Proteins, types and functions , classificatiion

Peptides and Proteins
20 amino acids are commonly found in protein.
These 20 amino acids are linked together through “peptide
bond forming peptides and proteins.
Peptides and proteins:
- The chains containing less than 50 amino acids are called
“peptides”, while those containing greater than 50 amino
acids are called “proteins”.

Peptide bond formation:
α-carboxyl group of one amino acid forms a covalent bond
(peptide bond) with α-amino group of another amino acid by
removal of a molecule of water.
 The result is a dipeptide (i.e. two amino acids linked by one
peptide bond).

 By the same way, the dipeptide can then forms a second
peptide bond with a third amino acid to give tripeptide.
 Repetition of this process generates a polypeptide or protein
of specific amino acid sequence.

Protein with amino acid = n
Peptide bond = n-1

It generally exist in the trans configuration.
Both –C=O and –NH are polar and involved in the
formation of H-bond.
Peptide bond is rigid and planer with partial double
bond character.
Properties of peptide bond:

Each polypeptide chain starts on the left side by free amino group of the
first amino acid enter in chain formation . It is termed (N- terminus).
- Each polypeptide chain ends on the right side by free COOH group of the
last amino acid and termed (C-terminus).
N and C terminus of the protein:

Examples of Peptides:
1- Dipeptide (two amino acids joined by one peptide bond):
Example: Aspartame which acts as sweetening agent being used in
replacement of cane sugar.
It is composed of aspartic acid and phenyl alanine.

2- Tripeptides (three amino acids linked by two peptide bonds)
Example:
Glutathione (GSH) which is formed from 3 amino acids: glutamic
acid, cysteine and glycine.
It helps in absorption of amino acids, protects against hemolysis of
RBC by breaking H2O2 which causes cell damage.
3- octapeptides: (8 amino acids linked by 7 peptide bonds)
Examples:
Two hormones; oxytocine and vasopressin (ADH).
4- polypeptides: 10- 50 amino acids: e.g. Insulin hormone

Protein structure
There are four levels of protein structure
Primary
Secondary
Tertiary
Quaternary

1- Primary structure
The primary structure of a protein is its unique sequence of
amino acids.
– Lysozyme, an enzyme that attacks bacteria, consists of a
polypeptide chain of 129 amino acids.
– The precise primary structure of a protein is
determined by inherited genetic information.

– At one end is an amino acid with a
free amino group the (the N-
terminus) and at the other is an
amino acid with a free carboxyl
group the (the C-terminus).

1- Many genetic diseases result due to the alteration or change of the
amino acid at particular position of the protein.
2- Sequence is important to understand the mechanism of action of the
protein.
3- The secondary and tertiary structures of the protein can be predicted.
4- Trace the evolutionary relationships.
Importance of the primary sequence of protein

High orders of Protein structure
A functional protein is not just a polypeptide chain, but one or
more polypeptides precisely twisted, folded and coiled into a
molecule of unique shape (conformation).
This conformation is essential for some protein function e.g. enables
a protein to recognize and bind specifically to another molecule e.g.
hormone/receptor; enzyme/substrate and antibody/antigen.

2- Secondary structure
Results from hydrogen bond formation between hydrogen of
–NH group of peptide bond and the carbonyl oxygen of
another peptide bond.
Noncovalent interactions.
According to H-bonding there are two main forms of
secondary structure:
Alpha helix
Beta sheets

α-helix:
It is a spiral structure resulting from hydrogen
bonding between one peptide bond and the fourth one
This type of secondary structure was identified by
Pauling and Corey in 1951.

The salient features of α-Helix are as below;
1- The backbone of α-Helix is made of peptide bond.
2- Side chains extend outward.
3- The α-Helix is stabilized by the extensive H-bonding. It is
formed between H atom of peptide N and O atom of peptide C.
Although individual H-bond is weak but collectively they are
strong enough to stabilize the helix. These H-bonds are intra-chain
because they are within one polypeptide chain.

4- Each turn of the α-Helix contains
3.6 amino acids and α-Helix has a
pitch (length of one turn) of 0.54 nm
or 5.4 angstrom.
5- Certain amino acids particularly
proline disrupt the α-Helix and
therefore they do not occur in α-
helix

6- Every amino acid (n) form H-bond with the fourth amino
acid (n+4).
Example: Keratins are a family of closely related, fibrous
proteins whose structure is nearly entirely α-helical

β-sheets: is another form of secondary structure in which two or
more polypeptides (or segments of the same peptide chain) are
linked together by hydrogen bond between H- of NH- and
carbonyl oxygen.

