1

LECTURE 3
AMINO ACIDS

1. AMINO ACIDS- THEIR GENERAL FORMULA AND THREE-

DIMENSIONAL STRUCTURE
• Building blocks of proteins
• Amino acids are named as such because each amino acid
consists of an amine portion and a carboxylic acid part
♦ About 300 amino acids (aa) known to occur in nature
♦ Some only in certain life species while others, only one organism
♦ ALL ORGANISMS use only 20 in biosynthesis of proteins
♦ Most aa are alpha amino acids
 Both an amino (-NH 2 ) and carboxyl (-COOH) group attached to
the same alpha (α) carbon atom
 Long chains of aa linked by peptide bonds
 α -carbon also bonded to a hydrogen and to a side chain group
(represented by R)
 R- group determines identity of particular amino acid
e.g.
H H

NH3+ COOH H2N COO-

R R
Fully Protonated Fully De-protonated
 Amino acids are usually in the ionised form at neutral pH.
Varies with pH.

Acid pH: COOH, NH 3 +

Basic pH: COO-, NH 2
e.g.

BIOCHEMISTRY 2
 2

Linkage of 2 aa
 Dipeptide
♦ Linkage of 3 aa
 Tripeptide
♦ Many aa linked
 Polypeptide (protein)
♦ Sequence in which aa linked extremely important
♦ Chain may contain any 20 different aa > 1 BILLION POSSIBLE
SEQUENCES
♦ SEQUENCE DETERMINES THE MESSAGE TRANSCRIBED =
WHICH IN TURN DETERMINES:
 Type of protein
 How proteins form 3D conformation
 Function of protein
♦ 3D Shape of molecule (e.g. aa) – STERIOCHEMISTRY

♦ 19 of the 20 amino acids are chiral i.e. four different groups bonded to
α-carbon (asymmetric). The exception is glycine, which has a
hydrogen R-group, and is therefore symmetric.

COO-
!
H 3 N -C -H
!
H (R group)
Stereoisomers: All amino acids are found biologically as L-isomers.

• L and D isomers are mirror images of each other

• Glycine – 2 H atoms bonded to it - R-group is Hydrogen,

• Glycine is thus not chiral but achiral because of symmetry

BIOCHEMISTRY 2
 3

• Chiral centre aa - α -carbon

• All other commonly occurring aa - α -carbon has 4 different
groups bonded to it THUS giving rise to 2 nonsuperimposable
mirror images CALLED sterioisomers
• 2 steriosisomers of each aa
• L AND D AMINO ACIDS – L (Latin): “laevus” – left
D (Latin): “dexter” – right

NH2 NH2
! !
R -C -H H -C -R
! !
COOH COOH

L D
• D amino acids – most often bacterial cell walls and some
antibiotics
2. THE STRUCTURE AND PROPERTIES OF INDIVIDUAL AMINO
ACIDS
♦ Classified according to R-groups
 In turn classified according to criteria
 Polar/Hydrophilic
• Charged R groups : + (Basic R-group) and – (Acidic R-group)
• uncharged R groups (electrically neutral- no charge)
 Nonpolar/Hydrophobic
• Aliphatic R-group (no benzene ring or related structure)
• Aromatic R-group (benzene ring structure or similar)
♦ NOMENCLATURE (classification):
 Amino acids
• Full name (e.g. Alanine)
• Three letter abbreviation (e.g. Ala)

BIOCHEMISTRY 2
 4

• One Letter abbreviation (e.g. A)

Table 3.1 (revised Campbell) Names and Abbreviations of the Common Amino
Acids
Amino acid 3- letter 1- letter Criteria for Classification
abbreviation abbreviation
Alanine Ala A Hydrophobic- aliphatic
Arginine Arg R Hydrophilic – charged (+)
Asparagine Asn N Hydrophilic – charged (-)
Aspartic acid Asp D Hydrophilic – uncharged
Cysteine Cys C Hydrophobic- aliphatic
Glutamic acid Glu E Hydrophilic – charged (-)
Glutamine Gln Q Hydrophilic – uncharged
Glycine Gly G Hydrophobic – aliphatic
Hydrophilic – uncharged
Histidine His H Hydrophilic – charged (+)
Isoleucine Ile I Hydrophobic- aliphatic
Leucine Leu L Hydrophobic- aliphatic
Lysine Lys K Hydrophilic – charged (+)
Methionine Met M Hydrophobic- aliphatic
Phenylalanine Phe F Hydrophobic- aromatic
Proline Pro P Hydrophobic- aliphatic
Serine Ser S Hydrophilic – uncharged
Threonine Thr T Hydrophilic – uncharged
Tryptophan Trp W Hydrophobic- aromatic
Tyrosine Tyr Y Hydrophobic- aromatic
Valine Val V Hydrophobic- aliphatic

