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Department of botany
Mid Term Assignment

Course code: CHEM-5404 Course Name: Basic Biochemistry

Due Date: 25-4-2020 Submission Date: 25-4-2020

Teacher: Sir M.Mahmood Anwar Student Name: Zarmeena Maryam

Student ID: BBOF18E007 Session: 2018-2020

Program: BS-Botany Semester: 4th

(Self-support) Main campus/Ex-PPP: Main-campus

ASSIGNMENT COVER SHEET

Title of the Assignment: Structure and Properties of Proteins
Word count: 2750
Marks awarded by Teacher:
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Topic: Structure and properties of

Proteins

Proteins:

Any of the complex organic macromolecules containing carbon, hydrogen, oxygen, nitrogen,
and usually sulfur, composed of one or more amino acid chains.

The general structure of α-amino acids is shown. The α-amino acids are so called because the α-
carbon atom in the molecule carries an amino group (―NH2); the α-carbon atom also carries a
carboxyl group (―COOH).

Shortly after synthesis, some amino acids were chemically modified. This changes the folding,
stability, activity and function of the protein.

It is customary to write the structure of the peptides (formed as a result of bond formation
between amino acids) in such a way that the α-amino free group (also called the N terminal of
the peptide) is on the left side and the free carboxylic group (the C terminal) on the right side.
Protein is the basic component of all living cells, including many substances, such as enzymes,
hormones and antibodies, is necessary for the normal functioning of organisms. They are also
essential for the growth and can be obtained from meat, fish, eggs, milk and other.
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Protein structure:

The protein structure describes how protein molecules are organized. Proteins are important
biological macromolecules present in all organisms. They are polymers made up of 20 possible
amino acids by translating RNA. Protein structures have sizes ranging from tens to several
thousand amino acids. After translation, proteins fold into specific forms. This is not done by
chemical bonds but by weaker forces such as hydrogen bonds.

To understand how proteins work, it is often necessary to find out their three-dimensional
structure. To do this, biophysics uses techniques such as X-ray crystallography, NMR
spectroscopy and double polarization interferometry.A protein can pass from one form to
another while doing its job. Alternative states of the same protein are called conformations.

Protein structure level: There are four different levels of protein structure as shown below:
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1)Primary structure of protein:

The primary structure of a protein refers to the total number and sequence of amino acids in
that particular protein. A fixed number of amino acids are arranged in a specific order. Different
proteins have different sequences. Therefore, the study of the total number and sequence of
amino acids in proteins is the study of the primary structure of proteins.

• Normal and abnormal protein:

The primary structure distinguishes normal proteins from abnormal proteins. Any changes in the
sequence will cause abnormal functioning. An example is given below: that is sickle cell disease.

Sickle cell disease:

The oxygen transport protein hemoglobin is composed of four polypeptide chains, two
identical α chains and two identical β chains. Each α chain has 141 amino acids, and each β
chain has 146 amino acids, which are arranged in a specific order. In sickle cell anemia, a single
amino acid substitution occur in the beta chain of hemoglobin causes a change in the structure of
the entire protein and it does not work in proper way. When the amino acid glutamic acid is
replaced by valine in the β-chain, the polypeptide will fold into a slightly different shape,
thereby forming abnormal hemoglobin.
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Therefore, only one amino acid substitution can cause drastic changes. These dysfunctional
hemoglobins begin to combine with each other under some conditions, forming long fibers made
of millions of aggregated hemoglobins, which deform red blood cells into a crescent or
"sickle" shape, thereby blocking the arteries and the normal cells are disc-shape.

Effect:

People affected by this disease often have difficulty breathing, dizziness, headache and
abdominal pain.

2) Secondary structure of proteins:

It refers to the twist of the polypeptide chain in a helical form. These types of helical
structures have been identified:

Alpha helix and Beta pleated sheets.

• Alpha helix:

α , means the first and the structure described below is the first among the helical structures
that are found, hence known as the alpha (α) helix.

In the α-helix chain, a hydrogen bond is created between the oxygen atom in the polypeptide
backbone carbonyl group in one amino acid and the hydrogen atom in the amino group of the
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polypeptide backbone of another amino acid, which is four amino acids further down the chain.
This keeps the stretching of amino acids in the right winding.

Each helical turn in the alpha helix has 3.6 amino acid residues. The R groups (side chains) of
the polypeptide protrude from the α-helical chain and do not participate in the H bonds that
support the α-helical structure. This type of structure is found in many proteins in combination
with other structures.

The pure α-helical structure is observed in the hair protein, keratin.

• Beta pleated:

β ,means the second and the structure described below is the second discovery after the α
helix.In β-pleated sheets, the amino acid regions are held in an almost completely elongated
conformation that "pleats" or zigzags due to the nonlinear nature of single C-C and C-N covalent
bonds. β pleated sheets never occur alone. They should be kept in place by other β pleated
sheets.

