The University of Zambia

C 2112
Fundamentals of Biochemistry
Protein Biochemistry
Mr. Danny Banda

2022
 Definition
• any of a class of nitrogenous organic
compounds which have large molecules
composed of one or more long chains of
amino acids
• Contain a an array of amino acids- polymers
of amino acids .
are very important biological molecules that
play crucial roles in virtually all biological
processes
 BIOLOGICAL FUNCTIONS OF PROTEINS

1. Catalytic function:
Nearly all chemical reactions in biological systems are catalyzed by specific
enzymes.

2. Transport and storage:

For example;
➢ Hemoglobin transports oxygen in erythrocytes
➢ Myoglobin carries & stores oxygen in muscle.
➢ Albumin transports free fatty acids in blood.
➢ Transferrin transports iron in blood.

3. Coordinated motion:Actin and myosin are contractile proteins in

muscle.
BIOLOGICAL FUNCTIONS OF PROTEINS (cont.)

4. Structural and Mechanical support:

For Example; collagen, a fibrous protein in skin and bone.

5. Defense function:
For Example Clotting factors prevent loss of blood.
Immunoglobulins protects against infections.

6. Generation and transmission of nerve impulses:

For example, rhodopsin is the photoreceptor protein in retinal rod
cells.

7. Control of growth and differentiation:

For Example
➢ growth factor proteins.
➢ hormones such as insulin and thyroid-stimulating hormone.
 General structure of protein
• All biologically known protein are polymers of a
set of twenty known amino acids.

• All biologically known amino acids are α-L amino

acids.
 AMINO ACIDS

are the basic building blocks of

PROTEINS
 Each AMINO ACID
has
An amino group,
A carboxyl group,
A hydrogen atom and
a specific side chain (R group)
Bonded to
the α-carbon atom
• This side chain is unique for every amino
acid.
 Classification of amino acids

• Side chain reaction classification

• Biological classification
• Metabolic classification
 Side chain classification
1- Hydrophobic (non- 2- Hydrophilic (polar) R-group
polar) R-group)

Glycine (Gly-G) Uncharged Positively Negatively

Alanine (Ala-A) Aspargine charged charged
Valine (Val-V) (Asn – N) Lysine Aspartic acid
Leucine (Leu-L) Glutamine (Lys – K ) (Asp – D)
(Gln – Q ) Arginine Glutamic acid
Isoleucine (Ile– I) Serine
Methionine (Met– M) (Arg – R) (Glu – E )
(Ser – S)
Proline (Pro– P) Threonine Histidine
Phenylalanine (Phe– F) (Thr – T ) (His – H )
Tryptophan (Trp–W) Tyrosine
(Tyr – Y)
Cysteine
(Cys – C )
 Non polar (hydrophobic) amino acids

• Side chains of non polar (hydrophobic) a.a. can not participate

in hydrogen or ionic bonds, but they form hydrophobic
interactions.
• In aqueous environment, non polar a.a. tend to be present in
the interior of proteins.
• They include:
• Amino acids with aliphatic R group (glycine, alanine,
• Amino acids with aliphatic branched R group (valine, leucine
and isoleucine).
• Amino acids with aromatic R group (phenylalanine,
tryptophan)
• Amino acids with sulfur group (methionine) and
• Imino acid (proline).
 Polar (hydrophilic) amino acids
• Side chains of polar (hydrophilic) a.a. can participate in
hydrogen or ionic bonds.
• Therefore, in aqueous environment polar a.a. tend to be
present on the surface of proteins.
• Polar (hydrophilic) amino acids are classified into:
- Polar charged amino acids include
• acidic (Negatively charged): (aspartic and glutamic a.)
and
• basic (Positively charged group): (arginine, lysine,
histidine) amino acids.
– Polar non charged amino acids include:
• Amino acids with OH group (serine, threonine,
tyrosine)
• Amino acids with SH group (cysteine)
• Amino acids with amide group (glutamine, asparagines)
 Biological classification
1- Non essential amino acids: These are
Glycine, Alanine, Serine, Tyrosine, Cysteine,
Arginine, Asparagine, Aspartic, Glutamic
acid , Glutamine and Proline.
2- Essential amino acids:
They include Valine, Leucine, Isoleucine,
Threonine, Methionine,, Lysine, Histidine,
Phenylalanine and Tryptophan.
 Metabolic classification
– Glucogenic amino acids: These amino acids could give
intermediates which finally can give glucose.
– Purely ketogenic amino acids: They include Leucine &
Lysine. They give ketone bodies after its degradation in
the body, but no glucose.
– Mixed amino acids: These are amino acids that can give
both ketone bodies and glucose intermediates. These are
Phenylalanine, Tyrosine, Tryptophan, Isoleucine and
Lysine.
* The rest of amino acids are all purely glucogenic.
 Mirror image forms of amino acids

