1.

4 Protein
At the end of the lesson, student should be able to
explain:
a. Describe the basic structure of amino acid
b. State how amino acids are grouped
c. Describe primary(10), secondary(20), tertiary(30) and
quaternary(40 ) levels and types of bonds involved
d. Describe the effect of pH and temperature on the
structure of protein
e. Explain the formation and breakdown of dipeptide
f. Classify proteins according to their structure &
compoosition
 1.4 Protein
• Proteins contain the elements carbon,
hydrogen, oxygen and nitrogen
• Many proteins contain sulfur and phosphorus
• Proteins are built up from more than one
amino acids.
• Amino acid is a monomer of protein.
Learning Outcomes :
1.4 (a) Describe the basic structure of amino acids

BASIC STRUCTURE OF AMINO ACIDS

Amino acids consist of 4 components attached to a central
carbon
These components include:
a. a hydrogen atom
b. a carboxyl group
c. an amino group
d. a variable R group (or side chain).
R

amino group H2N C COOH carboxyl group

H
Learning Outcomes :
Learning Outcomes :
1.4 (a) Describe the basic structure of amino acids
1.4 (a) Describe the basic structure of amino acids

BASIC STRUCTURE OF AMINO ACIDS

2 functional groups:
i. COOH (carboxyl group) : acidic
ii. NH2 (amino group) : basic
Amino acids are amphoteric; have both acidic &
basic properties
R

amino group H2N C COOH carboxyl group

H
 Group of Amino acid

1. Non- polar Amino acid

2. Polar Amino acid

3. Basic Amino acid

4. Acidic Amino acid

** Amino acids are group according to the
properties of their side chain
 1. Non- polar Amino acid
• Amino acid that have hydrocarbon side chain
• Hydrophobic / insoluble in water and non-reactive
 2. Polar Amino acid
• Hydrophilic, enable hydrogen bonding
between polypeptide chain
• Increases the solubility of the protein
 3. Basic Amino acid
 Generally positive in charge
 The R group contains additional amino group
 4. Acidic Amino acid
 Side chain generally negative in charge
 The R group contains additonal carboxyl group
Fig. 5-17c

Basic and acidic amino acid

Electrically
charged
Acidic Basic

Aspartic acid Glutamic acid Lysine Arginine Histidine

(Asp ) (Glu ) (Lys ) (Arg) (His)
 Structure Levels of Protein
• There are four structure levels of protein

1. Primary structure (10)

2. Secondary structure (20)

3. Tertiary Structure (30)

4. Quaternary structure (40)

 Fig. 5-21

Structure Levels of Protein

Primary Secondary Tertiary Quaternary

Structure Structure Structure Structure

pleated sheet
+H N
3 Examples of
Amino
amino acid
end
subunits
 helix

α- helix
 1. Primary structure
Primary Structure
 Linear polypeptide is a
linear sequence of amino H3 N
+

acids in a polypeptide Amino end

chain.
 Amino acid held together
by peptide bonds Amino acid
subunits
 Examples : Insulin,
glucagon and lysozyme
 2. Secondary structure

 The secondary structure

refers to the way a
particular polypeptide
chain is coiled either:
 α-helix
 β-pleated sheet
 This shape forms as a
result of hydrogen
bonding
 α-helix

A delicate coil held

together by
hydrogen bonding
between every
fourth amino acid
E.g. :
α-keratin
(structural protein
of hair)
 β- pleated sheet
Two or more regions of
the polypeptide chain
lying side by side
(parallel) and connected
by hydrogen bonds.
β- pleated sheet has high
resistance to stretching.
E.g. :many globular
proteins, some fibrous
proteins
Fig. 5-21d

β- pleated sheet

Abdominal glands of the

spider secrete silk fibers
made of a structural protein
containing  pleated sheets.
The radiating strands, made
of dry silk fibers, maintain
the shape of the web.

