LECTURE 6:

PROTEINS

Protein Outline
Proteins (structure and function)
Major roles in physiology & structural
frameworks
Amino acid structure
Levels of structural organization:
(primary, secondary, tertiary,
quaternary)
Properties (relate to structure)
Major classes of proteins
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Objectives
1. Describe the structure of amino acids
2. Outline how proteins are formed by

peptide bonds.
3. Describe how proteins are organized
at the primary, secondary, tertiary,
quaternary levels.
4. State the functions of proteins
5. Classify proteins according to
structure/solubility, composition,
function.

Proteins
More than 50% of the dry mass of an

organism consists of proteins.

Macromolecules with numerous and very
important functions
Regulation of movement of

substances into and out of cells

(channel & carrier proteins).
Regulation of gene expression
Structural roles
Metabolic roles
Diet

Proteins
Contains elements C, H, O, N and

sometimes S.
Consist of monomers called amino
acids.
Has a very high molecular mass
Each has a unique sequence of amino
acids, giving it unique properties.
All are made from combinations of 20
amino acids. (the same 20 amino acids, in
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different arrangements, are present in all

living things).

Amino acids - Basic

structure

a carbon atom (asymmetric) is bonded to

a carboxyl group (COOH)
an amino group (HNH)
a hydrogen atom and
a variable group (R)

Amino acids
Type of R group determines the property

of the amino acid

Property of the amino acid determines the
final shape and function of the protein. For
e.g.,
Extra NH3 groups in the R group would give

the protein basic properties while more

COOH groups would make it acidic
More C-H groups would mean a non-polar
amino acid while more OH groups would
make it polar.
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Amino acids
(except proline)
have the formula
HHN-CHR-COOH

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http://www.cem.msu.edu/~cem252/sp97/ch24/ch24aa.html

Protein Formation
Proteins are made by the joining of

amino acids by condensation

(removal of a molecule of water).
Amino acids are joined by a

peptide bond (covalent) between

the carboxyl group of one amino
acid and the amino group of the
neighbouring one.
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Protein Formation
Two amino acids joined by a peptide bond

form a dipeptide
H2O is lost.
OH from the carboxyl end of one amino
acid and H from the amino end of another.
Dehydration Synthesis/ Condensation
Reaction.

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Protein Formation

Amino acids are bipolar

COOH donates a proton to form COO NH2 accepts a proton to form NH3+
Side chains (R groups) may be
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polar (and hydrophilic) or nonpolar

(and hydrophobic)

Protein Formation
Continued condensation leads to the
addition of further amino acids resulting
in the formation of a long chain called a
polypeptide.
OH (from COOH) + H (from NH2)=H2O
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Protein Formation
Peptide chains of any length have definite

direction or polarity because of the

difference in the orientation of their
component amino acids.
There is always a free amino group, not
joined to another amino acid, at one end
and at another end a free carboxylic
group.
The amino acid with the free amino group
is known as the N-terminal (amino) and
the amino acid with the free carboxylic
group, the C- terminal (carboxy)
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Levels of structural
organization: The three
dimensional structure of
proteins
Polypeptide molecules

that
make up the proteins are
folded into characteristic
three-dimensional
configurations determined by
the chemical properties of
the constituent amino acids.

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Three dimensional structure

of proteins
The structure may have four
levels of organization:
Primary,
Secondary,
Tertiary &
Quaternary (where proteins

consists of 2 or more polypeptide

chains arranged together).
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Primary structure
The specific linear sequence of

amino acids in a polypeptide.

The chain of amino acids of
which the peptides are
composed.
Plus any disulphide bridges
formed by the presence of more
than one cysteine molecule
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Primary structure
Different proteins have different

sequences which determine their

function.
The sequence is dependent on
the genetic code in the DNA of
the cell.
The sequence is named from the
amino to the carboxylic end
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Secondary structure
The organization of portions of the

polypeptide chain based on how

amino acids react with each other.
Three major types of secondary
structure are recognized:

alpha helix,
beta-pleated sheet and
a random coil.
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Secondary structure - Alpha

helix
Formed by some polypeptide
chains or parts of the chain.
Formed when hydrogen
bonds form between the
amino group in one peptide
bond and the carbonyl (C0)
group (of the COOH) of another
close by peptide bond.
E.g., found in alpha keratin;
the major protein of wool, hair,
nails, feathers, horns.
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Secondary structure - Beta

pleated sheet

Formed when two or more

sections of the polypeptide

chain lie side by side, forming an
accordion-like sheet that is held
together by hydrogen bonds.
Fibroin (major protein in silk) is
composed largely of pleated
sheets stacked on each another.
Unlike the fibres of wool (alpha

helix), silk cannot be stretched

because the polypeptide chains
are already extended.

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Secondary structure - Random

coil
Any portion of a

polypeptide chain not

organized into an alpha
helix or a beta sheet is
said to be a random coil.

E.g., the sites in the

myoglobin where the

polypeptide makes a sharp
turn are regions of random
coil.

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Tertiary structure
Further folding and coiling of the

secondary structure of the polypeptide

results in the final compact 3D shape.
Strongly influenced by the interactions
of R groups in different parts of the
chain.
Formed by hydrogen, ionic,
disulphide, and covalent bonds or by
hydrophobic interactions between R
groups.
E.g., myoglobin, enzymes.
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Tertiary Interactions
Hydrogen bonds occurs between CO

(of carboxyl) and NH (of amino group).