• Tetrahedral alpha-carbon atom,

• alpha amino acids acids are chiral exist in one
or two mirror image forms called the L
isomer and D isomer (orientation of the NH3
group) determines the isomer, L isomer-left
side, D isomer right hand side)
• Only L isomers are constituents of proteins
 Ionic properties of amino acids

• Amino acids have amphoteric properties .

• They contain acidic (COOH) and Basic (NH2) groups.
• The amino acids are usually ionized at physiological pH
.
• In acidic medium ; amino acid is positively charged (
behave as a base : proton acceptor )
• In alkaline medium ; the carboxylic acid is negatively
charged ( behave as an acid: Proton donor)
 Isoelectric point or “pI”
• At certain pH “ specific for each amino acid “ the amino
acid can exist in the dipolar from : fully ionized but with no
net electric charge .
• The characteristic pH at which the net electric charge is zero
is called the Isoelectric point or “pI”.
• The amino acid at the isoelectric pI is called
“ Zwitter Ion “ and is electrically neutral not migrating in an
electric field
• “Zwitter in German means hybrid or hermaphrodite”.
 Isoelectric point or “pI”
• At certain pH
“specific for
each amino
acid” the
amino acid
can exist in the
dipolar from :
fully ionized
but with no net
electric
charge.
Zwitter ion
 Polymerization of amino acids
• Amino acids polymerize by forming peptide bonds joining amino
acid monomer units in a dehydration synthesis reaction.
• The macromolecule formed is called a polypeptide/amino acid
residues/protein
 Polypeptide
• A series of a.a joined by peptide bonds forms a
polypeptide chain
• Peptide bond is resistant to corrosion
• Each a.a in a polypeptide chain is called a residue
• Has polarity-two ends that are different; amino
group at one end, carboxyl at other end
• Amino end-beginning of a polypeptide
• Sequence of a.a is written starting with the
amino-terminal residue
• Tyr-Gly-Phe-Leu, tyrosine is the amino terminal,
Leucine carboxyl terminal
Polypeptide contains a regularly repeating part called
main chain or backbone
Rich in hydrogen bonding potential
 Titration of amino acids
❑ One important piece of information derived from the titration curve of
an amino acid is the relationship between its net electric charge and
the pH of the solution.
❑ At pH 5.97, the point of inflection between the two stages in its
titration curve, glycine is present predominantly as its dipolar form,
fully ionized but with no net electric charge
❑ The characteristic pH at which the net electric charge is zero is called
the isoelectric point or isoelectric pH, designated pI.
❑ For glycine, which has no ionizable group in its side chain, the
isoelectric point is simply the arithmetic mean of the two pKa values:
 Amino Acids Differ in Their Acid-Base
Properties
❑The shared properties of many amino acids permit some
simplifying generalizations about their acid-base behaviors.
❑First, all amino acids with a single -amino group, a single -
carboxyl group, and an R group that does not ionize have
titration curves resembling that of glycine.
❑Second, amino acids with an ionizable R group have more
complex titration curves, with three stages corresponding to
the three possible ionization steps; thus they have three pKa
values.
❑The additional stage for the titration of the ionizable R
group merges to some extent with the other two
Titration of an amino acids with ionisable side
chain
 Protein Structure
• Proteins are the most abundant and
important organic molecules
• Basic elements:
– carbon (C), hydrogen (H), oxygen (O), and
nitrogen (N)
• Basic building blocks:
– 20 amino acids
 Protein Structure – 4 levels
❑ Primary structure: the exact sequence of the different
α-amino acids along the protein chain
➢amino acid sequence determined by gene (DNA)
❑Primary structure determines the 3-D structure
of a protein, and the 3D structure determines
the protein’s function
❑ slight change in amino acid sequence can affect
protein’s structure & it’s function
• even just one amino acid change can make all the
difference!
Sickle cell anaemia
 Secondary structure
• “Local folding”
– folding along short
sections of polypeptide
• interaction between
adjacent amino acids
• H bonds between
backbones (O:H)
 -helix
 -pleated sheet
• Fibrous proteins – only
have secondary structure
– Keratin
– Silk
Secondary (2°) structure
 Alpha helix
❑ Rod-like structure with a tightly coiled backbone
❑ Stabilised by H-bonds between NH and CO group of the main
chain
❑ CO group forms H bonds with NH group of a.a situated four
residues ahead in the sequence
❑ Has a rise of 1.5A, also called translation
❑ There are 3.6 a.a. residues per turn of the helix
❑ Left or right handed helix, right handed helices are
energetically more favorable due to fewer steric clashes btwn
side chains & backbone
❑ All helices in proteins are right handed
 Beta sheet
❑A polypeptide chain, called a β- strand, has almost fully
extended rather than being tightly coiled as in the α-
helix. A range of extended structures are sterically
allowed .
❑The distance between adjacent amino acids along a β
strand is approximately 3.5 Å, in contrast with α
distance of 1.5 Å along an α helix.
❑The side chains of adjacent amino acids point in
opposite directions .
Parallel / Anti-parallel stands
 Tertiary (3°) structure
 “Whole molecule folding”
 created when the secondary structure fold and form
bonds to stabilize the structure into a unique shape
 determined by interactions
between R groups
 Hydrophobic interactions
 anchored by disulfide bridges
 Ionic Bonds between R groups
 Hydrogen bonds between backbones
 Van der Waals Force
 Globular (spherical) proteins – have tertiary structure
 enzymes
 Tertiary structure
❑Refers to the 3 D structure formed from the polypeptide
chains.
❑Tertiary structures of water-soluble proteins have
common features
1. An interior formed by a.a with hydrophobic side chains
2. A surface formed largely by hydrophilic a.a that interact with the aqueous
environment
Such interactions are important for the formation of cell membranes
❑ Many a helices and b strands are amphipathic; that is, the a
❑ helix or b strand has a hydrophobic face, which points into the
protein interior, and a more polar face, which points into solution.
❑ Each polypeptide is called a subunit
➢ It involves twisting and folding
of the polypeptide chain
caused by hydrophobic and
hydrophilic interactions
between the side chains of
the amino acids.

