure at another site, the protein is said to be allosteric. Many enzymes exhibit allosteric control features. Hemoglobin is a classic example of an allosteric protein. – oxygen = positive cooperativity Has four subunits = tetramers Structure of Hemoglobin Overall structure  2  2 Heme - Fe

42. Classification of protein Proteins are classified in two ways: 1.Shape 2.Composition

43. Fibrous Proteins Fibrous proteins: contain polypeptide chains organized approximately parallel along a single axis. They – consist of long fibers or large sheets – tend to be mechanically strong – are insoluble in water and dilute salt solutions – play important structural roles in nature

44. Globular Proteins Globular proteins: proteins which are folded to a more or less spherical shape – they tend to be soluble in water and salt solutions – most of their polar side chains are on the outside and interact with the aqueous environment by hydrogen bonding and ion-dipole interactions – most of their nonpolar side chains are buried inside – nearly all have substantial sections of  -helix and  - sheet

45. Comparison of Shapes of Fibrous and Globular Proteins

46. Proteins by Composition Simple protein (apoprotein) Contain only amino acids ex. serum albumin and keratin Conjugated protein 1.simple protein (apoprotein) 2.prostetic group (nonprotein) ex. Glycoproteins, lipoproteins, metaloproteins - hemoglobin Holo- protein

47. Denaturation  Definition – complete loss of organized structure in a protein,  destroys the physiological function of the protein.  Definition – The unfolding of protein  Eg. During cooking of egg – Albumin (white egg) – denatured by heat and changes from a clear, colorless solution to a white coagulum – Often irreversible – denatured protein cannot returned to its native biological form – lost of biological function – why microbes die when boiling

48.  Due to loss of 2 o  4 o of protein structure, but not 1 o, the amide bond (peptide bond) is intact

49. Denaturation Several ways to denature proteins Heat –  in temp,  vibrations within the molecule, the energy of these vibrations can disrupt the 3 o pH –  or  pH, affect the charges of protein, the electrostatic interactions that normally stabilize the native conformation is reduced. Detergents (eg. SDS) - disrupt hydrophobic interactions, if the detergent is charged, this can also disrupt electrostatic interactions Reducing agents(eg. Urea) – will form stronger H bonds, stronger than within the protein. Also disrupt the hydrophobic interaction Heavy metal ions Mechanical stress

50. Denaturation  Reversible denaturation – organic solvents (ethyl alcohol or acetone), urea, detergents and acid or base  Denaturants disrupt only noncovalent interactions not the covalent linkages of the primary structure – If removed, possible protein to unwound to native structure – eg. pH – addition of picric acid, protein (casein) precipitate addition of NaOH, the solution clear

51. Denaturation  -mercaptoethanol example of reversible denaturation. -  -mercaptoethanol reduced the disulfide bridges of protein  the unfolding of 3 o structure, -the removal of  -mercaptoethanol will cause the oxidation of SH group to form disulfide bridges again and the 3 o structure is recovered.

52. ProteinProteinFunctionsFunctionsProteinProteinFunctionsFunctions