PROTEINS

BIOCHEMISTRY
OVERVIEW
• When scientists began studying nutrition in the early 19th
century, they quickly discovered that natural products
containing nitrogen were very essential for the survival of
animals.

• This class of compound was then coined as protein by

the Swedish chemist Jacob Berzelius in 1939 which was
derived from the Greek word “proteios” which means of
first importance.

• Proteins are the most important macromolecule in the

body because it plats a lot of important physiological
functions. It accounts for 15% of total cell’s mass and for
almost 50% of its dry weight.
IMPORTANCE OF PROTEINS
1. Growth and Maintenance
2. Causes Biochemical Reactions
3. Acts as a messenger
4. Provides structure
5. Maintains proper pH level
6. Balances fluids
7. Bolster Immune Health
8. Transport and Store Nutrients
9. Provides energy
What makes a protein protein?
• Proteins are naturally occurring unbranched polymers
(long chain) of amino acids connected together by
peptide bonds.

• FUN FACT: When proteins were first discovered,

physiological chemists (the term biochemist was not yet
used before) did not realize that proteins were made up of
smaller units, amino acids, although the first amino acid
has already been isolated in 1830. In fact, they believe
that proteins were incorporated whole into tissues of
animal. This misconception was laid to rest when the
process of digestion came to light. It became clear that
ingested proteins were broken down into smaller
compounds.
AMINO ACIDS
• An amino acid is a compound containing a carboxyl (-
COOH) group and amino (-NH2) group at the same time.

• There are more than 300 naturally occurring amino acids,

but only 20 of them are found in humans. These are
known as the Standard Amino Acids (SAA). - Nineteen
(19) of these Standard Amino Acids are α-amino acids.
Proline is the only SAA that is not an α-amino acid.

• An α-amino acid has its carboxyl group and amino group

in the same carbon, known as the α-carbon.
GENERAL STRUCTURE OF AMINO
ACIDS

• The nature of the side chain distinguishes amino acids

from each other
CLASSIFICATION OF STANDARD AMINO
ACIDS
• Because the standard amino acids are distinguished from
each other by their side chains, we can classify them
according to the characteristics of their side chains.

• The most common way to classify standard amino acids

is based on the polarity of their side chains.

• Thus, standard amino acids can either be polar or non-

polar.

• Polar amino acids can be further categorized as polar

neutral, polar acidic, or polar basic.

• The table on the next page demonstrates the differences

among the different classes of amino acids.
CLASSIFICATION OF STANDARD AMINO
ACIDS
THE 20 STANDARD AMINO ACIDS
• The standard amino acids are referred by their common
names. These names are often abbreviated as three-
letter code or one-letter code.

• The illustration below displays the names and complete

structures of the 20 standard amino acids.
CLASSIFICATION OF STANDARD AMINO
ACIDS
NON-POLAR
CLASSIFICATION OF STANDARD AMINO
ACIDS
POLAR NEUTRAL
CLASSIFICATION OF STANDARD AMINO
ACIDS
POLAR NEUTRAL
CLASSIFICATION OF STANDARD AMINO
ACIDS
POLAR BASIC
CLASSIFICATION OF STANDARD AMINO
ACIDS
POLAR ACIDIC
ESSENTIAL AMINO ACIDS
• Essential amino acids are Standard Amino Acids that the
human body cannot adequately synthesize and must,
therefore, be obtained from dietary sources.
• There are 10 essential amino acids necessary for normal
growth of a child. These amino acids can be easily
memorized easily using the mnemonic PVT. TIM HALL
which stands for:

Phenylalanine, Valine, Threonine,

Tryptophan, Isoleucine, Methionine, Histidine,
Arginine, Leucine, and Lysine.
ESSENTIAL AMINO ACIDS
• Arginine is only essential for infants for normal growth,
but becomes nonessential amino acid as they grow into
adulthood.

• Infants that are born prematurely cannot make sufficient

quantities of some nonessential amino acids and these
amino acids become conditionally essential amino acids
until the baby matures. In this situation the conditionally
essential amino acids must be obtained through diet. The
human milk and infant formula milk contain adequate
amounts of these conditionally essential amino acids.
ESSENTIAL AMINO ACIDS
• A complete dietary protein (high-quality protein) is a
protein that contains all of the essential amino acids in
adequate amounts as the body needs them. Proteins
from animal sources are usually complete dietary protein.
Example, casein from milk and albumin from eggs are
considered complete dietary proteins.

