Chemical Properties of Amino Acids

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1 hemical Properties of Amino Acids

2 Protein Function Make up about 15% of the cell and have many functions in the cell 1. atalysis: enzymes 2. Structure: muscle proteins 3. Movement: myosin, actin 4. Defense: antibody 5. Regulation: enzymes, hormones 6. Transport: globins 7. Storage: Mb, ferritin 8. Stress Response: hormones 5P2-2

3 The polymeric Nature of Protein Peptides: A short chain of residues with a defined sequence No max number of residues in a peptide Its physical properties are those expected from the sum of its amino acid residues No fixed 3D conformation Polypeptide: A longer chain with a defined sequence and length Polyamino acids: Nonspecific polymerization of one or a few amino acids Protein: Polypeptides that occur naturally ave a definite 3D structure under physiological conditions

4 Amino acid composition Basic Amino Acid Structure: The side chain, R, varies for each of the 20 amino acids In aqueous solution, the amino and carboxylic acid groups will ionize to give the zwitterionic form: + 3 N R O 2 Side chain N Amino group R α O O arboxyl group

5 General Amino Acid Structure At p N α OO- R

6 guanido ~50% at p7

7 Stereochemistry Note that the R group means that the α carbon is a chiral center. All natural amino acids are L amino acids. This means that almost all have the S configuration. Rules for assigning R/S configuration: onfiguration is assigned by "looking" down the bond to the lowest priority substituent and assigning R to the configuration where the remaining subtituents are arranged clockwise in decreasing priority Group Priorities: S > O > N 2 > OO > O > 2 O > 6 5 > 3 > lockwise: R, counterclockwise: S configuration (Exceptions: glycine and cysteine R configuration)

9 Amino acid abbreviations

10 Numbering (lettering) amino acids alpha-amino ε δ γ β ε-amino group alpha-carboxyl (attached to the α-carbon) alpha-carbon

11 Side chain nomenclature: Numbered according to the Greek αλφαβετ! Branches: Same alphabetic subscript. "eavier" atom = 1. omputer storage: no Greek alpha s/subscripts E.g. OE2 means O ε2. O δ1 O O 2 O δ2 γ1

12 Aromatic ring numbering/naming (IUPA) 7 1 7a 6 N a 4 β 2 N 2 O α O 3 (τ) 2 N N 1 4 (π) 5 β 2 N 2 O α O O β 2 N 2 α 3 2 O O IUPA nomenclature:

13 Amino Acid Groups 1 Based on chemical characteristics of R groups 1. Polar and negative charge (aspartic acid and glutamic acid) 2. Polar and positive charge (arginine, lysine, histidine) 3. Polar and uncharged (asparagine, glutamine, serine, threonine, tyrosine) 4. Nonpolar (alanine, glycine, valine, leucine, isoleucine, proline, phenylalanine, methionine, tryptophan, cysteine)

14 haracter of amino acid side chains Amino acids don t fall neatly into classes--they are different combinations of small/large, charged/uncharged, polar/nonpolar properties ow we casually speak of them can affect the way we think about their behavior. The properties of a residue type can also vary with conditions/environment

17 Absorption spectra of Trp & Tyr Beer s law: A = εcl. Used to estimate protein concentration

20 Grouping of Amino Acids 2 By side chain properties Size harge Polarity Gly, yclic imino acid, Aliphatic, ydroxyl, Acidic, Amide, Basic, is (imidazole), Aromatic, Sulfur containing

21 Glycine 2 N G OO No D- and L-isomer

22 yclic Imino Acid Proline N OO P

23 Aliphatic Amino Acids V A 2 N 2 N 3 3 OO 3 OO 2 N 2 N 3 3 OO 3 3 OO I L

24 ydroxylic Amino Acids 2 N 3 O T OO Thr 2 N O S OO Ser

25 Acidic Amino Acids D OO - E OO - 2 N OO 2 N OO Asp Glu

26 Amide Group N 2 N ON2 OO Q 2 N ON2 OO Asn Gln

27 Basic Amino Acids N3 + N + N3 R K N 2 N OO 2 N OO Lys Arg

28 Imidazole Side hain istidine N 2 N N is OO

29 Aromatic Amino Acids N O 2 N W OO Trp Phe 2 N Y OO Tyr 2 N F OO

30 Sulfo Amino Acids S 3 S 2 N OO 2 N OO M

31 ysteine and cystine Pairs of cysteines frequently undergo oxidation to a disulfide bonded form called cystine disulfide formation 2 2 S 1/ 2 O 2 2 S S 2 2 O 2 cysteines cystine more hydrophobic than cysteine disulfide exchange R 1 S R 2 S SR 2 R 2 S R 1 S SR 2 disulfide exchange occurs through the thiolate anion at neutral to basic p Basis of Ellman assay assay of thiol group. Use dithionitrobenzoic acid (DTNB) results in formation of nitrobenzoic acid (yellow aromatic thiol).

