PROTEINS (2)

Proteins are among the most abundant

organic molecules in living systems and
are way more diverse in structure and
function than other classes of
macromolecules. You can find it in every
single cell, from your hair and facial
muscles to your toenails. Protein is
composed of amino acids, which are
organic compounds made of carbon,
hydrogen, nitrogen, oxygen or sulfur. A
protein molecule is very large compared
with molecules of sugar or salt and
consists of many amino acids joined
together to form long chains, much as
beads are arranged on a string. Virtually
all the complex chemical functions of the
living cell are performed by protein-based catalysts called enzymes. Specifically,
enzymes either make or break chemical bonds. Further, most of the scaffolding that
holds cells and organelles together is made of proteins. In addition to their catalytic
functions, proteins can transmit and commute signals from the extracellular
environment, duplicate genetic information, assist in transforming the energy in light and
chemicals with astonishing efficiency, convert chemical energy into mechanical work,
and carry molecules between cell compartments.

Classification of Proteins:

A) Based on Composition:

Simple Proteins - the proteins which contain only amino acids.

a) Albumins
b) Globulins
c) Glutelins
d) Histories
e) Protamine
f) Prolamines
g) Scleroproteins
Conjugated Proteins - contain amino acid + prosthetic group (non-amino acid).

a) Glycoproteins
b) Chromoproteins
c) Lipoproteins
d) Nucleoproteins
e) Phosphoprotein

B) Based on Structure:

Fibrous - These are fibre like in shape and insoluble in water and resistance to
digestion. These are mainly of animal origin. Most fibrous proteins serve as structural
components of our body eg; Keratins, elastins, collagens. The collagens and elastins
are found as a component of skin, connective tissues and blood vessels wall whereas
keratin is found in skin and hair. The important fibrous proteins are:

1. Collagens
2. Elastins
3. Keratins
4. Fibroin

Globular - They are usually soluble in water and in aqueous media containing acid,
base, salt and alcohol. The globular proteins are more complex in configuration than
fibrous proteins. They have the greater variety of function, nearly all enzymes are
globular. Examples: Hemoglobin.

Function of Protein:

Role Examples Functions

Act as catalysts in biochemical reactions,

meaning that they speed the reactions up. Break
Digestive Amylase, lipase, down nutrients in food into small pieces that can
enzyme pepsin be readily absorbed

Carry substances throughout the body in blood

Transport Hemoglobin or lymph
Role Examples Functions

Actin, tubulin,
Structure keratin Build different structures, like the cytoskeleton

Coordinate the activity of different body systems.

Hormone These protein-based hormones are commonly
signaling Insulin, glucagon called peptide hormone

Defense Antibodies Protect the body from foreign pathogens

Contraction Myosin Carry out muscle contraction

Legume storage
proteins, egg white Provide food for the early development of the
Storage (albumin) embryo or the seedling

Formation of Proteins:

Amino Acids –> Peptide and Polypeptides -> Proteins

Links:

https://en.wikibooks.org/wiki/Biochemistry/Proteins

https://www.britannica.com/science/protein

https://ghr.nlm.nih.gov/primer/howgeneswork/protein

https://www.slideshare.net/kareemhussien5/protiens-biochemistry

https://en.wikibooks.org/wiki/Biochemistry/Proteins/Introduction

https://www.khanacademy.org/science/biology/macromolecules/proteins-and-amino-
acids/a/introduction-to-proteins-and-amino-acids

https://www.kullabs.com/classes/subjects/units/lessons/notes/note-detail/6127

http://www.agriinfo.in/default.aspx?page=topic&superid=4&topicid=1576
AMINO ACIDS (1)

Amino acids are the building blocks of proteins. Specifically, a protein is made up of one
or more linear chains of amino acids, each of which is called a polypeptide.

 The sequence of amino acids in the chain

determines how the chain will fold up to make
the protein, so different proteins have different
three-dimensional shapes.
 The three-dimensional shape of a protein
determines its function. This is because proteins
form attachments and interact with many other
molecules and structures inside organisms.
 The shape of a protein determines what it
can interact with, just like the shape of a key
determines which locks it can operate.

Structure

Amino acids share a basic structure, which consists of a central carbon atom, also
known as the alpha (α) carbon, bonded to an amino group (NH2), a carboxyl group
(COOH) and a hydrogen atom.
Every amino acid also has another atom or group of atoms bonded to the central atom,
known as the R group, which determines the identity of the amino acid. The R group is
often referred to as the side chain. For instance, if the R group is a hydrogen atom, then
the amino acid is glycine, while if it’s a methyl (CH3) group, the amino acid is alanine.

The properties of the side chain determine an amino acid’s chemical behavior (that is,
whether it is considered acidic, basic, polar, or nonpolar).