• An incomplete dietary protein is a protein that does not

contain in adequate amounts, relative to the body’s
needs, of one or more of the essential amino acids. The
essential amino acid that is missing or present in an
inadequate amount in a incomplete dietary protein is
known as a limiting amino acid. Gelatin is an incomplete
dietary protein having tryptophan as its limiting amino
acid.
ESSENTIAL AMINO ACIDS
• Protein from plant sources are generally incomplete
dietary proteins, with three common limiting amino acids
lysine, methionine, and tryptophan. Soy protein is the only
common plant protein that is considered complete dietary
protein.

• However, mix of plant proteins generally provide complete

dietary protein, such as in the case of rice and beans.
Proteins from rice and beans when eaten together are
known complementary dietary protein.
CHIRALITY OF STANDARD AMINO
ACIDS
If you noticed in the general structure of the Standard Amino
Acids, there are four different group around the α-carbon.
CHIRALITY OF STANDARD AMINO
ACIDS
This means that the α-carbons of the Standard Amino Acids
are stereogenic centers, except glycine since the side chain
of glycine is H resulting to 2 identical hydrogens in its α-
carbon.
ESSENTIAL AMINO ACIDS
• Because 19 of the Standard Amino Acids have
stereogenic centers, they also exist as enantiomers – D
or L.
• To represent the D and L enantiomers of the Standard
Amino Acids, we use the Fischer projection like in
monosaccharides.
ESSENTIAL AMINO ACIDS

The location of the amino group (-NH2) of the α-carbon of a

Standard Amino Acid in its Fischer projection determines its
type of enantiomer.
- For L amino acids, the amino group of the α-carbon is
directed to the left.
- For D amino acids, the amino group of the α-carbon is
directed to the right. - In nature and in proteins, the Standard
Amino Acids are L isomers.
AMPHOTERISM OF
STANDARD AMINO ACIDS
- An amphoteric substance is a substance that can act as
an acid in basic environment and can act as a base in an
acidic environment.
- Some organic compounds exhibit amphoterism, such as
your amino acids.

How is amphoterism possible in amino acids?

The Standard Amino Acids have both carboxyl group

(-COOH) and amino group (-NH2) in one molecule. We
learned in organic chemistry that –COOH is an acidic group
while –NH2 is a basic group
 AMPHOTERISM OF STANDARD
AMINO ACIDS

At neutral pH, carboxyl groups (-COOH) have the tendency to lose

protons (H+ ), producing a negatively charged species known as
carboxylate ions.
 AMPHOTERISM OF STANDARD
AMINO ACIDS

At neutral pH, amino groups (-NH2) have the tendency to accept

protons (H+ ), producing a positively charged species known as
quaternary ammonium ions.
AMPHOTERISM OF STANDARD
AMINO ACIDS

Because of this acid-base property of

the carboxyl and amino groups, in
aqueous solutions, the –COOH of
the Standard Amino Acids donates a
proton to its –NH2. We can
characterize this as an intramolecular
acid-base reaction.
AMPHOTERISM OF STANDARD
AMINO ACIDS

Because of this acid-base property of

the carboxyl and amino groups, in
aqueous solutions, the –COOH of
the Standard Amino Acids donates a
proton to its –NH2. We can
characterize this as an intramolecular
acid-base reaction.
AMPHOTERISM OF STANDARD
AMINO ACIDS

This structure is known as the zwitterion form of a Standard Amino

Acid.

- A zwitterion is a molecule having a positive charge on one side

and negative charge on the other. Take note that while a zwitterion
has charged groups it is neutral molecule because the number of
groups with positive charge is equal to the number of groups with
negative charge resulting to zero net charge.

- In solution near neutral pH and in solid state, the standard amino

acids exist as zwitterions.
AMPHOTERISM OF STANDARD
AMINO ACIDS

This structure is known as the zwitterion form of a Standard Amino

Acid.

- A zwitterion is a molecule having a positive charge on one side

and negative charge on the other. Take note that while a zwitterion
has charged groups it is neutral molecule because the number of
groups with positive charge is equal to the number of groups with
negative charge resulting to zero net charge.

- In solution near neutral pH and in solid state, the standard amino

acids exist as zwitterions.
PEPTIDES
A peptide is a chain of amino acids that is formed when
the carboxyl group of the α-carbon of an amino acid
reacts with the amino group of the α-carbon of the second
amino acid.

The bond formed in this reaction is generally an amide bond.

However, for peptides proteins, the bond is called a peptide bond.

The formation of peptide is clearly a type of dehydration reaction,

since water is a product after the reaction. For every peptide bond
that is formed in a reaction, there is also a production of 1 water
molecule
CLASSIFICATION OF
PEPTIDES
- Peptides are classified according to the number of
amino acid residues present.

