CHAPTER 6

Biomolecules: Amino Acids, Peptides, and Proteins

Introduction
 In every living organism, there are many different types with many
different biological functions of proteins.
 Proteins are made up of many amino acids linked together in a long
chain.
 Amino acids contain both basic amino group and acidic carboxyl
group  difunctional.
 Forming amide bonds between –NH2 of one amino acid and the –CO2H
of another.
 Classification of amino acids:
 Peptides: <50 amino acids
 Proteins: >50 amino acids

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Why this Chapter?
 Amino acids are the fundamental building blocks of
proteins

 To see how amino acids are incorporated into proteins

and the structures of proteins

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Structures of Amino Acids
 At physiological pH (pH = 7.3):
 COOH deprotonates to be carboxylate anion
 NH2 protonates to be ammonium cation.
 Amino acids in the form of dipolar ion or zwitterion
 They are like ionic salts in solution:
 Large dipole moment
 Soluble in water not in organic solvents
 Relatively high melting point
 Amphiprotic – react as acid or base

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The Common Amino Acids
 Table 26.1 shows 20 amino acids form amides in proteins
 All are -amino acids - amino group is a substituent on the 
carbon.
 19 out of 20 are primary amines, RNH2 with different side
chain – substituent attached to the  carbon.
 Proline is a five-membered secondary amine, with N and the 
C part of a five-membered ring

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Chirality of Amino Acids
 The  carbons of the amino acids are chiral centers.
 Except for glycine, H2NCH2CO2H
 Fisher projections:
 -CO2- at the top
 -NH3+ on the left
 Naturally occuring -amino acids are referred to as L amino
acids.

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Types of side chains
 Classification of the amino acids depend on the side
chains:
 Neutral – 15 of 20 have neutral side chains
 Acidic – 2 have extra carboxylic acid function: Aspartic acid
and glutamic acid
 Basic – 3 have basic amino groups: lysine, arginine and histidine
 Cysteine and tyrosine are neutral amino acids that can be
deprotonated in strongly basic solution due to the weakly
acidic side chains.

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Types of side chains
 At physiological pH, acidic amino acids deprotonated and the
basic amino acids will protonated.
 Histidine:
 Contains a heterocyclic imidazole ring as side chain – not quite basic
enough to be protonated.
 Pyridine-like is basic, pyrrole-like is nonbasic because its lone pair of
electrons is part of the 6  electron aromatic imidazole ring.

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Essential Amino Acids
 All 20 of the amino acids are necessary for protein
synthesis
 Humans can synthesize only 10 of the 20
 The other 10 must be obtained from food

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Henderson-Hasselbach Equation
 Both pH of the solution and the pKa of an acid HA is
known, we can calculate the ratio of [A-] to [HA] in the
solution.

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Henderson-Hasselbach Equation
 What species are present in a 1.00 M solution of alanine at pH
= 9.0.
 protonated alanine [H3NCH(CH3)CO2H] has pKa1 =2.34,
 neutral zwitterionic alanine [H3NCH(CH3)CO2] has pKa2 = 9.69
 Since pH is much closer to pKa2 so use pKa2

 Know that :
 At pH = 9.00, 83% of alanine molecules in 1.00 M solution are
neutral (zwitterionic) and 17% are deprotonated.

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Henderson-Hasselbach Equation
 Calculations can be done at other pH and titration curve
is plotted:
 1st leg: pH 1-6, dissociation of protonated alanine, H2A+
 2nd leg: pH 6-11, dissociation of zwitterion alanine, HA

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Isoelectric Points, pI
 In acid solution – protonated amino acids exist as cation.
 In basic solution – deprotonated amino acids exist as anion.
 At pH where cation and anion of amino acids are balance and
exist as neutral dipolar zwitterion – isoelectric point (pI)
 This pH where the overall charge is 0 is the isoelectric point,
pI

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Isoelectric Points, pI
 Neutral amino acids pI :
 pH 5.0 to 6.5
 Average pI is average of pKa1 and pKa2
 Acidic amino acids pI:
 lower pH (no deprotonation of the –COOH)
 Average pI is 2 lowest pKa values.
 Basic amino acids pI:
 higher pH (no protonation of the amino acids group)
 Average pI is 2 highest pKa values.

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Electrophoresis
 Proteins have an overall pI that depends on the net
acidity/basicity of the side chains
 The differences in pI can be used for separating proteins on a
solid phase permeated with liquid
 Different amino acids migrate at different rates, depending on
their isoelectric points and on the pH of the aqueous buffer

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Synthesis of Amino Acids
Bromination
 Oldest method.
  bromination of a carboxylic acid by treatment with Br2
and PBr3 then use NH3 or phthalimide to displace Br
 SN2 substitution of the -bromo acid with ammonia

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Synthesis of Amino Acids
Amidomalonate Synthesis
 General method
 Based on malonic ester synthesis.
 Convert diethyl acetamidomalonate into enolate ion with base,
followed by alkylation with a primary alkyl halide
 Hydrolysis of the amide protecting group and the esters in
warm aqueous acid and decarboxylation yields an -amino

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Synthesis of Amino Acids
Reductive Amination of -Keto Acids
 Reaction of an -keto acid with NH3 and a reducing agent (see
Section 24.6) produces an -amino acid
 Treatment of pyruvic acid with ammonia in the presence of
NaBH4
 Formation of imine
 reduction