The structures and properties of the individual amino acids

The 20 amino acids can be classified on the basis of their side chains (R-
groups).

SOME AMINO ACID FEATURES

Group 1: Amino acids with non-polar (type of chemical bond which
has no positive or negative end) side-chains:

BIOCHEMISTRY 2
 5

♦ Alanine, valine, leucine, isoleucine, proline, phenylalanine, tryptophan

and methionine
 Proline - Aliphatic cyclic structure
 Nitrogen bonded to two Carbon atoms
 Terminology of organic chemistry – amino group of proline –
secondary amine
 In contrast amino group of all other common amino acids –
primary amines
 Phenylalanine and tryptophan – aromatic (Contains a cyclic
structure similar to a benzene ring)
 Methionine
 Aliphatic hydrocarbon + Sulphur atom

Group 2: Amino acids with electrically neutral polar side chains:

♦ Serine, threonine, tyrosine, cysteine, glutamine and asparagine

BIOCHEMISTRY 2
 6

♦ Glycine is also included here for convenience as it lacks a nonpolar

side chain.
♦ In Serine and threonine – polar group is a hydroxyl (-OH) bonded to
aliphatic hydrocarbon group
♦ Tyrosine hydroxyl group bonded to aromatic hydrocarbon group
♦ Cysteine - Polar side chain contains – thiol group (-SH)
 Can react with other –SH groups
 Thus forming disulfide (S-S) bridges in proteins
Group 3: Amino acids with carboxyl groups in their side chains:

♦ Glutamic acid and Aspartic acid

 Carboxyl group in side chain (-COOH) in addition to the one
present in all amino acids
 -COOH can loose proton and from COO- (carboxylate anion)
 GLUTAMIC ACID – GLUTAMATE (-COOH VS COO-)
 ASPARTIC ACID – ASPARTATE (-COOH VS COO-)
 Side chain -COOH also capable of bonding to amino group (-NH 2 )
to form side-chain amide groups
 E.g. Asparagine and Glutamine

Group 4: Amino acids with basic side chains:

BIOCHEMISTRY 2
 7

♦ Histidine, lysine and arginine

♦ In lysine - side-chain amino group attached to an aliphatic
hydrocarbon
UNCOMMON AMINO ACIDS
♦ Many other aa are known to exist.
♦ Occur in some but not all proteins
♦ derived from common amino acids
♦ Produced by modification of parent amino acid after the protein is
synthesised by process called POSTTRANSLATIONAL
MODIFICATION
e.g.
1. Hydroxyproline (OH-Pro) and hydroxylysine (OH-Lys)
 differ from parent in having hydroxyl groups on their side chains
 found in only a few connective tissue proteins e.g. Collagen
2. Thyroxine
 Differs from tyrosine (have an extra iodine-containing aromatic
group side chain)
 Found only in thyroid gland bound to protein thryroglobulin

3. TITRATION CURVES OF THE AMINO ACIDS

♦ A free amino acid at neutral pH contains
 Carboxyl group negatively charged (COO-)

BIOCHEMISTRY 2
 8

 Amino group positively charged (NH 3 +)