- For example, the peptide below is considered a

dipeptide because it contains 2 amino acid residues:
CLASSIFICATION OF
PEPTIDES
- Tripeptide is the classification of peptides with 3 amino
acid residues, tetrapeptide for those with 4 amino
acids, and so on.

- Normally, when a peptide has 10-20 amino acid

residues it is already referred as an oligopeptide. When it
contains more than 20 amino acid residues already it is
already referred to as polypeptide.

NOTE: Peptides are not proteins. However, proteins are

composed of polypeptides. As we will later find out, some
proteins may contain more than one polypeptide chain
and other non-amino acid group
NOMENCLATURE OF
PEPTIDES
Peptides are named using the following rules:

1. The C-terminal amino acid residue keeps its full name.

2. All other amino acids have names that end in –yl. The –yl
suffix replaces the -ine or –ic acid ending of the amino acid
name, except for tryptophan (tryptophyl), cysteine
(cysteinyl), glutamine (glutaminyl), and asparagine
(asparaginyl).

3. The amino acid naming sequence begins at the N-terminal

acid residue.
NOMENCLATURE OF
PEPTIDES

alanylcysteinylphenylalanylserine

Abbreviation
Ala-Cys-Phe-Ser
ISOMERIC PEPTIDES
• Given 20 different amino acids, there are countless possible
combination of peptides.

• The number of possible of isomers in a peptide is given by

20n , where n is the number of amino acid residues.

• Peptides that contain the same kind and number of amino

acids but differ in order are called isomeric peptides.
PROTEINS
- The term protein is reserved for polypeptides with a
large number of amino acid residues, usually more
than 40 residues.

- A protein may contain only one or more than one

polypeptide chain. For this reason, proteins can be
classified as:

1. Monomeric proteins – contain only one polypeptide

chain (protein subunit)

2. Multimeric proteins – contain more than one protein

subunits. The protein subunits in a multimeric protein
may be all identical to each other or completely
different from each other. An example of a multimeric
protein is insulin, composed of 2 protein subunits that
are different from each other.
PROTEINS

Proteins may also contain non-amino

acid groups known as prosthetic groups.
Thus, proteins can also be classified as:

1. Simple proteins – only amino acid is

present

2. Conjugated proteins – contain amino

acids and prosthetic groups
PROTEINS
PRIMARY STRUCTURE OF
PROTEINS
• The amino acid sequence (the primary
structure) of a protein determines its three-
dimensional structure, which, in turn,
determine its functions.

• The sequence of amino acids in a protein’s

primary structure is decided by the genes.

What is the importance of knowing the

primary structure of a protein?

A change in amino acid sequence of a

protein may or may not matter, depending on
what kind of change it is.
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CLEAVAGE OF PROTEINS INTO
POLYPEPTIDES

• Polypeptides are cleaved at specific

sites by chemical reagents or by
enzymes.

• The following reagents and enzymes

are often used in breaking a protein
into smaller peptide fragments
CLEAVAGE OF PROTEINS INTO
POLYPEPTIDES
CLEAVAGE OF PROTEINS INTO
POLYPEPTIDES
CLEAVAGE OF PROTEINS INTO
POLYPEPTIDES
 SECONDARY STRUCTURE
OF PROTEINS
• The next level of protein structure is the
secondary structure, which refers to
regular localized arrangement of
polypeptide backbone of the protein.

• There are two commonly occurring

secondary structures in proteins – the α
helix and the β pleated sheet. These 2
are periodic structures, meaning their
features repeat in regular intervals
 SECONDARY STRUCTURE
OF PROTEINS
The α Helix

• The α helix is helical (spiral) repeating

structure of a polypeptide chain.

• The shape of the helix is maintained by

hydrogen bond between the carbonyl (–
C=O) of one amino acid and an N-H of
another amino acid located four
residues further along the polypeptide
chain
 SECONDARY STRUCTURE
OF PROTEINS
The α Helix
 SECONDARY STRUCTURE
OF PROTEINS
The α Helix

DNA is an example of a helix structure

 SECONDARY STRUCTURE
OF PROTEINS
The β Pleated Sheet

• In this type of secondary structure, the

peptide backbone is almost fully
extended
TERTIARY STRUCTURE OF
PROTEINS
The α Helix

• The α helix is helical (spiral) repeating

structure of a polypeptide chain.

• The shape of the helix is maintained by

hydrogen bond between the carbonyl (–
C=O) of one amino acid and an N-H of
another amino acid located four
residues further along the polypeptide
chain
 QUARTERNARY
STRUCTURE OF PROTEINS