Chemical classification of Amino Acids:

 There are 20 types of amino acids commonly found in proteins.
General chemical characteristics of their R groups:

1. Hydrophobic amino acids with nonpolar R groups

2. Polar amino acids with neutral R groups but the charge is not evenly distributed

3. Positively charged amino acids with R groups that have a positive charge at
physiological pH

4. Negatively charged amino acids with R groups that have a negative charge at
physiological pH

Links:

https://www.khanacademy.org/science/biology/macromolecules/proteins-and-amino-
acids/a/introduction-to-proteins-and-amino-acids

http://kidshealth.org/en/kids/protein.html#

https://www.bbc.co.uk/education/guides/zcr74qt/revision/1

http://www.aminoacidsguide.com/

https://www.slideshare.net/kareemhussien5/protiens-biochemistry

https://www.coursehero.com/file/p3bfea8/unctional-groups-these-groups-have-hydrogen-bonding-
potential-or-the-ability-to/

Essential and Non-essential Amino Acids (1)

 Of those 20 amino acids, nine of which are called “essential” and 11 of which are
labeled as “non-essential.” All 20 have distinct chemical structures and are used
for different roles – such as forming neurotransmitters, forming hormones and
producing energy. But their primary role is to build proteins.
Essential
First up are the essential amino acids. These are the nine amino acids that your body
cannot create its own, and that you must obtain by eating various foods. Adults need to
eat foods that contain the following eight amino acids: methionine, valine, tryptophan,
isoleucine, leucine, lysine, threonine and phenylalanine. Histidine, the ninth amino acid,
is only necessary for babies.

Instead of storing up a supply of the essential acids, the body uses them to create new
proteins on a regular basis. Therefore, the body needs a continual – ideally daily –
supply of these amino acids to stay healthy.

Non-Essential
The other type is the non-essential amino acid, 11 of which exists and is synthesized by
the body. Thus, although they are an important part of building proteins, they do not
need to be included in an everyday diet. Eight of these non-essential acids are also
known as “conditional,” meaning that the body may not be capable of producing enough
of them when presented with substantial stress or illness.

Link: https://www.sproutliving.com/what-are-essential-and-nonessential-amino-acids/

Peptide bonds (1)

 Each protein in your cells consists of one or more polypeptide chains. Each of
these polypeptide chains is made up of amino acids, linked together in a specific
order.
 The amino acids of a polypeptide are attached to their neighbors by covalent
bonds known as peptide bonds. Each bond forms in a dehydration synthesis
(condensation) reaction (removal of the water molecules - one hydrogen atom
from one amino acid and an OH group from the other). This process can then
continue to join other amino acids and yield in an amino acid chain. When there
are few amino acids in a chain, it is called an oligopeptide, when there are many
it is called a polypeptide. .
 During protein synthesis, the carboxyl group of the amino acid at the end of the
growing polypeptide chain reacts with the amino group of an incoming amino
acid, releasing a molecule of water. The resulting bond between amino acids is a
 peptide bond because of the structure of the amino acids; a polypeptide chain
has directionality, meaning that it has two ends that are chemically distinct from
one another. At one end, the polypeptide has a free amino group, and this end is
called the amino terminus (or N-terminus). The other end, which has a free
carboxyl group, is known as the carboxyl terminus (or C-terminus).

Link: https://www.khanacademy.org/science/biology/macromolecules/proteins-and-amino-
acids/a/introduction-to-proteins-and-amino-acids

Four Levels of Protein Structure (1)

Primary Structure: Amino Acids Are Linked by Peptide Bonds to Form Polypeptide
Chains

 Simply the sequence of amino acids in a polypeptide chain. Proteins are linear
polymers formed by linking the a-carboxyl group of one amino acid to the a-
amino group of another amino acid. The formation of a dipeptide from two amino
acids is accompanied by the loss of water. A polypeptide chain consists of a
regularly repeating part, called the main chain or backbone, and a variable part,
comprising the distinctive side chains. The polypeptide backbone is rich in
hydrogen-bonding potential. Each residue contains a carbonyl group (CPO),
which is a good hydrogen-bond acceptor, and, with the exception of proline, an
NH group, which is a good hydrogen-bond donor.
Secondary Structure: Polypeptide Chains Can Fold into Regular Structures Such As the
Alpha Helix, the Beta Sheet, and Turns and Loops

 This refers to local folded structures that form within a polypeptide due to
interactions between atoms of the backbone. (The backbone just refers to the
polypeptide chain apart from the R groups – so all we mean here is that
secondary structure does not involve R group atoms.) The most common types
of secondary structures are the α helix and the β pleated sheet. Both structures
are held in shape by hydrogen bonds, which form between the carbonyl O of one
amino acid and the amino H of another.