The polypeptide chains in the β-Sheet may be arranged either in
parallel (same direction) or antiparallel (opposite direction)

Supersecondary structure or motifs:
Combination of secondary structure.
The combination may be:
 α-helix- turn- α-helix- turn…..etc
 β-sheet -turn- β-sheet-turn………etc
 α-helix- turn- β-sheet-turn- α-helix
Turn (or bend): is short segment of polypeptides (3-4 amino
acids) that connects successive secondary structures.
e.g. β-turn: is small polypeptide that connects successive strands
of β-sheets.

3- Tertiary structure
Tertiary structure is determined by a variety of
interactions (bond formation) between R groups
of the polypeptide backbone.
These interactions include noncovalent and
covalent.

a- The weak interactions include:
Hydrogen bonds among polar side chains.
Ionic bonds between charged R groups (basic and acidic amino
acids).
Hydrophobic interactions among hydrophobic (non polar) R
groups.
b- Strong covalent bonds include disulfide bridges, that form
between the sulfhydryl groups (SH) of cysteine monomers, stabilize
the structure.

Proteins, types and functions , classificatiion

4- Quaternary structure
Combination of two or more polypeptide subunits held together by non-
covalent interaction like H-bonds, ionic or hydrophobic interactions.
Examples on protein having quaternary structure:
1- Collagen is a fibrous protein of three polypeptides (trimeric) that are
supercoiled like a rope. This provides the structural strength for their role in
connective tissue.
2- Hemoglobin is a globular protein with four polypeptide chains (tetrameric)
3- Insulin two polypeptide chains (dimeric)

Classification of proteins
I- Simple proteins
They are composed of only amino acids and on hydrolysis
gives only amino acids.

b- Fibrous proteins:
These are fiber like in shape, insoluble in water and resistant to
digestion.
Example: Keratin, Collagen, Elastin
Types: Simple proteins are further categorized into two types;
a- Globular proteins:
These are spherical or oval in shape, soluble in water or other
solvents and digestible.
Example: Albumin, Globulin, Histones

Examples of simple protein:
1- Albumin and globulins: present in egg, milk and blood
They are proteins of high biological value i.e. contain all essential
amino acids and easily digested.
Types of globulins:
α1 globulin: e.g. antitrypsin
α2 globulin: e.g. hepatoglobin: protein that binds hemoglobin to
prevent its excretion by the kidney
β-globulin: e.g. transferrin: protein that transport iron
γ-globulins = Immunoglobulins (antibodies) : responsible for
immunity.

3- Gliadines are the proteins present in cereals.
a - combined with DNA
b - combined with heme to form hemoglobin of RBCs.
2- Globins (Histones):
They are basic proteins rich in positively charged amino acid.

4- Scleroproteins:
These are structural proteins, not digested.
These include: keratin, collagen and elastin.
a- α-keratin:
Protein found in hair, nails, enamel of teeth and outer layer of skin.
It is α-helical polypeptide chain, rich in cysteine and hydrophobic
(non polar) amino acids so it is
water insoluble.
b- collagens:
Protein of connective tissues found in bone, teeth, cartilage, tendons,
skin and blood vessels.

Collagen
Collagen may be present as gel e.g. in extracellular
matrix or in vitreous humor of the eye.
•Collagens are the most important protein in mammals.
They form about 30% of total body proteins.
•There are more than 20 types of collagens, the most
common type is collagen I which constitutes about 90%
of cell collagens.

Structure of collagen
Three helical polypeptide chains (trimeric) twisted
around each other forming triplet-helix molecule.
⅓ of structure is glycine, 10% proline, 10%
hydroxyproline and 1% hydroxylysine.
Glycine is found in every third position of the
chain. The repeating sequence –Gly-X-Y-, where
X is frequently proline and Y is often
hydroxyproline and can be hydroxylysine.

Solubility:
Collagen is insoluble in all solvents and not digested.
•When collagen is heated with water or dil. HCl it will be
converted into gelatin which is soluble , digestible and used as
diet ( as jelly). Gelatin is classified as derived protein.

