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5 - Protein and Their Structures

The document discusses the structure of peptides and proteins. It covers the 20 common amino acids, peptide bond formation, and the four levels of protein structure - primary, secondary, tertiary, and quaternary. Examples of different protein types and structures like collagen are also provided.

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27 views33 pages

5 - Protein and Their Structures

The document discusses the structure of peptides and proteins. It covers the 20 common amino acids, peptide bond formation, and the four levels of protein structure - primary, secondary, tertiary, and quaternary. Examples of different protein types and structures like collagen are also provided.

Uploaded by

hussnain zaffar
Copyright
© © All Rights Reserved
We take content rights seriously. If you suspect this is your content, claim it here.
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Download as PPT, PDF, TXT or read online on Scribd
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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).
The amino acids linked by peptide bond are called residue
 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
N and C terminus of the protein:

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).
The acid – base behavior of the protein or its polarity depends
upon the ionization of the side chain.
Properties of peptide bond:

 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.
Peptides are also functional
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.
A number of vertebrate hormones are small peptides.
These include oxytocin (nine amino acid residues),
which is secreted by the posterior pituitary gland and
stimulates uterine contractions
Classification of proteins

Simple proteins
Many proteins, contain only amino acid residues and no other
chemical constituents; these are considered simple proteins.

Example: Ribonuclease A and chymotrypsin

conjugated proteins:
Some proteins contain permanently associated chemical
components in addition to amino acids; these are called
conjugated proteins.
Conjugated proteins are classified on the basis of the chemical
nature of their prosthetic groups.

Lipoproteins contain lipids,


Glycoproteins contain sugar groups
Metalloproteins contain a specific metal.
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).
Importance of the primary sequence of protein

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.
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)
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.
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- Hemoglobin is a globular protein with four polypeptide chains (tetrameric)


2- Insulin two polypeptide chains (dimeric)
Based on the structures proteins fall into two
groups
a- Globular proteins:
These are spherical or oval in shape, soluble in water or other
solvents and digestible.
Example: Albumin, Globulin, Histones

b- Fibrous proteins:
These are fiber like in shape, insoluble in water and resistant to
digestion.
Example: Keratin, Collagen, Elastin
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.

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