Amino Acids · B. Peptide Bonds Link Amino Acids •Amino acids can be polymerized to form chains •This process can be represented as a condensation reaction, bond formation with

Amino Acids• In 1839, the Swedish chemist Jacob Berzelius coined

the term protein (Greek: proteios, ) for thisclass of compounds

• The first amino acids had been isolated in 1830

• Scientists began to consider the nutritive qualities ofAmino Acids ( )

• The central role of amino acids in biochemistry:

1. Several amino acids are among the organiccompounds believed to have appeared early in theearth’s history

2. Amino acids have been co-opted by evolution for avariety of purposes in living system

Amino AcidsAmino Acid Structure

• All proteins are composed of 20“standard” amino acids

• Not every protein contains all 20types of amino acids

• The common amino acids areknown as α-amino acids

• The sole exception is proline,which has a secondary aminogroup (—NH—), although foruniformity we will refer to prolineas an α-amino acid


A. Amino Acids Are Dipolar Ions

• The amino and carboxylic acid groupsof amino acids ionize readily

• The pK values of the carboxylic acidgroups lie in a small range around 2.2

• The pK values of the α-amino groups(pK2) are near 9.4

• At physiological pH (∼7.4), the aminogroups are protonated and thecarboxylic acid groups are in theirconjugate base (carboxylate) form

See Table 4-1page 82


A. Amino Acids Are Dipolar Ions

• An amino acid can therefore act as both an acidand a base

• Molecules such as amino acids, which bear chargedgroups of opposite polarity, are known as dipolarions or zwitterions

• Amino acids, like other ionic compounds, are moresoluble in polar solvents than in nonpolar solvents

• The ionic properties of the side chains influencethe physical and chemical properties of free aminoacids and amino acids in proteins


B. Peptide Bonds Link Amino Acids

• Amino acids can be polymerized to form chains

• This process can be represented as a condensationreaction, bond formation with the elimination of a watermolecule

• The resulting linkage, an , is knownas a

• Polymers composed of , , a , andamino acid units are known, respectively, as ,

, , and

• Amino acid residues & peptides (Terminologies to know!)


B. Peptide Bonds Link Amino Acids

• Polypeptides are linear polymers rather thanbranched chains; that is, each amino acid residueparticipates in two peptide bonds and is linked to itsneighbours in a head-to-tail fashion

• The residues at the two ends of the polypeptide eachparticipate in just one peptide bond

• The residue with a free amino group is called theamino terminus or N-terminus

• The residue with a free carboxylate group (at theright) is called the carboxyl terminus or C-terminus


C. Amino Acid Side Chains Are Nonpolar, Polar, or Charged

• The most useful way to classify the 20 standard aminoacids is by the polarities of their side chains

• According to the most common classification scheme,there are three major types of amino acids:

1. those with nonpolar R groups

2. those with uncharged polar R groups, and

3. those with charged polar R groups



• Nine amino acids are classified as having nonpolarside chains

• The three dimensional shapes of some of these aminoacids are shown in Fig. 4-4, page 85

• Glycine has the smallest possible side chain, an Hatom

, , , and haveside chains ranging in size

from a methyl group for to isomeric butylgroups for and



has a side chain thatresembles an n-butyl group in many of its physicalproperties

has a cyclic side group

(with its moiety) and(with its group) contain

, which are characterized bybulk as well as nonpolarity



Uncharged Polar Side Chains Have Hydroxyl, Amide, or Thiol Groups

• Six amino acids are commonly classified as having uncharged polarside chains

and bear of differentsizes

and haveof different sizes

has a (and, like phenylalanine andtryptophan, is aromatic)

is unique among the 20 amino acids in that it has athat can form a disulfide bond with another cysteine

through the oxidation of the two thiol groups



Charged Polar Side Chains Are Positively or Negatively Charged

• Five amino acids have charged side chains

• The side chains of the basic amino acids are positivelycharged at physiological pH values

has a side chain, andbears a group

carries an moiety



Charged Polar Side Chains Are Positively or Negatively Charged

• The side chains of the acidic amino acids,and , are negatively charged

above pH 3

and are, respectively, theamides of and


D. The pK Values of Ionizable Groups Depend on Nearby Groups

• The α-amino acids have two or, for those withionizable side chains, three acid–base groups

• At values, these groups are fully, and at values, these groups

are

• At pH values, the tend tobe , and the tend to be



• Thus, for the amino acid , below pH 2.35 (thepK value of its carboxylic acid group), the+H3NCH2COOH form predominates

• Above pH 2.35, the carboxylic acid is mostly ionizedbut the amino group is still mostly protonated(+H3NCH2COO−)

• Above pH 9.78 (the pK value of the amino group), theH2NCH2COO− form predominates



• The at which a molecule carries no net electric charge isknown as its isoelectric point,

• where Ki and Kj are the dissociation constants of the twoionizations involving the neutral species

• For monoamino, monocarboxylic acids such as glycine, Ki andKj represent K1 and K2

• For aspartic and glutamic acids, Ki and Kj are K1 and KR

• For arginine, histidine, and lysine, these quantities are KR andK2





• Deprotonation of carboxylic acids gives

carboxylate anions

• these are resonance stabilized, because

the negative charge is delocalized over

the two oxygen atoms, increasing the

stability of the anion

• Each of the carbon–oxygen bonds in the

carboxylate anion has a partial double-

bond character



• Amino acid residues in the interior of a polypeptidechain do not have free α-amino and α-carboxylgroups that can ionize

• These groups are joined in peptide bonds


E. Amino Acid Names Are Abbreviated

• The three-letter abbreviations for the 20 standardamino acids given in Table 4-1, page 82, are widelyused in the biochemical literature

• Most of these abbreviations are taken from the firstthree letters of the name of the corresponding aminoacid and are pronounced as written

• The symbol Glx indicates Glu or Gln, and similarly, Asxmeans Asp or Asn



• The one-letter symbols for the amino acids are alsogiven in Table 4-1, page 82.

• This more compact code is often used whencomparing the amino acid sequences of severalsimilar proteins

• Note that the one-letter symbol is usually the firstletter of the amino acid’s name

• However, for sets of residues that have the same firstletter, this is true only of the most abundant residueof the set



• Amino acid residues in polypeptides are named bydropping the suffix, usually -ine, in the name of theamino acid and replacing it by -yl

• Polypeptide chains are described by starting at the N-terminus and proceeding to the C-terminus

• The amino acid at the C-terminus is given the name ofits parent amino acid

Amino AcidsStereochemistry

• Amino acids are chiral molecules whose configurations can be depicted by Fischer projections

• The amino acids in proteins all have the L stereochemical configuration

Amino AcidsStereochemistry

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Amino Acids · B. Peptide Bonds Link Amino Acids •Amino acids can be polymerized to form chains •This process can be represented as a condensation reaction, bond formation with