Lecture 3
Chemistry for Computer
Scientists
Joseph L. Hellerstein
jlheller@uw.edu
No Class
Tuesday
October 7
Agenda
Simple chemistry experiment
Atoms
Molecules
Line diagrams for organic
molecules
Reactions
Chemistry essentials in 2 UML
diagrams
4 Molecular Biology as a Computational Science. Joseph L. Hellerstein, 2014.
Chemistry Experiment
Motivating Question
Why don’t oil and water mix?
Chemistry in Brief
Chemistry is about the nature and
transformation of substances.
Atoms in Brief
•
Protons are positively charged.
•
Electrons are negatively charged.
•
An atom has the same number of protons
and electrons – no net charge.
8
Chemistry is about the configuration of electrons.
•
Atomic numbers count protons/electrons.
•
Electrons are arranged in shells (layers).
–
Successive rows in the periodic table have
another shell.
•
Right-most column lists the (inert) noble
gases.
Periodic Table of
Elements
10
•
Horizontal position of element indicates
electrons in outer “shell”
•
Atomic number indicates the number of
protons/electrons
•
The right-most column are the noble gases
•
Have a “complete collection” of electrons
•
Horizontal position of element indicates
electrons in outer “shell”
•
Atomic number indicates the number of
protons/electrons
•
The right-most column are the noble gases
•
Have a “complete collection” of electrons
1 2
3 4 5 6 7 8
•
Atomic numbers count protons/electrons.
•
Electrons are arranged in shells (layers).
–
Successive rows in the periodic table have
another shell.
•
Right-most column lists the (inert) noble
gases.
Elements Most
Relevant to Us
Molecular Biology as a Computational Science. Joseph L. Hellerstein, 2014. 12
CL
F Ne
Ar
Low Energy
Electron Configurations
Simple model
•
A low energy configuration has the
same number of electrons as a Noble
Gas.
Exampl
es
Noble Gas
Molecules
Molecules are formed by
combinations of atoms that
share electrons.
This is called a bond.
Chemistry is about the
distribution of electron densities
in molecules and changing these
distributions.
Simple Model for
Bonding
Bonds create an electron configuration that looks
like a Noble Gas for each atom in the molecule.
The lines indicate that a
pair
of electrons
is shared. In H2O:
•
Each H has 2
e
, like He.
•
Its original
e
plus one shared with O
•
The O has 8
e
, like Ne.
A Simple Molecule:
Methane
Methane production
•
Methane allows C to have 8 electrons in
its outer shell
–
4 in C’s outer shell
–
4 shared with 4 H’s
More Examples
Carbon dioxide.
•
C has 8 electrons
shared with 2
O’s.
•
Each O has 2
“lone pairs” plus
Double bond.
Sulfuric Acid.
•
But simple bond
model almost always
works in the class.
Representing Molecules
•
Rules for drawing organic (C-based)
molecules
–
Implied C:
dots
–
Implied H
’s: Sufficient so the C (N, P, S,
O) have a Noble Gas electron
configuration
1 implied C &
4 implied H’s
1 implied C
18
C
Molecule Names & Implied Bonds
How many carbons? Hydrogens?
How many carbons? Hydrogens?
Carbons? Hydrogens?
Ethane
Propane
Nonpolar, Polar, and Charged
Molecules
Nonpolar: “Balanced” distribution of
electrons
20
Polar Neutral
: Electrons are
“imbalanced”
Charged
: More
(less) electrons than
protons
Hydroxyl: OH
-
Hydronium: OH
+
Electrons are concentrated around O, creating a dipole.
Oil & Water
Long HydroC chains stackPolar molecules align
Oil & water don’t mix because they attract
H
yr
do
ph
ob
ic
H
yd
ro
ph
Hydro Types
What makes a
molecule hydrophylic
vs. hydrophobic?
CL
F Ne
Ar
1 2 3 4 5 6 7 8
Give electron
Grab electron Inert
Molecules with atoms in columns 5, 6, 7 are more hydrophylic.
Which are
hydrophobic? Which
are hydrophilic?
Molecular Biology as a Computational Science. Joseph L. Hellerstein, 2014. 24
R
i
is an
unspecified
group with
Carbon.
2
1
What is an implication of
the cytosol being largely
water for hydrophobic
proteins?
Chemical Reactions
•
A reaction is a transformation of one
set of chemical structures
(
reactants
) into other chemical
structures (
products
) by:
•
Breaking bonds
•
Making bonds
•
Reactions are generally
bi-directional.
Reactants
Products
Vinegar & Baking Soda
Reaction
Vinegar
Baking
Soda
Acetic
Acid
WaterSodium
Ion
CO
2
Understanding a reaction requires
answering:
•
Which bonds are broken?
Understanding the
Reaction
x
x
x
x
Prototypical Reactions (With Water)
‘
‘
Hydrolysis
: Separate functional groups.
Condensation
: Combine functional groups.
x
x
x
x
‘
‘
Chemistry is 3-d
30
(SparkNotes:
Organic
Chemistry)
Molecular Biology as a Computational Science. Joseph L. Hellerstein, 2014.