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Amino Acids (18.1-18.3) Amino acids have the same basic structure

20 common amino acids combine in different sequences to form thousands ofdifferent proteins

CH3N COO-

H RAll amino acids have

Amino acids differ here

General Structure

alpha carbon

C

CH3N COO-

H R

C

O

OCCCR

beta carbon

C

gamma carbon

C

alpha carbon

CCarboxylic acid amino acid

Beta and gamma carbons

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Which of the following are alpha amino acids and which are not?

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Classification of Amino AcidsH3N CH C

CH3

O

O

H3N CH C

H

O

O

H3N CH C

CH2

O

O

CH CH3

CH3

H3N CH C

CH

O

O

CH3

CH2

CH3H3N CH C

CH2

O

O

CH2

S

CH3

H3N CH C

CH2

O

O

H2N

C OO

H3N CH C

CH2

O

O

HN

H3N CH C

CH

O

O

CH3

CH3

H3N CH C

CH2

O

O

C

O

O

H3N CH C

CH2

O

O

CH2

C

O

O

H3N CH C

CH2

O

O

C

NH2

O

H3N CH C

CH2

O

O

CH2

C

NH2

O

H3N CH C

CH2

O

O

SH

H3N CH C

CH2

O

O

OH

H3N CH C

CH

O

O

CH3

OH

H3N CH C

CH2

O

O

OH

H3N CH C

CH2

O

O

CH2

CH2

NH

C

NH2

NH2

H3N CH C

CH2

O

O

CH2

CH2

CH2

NH3

H3N CH C

CH2

O

O

N

NH

Nonpolaramino acids

Polarunchargedamino acids

Polarchargedacidicamino acids

Polarchargedbasicamino acids

glycine alaninevaline

isoleucine leucine

methionine phenylalanine tryptophanproline

arginine

glutamine

cysteine serine threonine

tyrosine

glutamic acid(glutamate)

aspartic acid(aspartate)

lysine histidine

asparagine

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Name3-letter

abbreviationSingle-letter abbreviation

Glycine Gly GAlanine Ala AValine Val V

Leucine Leu LIsoleucine Ile I

Proline Pro PPhenylalanine Phe F

Tyrosine Tyr YTryptophan Trp W

Cysteine Cys CMethionine Met M

Lysine Lys KArginine Arg RHistidine His HAspartate Asp DGlutamate Glu EAsparagine Asn NGlutamine Gln Q

Serine Ser SThreonine Thr T

Amino Acid Abbreviations

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“many protons”

Amino acids are weak polyprotic acids (18.4)both the amino and carboxy

groups are protonated at lowpH. Carboxy loses proton firstand then amino loses at high pH.

N C

R

C

O

O H

H

H

H

H

N C

R

C

O

O

H

H

H

H

N C

R

C

O

OH

H

H

Amino acids are zwitterions (dipolar)zwitterions have charged residues but are electrically neutralthe amino and carboxy charges cancel each other out at neutral

pH so aa wo/ charged side chains are uncharged at neutral pH

CH3N COO-

H R Isoelectric point, pIpH where amino acid is electrically neutraldepends on the R group also

lower pH higher pHneutral pH

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Amino Acid pKa’s

Amino Acid-carboxylic

acid-amino

Side chain

Alanine 2.34 9.69Arginine 2.17 9.04 12.48Asparagine 2.02 8.80Aspartic Acid 2.09 9.82 3.86Cysteine 1.71 10.78 8.33Glutamic Acid 2.19 9.67 4.25Glutamine 2.17 9.13Glycine 2.34 9.60Histidine 1.82 9.17 6.00Isoleucine 2.36 9.68Leucine 2.36 9.68Lysine 2.18 8.95 10.53Methionine 2.28 9.21Phenylalanine 1.83 9.13Proline 1.99 10.60Serine 2.21 9.15Threonine 2.63 10.43Tryptophan 2.38 9.39Tyrosine 2.20 9.11 10.07Valine 2.32 9.62

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Titration of Amino Acids

H3N CH C

H

OH

O

H3N CH C

H

O

O

H2N CH C

H

O

O

X

X

XpI

pK1

pK2

net charge

0+1 -1

Netcharge

+1

Netcharge

0

Netcharge

-1

Amino acids have titration curves like diprotic or triprotic acids

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Alaninesimilar to diprotic acid

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Histidinesimilar to triprotic acid

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1. Given a peptide with the following amino acid sequence, identify the polar amino acids, the aromatic amino acids, and the sulfur-containing amino acids.

