1. Lecture 3: Amino Acids
Bonus seminar today at 3PM 148 Baker (bonus point assignment due on Wed. in class or electronically by )
Quiz next Wed. (9/7)
Introduction to amino acid structure
Amino acid chemistry

2. Uncharged polar side chains
COO-
H3N +
CH2 OH
Tyrosine
Tyr Y
CH2 C H
COO-
H3N +
Serine
Ser S OH C H
COO-
H3N +
Threonine
Thr T
CH3 OH H C
COO-
H3N +
Glycine
Gly G
Polar Aas are imortant since they provide chemical groups for interaction with water. Thus, the hydrogen bonding character of polar Amino acids is key in forming structures. Whie the ionic bonding character of charged polar Aas is also important for protein structures. They also provide chemically reactive groups in proteins.
Serine has a OH group that does not normally ionize so it is not charged in proteins (it is neutral). It is the smallest of the polar amino acids and very polar. The hydroxyl group on Ser provides enzymes a very giooid nucleophilic group for doing chemistry., It is also important to form esters with phosphate making phosphester proteins. Phosphyorylation of proteins and enzymes is very important in regulation of activity.
Thr adds a carbon on to Ser, which makes the hydroxyl group less accessible than in Ser. Thr is more oftten in a structural role in proteins and is not as chemically active as Ser. Thr can form esters with phosphoric acid and phospho-Threionine is often found in proteins.
Tyr is a hydrophobic aromatic alcohol but has some polar character. The hydroxyl of Tyr is like the hydroxyl group on phenol, so if the pH is high (basic) it can ionize. Tyr can also form phosphoesters like Ser and Thr. It is important in proteins and in enzymes for regulation of the cell cycle.

3. Uncharged polar side chains
COO-
H3N + C H
R-SH
R-S- + H+
CH2 SH
R-OH
R-O- + H+
Cysteine
Cys C
Cys is essentially a thiol-Ala. The thiol (-SH) group of Cys can ionize at about pH 8 so they are usually protonated at biological pH. Hydroxyl groups have a pK of about 15 and do not ionize normally.
Asn is a small and polar amino acid. Amides are neutral and do not ionize nor do they accept protons.
Gln is larger than Asn because of the longer side chain. Both of the amides are neutral derivatives of acidic amino acids (Asp and Glu).

4. Formation of cystine
The formation of Cystine can take place between 2 polypeptide chains to make a cross link between them. Extracellular proteins often contain Cys-Cys bonds, while cellular proteins rarely have them in the m since the environment in the cell is reducing. In the presence of oxygen or oxidizing conditions, the 2 thils react to form a disulfide bond between them. Since this is a redox reaction, the hydride ion released by each thil is usually coupled to an electonacceptor reaction or in simple oxidation with oxygen, hydrogen peroxide is usually formed with further reduction to water.

5. Uncharged polar side chains
COO-
H3N +
CH2
Glutamine
Gln Q O
NH2 C H
COO-
H3N +
Asparagine
Asn N
CH2 O
NH2
Asn is a small and polar amino acid. Amides are neutral and do not ionize nor do they accept protons.
Gln is larger than Asn because of the longer side chain. Both of the amides are neutral derivatives of acidic amino acids (Asp and Glu).

6. Amino acids Polar, uncharged amino acids
Contain R-groups that can form hydrogen bonds with water
Includes amino acids with alcohols in R-groups (Ser, Thr, Tyr)
Amide groups: Asn and Gln
Usually more soluble in water
Exception is Tyr (most insoluble at g/L at 25 C)
Sulfhydryl group: Cys
Cys can form a disulfide bond (2 cysteines can make one cystine)

7. Charged polar (acidic) side chains
COO-
H3N + C H
COO-
H3N +
CH2
CH2
CH2 C C O O- O O-
Aspartic acid
Asp D
Glutamic acid
Glu E

8. Amino acids Acidic amino acids
Amino acids in which R-group contains a carboxyl group
Asp and Glu
Have a net negative charge at pH 7 (negatively charged pH > 3)
Negative charges play important roles
Metal-binding sites
Carboxyl groups may act as nucleophiles in enzymatic interactions
Electrostatic bonding interactions

9. Charged polar (basic) side chains
COO-
H3N +
COO- C H
COO-
H3N +
H3N + C H
CH2
CH2
CH2
CH2
CH2
CH2
CH2 HC C
CH2 NH
H+N NH
LYSINE has a protonated alky amino group
Argining has a guanidinium
Histidine has an imidazolium ionized group C
NH3+ CH
NH2+
NH2
Lysine
Lys K
Histidine
His H
Arginine
Arg R

