Download Structure of a protein - Campus

The proteins
and nucleic acids
Proteins
The real importance of proteins is mainly
provided by the various growth and support
roles they play with regard to cell structures.
Moreover, metabolic reactions take place
with sufficient speed in the cellular
environment for the presence of enzymes.
Proteins with a specific catalytic function.
The proteins and nucleic acids > Proteins
Amino acids
Amino acids are molecules that contain
•a functional amine group (–NH2)
•a carboxyl group (–COOH)
The proteins and nucleic acids > Amino acids
The α carbon atom
In all the amino acids the α carbon
atom is asymmetric, with a highly
differentiated residual group.
Two molecular structures,
specular to each other, indicated
with letters L and D.
The amino acids naturally present in proteins all
belong to the L-series, called the “natural
series”.
The proteins and nucleic acids > The α carbon atom
The residual –R groups of amino acids
The chemical nature of the residual –R groups of amino
acids allow the protein they form to have a very specific
structure and thus to perform specific functions.
Alanine or phenylalanine
are NON-POLAR in
character and constitute
areas of hydrophobicity
in the protein chain.
The proteins and nucleic acids > The residual –R groups of amino acids
The –CH2–OH in serine
are polar in character an
d participate in the
formation of hydrogen
bonds.
The –CH2–SH in cysteine
is responsible for actual
covalent bonds, known
as disulphide bridges.
The peptide bond
Amino acids can link together using
a strong (peptide) bond
through a condensation reaction with
the elimination of a molecule of water between the carboxyl
group of one amino acid and the amino group of another.
The proteins and nucleic acids > The peptide bond
The structural organization of proteins
Structure of a protein depends on
1.the chain’s amino acid sequence;
2.how the chains are arranged in
three dimensions in space;
3.by further twists and folds;
4.by the presence of either a single
block or the association of several
subunits.
The proteins and nucleic acids > The structural organization of proteins
Corresponding to
these factors, there
are 4 ‘levels’ in the
structural
organization of
proteins.
The primary structure
1. The chain’s amino acid sequence
The primary structure of a protein is the exact sequence of
the amino acids which it is made of.
This also affects other factors upon which the overall
structure of the protein depends and determines its shape
and behaviour.
The proteins and nucleic acids > The primary structure
The secondary structure
2. The secondary structures of the most common
polypeptide chains are the twists:
• α-helix
globular proteins: keratin in hair.
• β-sheet
fibrous proteins: silk.
• triple helix
collagen, a protein which is found in the
tendons
The proteins and nucleic acids > The secondary structure
The tertiarity structure
3. The spatial structure that it assumes as a result of
the twisting of the protein chains due to the formation of
bonds between amino acid residual groups that are distant
from each other and in association with the presence of nontwisted sections that form the pivot for any folding.
3D structure characteristic of
globular proteins
The proteins and nucleic acids > The tertiarity structure
The quaternary structure
4. The spatial structure of its molecule resulting
from the association of polypeptide subunits to form
biologically active complexes that may also be associated
with non-protein elements.
The haemoglobin
molecule consists of 4
subunits (two α and two β
chains, of 141 and 146
amino acids respectively)
The proteins and nucleic acids > The quaternary structure
Denaturation of proteins
The forces that hold the subunits of a protein together are
weak and very sensitive to changes in the environment.
Changes in
temperature or pH
Modify secondary and
tertiary structure and
thus change 3D
configuration
The proteins and nucleic acids > Denaturation of proteins
Denatured protein can return
spontaneously to its ternary
3D configuration if its
primary structure has not
been changed.
Only the primary sequence
determines the over-riding
structures.
Functions of proteins in organisms
Proteins perform functions of growth and of support, but
also more sophisticated roles, linked for example to
defence, regulation and catalysis.
The main functions
• enzymatic catalysis
• contraction
• defence
• transport
• regulation
• structure
The proteins and nucleic acids > Functions of proteins in organisms
Enzymes
Enzymes are proteins of varying complexity, able to
change the speed of biological reactions under
conditions compatible with the life of the organisms.
Thanks to enzyme, a
reaction may require
less time or lower
activation energy to
take place.
The proteins and nucleic acids > Enzymes
Substrates and products
Enzymes as biocatalysts, greatly accelerating the speed of
reactions which otherwise would take place far more slowly.
The substances that are transformed by the
action of enzymes are called substrates,
While those that are formed by the reaction
are called products.
The proteins and nucleic acids > Substrates and products
Nucleic acids
Are polymers and their monomers are nucleotides.
Ribonucleic acid (RNA) and deoxyribonucleic acid
(DNA) are the main elements responsible for the
cellular characteristics.
The histones,
structures of 8
subunits, each of
which wraps around
two turns of the
nucleic
acid strand
The proteins and nucleic acids > Nucleic acids
The nucleotides of RNA and DNA
Each nucleotide is composed of three parts: a phosphate
group (orthophosphoric acid), a sugar with 5 carbon atoms
(a pentose) and a nitrogenous base.
Of these there are 2 types: one group with two rings, the
purines, and another with only a single ring called the
pyrimidines.
The proteins and nucleic acids > The nucleotides of RNA and DNA
The structure
TWO CHAINS
DNA is presented as a
linear molecule with 2
chains of nucleotides
coupled with opposite
spatial orientation.
The proteins and nucleic acids > The structure
OPPOSITE DIRECTION
The bases are oriented
towards the interior
and each base of a
filament binds by means
of hydrogen bonds with
the complementary
base of the other strand,
which develops in the
opposite direction.
The binding
THE DNA BINDING
As a result of the special structure of the bases,
the 2 DNA molecules can only bind to each
other in a single manner, with 2 hydrogen
bonds allowing only the union of adenine with
thymine (AT), while 3 hydrogen bonds only
allow guanine to bind with cytosine (GC).
The pairing also permits the maintenance of a
regular distance between the 2 strands.
The proteins and nucleic acids > The binding
The double helix
In 1953 J.D. Watson and F. Crick
hypothesize the double-helix
model for DNA.
The helical structure repeats itself
every 340 nm, which correspond
to 10 nucleobases.
The double helix of DNA is a
self-replicating molecule: it is in
fact able to reproduce chains
identical to itself in the
preparative phase before cell
division.
Biomolecules: carbohydrates and lipids / Metabolism: the role of energy