Download LACTURE 2 PROTEINS

Dh. DALIA AL-KHATEEB
LACTURE 2
PROTEINS
Proteins
Proteins are large, complex molecules that are critical for the normal
functioning of the human body. They are essential for the structure,
function, and regulation of the body’s tissues and organs. Proteins are
made up of hundreds of smaller units called amino acids that are attached
to one another by peptide bonds, forming a long chain. You can think of a
protein as a string of beads where each bead is an amino acid.
Image of beads on a string
Classification of Protein (with examples):
A) Based on composition
B) Base on structure
A) Based on Composition:
1) Simple Proteins
2) Conjugated Proteins
3) Derived proteins
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1) Simple Proteins: Classified according to solubility
a) Albumins
b) Globulins
c) Glutelins
d) Histones
e) Protamine
f) prolamines
g) Scleroproteins
2) Conjugated Proteins:
Contain amino acid + prosthetic group.
a) Glycoproteins
b) Chromoproteins
c) Lipoproteins
d) Nucleoproteins
e) Phosphoprotein
3) Derived Proteins: Derivatives of proteins due to action of heat, enzymes,
or chemical reagents.
a) Primary Derived
b) Secondary Derived
B) Based on Structure:
1) Fibrous
2) Globular
Function of Protein:
1) Storage
2) Transport
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3) Structural Material
4) Metabolic Growth Regulator
5) Control of Physiological Functions
6) Catalytic Activity
7) Hormonal
8) Toxicity by Foreign Proteins
Properties of Proteins:
1) Optical Property
2) Colloidal
3) Solubility
4) Amphoteric Nature
5) Denaturation of Proteins
Amino acid structure and its classification
An amino acid contains both a carboxylic group and an amino group.
Amino acids that have an amino group bonded directly to the alphacarbon are referred to as alpha amino acids. The simplest representation
of an alpha amino acid is shown below.
amino acid structure
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Every alpha amino acid has a carbon atom, called an alpha carbon,
bonded to a carboxylic acid, , group; an amino, , group; a hydrogen
atom; and an R group
that is unique for every amino acid. If you notice in the structure above, is
a chiral center, that is to say, this carbon atom is attached to four different
groups. Chirality refers to a molecule that has optical activity, so amino
acids are optically active molecules. The only exception is glycine, the
simplest amino acid, in which R = H.
Commonly, amino acids are represented as follows:
amino acid structures as fischer projections
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L and D amino acids;
Indicated by R and L As shown above, L and D amino acids are mirror
images of each other and are non-superimposable on each other, just like
our left and right hands. By non-superimposable, we mean that when the
mirror image of the object is placed over the original object, they do not
have a perfect overlap. Pairs of amino acids like these are called
enantiomers.
Only L-amino acids are constituents of proteins. Our body synthesizes
most of its own L-amino acids; these then get incorporated into proteins.
Proteins are catalysts for most of the biochemical reactions that take place
in our body. Along with DNA- DNAD and RNA- RNAR proteins
constitute the genetic machinery of living organisms. Proteins are often
called the building blocks of life.
Classification of different amino acids
Groups classified by different properties;
I: Non-polar side chains (hydrophobic).
II: Polar, uncharged side chains.
III: Charged Side Chains .

Acidic side chains .

Basic side chains .
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GROUP I: NON-POLAR (HYDROPHOBIC) SIDE
CHAINS
1 - Side chains of Group; aa’s are mainly hydrocarbons – very
unreactive amino acids.
2 –sub groups: Aliphatic hydrocarbons & Aromatic hydrocarbons
(have benzene rings) - These amino acids will tend to be buried (away
from water) in 3-D structure of proteins - Non-polar character.
GROUP II: NEUTRAL (UNCHARGED) POLAR SIDE CHAINS
Polar Residues are both buried as well as on the surface of proteins.
They either form hydrogen bonds with other polar residues in the
protein or with water. For example, the OH group of Serine can
both donate as well as accept a hydrogen bond:
GROUP III: Charged Amino Acids
A. ACIDIC SIDE CHAINS
a. Glutamate or glutamic acid (E, Glu) and Aspartate or aspartic
acid (D, Asp) Always negatively charged at physiological pH (~7.4)
--------CH2-COO-
B. BASIC SIDE CHAINS
All gain a proton at physiological pH (Positively charged) a. Lysine
(K, Lys) b. Arginine (R, Arg) c. Histidine (H, His) .
amino acid structure
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There are 20 common amino acids. Based on the nature of the R group,
they are classified as follows:
The types of amino acids;
1- Hydrophobic amino acids have nonpolar side chains, such as alkyl
groups or aromatic groups.
2- Hydrophilic—neutral—amino acids contain polar side chains, such
as hydroxyl, -OH negative and sulfhydryl, -SH, negative groups.
3-Hydrophilic—acidic—amino acids have side chains that contain
carboxylic acid, -COOH negative groups. . . Hydrophilic—basic—
amino acids have side chains that contain amine, -NH2negative start
subscript, 2, end subscript, groups.
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Peptides;
Peptide bond formation is a condensation reaction leading to the
polymerization of amino acids into peptides and proteins. Peptides
are small consisting of few amino acids. The simplest peptide, a
dipeptide, contains a single peptide bond formed by the
condensation of the carboxyl group of one amino acid with the
amino group of the second with the concomitant elimination of
water. The process of peptide bond formation can then continue to
join other amino acids and yield in an amino acid chain. A peptide
chain will have an unbound amino group free at one end (called the
N-terminus) and a single free carboxylate group at the other end
(called the C-terminus). When there are a few amino acids in a
chain (usually 10 - 20) , it is called an oligopeptide. When there
are many (usually more than 20) it is called a
polypeptide. Although the terms "protein" and "polypeptide" are
sometimes used to describe the same thing, the term polypeptide is
generally used when the molecular weight of the protein is below
10,000.
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Two a-amino acids are joined by a peptide bond in alanylglycine. It is a
dipeptide.
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