PROTEINS

CLASSIFICATIONS, REACTIONS, STRUCTURES AND MORE

PROTEINS
PROTEINS – are biomolecules that contain many amide bonds, formed by joining amino acids
together. It came from the Greek word proteios meaning “of first importance. It occurs widely in
the human body, accounting for approximately 50% of its dry weight.

Proteins are classified based on the function:

▪ Structural/Fibrous proteins: give support and structure to tissues and cells.
Examples: keratin in hair, skin, nails and collagen in connective tissue.
▪ Transport proteins : carry substances through the blood
▪ Storage proteins: store elements and ions in organs.
▪ Contractile proteins : control muscle movements
▪ Immunoglobulins: proteins that defend the body against foreign substances.
▪ Signal Proteins: communication with other cells
Amino Acids
What are Amino Acids?
▪ An organic compound containing the amino group and a carboxyl group.
▪ It contains two functional groups- an amino group (NH2) and carboxyl group (COOH).
▪ The 20 amino acids commonly found in proteins are alled alpha (α) amino acids.
▪ Humans can synthesize only 10 of the 20 amino acids needed for proteins. The
remaining 10, called essential amino acids, must be obtained from the diet and
consumed on a regular, almost daily basis.
Properties of Amino Acids
▪ Amino acids are colorless, crystalline solid.
▪ All amino acids have a high melting point greater than 200o
▪ Solubility: They are soluble in water, slightly soluble in alcohol and dissolve with
difficulty in methanol, ethanol, and propanol. R-group of amino acids and pH of the
solvent play important role in solubility.
▪ On heating to high temperatures, they decompose.
▪ All amino acids (except glycine) are optically active.
▪ Peptide bond formation: Amino acids can connect with a peptide bond involving their
amino and carboxylate groups. A covalent bond formed between the alpha-amino
group of one amino acid and an alpha-carboxyl group of other forming -CO-NH-
linkage. Peptide bonds are planar and partially ionic.
 THE 20 COMMON AMINO ACIDS

BE FAMILIARIZED WITH THE STRUCTURES, IT WILL BE INCLUDED ON THE QUIZZES AND EXAMS
STRUCTURE OF AMINO ACIDS
All 20 of the common amino acids are alpha-amino acids. They contain a carboxyl
group, an amino group, and a side chain (R group), all attached to the α-carbon.
▪ The 20 amino acids that occur naturally in proteins differ in the
identity of the R group bonded to the 𝛼 carbon.
▪ The R group is called the side chain of the amino acid.
▪ The simplest amino acid, called glycine, has R=H.
▪ Amino acids with an additional COOH group in the side chain are
called acidic amino acids. Those with an additional basic N atom in
the side chain are called basic amino acids. All other are neutral
amino acids.
CLASSIFICATIONS OF
AMINO ACIDS
Nonpolar, Aliphatic amino acids: The
R groups in this class of amino acids are
nonpolar and hydrophobic. Glycine,
Alanine, Valine, leucine, Isoleucine,
Methionine, Proline.
CLASSIFICATIONS OF
AMINO ACIDS
Aromatic amino
acids: Phenylalanine, tyrosine, and
tryptophan, with their aromatic side
chains, are relatively nonpolar
(hydrophobic). All can participate in
hydrophobic interactions. It has a
rings
CLASSIFICATIONS OF
AMINO ACIDS
Polar, Uncharged amino acids: The R
groups of these amino acids are more
soluble in water, or more hydrophilic, than
those of the nonpolar amino acids, because
they contain functional groups that form
hydrogen bonds with water. This class of
amino acids includes serine, threonine,
cysteine, asparagine, and glutamine.
CLASSIFICATIONS OF
AMINO ACIDS
Acidic amino acids: Amino
acids in which R-group is acidic
or negatively charged. Glutamic
acid and Aspartic acid
CLASSIFICATIONS OF
AMINO ACIDS
Basic amino acids: Amino acids
in which R-group is basic or
positively charged. Lysine,
Arginine, Histidine
ACID-BASE PROPERTIES OF AMINO ACIDS
As mentioned, an amino acid contains both a basic amino acid group (NH2) and an acidic carboxyl
group (COOH). As a result, proton transfer from the acid to the base forms a zwitterion, a salt that
contains both a positive and a negative charge. The zwitterions is neutral; that is, the net charge on
the salt is zero.
 An amino acid can exist in different forms, depending on the pH of the aqueous solution in
which it is dissolved. When the pH of a solution is around 6, alanine (R=𝐶𝐻3) and other
neutral amino acids exist in their zwitterionic form (A), having no net charge. In this form,
the carboxyl group bears a net charge- it is a carboxylate anion- and the amino group bears
a net positive charge (an ammonium cation).

