BIOCHEMISTRY ( I ) PROTEINS SALEM ELTUMI

PROTEINS

Proteins are organic compound with high molecular weight. Proteins are mainly formed of carbon,
hydrogen, oxygen and nitrogen in addition to S, Fe, Mg, Zn and etc.

Proteins are fundamental to all organisms and are the most versatile macromolecules in the
cell they serve crucial functions in all biological processes.

 The function of proteins within the organisms:

1- Catalysing metabolic reactions such as enzymes (all enzymes are proteins).

2- Transport molecules such as oxygen (haemoglobin).

3- Proteins also have structural or mechanical functions such as Collagen.

4- Regulation and control growth such as hormones.

5- Protection like as in antibodies.

6- Proteins are also necessary in animals' diets, since animals cannot synthesis all amino acids they
need and must obtain essential amino acids from food.

 Protein structure:

Proteins are linear polymers built of monomer units called amino acids. All amino acids are
linked together by peptide bonds.

 Amino Acids:

A typical amino acid has a central carbon atom called α-carbon. α- Carbon atom is attached to an
amino group (NH2), a carboxylic acid group (COOH), a hydrogen atom and a side chain (R-
group)that is specific to each amino acid and different in - Shape- Size- Polarity

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In all amino acids the α-carbon is attached to four different groups. This carbon is
known as an asymmetric atom and therefore has 2 different stereoisomers.

 1- Optical activity:
it's the ability of substance to rotate plane-polarized light either to the right or to
the left.

2- Optical isomerism:

it's the ability of substance to present in more than one form (isomer)

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 Ionization of amino acids:

Free amino acids have at least two ionizing groups, these are carboxyl group and amino group,
which is exist in several ionic states.

1- At low pH (i.e. high H+ concentration)

The carboxyl and amino groups both gain H+ so giving the cationic form (i.e. neutral COOH and
positively charged NH3+) and is expressed by its dissociation constant pk1

2- At neutral pH (physiological pH 7.4)

The carboxylic acid loss a proton (H+) and form a carboxyl group COO-, while the amino group
accepts a proton H+ to form NH3+. Thus at the physiological pH an amino acid can have both a
positive (+) and negative (-) charge which is known as a zwitterion.

3- At high pH (i.e. low H+ concentration)

The carboxyl and amino groups both loss H+ giving the anionic form (I.e. negative COO- and
neutral NH2) and is expressed by its dissociation constant pk2.

 Because amino acids contain both acidic and basic groups, they are AMPHOTERIC
(having both acidic and basic properties).

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 Zwitter ion definition:

It is an amino acid that can have both a positive and a negative charge
(it is dipolar ion).It bears no net charge (i.e. net charge is zero) and formed at neutral pH.
Zwitterion is electrically neutral and hence does not migrate in an electric field.

 Isoelectric point:

An amino acid bears a positive charge in acidic solution (low pH) and a negative charge in basic
solution (high pH). There must be an intermediate pH where the amino acid is evenly balanced
between the two forms, as the dipolar zwitterion with a net charge of zero. This pH is called the

isoelectric point .

 EXAMPLE: What is the isoelectric point of Alanine? pKa values: Alanine pKa1 for COOH
= 2.3, and pKa 2 for NH2 = 9.9,

 You must know you calculate the average value

Question: What is the isoelectric point of Methionine pKa1 for COOH =2.28, and pKa2 for NH2=
9.21? Solve it by yourself.

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 AMINO ACIDS CLASSIFICATION

Although over 300 different amino acids occur in nature. Proteins of all species, from bacteria to
human, are made up from the same set of 20 standard L-amino acids.

Amino acids can classify into different ways based on polarity, structure, nutritional requirement,
Metabolic etc. Generally used classification based on polarity. Based on polarity amino acids are
classified into four groups as follows:

i. -Non polar amino acids.

ii. -Polar amino acids with no charge.
iii. -Polar amino acids with positive charge.
iv. -polar amino acids with negative charge.

 Non polar amino acid

These amino acids are hydrophobic and have no charge on the R group. The amino acids of this
group are Glycine (Gly), Alanine (Ala), Valine (Val), Leucine (Leu), Isoleucine (Iso), Methionine
(Met), Phenyl alanine (Phe), Tryptophane (try), and Proline (pro).