10. Amino acids Basic amino acids
Amino acids in which R-group have net positive charges at pH 7
His, Lys, and Arg
Lys and Arg are fully protonated at pH 7
Participate in electrostatic interactions
His has a side chain pKa of 6.0 and is only 10% protonated at pH 7
Because His has a pKa near neutral, it plays important roles as a proton donor or acceptor in many enzymes.
His containing peptides are important biological buffers

11. Nonstandard amino acids
20 common amino acids programmed by genetic code
Nature often needs more variation
Nonstandard amino acids play a variety of roles: structural, antibiotics, signals, hormones, neurotransmitters, intermediates in metabolic cycles, etc.
Nonstandard amino acids are usually the result of modification of a standard amino acid after a polypeptide has been synthesized.
If you see the structure, could you tell where these nonstandard amino acids were derived from?

12. Nonstandard amino acids
These are amino acids derivatives found in proteins
4-hydroxyproline and 5-hydroxylysine are structural components of collagen a structural protein
N-formyl methionine is the N-terminal residue of all prokaryotic proteins but is usually removed as the protein matures
Gamma-carbocyglutamate is part of proteins involved in blood clotting
Methylated and acetylated amino acids are important parts of ribosomal proteins and chromosomal proteins called histones (important for chromatin formation in eukaryotes)

13. Nonstandard amino acids
Amino acids with specialized roles
GABA is a glutamate decarboxylation product, dopamine and glycine are neurotransmitters
Histamine is a mediator of allergic reactions
Thyroxine is an iodine-containing hormone that stimulates metabolism
Some amino acids are important intermediates in metabolic processes
Citrulline and ornithine are important in urea biosynthesis
Homocysteine is an intermediate in amino acid metabolism
S-adnosylmethionine is methylating agent (adds methyl groups to other compounds)
Azaserine is an antibiotic
Beta-cyanoalanine is an intermediate in cyanide production in plants.

14. Peptide bonds + + H2O H C R1 H3N + O OH N H C R2 O- O H C N R1 H3N + O
Proteins are sometimes called polypeptides since they contain many peptide bonds H C R1
H3N + O OH N H C R2 O- O + H C N R1
H3N + O R2 O-
+ H2O

15. Structural character of amide groups
Understanding the chemical character of the amide is important since the peptide bond is an amide bond.
These characteristics are true for the amide containing amino acids as well (Asn, Gln)
Amides will not ionize: O O R C
NH2 R C
NH2

16. Acid-base properties of amino acids
The dissociation of first proton from the -carboxyl group is
The dissociation of the second proton from the -amino group
Gly+ + H2O
Gly0 + H3O+
Gly0 + H2O
Gly- + H3O+
[Gly0][H3O+]
[Gly-][H3O+]
K1=
K2=
[Gly+]
[Gly0]
The pKa’s of these two groups are far enough apart that they can be approximated by Henderson-Hasselbalch
[Gly0]
[Gly-]
pK1 + log
pH =
pK2 + log
pH =
[Gly+]
[Gly0]

17. Titration curve of glycineH C
COO-
H3N +
Neutral
form
At low pH values both acid-base groups of glycine are fully protonated.
The pK values of glycine’s two ionizable groups are different enough that the Henderson-Hasselbalch equation closely approximates each phase of the titration.
pI = 1/2(pKi +pKj) Where Ki and Kj are the dissociation constants of the two ionizations involving the neutral species.
The pH at which the molecule carries no net electric charge is the isoelectric point.

18. Titration of Gly pK1 pK2 pH 2.3 pH 9.6 COOH COO- + H2N H3N C H
From the pK values we can calculate the pI (isoelectric point) where the amino acid is neutral.
pI ≈ average of (pK below neutral+ pK above neutral)
So, for Gly,
pI = (pK1 + pK2)/2
= ( )/2 ≈ 6

19. General rules for amino acid ionization
Alpha carboxylic acids ionize at acidic pH and have pKs less than 6; So in titrating a fully protonated amino acid, alpha carboxylic acids lose the proton first.
Alpha amino groups ionize at basic pH and have pKs greater than 8; So after acids lose their protons, amino groups lose their proton.
Most of the 20 amino acids are similar to Gly in their ionization properties because their side chains do not ionize at biological pHs.
However, there are 5 exceptions worth noting (the amino acids with polar charged side chains)
Glu, Asp, Lys, Arg, His
Each has 3 ionizible groups and thus, 3 pKs.

