Kwame Nkrumah University of

Science & Technology, Kumasi, Ghana

AMINO ACIDS
AND PROTEINS

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 OUTLINE

Amino acids
Protein structure
Protein denaturation
Functional properties of proteins

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 Amino Acids
• Compound containing an amino group, an acid group, a
hydrogen atom, and a side group.

• It is the side group that makes each amino acid unique.

• It is the unique side groups that result in differences in

the size, shape and electrical charge of an amino acid.

• All amino acids (except glycine) are chiral.

• Both D- and L- conformers occur in nature; the body

uses only the L- conformer to make proteins.

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  -amino acids
H
H2N COOH
R

Amino group Carboxylic Acid group

Side Chain
Chiral if R- is not H-, i.e. glycine.
In  -amino acids, amino group is in alpha position.
Amino acids are grouped on the basis of the chemical
nature of the side chains
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 Amino Acids
• All are primary amino acids except proline which is a
secondary amino acid.
• Also found in enantiomeric form, D- and L-

COOH COOH
H2N H H NH2
R R
L-amino acid D-amino acid

• Amino group on the left, similar to OH- on the left of sugars

• Most natural amino acids are in L- configuration.

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 Classification of Amino Acids

• Neutral, acid or basic.

• D- or L- amino acids.
• Essential or non-essential amino acids.
• Amino acid side chains: hydroxyl, aromatic, alkyl,
carboxylic acid, amino, amide or sulfur containing.
• Hydrophilic, hydrophobic or amphiphilic.
• Polar or non-polar. High levels of polar increase
water solubility

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Essential amino acids: the body does not synthesize them
and must be obtained from the diet

ESSENTIAL AMINO ACIDS

LEUCINE
ISOLEUCINE
LYSINE PVT TIM Hill

METHIONINE
PHENYLALALINE
TRYPTOPHANE
VALINE
THREONINE HISTIDINE
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 Characteristics of Amino Acids
• Amphoteric – able to react as acid or
as base
• May form zwitterions or dipolar ion
HO O O
-
O O
-
O
C pKa1 C pKa2 C
+ +
H3N C H H3N C H - H+ H2N C H
+ H+
R R R
Acidic condition Zwitterion Basic condition

Isoelectric point: pH at which amino acid is neutral or exist primarily as

zwitterion. Isoelectric point for each amino acid is different depending on its
structure.
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 Ionization
At acidic pH, the carboxyl
group is protonated and the
amino acid is in the cationic
form
At neutral pH, the carboxyl
group is deprotonated but
the amino group is
protonated. The net charge
is zero; such ions are
called Zwitterions
At alkaline pH, the amino
group is neutral –NH2 and
the amino acid is in the
anionic form.

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Amino Acids Carry a Net Charge of Zero
at a Specific pH
•Zwitterions predominate at pH values between the pKa
values of amino and carboxyl group
•For amino acid without ionizable side chains, the Isoelectric
Point (equivalence point, pI) is
• pK1  pK 2
pI 
2

• At this point, the net charge is zero

– AA is least soluble in water
– AA does not migrate in electric field
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How to Calculate the pI When the Side-
chain is Ionizable?
• Identify species that carries
a net zero charge
• Identify pKa value that
defines the acid strength of
this zwitterion: (pK2)
• Identify pKa value that
defines the base strength of
this zwitterion: (pKR)
• Take the average of these
two pKa values

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 Peptides and Peptide bonds
• Peptide bond in a
di-peptide

• “Peptides” are
small condensation
products of amino
acids

• They are “small”

compared to
proteins (di, tri,
tetra… oligo-)

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 Peptide Ends are Not the Same
Numbering starts from the amino terminus
AA1 AA2 AA3 AA4 AA5

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 The Three Letter Code
• Naming starts from
the N-terminus
• Sequence is written
as:
Ala-Glu-Gly-Lys

• Sometimes the one-

letter code is used:
AEGK

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Reactivity of Amino Acids

Functional groups
Carboxyl
Amino
Sulfhydryl - Disulfide bridges
Phenolic
Hydroxyl

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 Proteins
• Essential for building, maintaining, and
replacing body tissues, as well as providing
energy.

