Lecture 3: Amino Acids –Bonus seminar today at 3PM 148 Baker (bonus point assignment due on Wed....

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Lecture 3: Amino Acids

– Bonus seminar today at 3PM 148 Baker (bonus point assignment due on Wed. in class or electronically by email)

– Quiz next Wed. (9/7) – Introduction to amino acid structure– Amino acid chemistry

Uncharged polar side chains

Serine

Threonine

OHTyrosine

Glycine

Cysteine

R-SH R-S- + H+

R-OH R-O- + H+

Formation of cystine

Asparagine

Glutamine

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 0.453 g/L at 25 C)

– Sulfhydryl group: Cys• Cys can form a disulfide bond (2 cysteines can make one cystine)

Charged polar (acidic) side chains

H3N+ C H

Aspartic acid

Glutamic acid

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

Charged polar (basic) side chains

H3N+ C H

NH2+ NH2Lysine

Arginine

Histidine

CH2CH2

NH H+N NHCH

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

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?

Nonstandard amino acids

Peptide bonds • Proteins are sometimes called polypeptides since they contain many peptide bonds

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:

NH2 R C

Acid-base properties of amino acids

Gly+ + H2O Gly0 + H3O+

[Gly0][H3O+]

[Gly+]

Gly0 + H2O Gly- + H3O+

K2=[Gly-][H3O+]

[Gly0]

The dissociation of first proton from the -carboxyl group is

The dissociation of the second proton from the -amino group

The pKa’s of these two groups are far enough apart that they can be approximated by Henderson-Hasselbalch

pK1 + logpH =[Gly0]

[Gly+]pK2 + logpH =

[Gly-]

[Gly0]

Titration curve of glycine

H3N+ Neutral

Titration of Gly

pK1 pK2

Gly0Gly+Gly-

pH 2.3 pH 9.6From 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 = (2.3 + 9.6)/2 ≈ 6

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.

Aspartic acid

Glutamic acid

Charged polar (acidic) side chains

9.5 2.0

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.

Titration curve of aspartic acid

The neutral form of Asp is close to pH 2.8Take the pKs for +1 and -1 from this point and average to get approximate pI,pI = (pK3 + pK1)/2 = (2.0 + 3.9)/2 = 2.95

Charged polar (basic) side chains

H3N+ C H

NH2+ NH2Lysine

Arginine

Histidine

CH2CH2

NH H+N NHCH

9.21.8

Titration curve of arginine

The neutral form of Asp is close to pH 10.8Take the pKs for +1 and -1 from this point and average to get approximate pI,pI = (pK2 + pK3)/2 = (9.0 + 13.0)/2 = 11.0

Acid-base properties of amino acids Amino acid -COOH pKa -NH3

+ pKa R-group pKa

Gly 2.3 9.6 -

Ala 2.4 9.7 -

Val 2.3 9.6 -

Leu 2.4 9.6 -

Iso 2.4 9.7 -

Met 2.4 9.2 -

Pro 2.1 10.6 -

Phe 1.8 9.1 -

Trp 2.4 9.4 -

Ser 2.2 9.2 13

Thr 2.6 10.4 13

Tyr 2.2 9.1 10.1

Cys 1.7 10.8 8.3

Asn 2.0 8.8 -

Gln 2.2 9.1 -

Asp 2.1 9.8 3.9

Glu 2.2 9.7 4.3

Lys 2.2 9.0 10.5

Arg 2.2 9.0 12.5

His 2.4 9.2 6.0

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.

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

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

Asymmetry• Fischer projections are a shorthand way to write molecules with

chiral centers

Asymmetry• For -amino acids the arrangement of the amino, carboxyl, R,

and H groups about the C atom is related to glyceraldehyde

Asymmetry• All -amino acids from proteins have the L-stereochemical

configuration

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.

Diastereomers

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)

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)

Cahn-Ingold-Prelog or (RS) System

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

Prochiral centers

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

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

Nomenclature • Nonhydrogen atoms of the amino acid side chain are named in

sequence with the Greek alphabet

Lecture 3: Amino Acids –Bonus seminar today at 3PM 148 Baker (bonus point assignment due on Wed....

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