Transcript Organic Chemistry

Proteins: the basis of life diversity
• Proteins are a class of diverse macromolecules that determine
many characteristics of cells and, in turn, of the whole organisms.
• All proteins are polymers constructed of subunits called amino
acids. There are 20 types of amino acids in protein. Thus, the
biological language expressed in proteins is a huge vocabulary of
a complex words based on an alphabet (these 20 amino acids). The
meaning of a protein rests in the exact order of its amino acids.
The order gives the molecules its special characteristics as a
structural component in a cell, as an enzyme, as a carrier, or
whatever. In each amino acid there are one central carbon atom,
bound to a hydrogen atom, and amino group (NH2), a carboxyl
group (-COOH-), and a side chain, represented by R-group.
R - group can be as simple as a single hydrogen atom, or as
complex as the double ring structure. Some amino acids side
chains are hydrophobic; and the other are ambivalent.
Proteins
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Monomer – Amino Acids
Polymer – Polypeptide (a long string)
Proteins are the 3D structures formed
by one or more folded polypeptides
working together
There are about 20
common amino acids
that can make
thousands of
different kinds of
proteins.
Characteristics of Amino Acids
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Backbone is always the
same
Side chains can be
• Polar—hydrophilic
• Nonpolar—hydrophobic
• Acidic
• Basic
• Contain Sulfur
(cysteine)
Proteins
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Peptide bonds – covalent bonds formed
between amino acids.
Proteins
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A is a large, complex polymer composed of
carbon, hydrogen, oxygen, nitrogen, and
sometimes sulfur.
protein
• Like polysaccharides, proteins are polymers, but the
amino acid subunits are linked covalently by peptide
bonds. The bonds are the result of a condensation
reaction between the carboxyl group of one amino acid
and the amino group of another. Two joined amino acid
units are called dipeptide. A third amino acid can be
joined by the other condensation reaction, to form
tripeptide. The condensation reaction occurs again and
again, forming chains that are typically 50 to hundreds
of amino acids long. These polymer chain are called
polypeptides, and regardless of length, each chain will
have an amino terminus and a carboxyl terminus. A
protein molecule can consists of one, two or several
polypeptide chains bound to one another in various
ways.
•A second type of covalent bound called disulfide
bond or bridge (-S-S-) results from linking of two
sulfhydryl groups. These bonds can cause a kink or
loop in a chain and join two polypeptide chains into
one molecule.
• In the early 1950s, Frederick Sanger of Cambridge
University made one of the greatest discoveries in
the history of biology by exploring the precise
amino acid sequence of the protein hormone called
insulin. The work of Sanger and his colleagues
revealed than the order of amino acids is the key to
the structure and function of proteins and that a
specific sequence characterizes each type of
protein.
Protein Structure
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Primary Protein
Structure – the order of
amino acids in the
polypeptide chain.
Primary structure –the linear
sequence of amino acids in a
protein is referred to as its
primary structure. Whether a
protein functions as an
enzyme, a hormone, or a
structural component of a
cell depends on its primary
structure.
What determines the amino acid sequence?
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The amino acid sequence is determined by
information coded in that organism’s DNA
http://science.csumb.edu/~hkibak/241_web/index.html
•Secondary structure – the sequence of amino acids
in a long polypeptide determines not just the
biological meaning of the protein ‘word’, but the
way the chains twists, bends, and folds into a
characteristics of a series of high – order
configurations called secondary, tertiary, and
quaternary structure, which ultimately determine
the protein’s activity in a living thing. The works of
chemists L. Pauling and R, Corey helped reveal this
hierarchy of protein structure and function by
focusing on the spatial relationships of amino acids
in polypeptide chains. They proved that the
subunits of some proteins tend to occur in regularly
repeating patterns and these patterns form the
secondary structure of the protein.
Secondary Protein Structure
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3D shape starts to form
The amino acids in some proteins are stabilized by their
own hydrogen bonds.
Forms alpha-helix ( spiral), beta sheets (like crinkled
paper)
Secondary Structure
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Alpha Helix (Hbonds in
yellow)
Beta pleated
sheets
(parallel or
antiparallel)
•In the protein molecule there are zones
with a bend. It is because of these
bends that the helix and sheet sections
fold onto the tertiary structure – the
characteristic three-dimensional shape.
Virtually, all water-soluble proteins,
including blood proteins, enzymes,
and antibodies, form a compact,
roughly spherical globular shape
as a result of this tertiary folding.