The changes in the amino acids in the β-pleated sheets are seized in their pleated structure
because the hydrogen bonds are formed between the oxygen atom in the carbonyl group of the
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polypeptide backbone of one β-pleated sheet and the hydrogen atom in the amino group with the
polypeptide base of another β-pleated sheet.

The β , pleated sheets, which are held to each other, are aligned parallel or antiparallel to each
other. The R groups of the amino acids in the β-pleated sheet are at a 90 degree angle to the
hydrogen bonds holding the β-pleated sheets together, and are not concerned in maintaining the
β-pleated structure of the sheet.

Conversion:

α-Helices may be converted into β-sheets, as for example occurs when the a-keratin of hair or
wool is stretched in a moist and hot atmosphere.

The conversion of α-helices into β-sheets may also explain the abnormal folding of some
proteins that tend to aggregate in certain disorders such as Alzheimer (b-amyloid) and
Parkinson (a-synuclein) neurodegenerative diseases.

3) Tertiary structure:

The tertiary structure of a polypeptide chain is its general three-dimensional form, after all the
secondary structural elements are folded together. The interactions between polar, nonpolar,
acidic and basic R groups within the polypeptide chain create the complex three-dimensional
tertiary structure of the protein.

• Hydrophobic interactions:

When protein folding takes place in the aqueous environment of the body, hydrophobic R
groups of nonpolar amino acids are most frequently located inside the protein, while
hydrophilic R groups lie mostly outside.

• Hydrogen bonding:

In the polypeptide chain and between amino acid "R" groups helps to stabilize protein structure
by holding the protein in the shape established by the hydrophobic interactions.

• Ionic bonding:
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Due to protein folding, ionic bonding can occur between the positively and negatively charged
"R" groups that come in close contact with one another.

• Disulphide bridge:

Cysteine side chains form disulfide bonds in the existence of oxygen, the only covalent bond
formed during protein folding. All these interactions, weak and strong, determine the final three-
dimensional form of the protein.

When a protein loses its three-dimensional shape, it will no longer be useful.

4) Quaternary structure:

The quaternary structure of a protein is how its subunits are oriented and arranged relative to
each other. As a result, the quaternary structure is only suitable for multi-subunit proteins; that
is, proteins made from more than one polypeptide chain

Proteins made from a single polypeptide will not have a quaternary structure.

In proteins with more than one subunit, weak interactions between subunits help stabilize the
overall structure. Enzymes often play a key role in binding subunits to form the final functional
protein. For example: Hemoglobin is an example of a protein with a quaternary structure.
Hemoglobin in the blood is an iron-containing protein that binds oxygen molecules. It contains
four subunits: two alpha subunits and two beta subunits.
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This image shows a protein that is made of several protein subunits. Each color represents a
separate protein

Each protein subunit is produced individually by a ribosome. Then, each protein subunit attains
secondary and tertiary structure. Finally, the protein subunits come together to form a fully
functional protein.

Properties of proteins:

Physical properties:

Physical properties are those that can be observed without changing the identity of the substance.

Chemical properties:

Properties that describe how a substance changes to a completely different substance are called
chemical properties.

The physical and the chemical properties of protein are given below and these properties help us
to understand the proteins in an effective way and their behavior with other substances.

➢ Physical Properties of Proteins:

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• Colour and Taste:

Proteins are colourless and usually tasteless. These are homogeneous and crystalline.

• Shape and Size

The proteins range in shape from simple crystalloid spherical structures to long fibrillar
structures. Two distinct patterns of shape have been recognized :

(a)Globular proteins:

These are spherical in shape and occur mainly in plants, esp., in seeds and in leaf cells.
These are bundles formed by folding and crumpling of protein chains. e.g., pepsin,
edestin, insulin, ribonuclease etc.

(b) Fibrillar proteins :

These are thread-like or ellipsoidal in shape and occur generally in animal muscles. Most
of the studies regarding protein structure have been conducted using these proteins. e.g.,
fibrinogen, myosin etc..

• Colloidal Nature:
Because of their giant size, the proteins exhibit many colloidal properties, such as; Their
diffusion rates are extremely slow and they may produce considerable light-scattering in
solution, thus resulting in visible turbidity (Tyndall effect).
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• Denaturation:
The partial or complete unfolding of the natural (natural) conformation of the polypeptide
chain is called denaturation. This is caused by heat, acid, alkali, alcohol, acetone, urea.

• Weight:
If the protein contains only one amino acid molecule or one atom of iron, copper, or
another element, the minimum molecular weight of the protein or subunit can be
calculated; for example, protein myoglobin contains 0.34 grams of iron in 100 grams of
protein. The atomic weight of iron is 56; therefore, the minimum molecular weight of
myoglobin is (56 × 100) /0.34 = about 16,500. Direct measurement of the molecular
weight of myoglobin gives the same value. However, hemoglobin also contains 0.34%
iron with a molecular weight of 66,000 or 4 × 16,500. So hemoglobin contains four iron
atoms.
• Condensation:
When proteins are denatured by heat, they form insoluble aggregates, called coagulum.
All proteins are not heat coagulable, only a few like albumin, globulin is heat coagulable.