 Note: Glycine is the smallest amino acid with the simplest structure, has a hydrogen atom in
the side chain position, and thus does not exist as a pair of stereoisomers since there are two
identical groups ( 2 hydrogen atoms ) attached to the α-carbon atom.

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 Polar amino acids with no charge

These amino acids participate in hydrogen bonding of protein structure. The amino acids in this
group are: Serine (Ser), Threonine (Thr), Glutamine (gln), Cysteine (Cys). Asparagine (Asn), and
Tyrosine (Tyr).

Polar amino acids with positive charge.

Polar amino acids with positive charge have more amino group as compared to carboxyl group
make them basic. These amino acids are: Lysine (Lys), Arginine (Arg), and Histidine (His).

 Polar amino acids with negatively change.

Amino acids with negatively charge have carboxyl groups more than amino make them acidic.
These amino acids are: Aspartate (Asp) and Glutamate (Glu).

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 Amino acids can classify based on nutritional value and classified into essential and
nonessential amino acids

 Essential amino acids:

Essential amino acids are those that cannot be produce in human body and therefore have
to be obtained from food sources. There are 9 amino acids essential amino acids:

 Tryptophan, Valine, Leucine, Isoleucine, Lysine, Methionine,

Phenylalanine, Threonine and Histidine.

Recommended daily amount of essential amino acids are vary from one to other. While
adult humans need 4mg of Trp per Kg body weight but need 40 mg of Leu. Children need 20%
higher than adult levels and those for infants (up to one year old) can be as much as 150% higher.

 Arginine is essential for infants, since their bodies cannot

produce them yet.

 Non-essential amino acids:

Nonessential amino acids are those can be produce in human body. Their use and function
in our bodies are equally as important as the essential amino acids. These amino acids are:

Alanine, Cysteine, Glycine, Serine, Tyrosine, Aspartic acid, Glutamine

Glutamic acid, Asparagine, , and Proline.

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Reactions of amino acids.

1-Peptide bonds formation:

The peptide bond is formed by linking the carboxyl group of one amino acid to the amino group of
another amino acid, which accompanied by the loss of a water molecule.

When a polypeptide is named, all amino acid residues have their suffixes (-ine, -an, -ic, or -ate)
changed to "yl" with the exception of the C-terminal amino acid.
For example, a Dipeptide composed of an N-terminal valine, a glycine, and a C-terminal
leucine is called ( valylglycylleucine ).

Question: Give the name for the following tetrapeptide?

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 Classification of Proteins

 Simple proteins are those that hydrolyze to give only amino acids. All the protein structures we
have considered so far are simple proteins.
Examples are insulin, ribonuclease, and oxytocin.

 Conjugated proteins are bonded to a nonprotein prosthetic group such as a sugar, a nucleic
acid, a lipid, or some other group.

 Proteins are classified as fibrous or globular depending on whether they form long filaments or
coil up on themselves.
 Fibrous proteins are stringy, tough, and usually insoluble in water. They function primarily as
structural parts of the organism. Examples of fibrous proteins are α-keratin in hooves and
fingernails, and collagen in tendons.
 Globular proteins are folded into roughly spherical shapes. They usually function as enzymes,
hormones, or transport proteins.

 LEVELS OF PROTEIN STRUCTURE

1- Primary structure (polypeptide)

The primary level of structure in a protein is the linear sequence of amino acids that
covalently linked through peptide bond in the chain, in some proteins the polypeptide can cross-
linked by DISULPHIDE BONDS between cysteine residues (as shown in insulin structure).

Each polypeptide chain has polarity because its ends are different i.e. the polypeptide has a
free amino group at one end called N-terminal and a free carboxyl group at the other end called C-
terminal.

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Chemical structure of insulin

2- Secondary structure (α-helix and β-pleated sheet)

After synthesis, polypeptide chains are folded into different shapes called their secondary
structure. The two most common types of protein fold are α-helix and β-pleated sheet.

1- α-Helix

 The α-helix is rod like structure and right-handed.

 A tightly coiled polypeptide backbone core forms the inner part of the rod
 Side chains extended outward in the helical.
 The helix is stabilized by hydrogen bonds, where carbonyl oxygen of each peptide bond is
hydrogen bonded to the hydrogen on the amino group of fourth amino acid away.