♦ Amino acids without charged groups on side chains exist in neutral
solution as ZWITTERIONS with no net charge
 Zwitterion:
 Has equal positive and negative charges
 In solution is electrically neutral
♦ When an amino acid is titrated- titration curve indicates reaction of
each functional group with H+
♦ At very low pH all α-amino acids exist as ions with an overall positive
charge, while at high pH they exist as ions with an overall negative
charge. For each α-amino acid there is a pH between these
extremes at which its molecules are neutral overall. This value is
called the isoelectric point for the α-amino acid. At its isoelectric
point the α-amino acid molecules will not move when placed in an
electric field. The separation technique called electrophoresis relies
on molecules with different isoelectric points moving at different
speeds when kept at a fixed pH and placed in an electric field.
♦
♦ The isoelectric point is calculated by averaging the pKa values for the
carboxylic acid and the amine group. pK 1 applies to the carboxylic
acid and pK 2 applies to the amine.
pK 1 + pK 2
♦ pI =
2
♦ This formula does not take into account acidic or basic side chains. If
an acidic side chain is present you average the side chain pK a and
pK 1 . For a basic side chain you average the side chain pK a and pK 2 .

e.g. TITRATION OF ALANINE (neutral amino acid)

♦ Typical of a diprotic acid
♦ Carboxyl and amino groups the two titratable groups
♦ Thus 2 pK a values
♦ AT LOW pH
 Alanine has protonated (thus, uncharged) carboxyl group (viz.
COO- - COOH)

BIOCHEMISTRY 2
 9

 Also has protonated amino group (thus positively charged)

 Under these conditions – alanine has a net positive charge of 1
♦ Increase in pH (addition of base)
 Carboxyl group first to loose proton
 Becomes negatively charged carboxylate group (COO-)
 No net charge (positive charge of amino group = negative charge
of carboxylate group.
 Zwitterion of Ala
 pH at which molecule has no net charge called isoelectric pH
(given symbol pI)
♦ As pH increases further (addition of more base)
 Protonated amino group (a weak acid) looses its proton (now NH 2 )
 Net charge = +1
 deprotonated
♦ Amino acid may contain R-group which has titratable group
 Histidine has imidazole side chain
 Triprotic/polyprotic – 3 pK a values
 Initial net charge = +2
 Addition of base carboxyl group looses proton net charge = +1
 Addition of base imidazole group looses proton net charge = 0
 THUS zwitterion of histidine
 Addition of more base amino group looses proton net charge = -1
 deprotonated

MORE ABOUT K a , pK a and pI VALUES

♦ Similar to acids – amino acids have characteristic values for the K a
and pK a of their titratable groups
♦ pK a of carboxyl group fairly low, ∀2

BIOCHEMISTRY 2
 10

♦ pK a of amino groups much higher, 9 – 10.5

♦ pK a of side-chain groups (including side-chain carboxyl and amino
groups ) depend on groups chemical nature
♦ TABLE 3.2 lists the pK a of titratable groups of amino acids

BIOCHEMISTRY 2
 11

Table 3.2
Acid α-COOH α-NH 3 + RH or RH+

Gly 2.34 9.60

Ala 2.34 9.69
Val 2.32 9.62
Leu 2.36 9.68
Ile 2.36 9.68
Ser 2.21 9.15
Thr 2.63 10.43
Met 2.28 9.21
Phe 1.83 9.13
Trp 2.38 9.39
Asn 2.02 8.80
Gln 2.17 9.13
Pro 1.99 10.6
Asp 2.09 9.82 3.86*
Glu 2.19 9.67 4.25*
His 1.82 9.17 6.0*
Cys 1.71 10.78 8.33*
Tyr 2.20 9.11 10.07
Lys 2.18 8.95 10.53
Arg 2.17 9.04 12.48
* For these amino acids the R group ionisation occurs before the α-NH 3 + ionisation

♦ FACT: amino acids, peptides and proteins have different pK a

 THUS, can have different charges at a given pH
 E.g. Alanine and histidine both have net charges = -1 at high pH >
10
• at lower pH theses two molecules have different charges
• around pH 5 alanine is a zwitterion with no net charge BUT
histidine has a net charge of +1 (imidazole group is protonated)
• THIS IS THE BASIS FOR ELECTROPHORESIS – METHOD
FOR SEPARATING MOLECULES ON BASIS OF CHARGE

BIOCHEMISTRY 2
 12

• Method extremely useful in determining the structure of proteins

and nucleic acids
♦ pH at which molecule has no net charge called ISOELECTRIC pH
(symbol pI)
 at pI a molecule will not migrate in an electric field
 thus medium used in electrophoresis ALWAYS have higher/lower
pH than pI value(s) of molecule(s) to be separated

HOW TO CALCULATE THE pI OF AN AMINO ACID?

