1. Chapter - 1 Amino Acids

2. First Lecture Overview Structure of the Amino Acids:
A.A. with nonpolar side chains
A.A. with uncharged polar side chains

3. 1. Overview:
Proteins are the most abundant and functionally diverse molecules in living systems.
Every life process depends on this protein molecules.
For example,
enzymes and polypeptide hormones  direct and regulate metabolism in the body
contractile proteins in muscle  movement.

4. In bone:
Collagen forms a framework for the deposition of calcium phosphate crystals, acting like the steel cables in reinforced concrete.
In the bloodstream:
hemoglobin and plasma albumin shuttle molecules essential to life.
immunoglobulins  fight infectious bacteria and viruses.
Proteins share the common structural feature of being linear polymers of amino acids.

5. II. STRUCTURE OF THE AMINO ACIDS
Amino acids that described in nature are more than 300 different amino acids BUT, only 20 are constituents of mammalian proteins.
These 20 A.A. are the only A.A. coded for by DNA (the genetic material in the cell).
Each amino acid (except proline) has a carboxyl group, an amino group, and a distinctive side chain “R-group” bonded to the  -carbon atom (Figure 1.1A)

7. At physiologic pH (pH 7.4), the carboxyl group is dissociated  forming the negatively charged carboxylate ion (─COO- ), and the amino group is protonated (─NH3+).
In proteins, all the carboxyl and amino groups are combined in peptide linkage and, available only for hydrogen bond formation (Figure 1.1B).
The side chains ultimately dictate the role an amino acid plays in a protein.

9. Amino acids are therefore classified according to the properties of their side chains :
Nnonpolar: have an even distribution of electrons
Polar : have an uneven distribution of electrons, such as acids and bases (Figures 1 .2 & 1.3).
Each A.A. is shown in its fully protonated form, with dissociable Hydrogen ions represented in Red Bold print H.
The pK values for the -carboxyl and -amino groups of the nonpolar amino acids are similar to those shown for Glycine.

12. A. Amino acids with nonpolar side chains:
Each of these A.A. has a nonpolar side chain that does not bind or give off protons or participate in hydrogen or ionic bonds (Figure 1.2).

13. The side chains of the nonpolar amino acids can be thought of as "oily" or lipid-like, a property  promotion of hydrophobic interactions (Figure 2.9.).

14. 1. Location of nonpolar A.A. in proteins:
In proteins found in aqueous solutions, the side chains of the nonpolar A.A. tend to cluster together in the interior of the protein (Figure 1 .4).
This phenomenon is the result of the hydrophobicity of the nonpolar R-groups, which act like droplets of oil that coalesce in an aqueous environment.

15. The nonpolar R-groups thus fill up the interior of the folded protein  three-dimensional shape.
In proteins that are located in a hydrophobic environment, such as a membrane, the nonpolar R-groups are found on the outside surface of the protein, interacting with the lipid environment.
(Figure 1.4).

16. Proline:
The side chain of proline and its  -amino group form a ring structure, and thus proline differs from other amino acids in that:
it contains an imino group, rather than an amino group (Figure 1.5).
The unique geometry of proline contributes to the formation of the fibrous structure at collagen, and often interrupts the  - helices found in globular proteins.

17. B. Amino acids with uncharged polar side chains
These A.A. have zero net charge at neutral pH. although the side chains of cysteine and tyrosine can lose a proton at an alkaline pH
(Figure 1.3).

18. Serine, threonine and tyrosine each contain a polar hydroxyl group that can participate in hydrogen bond formation (Figure 1.6).
The side chains of asparagine and glutamine each contain a carbonyl group and an amide group, both of which can also participate in hydrogen bonds.

19. 1. Disulfide bond:
The side chain of cysteine contains a sulfhydryl group (─SH), which is an important component of the active site of many enzymes.
In proteins, the ─ SH groups of two cysteines can become oxidized  form a dimer, cystine, which contains a covalent cross-link called a disulfide bond (─ S ─ S ─).

20. 2. Side chains as sites of attachment for other compounds:
Serine, threonine and, rarely, tyrosine contain a polar hydroxyl group that can serve as a site of attachment for structures such as a phosphate group.
The side chain of serine is an important component of the active site of many enzymes.
The amide group of asparagines, as well as the hydroxyl group of serine or threonine, can serve as a site of attachment for oligosaccharide chains in glycoproteins .

21. Second Lecture Contents: A.A. with acidic side chain
A.A. with basic side chain
Abbreviations and symbols of the
commonly occurring A.A.
Optical properties of A.A.

22. C. Amino acids with acidic side chains
The amino acids aspartic and glutamic acid are proton donors. (Figure 1 .3).
At neutral pH, the side chains of these amino acids are fully ionized, containing a negatively charged carboxylate group (─ COO-) So, they are, therefore, called aspartate or glutamate.

23. At physiologic pH:
the side chains of lysine and arginine are fully ionized and positively charged.
In contrast,
histidine is weakly basic, and the free amino acid is largely uncharged at physiologic pH.