20. Charged polar (acidic) side chains
2.1
2.0 C H
COOH
H3N +
CH2
Glutamic acid
Glu E O OH
9.5
9.8 C H
COOH
H3N +
Aspartic acid
Asp D
CH2 O OH
3.9
4.1

21. How to calculate the pI of a compound with more than 2 pKs
Find the amino acid form with no net charge (total charge = 0).
Take the pK of the amino acid form going towards +1 form as the lower pK.
Next find the amino acid form going towards the -1 form.
Finally, average these two pKs to get the pI.

22. Titration curve of aspartic acid
At low pH values both acid-base groups of glycine are fully protonated.
The pK values of glycine’s two ionizable groups are different enough that the Henderson-Hasselbalch equation closely approximates each phase of the titration.
pI = 1/2(pKi +pKj) Where Ki and Kj are the dissociation constants of the two ionizations involving the neutral species.
The pH at which the molecule carries no net electric charge is the isoelectric point.
The neutral form of Asp is close to pH 2.8
Take the pKs for +1 and -1 from this point and average to get approximate pI,
pI = (pK3 + pK1)/2 = ( )/2 = 2.95

23. Charged polar (basic) side chains
2.2
1.8 C H
COOH
H3N +
1.8
COOH
9.2 C H
COOH
H3N +
H3N + C
9.3 H
9.0
CH2
CH2
CH2
CH2
CH2
CH2
CH2 C
6.0 HC
CH2 NH
H+N NH C
NH3+ CH
NH2+
NH2
Lysine
Lys K
10.8
Histidine
His H
Arginine
Arg R
12.5

24. Titration curve of arginine
At low pH values both acid-base groups of glycine are fully protonated.
The pK values of glycine’s two ionizable groups are different enough that the Henderson-Hasselbalch equation closely approximates each phase of the titration.
pI = 1/2(pKi +pKj) Where Ki and Kj are the dissociation constants of the two iionizations involving the neutral species.
The pH at which the molecule carries no net electric charge is the isoelectric point.
The neutral form of Asp is close to pH 10.8
Take the pKs for +1 and -1 from this point and average to get approximate pI,
pI = (pK2 + pK3)/2 = ( )/2 = 11.0

25. Acid-base properties of amino acids
-COOH pKa
-NH3+ pKa
R-group pKa
Gly
2.3
9.6 -
Ala
2.4
9.7
Val
Leu
Iso
Met
9.2
Pro
2.1
10.6
Phe
1.8
9.1
Trp
9.4
Ser
2.2 13
Thr
2.6
10.4
Tyr
10.1
Cys
1.7
10.8
8.3
Asn
2.0
8.8
Gln
Asp
9.8
3.9
Glu
4.3
Lys
9.0
10.5
Arg
12.5
His
6.0

26. More rules for amino acid ionization
Carboxylic acid groups near an amino group in a molecule have a more acidic pK than isolated carboxylic groups.
Amino groups near a carboxylic acid group also have a more acidic pK than isolated amines.
Aromatic amines like His have a pK about pH 6.
When titrating an amino acid that is fully protonated (ie starting at pH = 1), the alpha carboxylic acids lose their proton first (all free amino acids have this group), then side chain carboxylic acids, then aromatic amine side chains (His), then alpha amino groups, then side chain amino groups.
These rules apply to small peptides too.

27. Amino acids are optically active
All amino acids are optically active (exception Gly).
Optically active molecules have asymmetry; not superimposable (mirror images)
Central atoms are chiral centers or asymmetric centers.
Enantiomers -molecules that are nonsuperimposable mirror images
Enantiomers of fluorochlorobormomethane

28. Asymmetry
Molecules are classified as Dextrorotatory (right handed), D or Levrotatory (left handed) L depending on whether they rotate the plane of plane-polarized light clockwise or counterclockwise determined by a polarimeter

29. Asymmetry
Fischer projections are a shorthand way to write molecules with chiral centers
In Fisxher projections all horizontal bonds point above the page and all vertical bonds below the page.

30. Asymmetry
For -amino acids the arrangement of the amino, carboxyl, R, and H groups about the C atom is related to glyceraldehyde
Thus L glyceraldehyde and L-alpha amino acids are said to have the same relative configurations.

