Taiz University

Pharmacy department , Forth level

Proteins Overview

Dr: Eyad Al-sabaei

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 Proteins Overview
 Proteins are the most abundant and functionally diverse molecules
in living systems.
 Proteins Structure
 They are polymers of amino acids, connected together by a peptide
bond
 The monomer units: L-α-amino acids
 These are the only amino acids that are coded for by DNA
 Humans can’t synthesize 10 of the 20 L-α-amino acids
 Proteins Functions
 Proteins display a diversity of functions, such as:
 Direct and regulate metabolism “Enzymes and Hormones”
 Permit movement in muscle “Contractile Proteins”
 Shuttle molecules essential to life “Hemoglobin and Albumin”
 Fight infectious bacteria and viruses “Immunoglobulins”
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 Amino Acids: Structure
 Structure of the Amino Acids: Each amino acid has:
 A carboxyl group
 A primary amino group (except proline, Secondary amine)
 A distinctive side chain (“R-group”) bonded to the α-carbon
atom
 In proteins, almost all of carboxyl and amino groups are combined
through peptide linkage.

 The α-carbon of amino acids is chiral or optical active: Except of

glycine.

 Amino acids exist as D and L mirror images of each other:

Enantiomers.
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 Amino Acids: Classification
 Amino acids are classified according to polarity and charge of the
side chains into: 4 groups

 A) Amino acids with nonpolar side chains (9 Amino Acids)

 Does not gain or lose protons or participate in hydrogen or ionic

bonds
 In the interior of the protein found in aqueous solutions
 Due to the hydrophobic effect
 On the outside surface of protein located in a hydrophobic
environment
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 B) Amino acids with uncharged polar side chains (6 Amino Acids):
They have zero net charge at neutral pH

 cysteine and tyrosine can lose a proton at an alkaline pH

 Serine, threonine, and tyrosine contain a polar hydroxyl group
can participate in hydrogen bond formation.

 Asparagine and glutamine contain a carbonyl group and an amide

group
can participate in hydrogen bonds.

 Disulf ide bond (-S-S-): two cysteines oxidized to form a dimer,

cystine
an important component of the active site of many enzymes
stabilized many extracellular proteins; Albumin

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 C) Amino acids with acidic side chains (2 Amino Acids)
 They are proton donors.
 At physiologic pH (approximately pH 7.4), the side chains are
fully ionized, carboxylate group (–COO– ).

 D) Amino acids with basic side chains (3 Amino Acids)

 They are protons acceptors
 At physiologic pH the side chains of lysine and arginine are fully
ionized (–NH3+).
 Histidine is weakly basic,
 The free is largely uncharged
 In protein, can be either positively charged or neutral

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Protein Structure


 The protein structure is analyzed in terms of four organizational
levels
 Primary, Secondary, Tertiary, Quaternary

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 Primary Structure: The sequence of amino acids in a protein.
 Importance of primary structure:
 Understanding the primary structure of proteins is important
 Many genetic diseases result in proteins with abnormal amino
acid sequences(Hemophilia, Wilson disease)
 Leading to improper folding and loss or impairment of normal
function
 Comparison of the primary structures of the normal with
mutated proteins
 May be used to diagnose or study the disease.
 Peptide Bond:
 In proteins, amino acids are joined covalently by peptide
bonds.
 Amide bond between α-carboxyl group of one amino acid and
α-amino group of another.
 Peptide bonds are not broken by conditions that denature
proteins
 But hydrolyzed by prolonged exposure to a strong acid or base
at elevated temperatures.
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 Primary Structure: Peptide Bond
 Characteristics of the Peptide Bond:
 Has a partial double-bond character
• It is shorter than a single bond

 Rigid ▪ Planar
• This prevents free rotation

 trans bond in general

• Due to steric interference of the R-groups in cis position.

 Polarity of the peptide bond: Uncharged but Polar

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 Primary Structure: Quantitation
 Determination of the amino acid composition of a polypeptide
 A purif ied sample is f irst hydrolyzed by strong acid at 110°C for 24
hours.
 cleaves the peptide bonds and releases individual amino acids
(a.a)
 T h e se a m i n o a ci ds ca n be se pa r a t e d by Ion - e x ch a n ge
chromatography
 A mixture of a. a is applied to a column that contains a resin
 The a. a bind to the column with different affinities, depending
on their charges, hydrophobicity, and other characteristics.
 Each a. a is released from column by eluting with solutions.
 The separated a.a contained are quantitated by heating them
with ninhydrin a reagent that forms a purple compound with
most a.a

 The amount of each a.a is determined spectrophotometrically by

measuring the amount of light absorbed 12
 Secondary Structure of Proteins: α-
Helix
 The –backbone- regular arrangements of a. a that are located
near to each other

▪ ▪
 The examples of secondary structures:
• α-helix β-sheet β-bend (β-turn)
 α-Helix
 α-helix is the most common of different helices .
 Tightly packed, coiled polypeptide backbone core
 The side chains extending outward from the central axis from
the right side.
 2.3 Amino acids per turn

 Amino acids that disrupt an α-helix:

 Proline
with bulky (R)
▪ Large numbers of charged a.a ▪ a.a
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 Secondary Structure of Proteins: β-
Sheet & β-Bends
 β-Sheet
 Composed of two or more peptide chains or a single
polypeptide chain folding back on itself
 All of the peptide bond are involved in hydrogen bonding
 Parallel and antiparallel sheets

 β-Bends (reverse turns, β-turns)

 Composed of four amino acids, one of which may be proline.
 Glycine is also frequently found in β-bends
 They are usually found on the surface of protein molecules
 Stabilized by the formation of hydrogen and ionic bonds.

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 Tertiary & Quaternary Structure of
Proteins
 The primary structure of a polypeptide chain determines its
tertiary structure.
 “Tertiary” refers both to the folding of domains and to the final
arrangement of domains
 Domains:
 The functional and three-dimensional structural units of
polypeptides.
 Folding of the peptide chain within a domain usually occurs
independently of folding in other domains.

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 Protein Misfolding
 Misfolding may occur spontaneously, or be caused by a mutation
in a particular gene
 These misfolded proteins are usually tagged and degraded within
the cell. However, this quality control system is not perfect, and
intracellular or extracellular aggregates of misfolded proteins can
accumulate, particularly as individuals age.
 Deposits of these misfolded proteins are associated with a
number of diseases.
 Amyloid disease (Alzheimer disease)
 Accumulation of long, f ibrillar protein assemblies consisting of β-
pleated sheets.

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 Chemical Instability of Proteins

• 1-Hydrolysis.

• 2- Deamidation.

• 3- Racemization.

• 4- Oxidation.

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Good LUCK

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