Tertiary Structure: Water-Soluble Proteins Fold into Compact Structures with Nonpolar
Cores

 The overall three-dimensional structure of a polypeptide. The tertiary structure is

primarily due to interactions between the R groups of the amino acids that make
up the protein.
 R group interactions that contribute to tertiary structure include hydrogen
bonding, ionic bonding, dipole-dipole interactions, and London dispersion forces
– basically, the whole gamut of non-covalent bonds. Also important to tertiary
structure are hydrophobic interactions, in which amino acids with nonpolar,
hydrophobic R groups cluster together on the inside of the protein, leaving
hydrophilic amino acids on the outside to interact with surrounding water
molecules.
 Finally, there’s one special type of covalent bond that can contribute to tertiary
structure: the disulfide bond. Disulfide bonds, covalent linkages between the
sulfur-containing side chains of cysteines, are much stronger than the other types
of bonds that contribute to tertiary structure. They act like molecular "safety pins,"
keeping parts of the polypeptide firmly attached to one another.

Quaternary Structure: Polypeptide Chains Can Assemble into Multisubunit Structures

 Many proteins are made up of a single polypeptide chain and have only three
levels of structure. However, some proteins are made up of multiple polypeptide
chains, also known as subunits. Concerns interactions by which two or more
polypeptide chains associate in a specific manner to form biologically active
 proteins. It is formed by noncovalent association of tertiary structure. Two or
more polypeptides are called oligomer.

Links:
https://ia801303.us.archive.org/13/items/BiochemistryStryer7th/Biochemistry%20Stryer%207th.pdf

https://en.wikibooks.org/wiki/Biochemistry/Proteins/Protein_structure_and_folding

https://www.khanacademy.org/science/biology/macromolecules/proteins-and-amino-acids/a/orders-
of-protein-structure
LOSS OF PROTEIN STRUCTURE

Denaturation and Protein

Each protein has its own unique shape. If the temperature or pH of a protein's
environment is changed, or if it is exposed to chemicals, these interactions may be
disrupted, causing the protein to lose its three-dimensional structure and turn back into
an unstructured string of amino acids. When a protein loses its higher-order structure,
but not its primary sequence, it is said to be denatured. Denatured proteins are usually
non-functional.

For some proteins, denaturation can be reversed. Since the primary structure of the
polypeptide is still intact (the amino acids haven’t split up), it may be able to re-fold into
its functional form if it's returned to its normal environment. Other times, however,
denaturation is permanent. One example of irreversible protein denaturation is when an
egg is fried. The albumin protein in the liquid egg white becomes opaque and solid as it
is denatured by the heat of the stove, and will not return to its original, raw-egg state
even when cooled down.

PROTEINS AS ENZYMES

Enzymes are biological catalysts - catalysts are substances that increase the rate of
chemical reactions without being used up. Enzymes are also proteins that are folded
into complex shapes that allow smaller molecules to fit into them. The place where
these substrate molecules fit is called the active site. If the shape of the enzyme
changes, its active site may no longer work; we say the enzyme has been denatured.
They can be denatured by high temperatures or extremes of pH.
Active sites

Active sites are cracks or hollows on the surface of the enzyme caused by the way the
protein folds itself up into its tertiary structure. Molecules of just the right shape and with
just the right arrangement of attractive groups can fit into these active sites. Other
molecules won't fit or won't have the right groups to bind to the surface of the active site.
We would describe the molecule which is actually going to react as the reactant. The
reactant in an enzyme reaction is known instead as the substrate.

Enzyme Cofactors

What we have said so far is a major over-simplification for most enzymes. Most
enzymes aren't in fact just pure protein molecules. Other non-protein bits and pieces are
needed to make them work. These are known as cofactors. In the absence of the right
cofactor, the enzyme doesn't work.

The complete functional or active complex of an enzyme including its required cofactors
is known as holoenzyme; the protein part free of cofactors is called apoenzyme. There
are two basically different sorts of cofactors. Some are bound tightly to the protein
molecule so that they become a part of the enzyme - these are called prosthetic
groups. Some are entirely free of the enzyme and attach themselves to the active site
alongside the substrate - these are called coenzymes.

Links: https://www.khanacademy.org/science/biology/macromolecules/proteins-and-amino-
acids/a/orders-of-protein-structure

https://www.chemguide.co.uk/organicprops/aminoacids/enzymes.html

http://www.bbc.co.uk/schools/gcsebitesize/science/add_aqa_pre_2011/enzymes/enzymes1.shtml

http://nat5biopl.edubuzz.org/unit-1-cell-biology/5-proteins-enzymes

http://www.chem4kids.com/files/bio_enzymes.html