05_Proteins

5 PROTEINS
Summary taken from the books:

BIOCHEMISTRY by L. Stryer
August, 2013
Summarized by Eugenia Olivera
Each amino acid presents a specific weight,
charge and solubility
Proteins are interesting three-
dimensional structures because their
three-dimensional structure depends
simply on their primary structure.
Proteins can be understand by their

structure:
• Primary
• Secondary
• Tertiary
• Quaternary
These structures are possible due
different types of stabilizing forces:
 Covalent Bonds
 Hydrogen Bonds
 Van der Waals Forces
 Disulfur Bonds
 Ionic Interactions
 Hydrophobic Interactions
PRIMARY STRUCTURE
Consists on the linear polymer formed by

linking the a-carboxyl group of an amino
acid to the a-amine group of another
amino acid.
This linkage is called PEPTIDE BOND
(also called amide bond) and the
reaction is followed by the loose of a
water molecule.
Rich in hydrogen-bonding
potential
Side chain
Backbone = main chain
Natural polypeptide
chains contain between
50 and 2000 amino
acids
Frederick Sanger  1953  determined the
amino acid sequence of insulin (protein
hormone).
This work is a landmark in biochemistry

because it showed for the first time that a
protein has a precisely defined amino acid
sequence consisting only of L amino acids
linked peptide bonds.
Today there are known complete amino acid

sequences of more than 2 million proteins.
Striking fact  each protein has a unique,

precisely defined amino acid sequence.
http://www.ncbi.nlm.nih.gov/protein
PEPTIDE BOND
Strong covalent
bond
Planar bond
Trans
There is rotation on
the other bonds
between the a-
carbon and the
amino group of one
amino acid and
between the a-
carbon and the
carboxyl group of
another amino acid
SECONDARY STRUCTURE
Occurs when a
polypeptide chain folds
into a regular repeated
structure:
a-helix
b-sheet
a-helix
(A) A ribbon depiction shows the –carbon atoms and
side chains (green).
(B) A side view of a ball-and-stick version depicts the
hydrogen bonds (dashed lines) between NH and CO
groups.
(C) An end view shows
the coiled backbone as
the inside of the
helix and the side
chains (green) projecting
outward.
(D) A space-filling view of
part C shows the tightly
packed interior core of
the helix. The CO group of each
amino acid forms a
hydrogen bond with the NH
group of the amino acid
that is situated four
residues ahead in the
a-helix
- All the main chain CO and NH groups are
hydrogen bonded
- Essentially all a helices found in proteins
are right-handed
- About 25% of all soluble proteins are
composed of a helices
- Many proteins that span biological
membranes also contain a helices
b-sheet
Antiparallel
Are stabilized by
hydrogen bonding
between polypeptide
strands.
Adjacent chains in a b
sheet can run in
opposite directions
(antiparallel b sheet)
or in the same
direction (parallel b
sheet)
Parallel
TERTIARY STRUCTURE
Occurs when a R groups

are interacting:
-Non polar groups – Van

der Waal
-Polar groups – Hydrogen
bounds
-Charged R groups –
Strong ionic bonds
-Among two cysteine
amino acids - Disulfide
bridge (strong covalent
bond)
QUATERNARY STRUCTURE
Occurs when multiple

polypeptide chains can
assemble into a single
protein.
-Not all proteins present

quaternary structure.
-Depending on the
number of subunits there
are:
- Dimers
- Trimers
- Tetramers
Proteins fall into two general
categories:
• FIBROUS proteins: are found only in animals. They

usually serve as structural entities such as
connective tissue, tendons, and muscle fiber.
They’re normally insoluble in water.
• GLOBULAR proteins: don’t usually serve as

structural function. They can act as transporters,
like hemoglobin, and are often enzymes. They’re
usually water-soluble.
Living organisms use proteins in a
number of ways:
• STRUCTURE: skin and bone contain collagen, a

fibrous protein.
• CATALYSIS: proteins called enzymes allow

reactions to occur in an organism under mild
conditions and with great specificity.
• MOVEMENT: proteins make up a large percentage