Val-Met-Ser-Ile-Phe-Arg-Cys-Tyr-Leu

2. Write equations to show the ionic dissociation reactions of the following amino acids:aspartic acid

valine

3. Draw the predominant ionized forms of the following amino acids at pH 7:glutamic acid histidine arginine

4. Based on the pKa information for amino acids, is there any amino acid that could serve as a buffer at pH 6? If so, which one(s)?

Amino Acid Questions. Explain in detail with structures and equations where applicable.

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5. Sketch a titration curve for the amino acid cysteine; indicate the pKa values for all titratable groups.

Amino acid questions continued.

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Amino acids have handedness (18.5-18.6)Chirality - an object or molecule that cannot be superimposed

on its mirror image image is chiralyour left and right hands are mirror images of each other.They are non-superimposable mirror images.You cannot exactly superimpose your left and right hands.

Molecular handednessMolecules with carbon are frequently chiralcarbon must have 4 different groups bound to it - calleda chiral carbon or chiral center.

The presence of one chiral carbon always produces a chiralmolecule

A molecule with more than one chiral carbon may or may notbe chiral overall

non-superimposablemirror images - chiral

superimposablemirror images - achiral

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In the type of chiral center we are intersted in, carbon must have 4 different groups attached:

Examples:

Propane Chloroethane

Amino acids

Groups attached to Cof amino acids

1. COO-

2. H3. NH3+

4. R group

CH3N COO-

H R

CH3

CH H

CH3

Cl

CH H

CH3

Has 2 sets ofidentical groupsattached (thehydrogens and themethyl groups) achiral

Has 2 identicalatoms attached(the hydrogens) achiral

4 different groups attachedin all amino acids exceptglycine (the R group is hydrogen)

C

C

NH3+

NH3+

COO-

COO-

CH3

H

H

Alanineenantiomers

CH3

The chiral atom thatmakes

the overall moleculechiral

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Label the chiral center in the following molecules if one is present.

H3C CH

OH

C

O

OH H3C C CH3

NH3H2C C CH3

NH3

H3C

H3CH2C CH

H2C CH3

Cl

H3C CHH2C

H2C CH3

Cl

Two of the 20 common amino acids have two chiral carbon atoms in their structures.Identify these amino acids, draw their structures below, and label their chiral centers.

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Enantiomers - molecules that are non superimposable mirror images of each other

Enantiomers have the same name but are distinguished by a prefixR vs. S system most commonly usedD vs. L is older nomenclature

only L amino acids are in making proteins (L for “Life”)

Enantiomers have many identical physical properties:melting and boiling pointssame pIsame solubility in watersame density

Enantiomers have some physical and chemical properities that differrotate plane polarized light in opposite directionsreactivity with other chiral molecules**biological activity**odors and tastes**activity as drugs

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Examples of the differing biological activity of enantiomers:

CH3

O

HCH2C

CH3

CH3

O

H C CH2

H3C

mirrorL-Carvone

(in spearmint)D-Carvone

(in caraway)

Chiral center

Chiralcenter

mirror

(R)-Limonene(smell of oranges)

(S)-Limonene(smell of lemons)

Chiral centerChiralcenter

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N

O

O

HN

O

O

H

N

O

O

NH

O

O

H

mirror

(S)-Thalidomide(fetal abnormalities)

(R)-Thalidomide(sedative)

Chiral centerChiral center

OCH3

H3C

HHO2C

H3CO

CH3

H CO2H

mirror(S)-Naproxen(anti-inflammatory)

(R)-Naproxen(liver toxin)

Must be soldas 97% S

enantiomer