24. D. Amino acids with basic side chains
The side chains of the basic A.A. accept protons (Figure 1.3).

25. The side chain of histidine can be either positively charged or neutral when is incorporated into a protein depending on the ionic environment provided by the polypeptide chains.
This is an important property of histidine explaining its role in the functioning of proteins such as hemoglobin.

26. E. Abbreviations and symbols for the commonly occurring amino acids
Each amino acid name has : three-letter abbreviation and a one-letter symbol (Figure 1 .7).
The one-letter codes are determined by the following rules:

27. 1. Unique first letter:
If only one amino acid begins with a particular letter, then that letter is used as its symbol.
For example, l = isoleucine.

28. 2. Most commonly occurring amino acids have priority:
If more than one amino acid begins with a particular letter, the most common of these amino acids receives this letter as its symbol.
For example, glycine is more common than glutamate, so G = glycine.

29. 3. Similar sounding names:
Some one-letter symbols sound like the amino acid they represent.
For example, F = phenylalanine, or W = tryptophan (“ twyptophan” ) as a letter replacing person will say

30. 4. Letter close to initial letter:
A one-letter symbol is close in the alphabet as possible to the initial of the amino acid.
B  Asx, signifying aspartic acid or asparagine
Z  Glx. signifying glutamic acid or glutamine
X  an unidentified amino acid.

31. F. Optical properties of amino acids
The -carbon of each amino acid is attached to four different chemical groups  a chiral or optically active carbon atom.
Glycine is the exception
because its -carbon has two hydrogen substituents  optically inactive.

32. Amino acids that have an asymmetric center at the -carbon can exist in two forms, designated D and L, that are mirror images of each other
(Figure 1 .8).

33. The two forms in each pair are termed stereoisomers, optical isomers, or enantiomers.
All amino acids found in proteins are of L- form
However, D-amino acids are found in some antibiotics and in bacterial cell walls.

34. Lecture 3 Contents: III. ACIDIC AND BASIC PROPERTIES OF AMINO ACIDS:
Derivation of the equation
Buffers
Titration of an Amino Acid
Other applications of the Handerson-Hasselbalch equation

35. III. ACIDIC AND BASIC PROPERTIES OF AMINO ACIDS
Amino acids in aqueous solution contain weakly acidic - carboxyl groups and weakly basic -amino groups.
In addition, each of the acidic and basic A.A. contains an ionizable group in its side chain.

36. Both free amino acids and some amino acids combined in peptide linkages can act as buffers.
The quantitative relationship between the [ weak acid ] (HA) and its conjugate base (A-) is described by the Henderson-Hasselbalch equation.

37. Henderson-Hasselbalch equation A. Derivation of the equation
Consider the release of a proton by a weak acid represented by HA:
HA H A-
weak proton salt form
acid or conjugate base
The " salt " or conjugate base (A-), is the ionized form of a weak acid.

38. By definition, the dissociation constant of the acid, Ka , is
Ka = [H+] [A-]
[HA]
The larger the Ka, the stronger the acid, because most of the HA has been converted into H+ and A- .
Conversely, the smaller the Ka , the less acid has dissociated  the weaker the acid.

39. By solving for the [H+] in the above equation;
- Taking the logarithm of both sides of the equation,
- Multiplying both sides of the equation by ─ 1, Substituting : pH = ─ log [H+] and
pKa = ─ log Ka
We obtain the Henderson-Hasselbalch equation:
pH = pKa + log [A- ]
[HA]

40. B. Buffers
A buffer is “ a solution that resists change in pH following the addition of an acid or base”.
A buffer can be created by mixing a weak acid (HA) with its conjugate base (A-).
If an acid ( HCl ) is added to the buffer A- can neutralize it  converted to HA.
If a base is added  HA can neutralize it  converted to A-.

41. Maximum buffering capacity occurs at a pH equal to the pKa, but
A conjugate acid / base pair can still serve as an effective buffer when the pH of a solution is within approximately ± 1 pH unit of the pKa.
[If the amounts of HA = A-  pH = pKa ]

42. A solution containing acetic acid (HA = CH3 –COOH) and acetate (A- = CH3-COO-) with a pKa of 4.8 resists a change in pH from pH 3.8 to 5.8, with maximum buffering at pH = 4.8
(Figure 1.9)
At pH values < pKa, the protonated acid form (CH3-COOH) is the predominant species.
At pH values > pKa, the deprotonated base form (CH3-COO-) is the predominant species in solution.

44. C. Titration of an amino acid
Dissociation of the carboxyl group:
The titration curve of an amino acid can be analyzed in the same way as described for acetic acid.
As the pH of the solution is , the — COOH group of form l can dissociate by donating a proton to the medium.

45. Consider alanine, for example, which contains both an -carboxyl and an -amino group.
At a low (acidic) pH, both of these groups are protonated (Figure 1.10).

