What we have to learn to do, we learn by doing
Aristole
Welcome to
Biology: A Molecular Approach
Bio 7505
Professors:
JM Crisman, PhD
EJ Lehning, PhD
www.ccuri.org
Lecture Block- Basic Chemistry
Basics of Quantum Mechanics
Protons, neutrons and electrons
Atomic number- total # of protons
Atomic mass- protons + neutrons
- dalton is the unit of atomic mass
Potential Energy vs. Kinetic Energy
(stored)
vs. (released)
What do the words “potential” and “kinetic” mean?
Free nrg (G)
Kinetic EnergyPotential
EnergyEnergy
Energyisisreleased
Stored
For Bonds Use
Kilocalories
Calories
X miles
(kcals)
Atoms store nrg and release nrg
1) Movement of electrons between nrg (energy)
levels (e.g. fluorescence)
2) Forming and breaking bonds
3) Radioactive Decay- Nrg is also released
when some atoms release subatomic particles
Fig. 2.3
Fig. 2.4
Radioactive Isotopes Decay
Radioactive Half-life
electrons occupy different energy levels
Nucleus
M
Highest nrg
L
K
Lowest nrg
Nrg = energy
Fig. 2.5
Fig. 2.8
Nrg in nrg levels can
be use
to create fluorescence
Fig.
2.6
Atoms can absorb energy (potential energy) and
release energy (kinetic energy)
An Example
Nucleus
M
Release
Absorb
nrg
nrg
Highest nrg
L
K
Lowest nrg
Nrg = energy
Ionic Bonds- AKA electrovalent bonds
- Atoms are in close association and
electrons are donated and change the
charge of the atom.
Ions:
Number of electrons does not equal the
number of protons…..
So there is a charge
Cations- ions with positive charge (e.g. Na+)
Anions- ions with negative charge (e.g. Cl-)
Redox Reactions
Redox = reduction/oxidation reactions
e- can be gained and lost
during chemical reactions (rxns).
Gain of e- ---reduction
Loss of e- ---oxidation
LEO
SAYS
GER
Used for energy transfer in biochemical reactions
Bonds and Basic Reactions
Atoms interact to form molecules by forming bonds
Bonds store energy
Covalent bonds- pairs of electrons are shared
between atoms
Strong bonds that require significant amounts
of energy to break
These bonds take tons of nrg to form!
-So cells use molecules called enzymes that make reactions
go faster!
Explain the example of making a protein from amino acids
When chemical combine they form an intermediary state called
a transition state….takes a ton of energy to get there…and when
achieved the transition state allows bonds to break and new
bonds to form
Enzymes lower the amount of energy needed to break and reform
New bonds…they hold reactants close together and
move electrons themselves!...usually within their own molecular
structures!
What is an enzyme?
Free nrg (G)
kcal
Chemical reactions pass through a transition state
and enzymes speed-up reactions by lowering the
nrg needed to get there
Activation nrg (Ae)nrg needed
to get to the
transistion
state
from
Enzymes
are
biological
reactant nrg level
+
catalysts that
lower the Ae
reactants
products
A+B
C
Use the example of two amino acids!!!!!!
Besides true bonds, there are other ways
atoms interact with each other
• Van der Waal forces
• Hydrogen bonds (H Bonds)
• Hydrophobic interactions
Low nrg associations
- are like velcro
individually these interactions are weak but
collectively they are very strong
Van der Waals Interactions
Molecules naturally attract each other
Within a certain radius atoms attract each other.
If they get too close…they repel each other
Van der Waal Radius
Distance that atoms of a molecule will
stably interact
individually these interactions are weak
but are stronger collectively
H Bonds
DIPOLE
Water (H2O)
dH
d+
O
H
Polar
Molecule
O and N can form Hydrogen bonds
-very weak individually but collectively strong
In fact the DNA double helix is stabilized
by these interactions
Hydrophobic Interactions
What does “hydro” and “phobic” mean?
Hydrophobic molecules (i.e. do not
interact with water…and thus
tend to interact with each other…
to “drive” water out
Very important to stabilize many
molecular structures
(e.g. cell membranes, some protein structure)