When strong acid is added to lower

the pH to 2 or less, the carboxylate
anion gains a proton and the amino
acid has a net positive charge (form
B).
When the strong base is added to A to raise the pH to 10 or higher, the ammonium
cation loses a proton and the amino acid has a net negative carge (form C).

Thus, alanine exists in one of three different forms depending on the pH of the solution in
which it is dissolved. At the physiological pH of 7.4, neutral amino acids are primarily in their
zwitterionic forms.
The pH which the amino acid exists primarily in its neutral form is called isoelectric point,
abbreviated as “pI”. The isoelectric points of neutral amino acids are generally around 6
Acidic amino acids (refer to the table below), which The three basic amino acids, which have additional
have an additional carboxyl group that can lose a basic nitrogen atom that can accept a proton, have
proton, have lower pI values (around 3). higher pI values ( 7.6-10.8)
PEPTIDES
When amino acids are joined together by amide bonds, they form larger molecules
called peptides and proteins.
A dipeptide has two amino acids joined together by one amide bond.
A tripeptide has three amino acids joined together by two amide bonds.
Polypeptides and proteins both have many amino acids joined together in long linear
chains, but the term protein is usually reserved for polymers of more than 40 amino
acids.
• The amide bonds in peptides and proteins are called peptide bonds
• The individual amino acids are called amino acid residues.

Peptide bond – a covalent bond between the carboxyl group of one amino acid and the
amino group of the other amino acid.
Amino acid residue – portion of amino acid structure that remains after release of H2O,
when an amino acid participates in peptide formation as it becomes part of a peptide
chain.
Peptide chain – an amide bond that links two amino acids
STRUCTURE OF PROTEINS
(based on complexity)
1. PRIMARY STRUCTURE
- It is the particular sequence of amino acids
that is joined together by peptide bonds.
- the most important element of this structure
is the amide bond that joins the amino
acids.
- the primary structure of a protein-the exact
sequence of amino acids- determines all
properties and function of a protein.
 STRUCTURE OF PROTEINS
(based on complexity)
SECONDARY STRUCTURE
- It is the three-dimensional arrangement of localized regions of a protein.
- These regions arise due to hydrogen bonding between the N—H proton of one amide and the C=O
ocygen of another. Two arrangements that are particularly stable are called the 𝛼-helix and the 𝛽-
pleated sheet.
𝜶-helix – this forms when a peptide chain twists into a right-handed or clockwise spiral.
Important features of 𝜶-helix :
- Each turn of the helix has 3.6 amino acids
- The N—H and C=O bonds point along the axis of the helix in opposite directions.
- The C=O group of one amino acid is hydrogen bonded to an N—H group four amino acid residues
father along the chain.
- The R groups of the amino acids extend outward from the core of the helix.
- Both myosin in muscle and the 𝛼-keratin in hair are proteins composed almost entirely of 𝛼-helices.
Two Different Illustration of the 𝛂-Helix

THE BACKBONE THE RIGHT-HANDED

OF THE HELIX : 𝛼-HELIX : All atoms of
Only the peptide the 𝛼-helix are drawn
backbone is in this representation.
drawn in this All C=O bonds are
representation. pointing up and all the
The Hydrogen N—H bonds are
bonds between pointing down.
the C=O and
N—H of amino
acids four
residues away
from each other
are shown.
𝜷- Pleated Sheet – This forms when two or more peptide chains, called strands, line up side-by-side.
✓ Characteristics of the 𝛽- Pleated Sheet:
- The C=O and N—H bonds lie in the plane of the sheet.
- Hydrogen bonding often occurs between N—H and C=O groups of nearby amino acid
residues.
- The R groups are oriented above and below the plane of the sheet, and alternate from one side to the
other along a given strand.
- The 𝛽- Pleated Sheet arrangement is
favoured by amino acids with small R groups,
like alanine and glycine. With larger R groups,
steric interactions prevent the chains from
getting close together, so the sheet cannot be
stabilized by hydrogen bonding.