46. The release of a proton  the formation of the carboxylate group, — COO- .
This structure is shown as form ll, which is the dipolar form of the molecule ( Figure ).
[Note: This form, also called a zwitterion, is the isoelectric form of alanine — that is, it has an overall charge of zero.]

47. 2. Application of the Henderson-Hasselbalch equation:
The dissociation constant of the carboxyl group of an amino acid is called K1 rather than Ka, because the molecule contains a second titratable group.

48. The Henderson-Hasselbalch equation can be used to analyze the dissociation of the carboxyl group of alanine in the same way as described for acetic acid.
K1 = [ H+ ] [ ll ]
[ l ]
l is “ the fully protonated form of alanine”
ll is “the isoelectric form of alanine”
(Figure 1.10).

49. The equation can be rearranged and converted to its logarithmic form to yield:
pH = pK1 + log [ ll ]
[ l ]

50. 3. Dissociation of the amino group:
The second titratable group of alanine is the amino (—NH3+) group (Figure 1.10).
This is a much weaker acid than the —COOH group and, therefore, has a much smaller dissociation constant, K [Note: Its pKa is therefore larger.]
Release of a proton from the protonated amino group of form ll  fully deprotonated form of alanine (form lll)
(Figure 1.10).

51. 4. pKs of alanine:
The sequential dissociation of protons from the carboxyl and amino groups of alanine ( Figure1.10).
Each titratable group has a pKa, that is numerically equal to the pH at which exactly one half of the protons have been removed from that group.
The pKa for the most acidic group (—COOH) is pK1
The pKa for the next most acidic group (—NH3+) is pK2.

52. 5. Titration curve of alanine:
By applying the Henderson Hasselbalch equation to each dissociable acidic group, it is possible to calculate the complete titration curve of a weak acid.
Figure 1.11 shows the change in pH that occurs during the addition of base to the fully protonated form of alanine (l)  completely deprotonated form (lll).

54. Note the following:
a. Buffer pairs:
The -COOH / - COO- pair can serve as a buffer in the pH region around pK1 and the -NH3+/ -NH2 pair can buffer in the region around pK2.
b. When pH = pK: - When the pH is equal to pK1 (2.3)  equal amounts of forms l and ll of alanine exist in solution. - When the pH is equal to pK2 (9.1)  equal amounts of forms ll and lll are present in solution.

55. c. Isoelectric point:
At neutral pH, alanine exists predominantly as the dipolar form ll in which the amino and carboxyl groups are ionized, but the net charge is zero.
The isoelectric point (Pl) “ is the pH at which an amino acid is electrically neutral”— that is,
the sum of the +ve charges = the sum of the -ve charges.

57. For an amino acid, e.g. alanine, that has only two dissociable hydrogens (one from the -carboxyl and one from the -amino group),
pl = (pK1 + pK2) / 2
pI = ( ) / 2 = 5.7
( Figure 1.10)
pI corresponds to the pH at which:
form ll (with a net charge of zero)
predominates, and
the amount of form l (net charge of +1) = form lll (net charge of -1).

58. 6. Net charge of amino acids at neutral pH:
At physiologic pH, all amino acids have a negatively charged group (-COO-) and a positively charged group (- NH3+ ) both attached to the -carbon.
[ Glutamate, aspartate, histidine, arginine and lysine have additional potentially charged groups in their side chains].

59. Substances, such as amino acids, that can act either as an acid or a base are defined as amphoteric and are referred to as ampholytes ( amphoteric electrolytes ).

60. D. Other applications of the Henderson-Hasselbalch equation
The Henderson-Hasselbalch equation can be used to calculate how the pH of a physiologic solution responds to changes in the concentration of weak acid and / or its corresponding “salt” form.
For example, in the bicarbonate buffer system, the Henderson-Hasselbalch equation predicts how shifts in [HCO3-] and pCO2 influence pH (Figure 1.12A).

62. The equation is also useful for calculating the abundance of ionic forms of acidic and basic drugs.
For example, most drugs are either weak acids or weak bases (Figure 1.12 B).

64. Acidic drugs (HA)  a proton (H+),  a charged anion (A-) to form.
HA H A-
Weak bases (BH+) can also  H+.

65. The protonated form of basic drugs is usually charged and the loss of a proton  the uncharged base (B).
BH B H+

66. A drug passes through membranes more readily if it is uncharged.
For a weak acid,
the uncharged HA can permeate through membranes and A- cannot.
For a weak base, e.g. morphine, the uncharged form B, penetrates through the cell membrane and BH+ does not.

67. The ratio between the two forms is determined by:
The effective concentration of the permeable form of each drug at its absorption site is determined by the relative concentrations of the charged and uncharged forms.
The ratio between the two forms is determined by:
the pH at the site of absorption, and
the strength of the weak acid or base, which is represented by the pKa of the ionizable group.

68. The Henderson Hasselbalch equation is useful in determining how much drug is found on either side of a membrane that separates two compartments that differ in pH,
for example,
stomach (pH )
blood plasma (pH 7.4).