• Amphoteric Nature:
Like amino acids, the proteins are amphoteric, i.e., they act as acids and alkalies both.
These migrate in an electric field and the direction of migration depends upon the net
charge possessed by the molecule. The net charge is influenced by the pH value. Each
protein has a fixed value of isoelectric point (pl) at which it will move in an electric field.
Isoelectric pH (pH1), the pH at which proteins have equal numbers of positive and
negative charges is called isoelectric pH. When subjected to an electric field, proteins do
not move toward the anode or cathode, so this feature can be used to separate proteins.
The protein has the lowest solubility at pHI and precipitates out. The pHI of casein is 4.5,
and at this pH, the casein in buttermilk produces curd.
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• Ion Binding Capacity:

The proteins can form salts with both cations and anions based on their net charge.

• Solubility:
The solubility of proteins is influenced by pH. Solubility is lowest at isoelectric point and
increases with increasing acidity or alkalinity. This is because when the protein
molecules exist as either cations or anions, repulsive forces between ions are high, since
all the molecules possess excess charges of the same sign. Thus, they will be more
soluble than in the isoelectric state.

• Optical Activity
All protein solutions rotate the plane of polarized light to the left, i.e., these are
levoratotory.Although the specific rotation (a function of the concentration of a protein
solution and the distance the light travels in it) of most L-amino acids varies from −30° tο
+30°, the amino acid cystine has a specific rotation of approximately −300°.
Although the optical rotation of a protein depends on all of the amino acids of which it is
composed, the most important ones are cystine and the aromatic amino acids
phenylalanine, tyrosine, and tryptophan. The contribution of the other amino acids to the
optical activity of a protein is negligibly small.

➢ Chemical Properties of Proteins:

• Hydrolysis:
Hydrolysis breaks bonds by reacting with water. It can be catalyzed by acids or bases.
Proteins and peptide chains can be hydrolyzed to break peptide bonds and form their
constituent amino acids.
(a)Acid hydrolysis:It usually involves heating the protein with an acid, such as
hydrochloric acid, under reflux of the protein. 6moldm-3 HCl (aqueous solution). Since
low pH depends on their isoelectric point, this will use water to break bonds and often
form positively charged amino acids.
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(b)Alkaline hydrolysis:It usually involves heating with NaOH to slightly above 100 ° C.
This will form an amino acid salt, so the carboxyl group is COO-Na +

• Reactions involving COOH Group:

The following types of reactions takes place that are given below,
(a) Reaction with alkalies:It result in salt formation.

(b)Reaction with alcohols: It results in esterfication.

• Reactions involving NH2 Group:

(a) Reaction with mineral acids (Salt formation): When any free amino acids or
proteins are treated with mineral acids like HCl, the acid salts are created.

(b) Reaction with formaldehyde: It react with formaldehyde, the hydroxy-methyl

derivatives are formed.

(c)Reaction with benzaldehyde: It react with benzyldehyde and Schiff‘s bases are
formed.

(d) Reaction with nitrous acid (Van Slyke reaction): The amino acids treat or react with
HNO2 to release N2 gas and to produce the corresponding α-hydroxyl acids.

• Reactions involving both COOH and NH2 Group:

(a) Reaction with phenyl isocyanate: When it react with phenyl isocyanate, hydantoic
acid is formed which in turn can be converted to hydantoin.

(b)Reaction with phosgene: When it react with phosgene, then N-carboxyanhydride is

formed.
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(c) Reaction with carbon disulfide:When it react with carbon disulfide, then 2-thio-5-
thiozolidone is produced.

• Reactions involving R Group or Side Chain:

(a) Biuret test: The biuret test, also known as Piotrowski's test, is a chemical test used
for detecting the presence of peptide bonds. In the presence of peptides, a copper(II) ion
forms mauve-colored (Mauve is a pale purple color named after the mallow flower) coordination complexes
in an alkaline solution.

(b) Millon’s test: Millon reagent is an analytical reagent used to detect the presence of
soluble proteins. Add a few drops of reagent to the test solution, then heat it. Reddish
brown or precipitation indicates presence of tyrosine residues in almost all proteins.

(c) Pauly test: The Pauli reaction is a chemical test used to detect the presence of
tyrosine or histidine in proteins. It was named after the German chemist Herman Pauly,
who first described the reaction. When proteins containing either tyrosine or histidine
react with diazotized sulfanilic acid under alkaline conditions, a red color is formed.

• Reactions involving SH Group:

(a)Nitroprusside test: Red colour develops with sodium nitroprusside in dilute NH4.OH.
The test is specific for cysteine.
(b)Sullivan test: Cysteine develops red colour in the presence of sodium 1, 2-
naphthoquinone- 4-sulfonate and sodium hydrosulfite
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