Download Shell configurations of electrons

Chemicals common in biology



Carbon, Oxygen, Hydrogen and Nitrogen most
abundant
Phosphorus, Calcium, Sodium, Magnesium,
Potassium and Sulfur are also common
Most organic material comprises only 25
elements
Table 2-1
Fig. 2-5
Cloud of negative
charge (2 electrons)
Electrons
Nucleus
(a)
(b)
Atomic Structure

Protons and
neutrons in
nucleus
Protons +
charge
 Neutrons are
neutral


Electrons
“orbit” nucleus
in electron shell

Electrons charge
Atomic characteristics




Number of protons and electrons is equal
under most conditions (no net charge)
Atomic number=number of protons
Atomic mass=combined number of protons
plus neutrons in nucleus
Isotopes=atom that contains the same number
of protons, but different numbers of neutrons
Fig. 2-9
Hydrogen
1H
Atomic mass
First
shell
2
He
4.00
Atomic number
Helium
2He
Element symbol
Electrondistribution
diagram
Lithium
3Li
Beryllium
4Be
Boron
5B
Carbon
6C
Nitrogen
7N
Oxygen
8O
Fluorine
9F
Neon
10Ne
Silicon
14Si
Phosphorus
15P
Sulfur
16S
Chlorine
17Cl
Argon
18Ar
Second
shell
Sodium Magnesium Aluminum
12Mg
11Na
13Al
Third
shell
Shell configurations of electrons
Chemical Bonding



Atoms or molecules with full valence shells
are very stable (inert gases)
Chemical Bonding takes place to allow filling
of valence shells
Two types of chemical bonds



Covalent bonds
Ionic bonds
New molecule often has characteristics unique
from parent atoms (NaCl)
Fig. 2-12
Name and
Molecular
Formula
Covalent Bonding



Multiple atoms
share electrons to
fill outer shell.
Can take place
between two
identical atoms (O2
or H2)
Carbon-based
molecules are
typically
covalently linked
(a) Hydrogen (H2)
(b) Oxygen (O2)
(c) Water (H2O)
(d) Methane (CH4)
ElectronLewis Dot
Spacedistribution Structure and filling
Model
Diagram
Structural
Formula
Fig. 2-13
Polar Covalent Bonds


–
O
+
H
H
H2O
+

Attraction of atom
for electrons is called
electronegative force
In some compounds
the difference in
electronegative force
is large enough that
one atom pulls shared
electrons to itself
Results in a molecule
with slightly charged
regions
Fig. 2-14-2
Ionic Bonds
Na
Cl
Na
Cl
Na
Sodium atom
Cl
Chlorine atom
Na+
Sodium ion
(a cation)
Cl–
Chloride ion
(an anion)
Sodium chloride (NaCl)




Caused by strong electronegative differences between atoms
One atom donates an electron to another
Both atoms become charged and their opposite charges
causes an attractive force
Strong bonds outside of aqueous solution, weak in solution
Hydrogen bonding



Weak bonds that are
made and broken
easily
Hydrogen of a polar,
covalent molecule
has attraction to
Nitrogen or Oxygen
of similar molecule
Results from weak
charge of regions on
polar molecules
Fig. 2-17
s orbital
Four hybrid orbitals
z
x
Three p
orbitals
y
Tetrahedron
(a) Hybridization of orbitals
Space-filling
Model
Ball-and-stick Hybrid-orbital Model
Model
(with ball-and-stick
model superimposed)
Unbonded
electron
pair
104.5º
Water (H2O)
Methane (CH4)
(b) Molecular-shape models
s orbital
Four hybrid orbitals
z
x
Three p
orbitals
Molecular Shape
y
Tetrahedron
(a) Hybridization of orbitals
Space-filling
Model
Ball-and-stick Hybrid-orbital Model
Model
(with ball-and-stick
model superimposed)

Unbonded
electron
pair
104.5º
Water (H2O)
Methane (CH4)
(b) Molecular-shape models

Determined by
electron shells
and the size of
atoms included
Space-filling
models
attempt to
demonstrate
the shape of a
molecule
Biological Activity

Biological activity of molecules is largely
determined by:

Shape of molecule


Charge of molecule of on portions of molecule


3D structure allows molecule to interact with other
molecules
Charged regions often interact with oppositely
charged molecules
Bond type

Covalent bond is more easily broken and assembled
Molecular Mimicry



One molecule
has a shape that
is similar to
another molecule
The similarity in
shape often
results in a
similarity in
function
Seen in
pharmaceutical
development and
pathogenic
microbiology