A protein’s tertiary structure can
be also filament – shaped. For
example, collagen, the structural
protein that makes up the fibrous
component of skin, tendons,
ligaments, cartilage, and bone - its
build up of molecules shaped like thin cigars some
Tertiary Structure
•Some proteins have a fourth level Quaternary Structure
of organization, called quaternary
structure. These molecules are
made up of two, three or more
polypeptides, each folded into a
secondary and tertiary shapes and
then intertwined in a complex
multichain unit. This kind of
structure has a three – dimensional
shape held together by week
bonds. The hemoglobin molecule,
which is composed of four hemo bearing polypeptide chains, has
the quaternary structure.
•Not all proteins have this structure. When multiple
polypeptide chains assemble to form one functional unit.
Hemoglobin (4 chains), ATP Synthase, collagen (3 chains)
•Biologists often classify proteins
according to the functions they perform.
Structural proteins, for example help to
form bones, muscles , shells, leaves,
roots, and even the microscopic cell
‘skeleton’ that provides shape and allow
cell movement. Other examples are
protein hormones, which serve as
chemical messengers; antibodies, which
fight infections; and transport proteins,
which act as carriers of other substances
(the hemoglobin protein in blood, for
example transport oxygen). One of the
most important kind of proteins in the
enzymes, which change the speed (or
catalyze) chemical reaction and thus
underlie every biological activity.
Proteins
There are tens of thousands of different
kinds of proteins;
they have 5 main
functions:
• STRUCTURAL
• STORAGE
• TRANSPORT
• DEFENSIVE
• ENZYMES
Enzymes
•Enzymes are the classic mediators of biological
change, and change is central to life – change within
atoms and molecules. Except in a few rare cases, the
organism that is no longer changing is no longer living.
•The study of enzymes began more than a century and
a half ago. Since then, biologists have learned a great
deal more about the roles of enzymes in living cells
and about enzyme structure and function, including
three unique characteristics. First, enzymes are
specific. A given enzyme can act on only one type of
compound or pair of reacting compounds, which is
called its substrate. One enzyme can catalyze only one
type of reaction. Second, the presence or absence of
critical compounds can control enzymes. Third, at the
end of the reaction enzymes are not changed they can
act again and again with new substrates.
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Bio-molecule: Proteins
Enzymes are important proteins found in
living things. An enzyme is a protein that
changes the rate of a chemical reaction.
Example: they speed
the reactions in
digestion of food.
In living cells, enzymes serve
as catalysts by reducing the
activation energy necessary
for biochemical reactions to
take place.
Enzymes
Enzymes act to bring substrates together or
break them apart
•Most enzymes are globular proteins, and the
substrates on which they act often much smaller
molecules than the enzymes themselves. Each
protein enzyme has a unique three-dimensional
shape arising from its primary, secondary, tertiary
and (sometimes) quaternary structure. On the
surface of each enzyme molecule there is one small
area called the active site. The key to enzyme
specificity is the shape of that site. The conformation
of the active site complements the shape of the
substrate (S) the enzyme acts on in much the same
way that the key – hole of a lock fits around the key.
It is this reciprocal matching of the threedimensional shapes of active sites
and substrates that accounts for enzyme specificity.
•Enzymes function as catalysts by forming
complexes with the reacting molecules. The first
step in enzyme function is the formation of an
enzyme –substrate complex. They change their own
shapes slightly to improve the fit between enzyme
and substrate. Such a change is called induced fit.
The binding of substrates to an enzyme can
increase the local concentration of the molecules,
orienting the molecules correctly so than the
reaction can take place most efficiently. All such
changes act to lower the activation energy. Then
they distort the shape of the substrate molecules
slightly, as well, thereby helping them reach its
transition state. Once substrate collides with and
binds to an enzyme’s active site, the enzyme can
perform its functions.
•It distorts the bonds in the substrate molecule,
and form the so called products from the
substrate molecule, which can be released
from the active site. The active site is
unchanged and ready to catalyze a new
reaction.
•Three factors – temperature, concentration of
enzymes, and concentration of substrates can
affect the rates of enzyme-catalyzed reactions.
If enzymes become saturated with substrate
the reaction shows no further rate increase.
•Because an enzyme’s activity depends on it precise
three-dimensional shape, factors that affect its
shape, can also affect, or even destroy, enzyme
activity. One of the most important factors is the
temperature. Enzymes intensity their activity up to
40°C. Over 60°C they stop their actions because the
active site looses its three-dimensional structure.
Most enzymes have a pH optimum or level of H+
concentration in which they function best. Cell and
organisms have many mechanisms that help keep
salt and H+ concentrations within narrow limits. There
are factors which affect the three-dimensional shape
of the active site and respectively can change
enzyme’s activity. Some of them increase it – these
are called activators. Others decrease enzyme’s
activity – these are inhibitors.
Protein Folding in Sickle Cell Anemia