Ionic bonds formed between R groups
with positive and negative charges.
Disulphide bonds links the S atoms of
the sulphydryl group of two cysteine
amino acids.
Hydrophobic interactions protein folds
in such a way as to shield hydrophobic
groups while exposing hydrophilic groups
to aqueous surroundings.
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Tertiary Interactions

The secondary,

tertiary and
quaternary
structures are not
random, but highly
specific, and
precisely dictated by
the primary structure
that is by the
sequence of amino
acids in the chain.

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Quaternary structure
Interaction of

more than one

polypeptide chain
E.g., haemoglobin consists

of four polypeptide chains

(two alpha and two beta).

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10

20

40
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Biuret test
biuret test" is a generic term for the testing

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of proteins by using copper (II) sulfate

solution in an alkaline environment. Thus,
the process of testing for proteins in a
solution by first adding a small amount of
sodium hydroxide, and then adding copper
(II) sulfate drop by drop, is also known as a
biuret test.
These copper ions reflect off closely
clustered amide groups of proteins casting
a violet color to a solution with proteins.
This violet color is a positive reaction in a
Biuret Test.

Properties of proteins
Anything that affects the specific 3D

structure of a protein will affect its

properties.
Disruption of structure is called
denaturation
The protein unfolds, losing its

tertiary and secondary structure.

Primary structure is unaffected.
Under suitable conditions, reforming of

the structure can occur (renaturation).

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Factors Affecting Protein

Structure
Heat
Destroys the ionic and

hydrogen bonds by causing the

atoms to vibrate more.
In extreme cases coagulation
occurs e.g., boiling an egg.

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Factors Affecting Protein

Structure
Acids and alkali
Disrupt the ionic and H bonds.
Above pH 7 almost all H bonds in an

alpha helix are broken. (Additional H+

ions will combine with COO- group to
form COOH thus breaking the ionic
bonds)
Inorganic chemicals e.g., Hg and Ag
combine with COOH.
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Factors Affecting Protein

Structure

Organic solvents and detergents

Alcohols disrupt hydrophilic

hydrophobic interactions and form

bonds with hydrophobic groups. H
bonds are then disrupted.
This is the principle behind the
use of alcohol as a disinfectant
they denature bacterial proteins.
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Protein Classification
1. Structure and solubility
2. Composition
3. Function

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Classification of proteins
Classification according to
structure and solubility.

1.

a. Fibrous proteins e.g., keratin

b. Globular protein e.g., enzymes,
albumins
c. Intermediate Protein e.g.,
fibrinogen
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Structure/Solubility
Classification

Fibrous proteins e.g., keratin

Secondary structure important; consist
of long parallel polypeptide chains crosslinked at many parts along their length.
Insoluble in water
Structural function e.g., collagen
(tendon, bone, connective tissue);
myosin (muscle); silk; keratin (hair,
nails).
a.

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Structure/Solubility
Classification
b.
Globular proteins e.g., enzymes, albumins
Tertiary structure important; polypeptide

chains tightly folded to form spherical shape.

Readily soluble, e.g. globulin in blood.
Readily forms colloidal suspensions; and enter
various structures in the body in this form.
E.g. collagen and elastin which form
connective tissue.
Metabolic function, e.g., enzymes, antibodies,
some hormones e.g., insulin
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Structure/Solubility
Classification

c. Intermediate e.g., fibrinogen

Fibrous but soluble; when

blood clots it forms

insoluble fibrin.

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Classification of proteins
II Classification according to
composition
a. simple
b. conjugated
a. Simple proteins e.g., albumins,
globulins
Have only amino acids in their structure
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Composition Classification
b. Conjugated proteins e.g.,
glycoprotein's, lipoproteins (protein
conjugated to a lipid)
Consists of more than just polymers of

amino acids.
Have non-protein material tightly
bound (prosthetic group)
Sugars, lipids, etc may be bound to a
protein to form a conjugated protein.
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Classification of proteins by
composition - conjugated proteins

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Conjugated
protein

Prosthetic
Group

Example

Glycoprotein

Carbohydrate

Cell membranes

Lipoprotein

Lipid

Cell membranes

Metalloprotein

Metal e.g., Fe

Haemoglobin

Nucleoprotein

Nucleic acid

Chromosomes

Phosphoprotein Phosphoric acid

Casein of milk

Chromoprotein

Cytochrome

Pigment

Classification of proteins
III. Classified according to function
a. Structural

component of bone, cartilage, feathers, fur,

and hair
component of all biological membranes and
chromosomes e.g., Collagen, keratin,

b. Catalysis

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majority of enzymes are proteins. They play

a unique role in determining the pattern of
all chemical transformations and thus of all
growth and metabolism.

Function Classification

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c.
Coordination

Several hormones are proteins;

others are transported by proteins.
Physical activities of living systems
are regulated and coordinated by
hormones.

d. Respiratory
pigments

Haemoglobin, myoglobin

e. Transport

Haemoglobin

f. Growth

Hormones

Classification of proteins by
function
g. Storage

Casein

h. Protective

Immunoglobins - highly specific

protein molecules that chemically
recognize and combine with
potentially dangerous foreign
invaders of the body like bacteria
and viruses.

i. Toxins

Snake venom

j. Nutrition

Digestive enzymes

K. Reproduction Hormones
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