31. Asymmetry
All -amino acids from proteins have the L-stereochemical configuration
The designation of the relative configuration of chirl centers is the same as the absolute configuration. We can use the CORN crib mnemonic.
We look at the alpha carbon from its H atom the other substituents should read CO-R-N in the clockwise direction.

32. Diastereomers
Stereoisomers or optical isomers are molecules with different configurations about at least one of their chiral centers but are otherwise identical
Since each asymmetric center in a chiral molecule can have two possible configurations, a molecule with n chiral centers has 2n different possible stereoisomers and 2n-1 enantiomeric pairs
Ex. Threonine and Isoleucine both have two chiral centers, and thus 4 possible stereoisomers.

33. Diastereomers * *
The mirror images on the top of this figure are the L and D forms.
The two other optical isomers are the Diastereomers or allo forms of the L and D forms.
The D-allo and L-allo forms are mirror images of one another just like the D and L forms
Neither allo form is symmetrically related to either of the D or L forms
Diastereomers are physically and chemically distinct. We see differences in melting points, spectra, and chemical reactivity. VERY Different from one another.

34. Diastereomers
Special case: 2 asymmetric centers are chemically identical (2 asymmetric centers are mirror images of one another)
A molecule that is superimposable on its mirror image is optically inactive (meso form)
D and L isomers are mirror images of one another but the meso has internal mirror symmetry and therefore lacks optical activity.

35. Cahn-Ingold-Prelog or (RS) System
The 4 groups surrounding a chiral center a ranked as follows: Atoms of higher atomic number bonded to a chiral center are ranked above those of lower atomic number.
Priorities of some common functional groups SH > OH > NH2 > COOH > CHO > CH2OH > C6H5 > CH3 > 2H > 1H
Prioritized groups are assigned letters W, X, Y, Z, so that W > X > Y > Z
Z group has the lowest priority (usually H) and is used to establish the chiral center.
If the order of the groups W X Y is clockwise, as viewed from the direction of Z, the configuration is (R from the latin rectus, right)
If the order of the groups W X Y is counterclockwise, as viewed from the direction of Z, the configuration is (S from the latin sinister, left)
The Fischer scheme can be ambiguous so an absolute nomenclature system was developed in 1956 by Cahn, Ingold and Prelog.

36. Cahn-Ingold-Prelog or (RS) System
So L-Glyceraldehyde is S-glyceraldehyde by the RS system representation.
The chiral C atom is represented by the large circle and H atom is located behind the plane of the screen.

37. Cahn-Ingold-Prelog or (RS) System
The Fischer scheme can be ambiguous so an absolute nomenclature system wad developed in 1956 by Cahn, Ingold and Prelog.

38. Cahn-Ingold-Prelog or (RS) System
Newman projection diagrams of the stereoisomer of threonine and isoleucine derived from proteins.
Here the C alpha - C beta bond is viewed end on.

39. Prochiral centers have distinguishable substituents
Prochiral molecules can be converted from an achiral to chrial molecule by a single substitution
Molecules can be assigned a right side and left side for two chemically identical substituents.
True for tetrahedral centered molecules
Example is ethanol
The Fischer scheme can be ambiguous so an absolute nomenclature system wad developed in 1956 by Cahn, Ingold and Prelog.

40. Prochiral centers
The two H atoms are prochiral. If assigned a and b then Hb is pro-R because in sighting from C1 towards Ha the order is clockwise whereas Hb is pro-S because substitutents decrease in a counterclockwise direction
Planar objects with no rotational symmetry are also prochiral.

41. Planar objects can also be prochiral
Stereospecific additions in enzymatic reactions
If a trigonal carbon is facing the viewer so that the substituents decrease in a clockwise manner it is the re face
If a trigonal carbon is facing the viewer so that the substituents decrease in a counterclockwise manner it is the si face
Acetaldehyde example
A represents the re face and b is the si face.
We are mostly going to use the DL convention of naming but the RS system is necessary for describing prochirality and stereospecific reactions.

42. Nomenclature Glx can be Glu or Gln Asx can be Asp or Asn
Polypeptide chains are always described from the N-terminus to the C-terminus
Amino acid residues in polypeptides are named by dropping of the suffix -ine and replacying it by -yl
The C- terminus is given the name of the parent amino acid.
So this compound is called alanyltyrosylaspartylglycine. We can replace this by Ala-Tyr-Asp-Gly or AYDG

43. Nomenclature
Nonhydrogen atoms of the amino acid side chain are named in sequence with the Greek alphabet
Greek letter used to identify the atoms in the glutamyl and lysyl R groups