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Synthesis of Amino Acids
Enantioselective Synthesis of Amino Acids
 Amino acids (except glycine) are chiral and pure
enantiomers are required for any protein or peptide
synthesis
 Resolution of racemic mixtures is inherently ineffecient
since at least half the material is discarded
 An efficient alternative is enantioselective synthesis

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Synthesis of Amino Acids
Enantioselective Synthesis of Amino Acids
 Chiral reaction catalyst creates diastereomeric transition
states that lead to an excess of one enantiomeric product
 Hydrogenation of a Z enamido acid with a chiral
hydrogenation catalyst produces S enantiomer selectively

 Most effective catalyst

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Peptides and Proteins
 Proteins and peptides are amino acid polymers in which
the individual amino acid units, called residues, are linked
together by amide bonds, or peptide bonds
 An amino group from one residue forms an amide bond
with the carboxyl of a second residue
 Two dipeptides can result from reaction between A and S,
depending on which COOH reacts with which NH2 we
get AS or SA
 The long, repetitive sequence of NCHCO
atoms that make up a continuous chain is called the
protein’s backbone

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Peptide Linkages
 Peptides are always
written with:
 N-terminal amino acid (the
one with the free NH2
group) on the left
 C-terminal amino acid (the
one with the free CO2H
group) on the right
 Alanylserine is abbreviated
Ala-Ser (or A-S), and
serylalanine is abbreviated
Ser-Ala (or S-A)

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Protein Structure
 Proteins classification:
 Fibrous proteins: polypeptide chains arranged side by side in long
filament e.g. collagen in tendons, connective tissues
 Globular proteins: polypeptide chains coiled into compact, roughly
spherical shapes – generally more soluble in water and are mobile
within cells.
 Levels of protein:
 Primary structure: amino acid sequence
 Secondary structure: how segments of the peptide backbone orient
into a regular pattern.
 Tertiary structure: how the entire protein molecule coils into an
overall three-dimensional shape
 Quaternary structure: how different protein molecules come
together to yield large aggregate structures

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Secondary structure - -Helix
 Right-handed coil of the protein backbone
 Each coil contain 3.5 amino acid residues
 -helix stabilized by H-bonds between amide N–H groups and
C=O groups four residues away -helical segments in their
chains

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Secondary structure - -Pleated Sheet
 Peptide chain is
extended between
residues in adjacent
chains
 β-pleated sheet
secondary structure
is exhibited by
polypeptide chains
lined up in a parallel
arrangement, and
held together by
hydrogen bonds
between chains Concanavalin A

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Tertiary structure
 Forces that determine the stabilisation of the structure:
 Hydrophilic (water-loving) interaction
 Formation of disulfide bridges between cysteine residues
 Formation of hydrogen bonds between amino acid residues
 Ionic attractions
 The tertiary structure of a globular protein is the result of many intramolecular attractions
that can be disrupted by a change of the environment, causing the protein to become
denatured
 Solubility is drastically decreased as in heating egg white, where the albumins unfold and
coagulate
 Enzymes also lose all catalytic activity when denatured

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Enzymes and Coenzymes
 Enzyme: protein that acts as a catalyst for a biological
reaction.
 Enzymes are usually specific in their action – will catalyse
only a single reaction of a single compound, enzyme’s
substrate e.g.:
 Enzyme amylase in human digestive tract catalyses only the
hydrolysis of starch glucose. Cellulose and other
polysaccharides are not affected.
 Coenzyme: non-protein – small organic molecule. Not a
catalyst but a reactant, mostly derived from vitamins.

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Types of Enzymes by Function
 Enzymes are usually grouped according to the kind of
reaction they catalyze, not by their structures

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Citrate Synthase
 Citrate synthase catalyzes aldol-like addition of acetyl
CoA with oxaloacetate to give citrate
 First step in the citric acid cycle, in which acetyl groups
produced by degradation of food molecules are
metabolized to yield CO2 and H2O

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The Structure of Citrate Synthase
 Determined by X-ray
crystallography
 Enzyme is very large
compared to substrates,
creating a complete
environment for the
reaction

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Mechanism of Citrate Synthetase
 side-chain carboxyl of an aspartate residue acts as base to
abstract an acidic  proton while at the same time the side-
chain imidazole ring of a histidine donates H to the carbonyl
oxygen
 enol thus produced then does a nucleophilic addition to the
ketone carbonyl group of oxaloacetate.
 first histidine acts as a base to remove the OH hydrogen from
the enol
 second histidine residue simultaneously donates a proton to
the oxaloacetate carbonyl group, giving citryl CoA.
 Water then hydrolyzes the thiol ester group in citryl CoA in a
nucleophilic acyl substitution reaction, releasing citrate and
coenzyme A as the final products.

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Quiz
1. Draw structure corresponding to the IUPAC names:
a) 4-Methylpentanoic acid
b) 2-Pentenenitrile
c) 3,3,3-Tribromopropene
d) 2-Chlorohex-3-yn-1-ol
e) 1-Ethylcyclobutanol
2. Write structural formulas for the products that form
when 1-butene reacts with each of the following
reagents:
a) Br2 in H2O
b) KMnO4, OH, heat, then H3O+
c) O3, then Me2S

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