Atoms and Molecules

in Biology

The hierarchy of biological order

BIO 202

Sizes of molecules, cells and organisms

Chemical elements in living cells

Elements
Element = a substance that cannot be broken
down by chemical reactions
There are 92 naturally occurring elements
(+artificial=>103)
Each element has a 1- or 2-letter symbol (e.g., O,
N, Na, Ca)
Life requires ~25 elements
Trace elements = elements required in minute
amounts, but their lack can cause severe
disorders
Elements are made of atoms
Atom is the smallest unit of matter that retains the
properties of an element

Structure of atoms
Atoms are made of subatomic particles:
Protons and neutrons
make up the atomic nucleus
Neutron mass = Proton mass
= 1.7 x 10-24 g = 1 Dalton
Neutron = 0 charge
Proton = +1 charge
Thus, atomic nucleus is
positively charged,
and its mass =
mass of protons+mass of neutrons

Structure of atoms
The nucleus is orbited by electrons
Electron charge = -1
The attraction between the nucleus and the
electrons keeps the electrons in the vicinity of
the nucleus, and thus preserves the atomic
structure
Atoms overall are neutral:
# protons = # electrons
Electron mass = 1/2000 (=0.05%) mass of a
proton (negligible in biological calculations)
Atomic mass mass of the nucleus = mass of
protons + mass of neutrons

Uniqueness of elements
Various elements differ in number of
subatomic particles in their atoms
Each element has a unique number of
protons in the nucleus of its atoms =
atomic number = # protons
Each element is also characterized by its
mass number
Mass number = # protons + # neutrons

Uniqueness of elements
23
11

Mass number = # of protons + # of neutrons

Na
Atomic number = # of protons = # of electrons

Therefore:

Sodium has 11 protons and 12 neutrons

Because mass # atomic weight, atomic weight 23
All atoms of an element have the same number of
protons
What about neutrons?

Number of neutrons can vary

Atomic forms of the same element (same number
of protons and electrons) with different number
of neutrons are called isotopes.
Isotopes differ in mass
(neutron releases
Example: isotopes of carbon
12
13
6

6 neutrons

7 neutrons

Stable isotopes

electron and
becomes proton)
Decays to 14 N

14
6

8 neutrons

Radioactive isotope

Radioactive isotopes in biology

1.

Radioactive isotopes are very valuable tools in biology

Determining the age of samples
Radioactive elements have specific and constant
periods of decay called half-life
e.g., half-life of 14C=5,715 years, 8C=2 x 10-21
seconds, 32P=2 weeks
2. Cytotoxic agents
Kill proliferating cells (treatment of cancer)
3. Induce mutations in DNA (usually large deletions)
4. Biological tracers
Radioactive labeling of biological molecules (DNA,
proteins, etc.), and following their fate in a cell or
organism

Chemical bonds
Atoms combine into chemical compounds
Combinations of atoms in a fixed ratio =
molecules
example: Na + Cl = NaCl (1:1 ratio)
Chemical characteristics of a compound can
be different from those of its combined
elements (atoms)

Chemical bonds
Atoms interact with each other through
their electrons. Atomic nuclei do not
directly participate in chemical reactions
Electrons are characterized by their
energy levels
Energy is the ability to do work
Potential energy = energy stored in matter
due to its location
In atoms, the potential energy of the electron
is determined by its distance relative to the
nucleusthe further it is, the more potential
energy it has

Bonding
Different states in electron potential energy are called
energy levels or energy shells
When electrons receive
energy, they jump to a higher
energy level
When electrons lose energy,
they drop to a lower level
These changes in energy
occur in discrete steps
e.g., the energy of the sun
excites electrons in plant
compounds; when they
lose this energy, it is used
for work (biosynthesis)

Orbitals
Orbital - volume of space in which
electron spends most of its time

Energy
- one orbital can contain a maximum of 2 electrons
- orbitals have characteristic shapes: spherical (s),
dumbbell-shaped (p), and more complex shapes

Chemical behavior
The chemical behavior of atoms depends
on its electron configuration
Mainly on the number of electrons (=valence
electrons) in the outermost shell (=valence
shell)
An atom with a full valence shell is nonreactive (e.g., inert elements He, Ne, Ar)
In atoms, electrons first fill all the orbitals in
the valence shell, and then start filling them to
capacity

Chemical behavior
Atoms with unfilled valence
shells strive to fill them. To do
so, they must grab electrons
from other atoms (=chemical
reaction)
Different atoms with the same
number of valence electrons
(=chemical valency) exhibit
similar chemical behavior;
e.g., Cl (chlorine), F (fluorine)
Two atoms that interact with
each other to fill their valency
shells share electrons and
form a chemical bond