Three-Dimensional Structure of the 𝛽 - Pleated Sheet

Shorthand symbols are often used to indicate these regions of secondary structure, as well
as disulfide bonds that are sometimes present. In particular, a flat helical ribbon is used for
the 𝛼-helix, while flat wide arrow is used for the 𝛽 - Pleated Sheet. These representations are
often used in ribbon diagrams to illustrate protein structure.
SHORTHAND SYMBOLS REPRESENTING PROTEIN STRUCTURE
TERTIARY STRUCTURE – The three-dimensional shape adopted by the entire peptide
chain. A peptide generally folds into a shape that maximizes its stability.
-Disulfide bonds are the only covalent bonds that stabilize tertiary structure. These strong
bonds form by the oxidation of two cysteine residues on either the same polypeptide chain
or another polypeptide chain of the same protein.
- For example, INSULIN, consists of two separate polypeptide chains (labelled Chain A and
Chain B) that are covalently linked by two intermolecular disulfide bonds. The A chain, which
also has an intramolecular disulfide bond, has 21 amino acid residues, whereas the B chain
has 30.
QUATERNARY STRUCTURE – The shape adopted when two or more folded
polypeptide chains come together into one protein complex.
- Each individual polypeptide chain is called a subunit of the overall protein.
Hemoglobin, for example, consists of two 𝛼 and two 𝛽 subunits held together by
intermolecular forces in a compact three-dimensional shape. The unique function of
haemoglobin is possible only when all four subunits are together.
Overview of Four Levels of
Proteins
CLASSIFICATION OF PROTEIN
FIBROUS PROTEINS – composed of long linear polypeptide chains that are bundled
together to form rods of sheets. These proteins are insoluble in water and serve
structural roles, giving strength and protection to tissues and cells. (SECONDARY
STRUCTURE)
Examples :
a. 𝜶- Keratins – the proteins found in hair, hooves, nails, skin and wool. They are
composed almost exclusively of long sections of 𝛼-helix units, having
large numbers of alanine and leucine residues.
b. Collagen – the most abundant protein in vertebrates, found in connective tissues
such as bone, cartilage, tendons, teeth and blood vessels.
CLASSIFICATION OF PROTEIN
GLOBULAR PROTEINS – are coiled into compact shapes with hydrophilic outer space that
makes them water soluble. Enzymes and transport proteins are globular to make them
soluble in blood and other aqueous environments. (TERTIARY STRUCTURE)
Examples : a. Hemoglobin – consists of four polypeptide chains, each of which
carries a heme unit.
- has more nonpolar amino acid residues that myoglobin.
- present in red blood cells, transports oxygen to wherever it is
needed in the body.
b. Myoglobin – stores oxygen in tissues.
- has 153 amino acid residues in a single polypeptide chain. It has 8 separate alpha-helical
sections and a heme group held in a cavity inside the polypeptide. It also gives cardiac
muscle its characteristic red color.
IMPORTANCE OF GLYCOPROTEINS
& LIPOPROTEINS
What is Glycoprotein?
- is a type of protein molecule that has had a carbohydrate attached to it. The process
either occurs during protein translation or as a posttranslational modification in a
process called glycosylation.
- The carbohydrate is an oligosaccharide chain (glycan) that is covalently bonded to the
polypeptide side chains of the protein. Because of the -OH groups of sugars,
glycoproteins are more hydrophilic than simple proteins. This means glycoproteins are
more attracted to water than ordinary proteins. The hydrophilic nature of the molecule
also leads to the characteristic folding of the protein's tertiary structure.
IMPORTANCE OF
GLYCOPROTEIN
a. Glycoproteins on the cell surfaces are important for communication between cells, for
maintaining cell structure and for self recognition by the immune system
b. Glycoproteins are also important for red blood cells. Blood type refers to the type of
glycoprotein on our red blood cells. If you have type A blood, you have A antigens, or A
glycoproteins, on your red blood cells. This helps the body to identify that your blood is
part of you and tells it not to attack it.
c. Glycoproteins also help to stimulate the process of coagulation of platelets to clot
blood when you get cut. People who are missing important proteins on platelets can't
clot their blood and have a disease called hemophilia, where any cut continues to
bleed indefinitely.
d. Glycoproteins are on the surface of skin cells, called epithelial cells. These help to
attach our skin cells to each other, forming a tough barrier to protect our body.
e. adherins are an example of a glycoprotein that helps our skin hold together.
What is Lipoprotein?
- Lipoprotein is a substance that carries cholesterol throughout your system. There are 2
main kinds:
1. Low-density lipoprotein (LDL). It’s often called the “bad cholesterol.”
2. High-density lipoprotein (HDL). That’s the “good cholesterol.”
- Lipoproteins are special particles made up of droplets of fats surrounded by a single
layer of phospholipid molecules.
CHOLESTEROL IS USED FOR:
HORMONE MAKING
VIT D MAKING
BILE MAKING
IMPORTANCE OF
LIPOPROTEINS:
a. Its main function is to transfer lipids such as cholesterol via blood stream.
b. It helps the body sustain its nerve cell and other vital cells in our body.
c. it also helps the lipids transport energy to the muscles.