• Polymers of amino acids.

• May be categorized based on source

– Animal protein
– Plant protein
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 Classes of Proteins
• Simple proteins
– Yield only amino acid residues on hydrolysis
• E.g. albumins (egg yolk, milk, cheese, soy)
• Globulins (cereals, hemp seeds)
• Glutenins (wheat, rye, barley)

• Conjugated proteins
– Simple proteins complexed with non-protein molecules
• E.g. nucleoproteins
• Glycoproteins
• Lipoproteins
• Phosphoproteins

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 Classes of Proteins
• Derived proteins
– Derived from simple or conjugated proteins by physical or
chemical means
• E.g. denatured proteins, peptides

• Other classification schemes based on biological

function
– Structural proteins, hormonal proteins, storage proteins,
enzymatic proteins, transport proteins, receptor proteins etc.
• Classification based on structure
– Fibrous proteins: long chain of polypeptides arranged in
bundles; insoluble in water.
– Globular proteins: roughly spherical shapes; soluble in water

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 Proteins

• Polymer of amino acids

• MW of protein > 10,000
• Subunits = 20 common amino acids
• Molecule < 50 amino acids subunit = peptide
• Dipeptide = 2 units of amino acids
• Tripeptide = 3 units of amino acids

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 Peptide bond
O R2
OH
H2N
OH
+ H2N

R1 O

O
R2
H2N OH dipeptide
NH
R1
O
peptide/amide bond

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 Structure of Protein

Four levels of protein structure

Primary
Secondary
Tertiary
Quaternary

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 Structure of Proteins
• Primary structure
– Amino acid sequence of the protein
– Amino acids joined by amide bonds to form polypeptides

• Secondary structure
– Alpha helix or beta sheet configuration
– Provides stability to the polypeptide chain

• Tertiary structure
– Three dimensional shape of the protein molecule

• Quaternary structure
– Overall spatial arrangement of protein with more than one
polypeptide chain

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 Primary Structure of Protein
Sequence of amino acids in the polypeptide chain

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 Secondary Structure
Specific geometrical arrangement of the polypeptide chain
along one axis - due to hydrogen bonding between peptide
bonds

This is to minimize hydrophobic sites of protein to water and

maximize hydrophilic sites exposure to water

Major types of secondary structure

α – helix
β - pleated sheets

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  -Helix
• Fibrous proteins are regularly
coiled to form a structure called
the α -helix
• Structures are stabilized by H-
bonding to neighboring molecules
• Right- or left- hand orientation
• Amphiphilic nature: One side of
the helical surface is hydrophobic
and the other hydrophilic
• R groups extend outward from
the backbone of the coiled
polypeptide chain

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 -pleated sheet
Polypeptide chains can also be in
an extended zigzag configuration,
the β-pleated sheet

Such chains are arranged

alongside each other to form a
structure called a pleated sheet, in
which the adjacent polypeptide
chains run in opposite directions

The adjacent chains of the pleated

sheet are held together by
hydrogen bonding

May join distance peptide chain through H-bonding

Very stable
May be parallel or anti-parallel. Anti parallel more stable.
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Secondary Structures of Protein

+
α-helix

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 Tertiary Structure
The three-dimensional structure of globular proteins, in which the
polypeptide chain is tightly folded and packed into a compact spherical
form. The structure is stabilized by:
1. Hydrophobic attraction - the close association/attraction of
hydrocarbon side-chains
2. Ionic bonds - between positively charged groups and
negatively charged groups
3. Hydrogen bonds
4. Disulfide bonds
Thus, a protein has size and shape as well as a unique arrangement through
hydrogen, ionic, hydrophobic and disulfide bonds

Due to spontaneous folding of protein to minimize exposure of hydrophobic

amino acid side chains and maximize hydrophilic chains to water
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Tertiary Structure of Protein

Hydrophobic
interaction

Protein with high hydrophobic sites – globular

Protein with high hydrophilic sites – rod
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 Quaternary Structure

