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Physical Chemistry
Biochemistry is the study of living systems using the methods of
chemistry and physics. Physical chemistry deals with the physicochemical phenomena, which are needed to understand biochemistry.
Organisms are complicated and highly organized. Each organism
consists of many organ systems ( e.g. respiratory and reproductive
systems). Each system is formed of many organs which are formed of
tissues. The tissues are formed of cells that contain cell organelles.
The cell and its organelles are made up from molecules.
Cells are composed of different types of molecules:
Water
70%
Proteins
15%
Nucleic acids
7%
Polysaccharides
3%
Lipids
1%
Minerals and others 4%
Molecules are formed of elements. Carbon (C), hydrogen (H), oxygen
(O), nitrogen (N), phosphorous (P) and sulfur (S) are the main
elements that constitute more than 99% of the human body.
Elements are substances that cannot be broken down further by
ordinary chemical means.
Atoms are the smallest unit of matter retaining the properties of an
element. Each atom is made up of positively charged protons, neutral
neutrons, and negatively charged electrons.
Electrons are generally affected by the following three chemical
phenomena:
1. Electrons tend to pair.
2. They are negatively charged and so are subject to the
electrostatic attraction-repulsion rules. The relative ability of an
atom to draw electrons in a bond toward itself is called the
electronegativity of the atom. Atoms with high
electronegativitiy attract the electrons more than those that have
small electronegativity.
3. Atoms tend to fill their outermost electron energy level (orbit)
either by transfer or sharing of electrons.
These three factors are the basis for the different types of chemical
bonds and chemical reactions that occur in nature.
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Chemical Bonds
The components of the system become more stable through the
formation of bonds.
There are several types of chemical bonds:
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1- Covalent Bonds
Covalent Bonds are formed by sharing of a pair of electrons. Electrons
are shared in pairs. Two atoms sharing a single pair of electrons have
a single bond, while two atoms sharing two pairs have a double bond
and two atoms sharing three pairs have a triple bond.
Covalent Bonds are the strongest chemical
Atoms
bonds, the energy of a single covalent
bond can vary from 50 kcal/mol to 110
Sharing a pair
kcal/mol depending on the elements
of electrons
involved. Once formed, covalent bonds
rarely break spontaneously at room
temperature because of the high amount of
energy required.
Carbon-carbon bonds (C—C), carbonCovalent bond in
a molecule
oxygen bonds (C—O) and carbon-hydrogen
bonds (C—H) are all examples of covalent
bonds. Methane is formed of one carbon atom covalently attached to 4
hydrogen atoms by 4 covalent bonds.
2- Ionic Bonds
Ionic bonds are formed when there is a complete transfer of electrons
from one atom to another to fill
Atoms
their outermost energy levels. This
electron transfer results in two ions,
one positively charged and the
Transfer of
other negatively charged. These
electrons
ions become attracted to each other
Negatively
by the resulting electrostatic charge
charged ion
differences. Ionic bonds are
generally weak. They are often 4-7
Ionic bond in
Positively
kcal/mol in strength.
a molecule
charged ion
So they can be broken easily when subjected to heat or submerged in
water. An example of this process is the formation of a sodium
chloride molecule.
Ionic bonds are also called electrostatic bonds as they result from the
electrostatic attraction between two ionized atoms or groups of
opposite charge
3- Hydrogen bonds
Hydrogen bonds result from electrostatic attraction between an
electronegative atom e.g. oxygen or nitrogen (O or N) and a hydrogen
atom that shares its electron with a second electronegative atom.
Hydrogen bonds occur between two or more polar molecules. A polar
molecule is a molecule that has a slight positive charge at one end and
a slight negative charge on the other (giving it poles). The bond is
quite weak (5 kcal/mol) and easily broken, unlike covalent bonds.
Accumulation of many hydrogen bonds provides specificity and
significant stability to macromolecular structures.
Hydrogen bonds are frequently found in proteins and nucleic acids in
large numbers and serve to keep the protein or nucleic acid structure
secure.
Perhaps the most famous example of hydrogen bonds is the bond
which is formed between oxygen of water molecule and the hydrogen
of another water molecules. Each water molecule can form up to 4
hydrogen bonds.
H O
H
Hydrogen bond
H O
H
Hydrogen bond between 2 water molecules
4- Van der Waals interactions
Van der Waals interactions are intermolecular forces of attraction that
occur when there is a transient asymmetry in the distribution of charge
around atoms in a molecule. The consequent charge imbalance affects
and attracts adjacent atoms. Van der Waals interactions are very weak
bonds (1 kcal/mol) formed between non-polar molecules or non-polar
parts of a molecule that have slight transient charge displacements.
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5- Hydrophobic Interactions
Hydrophobic interactions occur between clusters of nonpolar
molecules that tend to aggregate so as to minimize the surface area
that is exposed to water. Hydrophobic molecules tend to aggregate
together in avoidance of H2O molecules.
6- Steric Hindrance
Atoms occupy a fixed volume of space that is very difficult to
compress, except by covalent bond formation. Thus, atoms cannot
overlap in their position. The effect of this on protein structure is
called steric hindrance. Bulky side-chains such ( as that found in
isoleucine amino acid) restrict the possible side-chain angles in protein
structure.
Biological Functions where non-covalent interactions play roles
1. Binding specificity
Specificity of enzyme substrate binding is due to formation of enough
noncovalent bonds to hold the enzyme and substrate together. Also,
specificity of antigen antibody reactions is due to formation of enough
noncovalent bonds.
2. Protein structure
Secondary, tertiary and quaternary protein structures are stabilized by
noncovalent bonds. Collagen ,a protein whose function depends on its
ability to maintain a long and fibrous structure, is stabilized by
noncovalent bonds.
3. DNA base pairing
Hydrogen bonding between adjacent base pairs underlies the ability of
one strand of DNA to pair with another and serves to hold the two
strands of the DNA double helix together.
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