The spiral strands (capture

strands) are elastic, stretching
in response to wind, rain,
and the touch of insects.
Fig. 5-21c

Secondary Structure
 pleated sheet

Examples of
amino acid
subunits

 helix
 3. Tertiary Structure

 Due to the bending and twisting the

polypeptide helix into a compact structure.
 It is folded into a globular shape
 This structure is maintained by:
 hydrogen bond
 ionic bond
 disulphide bridge
 hydrophobic interactions & van der Waal
interaction/forces
Example: Globular proteins include enzymes, myoglobin
 3. Tertiary Structure

1. Hydrogen bond Hydrophobic

interactions and
bond between polar van der Waals
interactions
side chains
Polypeptide
backbone
2. Ionic bond Hydrogen
bond
bond between
positively and
negatively charged Disulfide bridge

side chains
Ionic bond
 3. Tertiary Structure

Hydrophobic
3. Disulphide bridge interactions and
van der Waals
covalent bond that form interactions
when 2 amino acids with Polypeptide
sulfhydryl groups (-SH) on backbone
their side chains Hydrogen
bond

4. Hydrophobic interactions
Disulfide bridge
& van der Waals forces
Nonpolar R group with
another nonpolar R group
Ionic bond
Fig. 5-21f
Hydrophobic
interactions and
van der Waals
interactions

Polypeptide
backbone
Hydrogen
bond

Disulfide bridge

Ionic bond
FIGURE:
4 types of bond that maintained
the tertiary structure of protein
Tertiary Structure
 4. Quaternary structure

 Consists of more than one polypeptide chains

to form a single functional molecule
 Held together by hydrophobic interactions,
hydrogen bonds, ionic bonds and disulfide
bridges
 Associated with non-protein/prosthetic
groups into a large complex protein molecule.
 4. Quaternary structure

Example: Hemoglobin
that carries oxygen
contains four globular
polypeptide chains
Two alpha (α) two beta
(β) polypeptide chains
 Each containing a haem
group with an iron atom
that can bind with a
single oxygen molecule.
Fig. 5-21g

Polypeptide  Chains
chain

Iron
Heme

 Chains
Hemoglobin
Collagen
 Factor affecting the structure of protein

• Structure of protein maintain by hydrogen

bond ( 2˚ , 3˚ and 4˚); ionic bond, hydrophobic
interaction, disulfide bridge and van de waals
interaction (3˚and 4˚)
• Breakage the bond causes loss of specific
three-dimensional shape of a protein
molecule .
 Factor affecting the structure of protein
• The change may be temporary or permanent
• But amino acid sequence remains unaffected
• Change shape of protein – denaturation
• Molecule unfolds and can no longer perform its
normal biological function
• Factor effecting the structure of the protein:
1. pH
2. temperature
 Factor affecting the structure of protein
1) pH
- extreme pH causes the bonds disrupted and
protein lost its conformation.

-In many cases the globular proteins go

back (revert) to more fibrous form
 Factor affecting the structure of protein
2) Temperature
• higher temperature supply
kinetic energy to protein
causing its atom vibrate
• the weak hydrogen and ionic
bonds is disturb.
• protein conformation is
changed.
• coagulation of protein occurs.
• denatured proteins are
insoluble and solidify.
 Factor affecting the structure of protein
• Sometimes protein will spontaneously refold
into its original structure and function after
denaturation.
• This is called renaturation
 Properties of enzymes related to
protein structure
• Enzymes are globular protein having
three dimensional shape held by:
i) covalent bonds,
ii) hydrogen bonds,
iii) van der Waal forces and hydrophobic
attractions
• When the bonds are broken, the
parts of a molecule have been
disturbed.
• Altering the shape of the active site.
 Formation of dipeptide
• Two amino acids can be joined together
through condensation process.
• In condensation, a hydrogen atom (-H) from
amino group and (-OH) from carboxyl group
are removed to release a molecule of water.
Peptide bond

condensation
+ H2O

Amino acid 1 Amino acid 2 Dipeptide Water

 Formation of dipeptide
 Two amino acids that linked together by
peptide bond is known as dipeptide.
 A peptide bond is formed between carbon
atom in carboxyl group of one amino acid
molecule with nitrogen atom in amino
group of another amino acids
 More than two amino acids that are linked
together is known as polypeptide
 Breakdown of dipeptide
• Protein are broken down by hydrolysis
process.