➢ The nonpolar amino side

chains end up in the interior
of the protein away from the
aqueous environment.

➢ The polar side chains appear

on the surface of the protein
since they are attracted to the
aqueous surroundings.
 Quaternary structure
• The quaternary structure is the interaction of two or more
polypeptide chains to form a biologically active protein.
• Subunits are held by noncovalent bonds
– Hemoglobin – 4 polypeptides
– Collagen – 3 polypeptides

collagen =
skin & tendons
• Hemoglobin, an oxygen transport protein, is an
example of a protein with a quaternary structure.
It consists of four polypeptide chains or subunits.
It has two identical alpha subunits and two identical
beta subunits.
All four subunits must be present for the protein to
function as an oxygen carrier.
Levels of Protein structure
 Shape and Function
• Protein function is based on shape
• Shape is based on sequence of amino acids
• Denaturation:
– loss of shape and function (due to heat, pH
change or other factors)
 Protein denaturation
❑ Is a process that disrupts secondary, tertiary, and quaternary structures.
❑ The primary structure is not destroyed during denaturation.
❑ Protein becomes insoluble and looses biological activity
❑ Denaturation can be caused by
-strong acids or bases
-concentrated inorganic salts
-an organic solvent (alcohol or chloroform)
-radiation or
heat
❑ The process of denaturation is used as an antidote for lead or mercury poisoning.
❑ Egg whites can be given to an individual who has ingested a heavy metal. Egg
whites are denaturated by the heavy metals and a precipitate is formed.
❑ Vomiting is induced to eliminate the metal-protein precipitate.
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