of muscle fiber and help in the movement of
various parts of our body.
• TRANSPORT: proteins transport small molecules

trough an organism.
Living organisms use proteins in a
number of ways:
• HORMONES: hormones that happen to be proteins

help regulate cell growth.
• PROTECTION: proteins called antibodies help rid

the body of foreign harmful substances.
• STORAGE: some proteins help store other

substances in an organism (for example iron is
stored in the liver in a complex with the protein
ferritin).
• REGULATION: proteins help mediate cell

responses, such as the protein rhodopsin, found in
Building a protein: Outlining the
process
During the synthesis of a protein, the chain of
amino acids is built one link at a time, roughly as
follows:
1. A transfer RNA (tRNA) molecule transfers

specific amino acids to the ribosomes of the cell
to connect to the growing chain.
2. Each amino acid joins to the chain through the
formation of a peptide bond.
3. The first peptide bond joins two amino acids to
form a dipeptide.
4. The second peptide bond joins three amino acids
to produce a tripeptide.
5. This process continues for hundreds, if not
Building a protein: Outlining the
process
The cell’s DNA ultimately controls the sequence of
amino acids.
This information goes from the DNA to the

messenger RNA (mRNA), which serves as the
template for the creation of the protein’s primary
structure.
Its like a string of pearls, where each pearl

represents an amino acid.
In order for the protein to be synthesized, energy

must be supplied.
The purification of the protein of interest
is the indispensable first step in a series
of studies aimed at exploring protein
function.
Proteins can be separated from one

another on the basis of solubility, size,
charge, and binding ability. When a
protein has been purified, the amino acid
sequence can be determined.
The strategy is to divide and conquer, to

obtain specific fragments that can be
readily sequenced.
PURIFICATION OF PROTEINS
TECHNIQUES
 Exercise 5
Isoelectric Point
The isoelectric point (pI), sometimes abbreviated to IEP, is
the pH at which a particular molecule or surface carries no
net electrical charge.
Amphoteric molecules called zwitterions contain both

positive and negative charges depending on the functional
groups present in the molecule.
The net charge on the molecule is affected by pH of their

surrounding environment and can become more positively or
negatively charged due to the loss or gain of protons (H+).
The pI is the pH value at which the molecule carries no

electrical charge or the negative and positive charges are
equal.
The isoelectric point of a protein is an important property
because it is at this point that the protein is least soluble, and
therefore unstable.
It should be noted that both below and above the isoelectric

point (isoelectric pH) the protein will be soluble.
Proteins with little or no net charge can aggregate and

precipitate out of solution.
FUNCTIONALITY OF PROTEINS
AND RELEVANCE IN
AGRICULTURE, BIOTECHNOLOGY
AND FOOD INDUSTRY
http://www.salk.edu/news/pressreleas
e_details.php?press_id=559

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5 PROTEINS

Summary taken from the books:

Proteins can be understand by their

Consists on the linear polymer formed by

This work is a landmark in biochemistry

Today there are known complete amino acid

Striking fact  each protein has a unique,

Occurs when a R groups

-Non polar groups – Van

Occurs when multiple

-Not all proteins present

• FIBROUS proteins: are found only in animals. They

• GLOBULAR proteins: don’t usually serve as

• STRUCTURE: skin and bone contain collagen, a

• CATALYSIS: proteins called enzymes allow

• MOVEMENT: proteins make up a large percentage

• TRANSPORT: proteins transport small molecules

• HORMONES: hormones that happen to be proteins

• PROTECTION: proteins called antibodies help rid

• STORAGE: some proteins help store other

• REGULATION: proteins help mediate cell

1. A transfer RNA (tRNA) molecule transfers

This information goes from the DNA to the

Its like a string of pearls, where each pearl

In order for the protein to be synthesized, energy

Proteins can be separated from one

The strategy is to divide and conquer, to

Amphoteric molecules called zwitterions contain both

The net charge on the molecule is affected by pH of their

The pI is the pH value at which the molecule carries no

It should be noted that both below and above the isoelectric

Proteins with little or no net charge can aggregate and

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