+ H2O hydrolysis

Amino acid 1 Amino acid 2

Dipeptide Water
 CHAPTER 1: MOLCULES 0F LIFE 1.4: Proteins

Formation & Breakdown of DIPEPTIDE

Condensation
reaction

Hydrolysis
reaction

LEARNING OUTCOMES: 1.4c) Explain the formation and breakdown of dipeptide.

 Classification of proteins according to
their structure
According to structure, protein are classified into:

1. Fibrous Protein

2. Globular Protein

3. Conjugated Protein
 Properties of fibrous protein
i. Fibrous protein
1. Long parallel polypeptide chains.
2. Protein structural level is secondary
structure.
3. Maintain by hydrogen bond only.
4. Stable structure
5. Insoluble in water
6. Eg: Keratin, actin, myosin, collagen, silk
 Properties of globular protein
• Globular proteins
1.Polypeptide chains folded or spherical shape
2.Protein structural level is tertiary or
quaternary structure
3.Maintain by ionic bond, disulfide bridge,
hydrophobic interaction and van de Waals
interaction
4. Relatively unstable structure
5. Soluble in water(can form colloid)
 1. Conjugated Protein

• Protein joined with non protein component

known as prosthetic group.
• Conjugated protein are further classified into
many group based on the properties of
different prosthetic group.
• E.g. : Nucleoprotein, mucin, casein,
haemoglobin, lipoprotein
 1. Conjugated Protein
Name of Prosthetic Location
conjugated group
protein
Haemoglobin  Haem group  erythrocytes in
(contains iron) the blood
 bind with oxygen

Mucin (Glycoprotein )  Carbohydrate  component of

saliva
 1. Conjugated Protein

Name of Prosthetic group Location

conjugated
protein
Nucleoprotein • Nucleic acid • Chromosomes
• Ribosomes
Myoglobin  Haem group  Muscles
(contains iron)

Lipoprotein  lipid  Membrane

structure
 Transport lipid in
blood
 Classification of proteins according to their function

TYPES OF PROTEIN FUNCTION EXAMPLE

Defense protein Immunity Antibody
Structural protein Support Collagen
Hormonal protein Coordination Insulin
Storage protein Storage of amino acids Ovalbumin
Transport protein Transport of respiratory Haemoglobin
gases
Contractile protein Movement Actin
Myosin
Enzymatic protein Catalyze chemical Lipase
reaction protease
Let's answer this questions..
1.Determine the structure Y and Z
2.Name the type of bonds V and W
•
•
 QUESTIONS
• 1. Amino acids can be grouped by the

• A. number of carbon-carbon double bonds

• B. characteristics of their side chains
• C. number of peptide bonds they can form
• D. number of disulphide bonds they can form
• 2. The primary structure of a protein is determined
by its
• A. sequence of amino acids
• B. branching
• C. three dimensional structure
• D. number of polypeptide chain

• 3. Which of the following bonds is principally

concerned in maintaining the α-helix shape of
secondary protein structure?
• A. disulphide bonds B. ester bonds
• C. hydrogen bonds D. peptide bonds
• 4. When a protein loses its three-dimensional structure
and becomes non-functional, it is said to be
• A. hydrolysed B. denatured
• C. reversed D. coiled
• 5. Which of the following occurs when a peptide
bond is formed?
• A. a disulphide linkage is formed
• B. a hydrophobic bond is formed
• C. a water molecule is formed
• D. a dipeptide is formed
 Answers
• 1. B
• 2. A
• 3. C
• 4. B
• 5. C