32 Sizes of amino acids a.a mass Van der Waals (dalton) Volume (A3) A R D N E Q G I a.a mass Van der Waals (dalton) Volume (A3) L K M F P S T W Y V Weighted Avg

33 an group into several categories: 1) alkanes: A V I L (P) 2) aromatics: F W Y () 3) carboxylates: D E 4) corresponding amides: N Q 5) positively charged: K R () 6) Sulfur containing: M 7) hydroxyls: S T Y

34 an group into several categories: 8) β branched: V T I 9) small: G A S (V T ) 10) large: W R Y F (M ) 11) bond donors: S T Y N Q K R W (D & E, if protonated) 12) bond acceptors: S T Y N Q D E R W

35 Grouping the amino acids by properties from which adapted it from Livingstone & Barton, ABIOS, 9, , 1993.

36 Acid-Base Properties of Amino Acids Amino acids form zwitterions (dipolar ions) at neutral p Therefore, amino acids can act as acids (proton donor) and bases (proton acceptor), often called ampholytes. ence a simple amino acid, like Alanine below, can yeild two protons. 3 O 3 O 3 O + 3 N O N + O - 2 N O - Net charge

37 Ionization state as a function of p Physiological p (measure of [ + ]) 37

38 Shifting of side chain titration curves 1 2 N base N eq. O - added is+ pk a 2 N physiological p p N acid

39 pk a of ionizable side chains pk a = p for 50% dissociation, Note range

40 Titration urves of Amino Acids with Ionizing Side hain pi = pi = Figure 5-12, p. 125: Lehninger Principles of Biochemistry

41 Ionization of Amino Acids Equilibrium dissociation constant; K a = + [ ] [ A ] [ A] enderson-asselbolch Equation; log + [ ] [ A ] = logk + log p = pk p = pk a a a + [ A ] [ A] [ A] [ A ] = [ A]

42 ow to calculate pi The isoelectric point (pi) of an amino acid or peptide is the p at which the charge of the molecule = 0. It can be calculated simply as the arithmetic mean of the 2 pk a 's corresponding to the transitions generating the +1 and 1 forms.

43 ow to calculate pi 1. Identify all ionizable groups 2. Assign pk a s to each ionizable group 3. Start with each ionizable group in protonated form (very low p maybe 0 or 1) and calculate its net charge 4. Slowly move up in p to the first ionizable group s pk a and deprotonate it (reduce charge by 1) 5. Do this until each group is deprotonated. Now you have identified all charged forms and at which p each transition occurs. 6. Identify the form with net charge = 0 7. Take the pk a on either side of the electrically neutral form and take their average. This is the pi.

45 ow to calculate pi Take Glycine as an example it has only 2 ionizable groups. The transition (from low to high p) would be: Gly +1 Gly 0 Gly 1 pk a ( O 2 ) = 2.34; pk a ( N 3+ ) = 9.60 pi =( )/2 = 11.94/2 = 5.97

47 ow to calculate pi Glutamate has an ionizable group ( O 2 ; pk a = 4.25) that generates a negative charge when deprotonated. Its transitions would be: Glu +1 Glu 0 Glu 1 Glu 2 The relevant pk a 's are pk a ( O 2 ) = 2.19; pk a (R) = 4.25 pi =( )/2 = 6.44/2 = 3.22

49 ow to calculate pi istidine has an ionizable group (imidazole; pk a = 6.00) that is positively charged when protonated. Its transitions would be: is +2 is +1 is 0 is 1 The relevant pk a 's are pk a (R) = 6.00; pk a ( N 3+ ) = 9.17 pi =( )/2 = 15.17/2 = 7.59

51 Peptide bond Primary structure of protein: Between AAs α-carboxyl group of one AA & α-amino group of another 2 amino acids Dipeptide Loss of 2 O

52 Making dipeptides + 3 N R O N R O N R ON R O O This process can be repeated to make a tripeptide and so on: + 3 N R ON R O N R O N R ON R ON R O 2

54 Making dipeptides The N bond has partial double bond character, making the ON moiety planar. This limits the orientations available to the polypeptide

55 Peptide bond Double bond character Prevents rotation about this bond Bond length: -N peptide = 1.32 A -N single bond = 1.49 A -N double bond = 1.27 A Two configurations (cis & trans) possible. Only trans used

56 onsequences of double bond character in the peptide bond 2 N 1.24 Å O 1.33 Å N Å R O the peptide -N bond is 0.12A shorter than the alpha-n bond. and the =O is 0.02A longer than that of aldehydes and ketones. R O 2 N R O N R O O All six of the atoms highlighted at left lie in the same plane, and as with carbon-carbon double bonds there are two configurations--cis and trans (trans shown at left)

57 ...and that means that the dihedral angle describing rotation around the peptide bond, defined by the four atoms α(i)--n-α(i+1), will generally be close to 180. This angle is known by the greek symbol ω. O R 2 N ω α O α N R O residue i residue i+1 So the properties of the peptide bond place a strong restriction on the backbone conformation or main-chain conformation of proteins, that is to say, the spatial configuration of the non side-chain atoms.

cis form, the R groups in adjacent residues tend to clash.

58 onsequences of double bond character in the peptide bond trans peptide bond cis peptide bond Still another consequence: in the cis form, the R groups in adjacent residues tend to clash. ence almost all peptide bonds in proteins are in the trans configuration.

59 Main chain or backbone onstant backbone: regularly repeating part Distinctive side chains (R-groups): variable part AA unit in a polypeptide is called a residue, which contains, a carbonyl group; good hydrogen-bond acceptor, an N group (except Pro); good hydrogen-bond donor

60 Polypeptide chain has direction 60

61 Proteins are chains of amino acids Polymer a molecule composed of repeating units

Amino Acids and Peptides

Amino Acids Amino Acids and Peptides Amino acid a compound that contains both an amino group and a carboxyl group α-amino acid an amino acid in which the amino group is on the carbon adjacent to the carboxyl