Everything is
made of matter. All matter is
composed of atoms. The properties
of matter are determined by atomic structure.
ATOM – The
smallest unit of an element that retains its properties.
Atoms are
composed of:
NEUTRONS no charge
PROTONS + charge
(positively charged)
ELECTRONS - charge
(negatively charged)
The electrons orbit around the NUCLEUS, which is composed of the protons and neutrons.
ELEMENT –
Atoms that have the same number of protons are the same element. An element is all atoms that have a
specific number of protons. For
example, the element Hydrogen has 1 proton, Helium has 2, Lithium has 3,
etc. This number is called the
ATOMIC NUMBER and is one of the organizing patterns of the PERIODIC TABLE. The
reason elements have different chemical properties (for example, carbon is
different than oxygen) is because their atoms have different number of protons
in the nucleus,
ATOMIC MASS
– Atomic mass equals the number of protons plus the number of neutrons in
an atom. (Compared to these,
electrons have almost no mass.)
If the number of protons in an atom were to change, it would
become a different element. If the
number of neutrons were to change, it would become a different isotope
(radioisotope) of that element. If
the number of electrons were to change, it would have a different electrostatic
(ionic) charge of that element.
IONS
– Atoms or molecules that have a positive or negative charge are called
ions.
25 elements are
essential to life. 5 elements are
especially common in biological molecules:
H –
hydrogen
O – oxygen
C – carbon
N –
nitrogen
P –
phosphorous
MOLECULE – Two or more atoms held together by covalent
bonds.
MOLECULAR WEIGHT
(MW) – Equal to sum of the atomic masses of all the atoms in a
molecule. For example, water has a
molecular weight of 18 Daltons because the water molecule, H2O, has
one oxygen atom with an atomic mass of 16 and two hydrogen atoms each with an
atomic mass of 1.)
When forming
covalent bonds:
1) AN ATOM MAKES A SPECIFIC NUMBER OF BONDS
2) THE BONDS HAVE SPECIFIC STRUCTURES IN
SPACE
H –
hydrogen makes one bond
O – oxygen
oxygen makes two bonds
N –
nitrogen makes three bonds
C – carbon
makes four bonds
P –
phosphorous makes five bonds
NONPOLAR COVALENT BOND – The valence electrons are
shared equally between the atoms because the atoms have similar
electronegativity. For example,
C-H bonds.
POLAR COVALENT BOND – The valence electrons are
shared unequally because the atoms have dissimilar electronegativity. For example, O-H bonds.
*** The electrons are unevenly distributed
in a polar covalent bond. The end
that has more electrons develops a slight negative charge and the other end
develops a slight positive charge.
This is called a dipole.
***
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NONCOVALENT
INTERACTIONS – These occur between molecules (or between different parts
of large molecules). The atoms do
not share electrons. These are
often called noncovalent ÒbondsÓ which is too bad because then they can get
confused with covalent bonds.
A noncovalent
bond is like a lab partner
Significant in
biology, but weak and short-lived.
A covalent bond
is like a marriage partner
Significant in
biology, strong and potentially very long-lived.
** All chemical
reactions in biology involve making and/or breaking covalent bonds.
Noncovalent
interactions are sometimes called Van der Waals forces. They are also often called bonds (for
example, noncovalent bonds, hydorogen bonds, ionic bonds) and that can lead to
confusion with COVALENT BONDS. The
key is whether electrons are shared (all covalent bonds) or not shared (all
noncovalent bonds). There are
three kinds of noncovalent bonds.
1)
Dipole-dipole interactions: Because they have slight positive and
negative charges, polar covalent bonds are attracted to other polar covalent
bonds. A special example of these
are HYDROGEN BONDS – These are sooo important! When H forms covalent bonds with O or N, the polar bond can
form hydrogen bonds with other atoms.
For example, water makes hydrogen bonds with other water molecules and
other POLAR molecules or IONS.
These are HYDROPHILIC
(water loving) interactions. Things that dissolve in water are hydrophobic. Molecules that lack this capability
(because they are composed of nonpolar covalent bonds) are HYDROPHOBIC
(water fearing).
Oil does not dissolve in water because the nonpolar bonds in the oil
molecules are hydrophobic.
2) London
Dispersion forces: Noncovalent
interactions between nonpolar covalent bonds. These are very weak but can add up to significant levels
when there are a lot of them. For
example, this is the major force that allows a gecko to walk straight up a very
smooth wall.
3) Ionic
interactions: Noncovalent
interactions between ions.
ION – an
atom or molecule that is charged.
For example, when table salt is dissolved in water, the sodium is
positively charged and the chlorine is negatively charged. Ions can interact with water because
the oxygen in the water can bind to CATIONS (positively charged) and the
hydrogens can bind to ANIONS (negatively charged). Ions are hydrophilic.
Salt dissolves very easily in water.
The HYDROPHILLIC
and HYDROPHOBIC story in biology is very important and is mostly rooted in the
fact that carbon and hydrogen share electrons equally and oxygen and hydrogen
share them unequally.
GRAM MOLECULAR WEIGHT – Equal to the
molecular weight in grams. Water
has a gram molecular weight of 18 grams, and therefore, one mole of water
molecules weighs 18 grams. This is
true for any molecule. For example: sucrose = 342 MW (C12H22O11), glucose = 180 MW (C6
H12 O6). One
mole of sucrose would weigh 342 grams and one mole of glucose would weigh 180
grams.
MOLARITY - The concentration of a molecule in a
solution. If one mole of the
molecule is dissolved in one liter it is called a 1 Molar (1M) solution. So, 3M = 3 moles/liter.