BIO105K
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, all atoms that
have one proton are the element Hydrogen, 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. Elements have different chemical properties (for example, carbon
is different than oxygen) because their atoms have different number of protons.
ATOMIC MASS – Atomic mass equals the number of protons plus the number of
neutrons in an atom. (All protons and neutrons have about the same mass and
compared to these, electrons have almost no mass.)
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
COVALENT BOND – When two atoms share a pair of electrons to help fill and stabilize
their outer shell of electrons (the valence shell). Many elements are more stable if they
share electrons with another atom.
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
ELECTRONEGATIVITY – the strength that the nucleus pulls on the pair of electrons
shared in a covalent bond. Different elements have different electronegativity.
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. For the two atoms
in a polar covalent bond, the atom that has more electrons develops a slight negative
charge and the other atom develops a slight positive charge. This is called a dipole. ***
NONCOVALENT INTERACTIONS – These occur between molecules (or between
different parts of large molecules). The atoms do not share electrons. These are often
called noncovalent “bonds” 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 do not dissolve in water are hydrophobic. These molecules are HYDROPHOBIC
(water fearing) because they are composed of nonpolar covalent bonds. For example,
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.
MOLE – This a specific number similar to the concept that 12 can also be called one
“dozen”. You can have a dozen of anything (eggs, donuts, etc.) and it means you
have twelve. Similarly, you can have a mole of anything (carbon, sucrose, etc.) and
it means you have 6.02 x 1023. This funny number was established to make the
following relationships convenient:
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.)
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.
One liter of a 3M glucose solution would have 540 grams of glucose (180 x 3 = 540).