Macromolecular analysis

Hierarch in protein structure

1. Primary structure: amino acid sequence

2. Secondary structure: local arrangement of peptide backbone

3. Tertiary structure: three dimensional arrangement of all atoms, peptide backbone

and amino acid side chains

4. Quaternary structure: spatial arrangement of subunits

PROTEINS

Each protein is made up of…

THINK: “CHONS”
 Amino acids are the basic structural unit of all proteins. A
'free' amino acid (a single amino acid) always has:
• an amino group -NH2,
• a carboxyl group -COOH
• a hydrogen -H
• a chemical group or side chain -"R".
These are all joined to a central carbon atom, the alpha -
carbon.

 Theamino group[ -NH2] is basic while thecarboxyl group [- COOH] is

acidic innature.

 There are about300 aminocids occur in nature. Only 20 ofthem occur

in proteins.
 α- carboxyl group of one amino acid (with side chain
R1) forms a covalent peptide bond with α- amino
group of another amino acid (with side chain R2 by
removal of a molecule of water).

 The result is : Dipeptide.

 The dipeptide can then form a second
peptide bond with a third amino acid ( with side chain
R3) to give tripeptide.
 Repetition of this process generates a polypeptide or
protein of specific aminoacid sequence.
 Has 40% double bond character, caused by resonance.
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 Polypeptide backbone is the repeating sequence of the N-C- C-N-
C-C… in the peptidebond.
 The side chain or R group is not part of the backbone or the peptide
bond.
Proteins have different levels of organisation

 Primary Structure
Secondary Structure
Tertiary Structure
Quaternary Structure
 Primary Structure

 The primary structure of protein refers tothe sequence of

amino acids present in the polypeptide chain.

 Amino acids are covalently linked by peptide bonds

or covalent bonds.

 Each component amino acid in a polypeptide is

called a "residue” or “moiety”.

 By convention the primary structure of protein starts

from the amino terminal (N) end and ends in the
carboxyl terminal (C) end.
It is a local, regularly
occurring structure inproteins
and is mainly formed through hydrogen bondsbetween
backboneatoms.

Pauling & Corey studied the secondary structures

and proposed2 conformations
α helix
β sheets.
Bonds holding the tertiary structure of
Proteins

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Protein functions
Proteins play an important role in many crucial biological processes and functions. They
are very versatile and have many different functions in the body, as listed below:

•Act as catalysts
•Transport other molecules
•Provide mechanical support
•Provide immune protection
•Generate movement
•Transmit nerve impulses
•Control cell growth and differentiation
 Enzymatic proteins
Function: Selective acceleration of chemical reactions
Example: Digestive enzymes catalyze the hydrolysis of
bonds in food molecules.

Enzyme

• Enzymes are a type of protein that acts as a catalyst to speed up chemical reactions
• Enzymes can perform their functions repeatedly, functioning as workhorses that carry out the
processes of life
Lipases – a group of enzymes that help to digest fats in the gut.
Amylase – helps change starches into sugars. Amylase is found in saliva.
Maltase – also found in saliva; breaks the sugar maltose into glucose. Maltose is found in foods such as
potatoes, pasta, and beer.
Trypsin – found in the small intestine, breaks proteins down into amino acids.
Lactase – also found in the small intestine, breaks lactose, the sugar in milk, into glucose and galactose.
 Storage proteins
Function: Storage of amino acids
Examples: Casein, the protein of milk, is the major
source of amino acids for baby mammals. Plants have
storage proteins in their seeds. Ovalbumin is the
protein of egg white, used as an amino acid source
for the developing embryo.

Ovalbumin Amino acids

for embryo

Storage proteins are a source of amino acids for growing organisms, such as this germinating garden
pea.
Storage proteins serve as reserves of metal ions and amino acids, which can be mobilized and utilized
for the maintenance and growth of organisms.
 Hormonal proteins
Function: Coordination of an organismʼs activities
Example: Insulin, a hormone secreted by the
pancreas, causes other tissues to take up glucose,
thus regulating blood sugar concentration

Insulin
High secreted Normal
blood sugar blood sugar

Some examples of protein hormones include growth hormone, which is produced by the pituitary
gland, and follicle-stimulating hormone (FSH), which has an attached carbohydrate group and
is thus classified as a glycoprotein.
FSH helps stimulate the maturation of eggs in the ovaries and sperm in the testes.
Insulin for Glucose transport

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 Contractile and motor proteins
Function: Movement
Examples: Motor proteins are responsible for the
undulations of cilia and flagella. Actin and myosin
proteins are responsible for the contraction of
muscles.

Actin Myosin

Muscle tissue
100 m

Myosin motors power movements on actin filaments, whereas dynein and kinesin motors power
movements on microtubules. The mechanisms of these motor proteins differ, but, in all cases, ATP
hydrolysis and subsequent release of the hydrolysis products drives a cycle of interactions with the
track (either an actin filament or a microtubule), resulting in force generation and directed movement.
 Defensive proteins
Function: Protection against disease
Example: Antibodies inactivate and help destroy
viruses and bacteria.

Antibodies

Virus Bacterium

Antibodies are defensive proteins that have binding sites whose three-dimensional structure allows them
to identify and bind to very specific foreign molecules. By binding to foreign proteins they can help
neutralize them and tag them, facilitating their engulfment and removal by defensive cells. IgG antibodies
have a quaternary structure with four subunits, two "light chains" and two "heavy chains."
Transport proteins
Function: Transport of substances
Examples: Hemoglobin, the iron-containing protein of
vertebrate blood, transports oxygen from the lungs to
other parts of the body. Other proteins transport
molecules across cell membranes.

Transport
protein

Cell membrane

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Many small molecules, organic and inorganic, are transported in the bloodstream and extracellular fluids, across
the cell membranes, and inside the cells from one compartment to another, by specific proteins.
•
Examples are:
hemoglobin, that carries oxygen from the alveolar blood vessels to tissue capillaries;
transferrin, which carries iron in the blood;

membrane carriers;
fatty acid binding proteins (FABP), that is, the proteins involved in the intracellular transport of fatty acids;
proteins of plasma lipoproteins, macromolecular complexes of proteins and lipids responsible for the transport of
triglycerides, which are otherwise insoluble in water;

albumin, that carries free fatty acids, bilirubin, thyroid hormones, and certain medications such as aspirin and
penicillin, in the blood
 Receptor proteins
Function: Response of cell to chemical stimuli
Example: Receptors built into the membrane of a
nerve cell detect signaling molecules released by
other nerve cells.

Receptor
Signaling protein
molecules

Receptors
These proteins are responsible for signal detection and translation into other type of signal. Sometimes
these proteins are active only in complex with low molecular weight compounds. Very well known
member of this protein family is rhodopsin - light detecting protein. Many receptors are transmembrane
proteins.
 Structural proteins
Function: Support
Examples: Keratin is the protein of hair, horns,
feathers, and other skin appendages. Insects and
spiders use silk fibers to make their cocoons and webs,
respectively. Collagen and elastin proteins provide a
fibrous framework in animal connective tissues.

Collagen

Connective
tissue 60 m

Structural proteins maintain cell shape, akin to a skeleton, and they compose structural elements in
connective tissues like cartilage and bone in vertebrates.