♦ pI calculated by using the average of the two pK a values on either
side of the zwitterion.
e.g. Calculate the pI of Ala.
pI = pK a1 + pK a2
2
= 2.34 + 9.69 = 6.02
2
4. THE PEPTIDE BOND
♦ Individual amino acids may be linked by covalent bonds
♦ Bond formed between the α-carboxyl group of one amino acid with
the α-amino group of another
♦ Water is eliminated (dehydration) during process
♦ Linked amino acid residues remain after water eliminated
♦ Bonds formed in this way called PEPTIDE BONDS
♦ PEPTIDE
 Compounds formed by linking a small number of amino acids (2-
99) – dipeptide, tripeptide, tetrapeptide etc.
 Many amino acids linked (> 100) linked by peptide bonds to form
polypeptides

BIOCHEMISTRY 2
 13

♦ carbon-nitrogen bond when two amino acids are linked in a peptide

bond usually written as single bond (one pair of electrons shared
between the two atoms)
 Simple shift in position of pair of electrons, possible to write this
bond as a double bond
 Shift in electrons result in RESONANCE STRUCTURES –
structures which differ from each other only in the positioning of
electrons
 Peptide bond stronger than an ordinary single bond DUE TO
resonance stabilisation
 Structural feature important for 3D conformations of peptides and
proteins
♦ Free rotation around bonds between α-carbon of one amino acid
residue and the amino nitrogen and carbonyl carbon of this residue
♦ NO FREE ROTATION AROUND PEPTIDE BOND
♦ Steriochemical constraint plays important role in determining how
protein backbone can fold

5. SOME SMALL PEPTIDES OF PHYSIOLOGICAL INTEREST

♦ Simplest possible covalent combination of amino acids – dipeptide
(two amino acids linked by a peptide bond)
 E.g. Carnosine found in muscle tissue
 E.g. Aspartame
• dipeptide – L-Aspartyl-Lphenylalanine
• methyl ester derivative of this dipeptide of great commercial
importance
• 200 times sweeter than sugar

BIOCHEMISTRY 2
 14

• methyl ester derivative called aspartame – marketed as sugar

substitute NutraSweet
• Table sugar consumed in amounts of ∀45 kg /person/year
• Cut out sugar:
1. Fight obesity
2. Diabetes
• Solution: drink diet soft drinks (one of the largest aspartame
markets)
• Although Food and Drug Administration (FDA) approved
aspartame in 1981 – still controversy with regard to safety
• Aspartame have phenylalanine present
• NOTE: both amino acids have L configuration
• If D configuration – derivative is bitter rather than sweet
 Oxytocin
• Peptide hormone
1. Induces labour in pregnant women
2. Controls contraction of uterine muscles
3. Stimulates milk flow during nursing
 Vasopressin
• Peptide hormone
1. Controls blood pressure

Synthesis of other amino acids

• humans can only synthesize 11 of the 20 amino acids (non-
essential amino acids)
• essential amino acids must be ingested (synthesized by plants and
bacteria)
• carbon skeletons derived from intermediates of glycolysis, pentose
phosphate pathway, or citric acid cycle
o six biosynthetic pathways

BIOCHEMISTRY 2
 15

Nonessential Essential
Alanine Histidine
Arginine Isoleucine
Asparagine Leucine
Aspartate Lysine
Cysteine Methionine
Glutamate Phenylalanine
Glutamine Threonine
Glycine Tryptophan
Proline Valine
Serine
Tyrosine
4. Feedback inhibition of amino acid synthesis pathways

Glutamine synthetase is allosterically and covalently regulated

• alanine and glycine are negative regulators as are other end
products of this pathway adenylation of a specific amino acid
residue by AMP reduces activity
4. Amino acids are precursors of many biomolecules
Example: glutathione is synthesized from glutamate and cysteine
• serves as sulfhydryl buffer
o cycles between reduced (GSH) and oxidized form (GSSG)
2 GSH + R-O-OH --------> GSSG + H 2 O + ROH
Example: Nitric oxide formed from arginine
Argninine + NADPH + O 2 ------> N-α-hydroxyarginine -------->
Citrulline + NO
• catalyzed by nitric oxide synthase

BIOCHEMISTRY 2