CHAPTER 3 Amino Acids, Peptides, Proteins

1. CHAPTER 3 Amino Acids, Peptides, Proteins • Structure and naming of amino acids • Structure and properties of peptides • Ionization behavior of amino acids and peptides • Purification and assay methods • Peptide sequencing and chemical synthesis • Protein sequence analysis

2. Proteins: Main Agents of Biological Function Catalysis: enolase (in the glycolytic pathway) DNA polymerase (in DNA replication) Transport: hemoglobin (transports O2 in the blood) lactose permease (transports lactose across the cell membrane) Structure: collagen (connective tissue) keratin (hair, nails, feathers, horns) Motion: myosin (muscle tissue) actin (muscle tissue, cell motility)

3. Amino Acids: Building Blocks of Protein • Proteins are heteropolymers of -amino acids • Amino acids have properties that are well suited to carry out a variety of biological functions: • Capacity to polymerize • Useful acid-base properties • Varied physical properties • Varied chemical functionality

4. Amino Acids: Atom Naming Organic nomenclature: start from one end Biochemical designation: start from -carbon and go down the R-group

5. Most -Amino Acids are Chiral • The -carbon has always four substituents and is tetrahedral • All (except proline) have an acidic carboxyl group, a basic amino group, and an alpha hydrogen connected to the -carbon • Each amino acid has an unique fourth substituent R • In glycine, the fourth substituent is also hydrogen

6. Amino Acids: Classification Common amino acids can be placed in five basic groups depending on their R substituents: Nonpolar, aliphatic (7) Aromatic (3) Polar, uncharged (5) Positively charged (3) Negatively charged (2)

7. Aliphatic Amino Acids • http://en.wikipedia.org/wiki/File:Aa.svg

8. Aromatic Amino Acids • http://en.wikipedia.org/wiki/File:Aa.svg

9. Charged Amino Acids • http://en.wikipedia.org/wiki/File:Aa.svg

10. Polar Amino Acids • http://en.wikipedia.org/wiki/File:Aa.svg

11. Special Amino Acids • http://en.wikipedia.org/wiki/File:Aa.svg

13. Uncommon Amino Acids in Proteins Not incorporated by ribosomes Arise by post-translational modificationsof proteins Reversible modifications, esp. phosphorylation is important in regulation and signaling

14. The Genetic Code is organized by Amino Acid Properties

15. Ionization At acidic pH, the carboxyl group is protonated and the amino acid is in the cationic form At neutral pH, the carboxyl group is deprotonated but the amino group is protonated. The net charge is zero; such ions are called Zwitterions At alkaline pH, the amino group is neutral –NH2 and the amino acid is in the anionic form.

16. Substituent effects on pKa Values -carboxy group is much more acidic than in carboxylic acids -amino group is slightly less basic than in amines

17. Amino Acids Can Act as Buffers Amino acids with uncharged side-chains, such as glycine, have two pKa values: The pKa of the -carboxyl group is 2.34 The pKa of the -amino group is 9.6 It can act as a buffer in two pH regimes.

18. Amino Acids Carry a Net Charge of Zero at a Specific pH Zwitterions predominate at pH values between the pKa values of amino and carboxyl group For amino acid without ionizable side chains, the Isoelectric Point (equivalence point, pI) is At this point, the net charge is zero AA is least soluble in water AA does not migrate in electric field

19. Ionizable Side Chains Can Show Up in Titration Curves Ionizable side chains can be also titrated Titration curves are now more complex pKa values are discernable if two pKa values are more than two pH units apart Why is the side-chain pKa so much higher?