Dimer

hydrophobic sites

Trimer Tetramer

Only proteins with more than one

chain have quaternary structure
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 Levels of protein structure: Summary

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 Protein classification based on solubility
Albumins: soluble in neutral salt free water
Globulins: soluble in neutral salt solutions
Glutelins: soluble in dilute acid or base solutions
Prolamins: soluble in 50-90 % ethanol
Scleroproteins: Insoluble in water. Structural proteins
Histones: Basic proteins, high content in lysine and
arginine. Soluble in water
Protamines: Strongly basic, low MW proteins

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 Protein classification based on
functionality
Enzymes
Structural
Contractile (myosin, actin)
Hormones (insulin, growth hormone)
Transfer proteins
Antibodies (immunoglobulins)
Storage proteins (egg albumen, seed proteins)
Protective proteins (toxins, allergens)
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 Protein Denaturation
• Major changes in secondary, tertiary or quaternary structure of
protein leading to a change in 3D spatial arrangement of the
molecule.
• Denaturation is regarded the loss of secondary, tertiary or
quaternary structures. Loss of ordered structure.
• In denaturation there is no peptide bond cleavage
• Caused by:
– pH change
– Increase in temperature
– Salts
– Agitation
– Solvent composition

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 Protein Denaturation
• Results of denaturation:
– Changes of physical
properties e.g.
coagulation, gelation.
– Inactivation e.g. loss of
enzymic properties
– Improvement of
digestibility/bioavailability

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 Temperature Change
• Increase of temperature causes increased vibration of
molecules.
• Strong vibrations breaks intramolecular interactions (does
not break bonds) of protein causing denaturation.
• Protein molecules starts to interact with each other
causing coagulation, e.g. egg white.
• Irreversible if interactions after denaturation cannot be
removed.
• Amino acid composition affects thermal stability. More
hydrophobic aa, more stable protein
• Water facilitates thermal denaturation. Dry powders are
stable
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 pH and denaturation
Proteins are most stable at their isoelectric point
Proteins unfold at extreme pH values.
Unfolding is greater at extreme alkaline pH values
than at extreme acid.
pH-induced denaturation is mostly reversible if there
is no peptide bond cleavage

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 Organic Solvents - Solutes

Affect mostly the stability of hydrophobic

interactions.
Hydrophobic interactions are weakened
Urea, guanidine hydrochloride: affect the
strength of hydrogen bonding
It can be reversible by removing the denaturant

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 Salts

• Salts that cause denaturation

• Competes with protein for interactions with
water molecules.
• Protein structure is influenced more by anions
than by cations
• Salting out = Protein precipitation
• Salting in = Protein solubilization

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 Mechanical Shear

• Agitation such as beating/whipping, shaking

and kneading
• Destabilize protein structure leading to the
stretching of protein molecule and denaturation
• Denaturation due to whipping is important in
foam formation.

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 Hydrolysis
Hydrolysis involves breaking peptide bonds yielding smaller
peptide chains or amino acids. Is achieved by acid or proteolytic
enzymes

Amino acids

Hydrolysis

Protein
Peptides

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Functional properties of proteins

Water absorption and binding

Viscosity
Coagulation/Gelation
Emulsification
Flavour binding
Foaming
Enzymic activity

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 Functional properties of proteins
Are influenced by
Size, shape of protein
Amino acid composition and sequence
Net charge and distribution of charges
Hydrophobicity / hydrophilicity ratio
Secondary, tertiary and quaternary structures
pH, temperature, ionic strength

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 Protein gelation
Proteins form two types of gels: opaque and translucent

Opaque Yogurt

Aggregation

Heat Cooling
Native state Denatured Translucent
Gelatin gel

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 Emulsification
Emulsion is a dispersion of one liquid in a second, largely
immiscible liquid. In foods the liquids are oil and an aqueous
solution.
μm

Water

Oil

Oil-in-water emulsion Water-in-oil emulsion

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Proteins create o/w emulsions and foams.
They are arranged at the oil-water interface.

oil

water

Globular protein
Surfactant
Random coil protein

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Proteins form a thin film surrounding the
droplet or gaseous phase

Protein film

Emulsion Foam
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