 Essentially all helices found in proteins are right-handed because less strain
clash between the side chains.

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2- β-Pleated sheet:
 The polypeptide is almost fully extended in a zig-zag manner.
 β-pleated sheets are composed of two or more polypeptide chains or a single
polypeptide chain folds on itself.
 They are arranged either parallel (when two strands run in the same direction)
or anti parallel (when two strands run in the opposite direction).
 Hydrogen bonds grouped in pairs between polypeptide chains stabilized the
β-sheet conformation, i.e. for each amino acid, the CO group of each peptide
bond is hydrogen bonded to the NH2 group of peptide bond of the amino acid
on the adjacent chain.

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3- Tertiary structure.

The tertiary structure of a protein is a description of the complex and irregular folding of the
peptide chain in three dimensional structure. It is essentially a picture of what the shape of the
entire protein actually looks like.

There are 4 forces affecting the 3-D shape of proteins. These include

1. hydrophobic interactions between nonpolar R-groups.

2. ionic bonds between charged R-groups.
3. hydrogen bonds between polar R- groups.
4. covalent bonds: The R-group of the amino acid cysteine contains a sulfur atom and this sulfur
atom is capable of forming a covalent bond with another sulfur atom on a different cysteine
molecule somewhere else on the chain.

 This bond is known as a DISULFIDE BOND and it acts to stabilize the tertiary structure of those
proteins that have such bonds.

1-Hydrophobic interaction:

It’s the main driving force behind the folding of the polypeptide chain. It’s the force that
causes nonpolar molecules to minimize their contact with water. In contrast, amino acids with
polar or charged side chains tend to be located on the surface of the molecule in contact with the
polar solvent.

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2-hydrogen bonds:

Amino acid side chains containing oxygen or nitrogen bound hydrogen, such as in the alcohol
groups of serine can form hydrogen bonds with electron-rich atoms, such as the oxygen of a
carboxyl group or carbonyl group.
3-Ionic interactions:
Negatively charged groups, such as the carboxyl group (COOˉ ) in the side chain of aspartate or
glutamate, can interact with positively charged groups, such as the amino group (NH3+) in the side
chain of lysine.

4-Covalent bonds:

These covalent bonds form between cysteine residues that are close together in the final
conformation.

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Four forces affecting the three dimensional shape of proteins.

4- Quaternary structure:

Proteins containing more than one polypeptide chain, exhibit a fourth level of protein
structure called quaternary structure. This level of structure refers to the spatial arrangement of the
polypeptide subunits that are held in association by the same non-covalent forces that stabilize the
tertiary structures of proteins. These non-covalent interactions(ionic interaction, hydrogen
interaction, and hydrophobic interaction).

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 Hemoglobin, the oxygen carrying protein of the blood, contains two α and two β subunits
arranged with a quaternary structure in the form, α2β2.

DENATURATION OF PROTEIN

 Process of partial or total alteration of the native secondary, tertiary, and quaternary
structures of proteins resulting in a loss of bioactivity.

 When the unique 3-D structure of proteins is destroyed it leads to temporary or permanent
loss of activity.

HOW ARE PROTEINS DENATURATED

I - Heating. II- Heavy metal. III- Changes in PH ( High PH ) and ( Low PH ).

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 Heating
Heat can be used to disrupt hydrogen bonds and non-polar hydrophobic interactions. This occurs
because heat increases the kinetic energy and causes the molecules to vibrate so rapidly and
violently that the bonds are disrupted. The proteins in eggs denature and coagulate during
cooking.

 Heavy Metals
Heavy metals act to denature proteins in much the same manner as acids and bases. Heavy metal
usually contain Hg+2, Pb+2, Ag+1, Cd+2 and other metals with high atomic weights. Since Heavy
metals are ionic they disrupt salt bridges in proteins. The reaction of a heavy metal with a protein
usually leads to an insoluble metal protein salt.

 Changes in PH
changes in pH (alters electrostatic interaction between charged amino acids). A protein consists of
amino acids. Some of these amino acids are polar, having positively charged sides and negatively
charged sides. A change in PH simply means a change in the availability of ( H+, ˉOH) atoms. As
you can see these atoms are positively and negatively charged, and attract the negative and
positive sides of the polar amino acids. so a change in the PH changes the stability of a protein
structure and can cause its denaturation.

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