20. How to Calculate the pI When the Side-chain is Ionizable? Identify species that carries a net zero charge Identify pKa value that defines the acid strength of this zwitterion: (pK2) Identify pKa value that defines the base strength of this zwitterion: (pKR) Take the average of these two pKa values

21. Peptides and Peptide bonds Peptide bond in a di-peptide “Peptides” are small condensation products of amino acids They are “small” compared to proteins (di, tri, tetra… oligo-)

22. Numbering starts from the amino terminus AA1 AA2 AA3 AA4 AA5 Peptide Ends are Not the Same

23. The Three Letter Code • Naming starts from the N-terminus • Sequence is written as: Ala-Glu-Gly-Lys • Sometimes the one-letter code is used: AEGK

24. Peptides: A Variety of Functions Hormones and pheromones: insulin (think sugar) oxytocin (think childbirth) sex-peptide (think fruit fly mating) Neuropeptides substance P (pain mediator) Antibiotics: polymyxin B (for Gram - bacteria) bacitracin (for Gram + bacteria) Protection, e.g. toxins amanitin (mushrooms) conotoxin (cone snails) chlorotoxin (scorpions)

25. Polypeptides (covalently linked -amino acids) + possibly – • cofactors, • coenzymes, • prosthetic groups, • other modifications Proteins are: Cofactor is a general term for functional non-amino acid component Metal ions or organic molecules Coenzyme is used to designate an organic cofactors NAD+ in lactate dehydrogenase Prosthetic groups are covalently attached cofactors Heme in myoglobin

26. Polypeptide Size in Some Proteins

27. Classes of Conjugated Proteins

28. Peptides and Proteins- Burning Questions Sequence and composition? Three-dimensional structure? Folding Mechanism? Biochemical role? Functional regulation? Molecular interactions with small and macro-molecules? Structural and sequence relatives? Cellular and sub-cellular localization? Physical and chemical properties?

29. Purification – Fractionation of Protein Mixtures • Separation relies on differences in physico-chemical properties • Solubility – Selective Precipitation (Centrifugation) • Thermal stability -- • Charge --Electrophoresis, Isoelectric Focusing, IEC • Size – Dialysis, Sedimentation (Centrifugation), GFC • Affinity for a ligand – “Pull down” assays (Centrifugation), AC • Hydrophobicity (HIC) • Chromatography is commonly used for preparative separation

30. Protein Fractionation http://www.salinesystems.org/content/figures/1746-1448-4-1-2-l.jpg

31. Separation by Charge Ion Exchange Chromatography Anion exchange Matrix positive Proteins negative Displaced by anions Cation exchange – Opposite pH determines net charge on Proteins Salt concentration gradient Native gel electrophoresis Iso-electric Focusing

32. Separation by Size • Size exclusion (Gel Filtration) Chromatography • Loading vol. <5% of column volume • Samples diluted • Dialysis or Centrifugal concentrators

33. Separation by Affinity • Affinity Chromatography • Free Ligand-Beads -- centrifugation • Ligand-Magnetic-Beads • Immuno-assays on solid supports

34. Electrophoresis for Protein Analysis Separation in analytical scale is commonly done by electrophoresis • Electric field pulls proteins according to their charge • Gel matrix hinders mobility of proteins according to their size and shape

35. SDS PAGE: Molecular Weight • SDS – sodium dodecyl sulfate – a detergent • SDS micelles binds to, and unfold all the proteins • SDS gives all proteins an uniformly negative charge • The native shape of proteins does not matter • Rate of movement will only depend on size: small proteins will move faster

36. Protein Sequencing

37. Spectroscopic Detection of Aromatic Amino Acids • The aromatic amino acids absorb light in the UV region • Proteins typically have UV absorbance maxima around 275-280 nm • Tryptophan and tyrosine are the strongest chromophores • Concentration can be determined by UV-visible spectrophotometry using Beers law: A = ·c·l

38. Chapter 3: Summary In this chapter, we learned about: • The many biological functions of peptides and proteins • The structures and names of amino acids found in proteins • The ionization properties of amino acids and peptides • The methods for separation and analysis of proteins

39. Nonpolar, Aliphatic R Groups

40. Aromatic R Groups Also Hydrophobic These amino acid side chains absorb UV light at 270-280 nm

41. Polar, Uncharged R Groups These amino acids side chains can form hydrogen bonding Cysteine can form disulfide bonds

42. Basic R Groups

43. Acidic R Groups