Some collagen diseases
1- Scurvy:
Disease due to deficiency of vitamin C which is important
coenzyme for conversion of proline into hydroxyproline and
lysine into hydroxylysine. Thus, synthesis of collagen is
decreased leading to abnormal bone development, bleeding,
loosing of teeth and swollen gum.
2- Osteogenesis Imperfecta (OI):
Inherited disease resulting from genetic deficiency or
mutation in gene that synthesizes collagen type I leading to
abnormal bone formation in babies and frequent bone
fracture in children. It may be lethal.

Elastin
Present in walls of large blood vessels (such as aorta).
It is very important in lungs, elastic ligaments, skin, cartilage.
It is elastic fiber that can be stretched to several times as its normal
length.
Structure:
Composed of 4 polypeptide chains (tetramer), similar
to collagen being having 33% glycine and rich in
proline but in that it has low hydroxyproline and
absence of hydroxylysine.

Elastin is a lung protein. Smoke stimulate enzyme called
elastase to be secreted form neutrophils (in lung). Elastase
cause destruction of elastin of lung.
α1-antitrypsin is an enzyme (secreted from liver) and inhibit
elastase and prevent destruction of elastin. So deficiency of α1-
antitrypsin especially in smokers leads to degradation of lung
and destruction of lung (loss of elasticity of lung, a disease
called emphysema.
Role of α1-antitrypsin:

Emphysema:
Emphysema is a chronic obstructive lung
disease (obstruction of air ways) resulting
from deficiency of α1-antitrypsin
particularly in cigarette smokers.

Conjugated proteins
Besides the amino acids, these proteins contain a non-protein moiety
known as prosthetic group or conjugating group.
On hydrolysis, give protein part and non protein part and
1- Phosphoproteins: These are proteins conjugated with phosphate
group. Phosphorus is attached to OH group of serine or threonine.
e.g. Casein of milk.
2- Lipoproteins:
These are proteins conjugated with lipids.
Functions: a- help lipids to transport in blood
b- Enter in cell membrane structure helping lipid soluble

3- Glycoproteins:
proteins conjugated with sugar (carbohydrate)
e.g. - Some hormones such as erythropoeitin
- present in cell membrane structure
- blood groups.
4- Nucleoproteins:
These are basic proteins (e.g. histones) conjugated with nucleic
acid (DNA or RNA).

5- Metalloproteins: These are proteins conjugated with metal like
iron, copper, zinc, ……
a- Iron-containing proteins:
Iron may present in heme such as in
- hemoglobin (Hb)
- myoglobin (protein of skeletal muscles and cardiacmuscle),
- cytochromes,
- catalase, peroxidases (destroy H2O2)
- tryptophan pyrrolase (desrtroy indole ring of tryptophan).
Iron may be present in free state (not in heme) as in:
- Ferritin: Main store of iron in the body. ferritin is
present in liver, spleen and bone marrow.
- Hemosidrin: another iron store.
- Transferrin: is the iron carrier protein in plasma.

b- Copper containing proteins:
e.g. - Ceruloplasmin which oxidizes ferrous ions into ferric ions.
- Oxidase enzymes such as cytochrome oxidase.
c- Zn containing proteins: e.g. Insulin and carbonic anhydrase
d- Mg containing proteins:e.g. Kinases and phosphatases.

6-Chromoproteins: These are proteins conjugated with pigment.
e.g.
- All proteins containing heme (Hb, myoglobin, ………..)
- Melanoprotein:e.g proteins of hair or iris which contain melanin.

Derived proteins
These are the denatured or degraded products of simple and
conjugated protein. The
degradation and denaturation
may be because of heat, acid or
alkali treatment or because of
enzymatic actions
Gelatin: from hydrolysis of collagen
Peptone: from hydrolysis of albumin

46
Electrophoresis: separation of polar compounds based on their
mobility through a solid support. The separation is based on
charge (pI) or molecular mass.

Proteins are:
• Polypeptides (covalently linked -amino acids) + possibly:
• cofactors
 functional non-amino acid component
 metal ions or organic molecules
• coenzymes
 organic cofactors
 NAD+
in lactate dehydrogenase
• prosthetic groups
covalently attached cofactors
heme in myoglobin
• other modifications

Proteins, types and functions , classificatiion

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