Note: convert H+ to H+ and Ca+2 to Ca+2
convert H2O to H2O
Life is a Chemical Process
I. Matter = ????????
A. examples:
1. ????????
2. _______
3. _______
4. _______
B. Matter on Earth composed of up to 92 different
naturally occuring elements
1. element = substance that cannot be broken down
to other substances by chemical reactions
a. examples:
-carbon
-hydrogen
-oxygen
-nitrogen
b. periodic table
2. compounds = substances made of two or more
elements combined in fixed ratios
a. examples:
-NaCl
-Na and Cl in a 1:1 ratio
-H2O
-H and O in a 2:1 ratio
C. life requires about 25 elements
1. 96% of mass of living things due to C, H, O, N
2. most of next 4% of mass due to P, Ca, K, S
3. Na, Cl and Mg present in small amounts
4. Trace elements = less than 0.01%
a. boron (B), chromium (Cr), cobalt (Co),
copper (Cu), fluorine (F), iodine (I), iron (Fe)
manganese (Mn), molybdenum (Mo),
selenium (Se), silicon (Si), tin (Sn),
vanadium (V), and zinc (Zn)
b. function of trace elements = 
-usually required by specific enzymes
-eg: see structure of cytochrome c with Jmol
-eg: cyt c gif file
-eg: alcohol dehydrogenase gif file
c. many trace elements are TOXIC at high
concentrations
eg: chromium, copper,
cobalt, selenium, etc
II. Atoms and Molecules
A. atomic structure
1. determines behavior of elements
2. atoms composed subatomic particles
a. neutrons
-mass = 1 dalton = 1 atomic mass unit (AMU)
-electric charge = none
b. protons
-mass = 1 dalton
-electric charge = +1
c. electrons
-mass = 0.0005 dalton
- it takes 2000 electrons to equal the mass of one proton
-electric charge = -1
-for many purposes, the mass of electrons
can be ignored
3. atomic number = # of protons
in atom's nucleus
a. see table of elements
b. periodic table
4. atomic mass number = # protons + # neutrons
in atom's nucleus
a. Note: Since many elements have multiple
isotopes in nature, the periodic table usually
lists an atomic weight that reflects the average
abundance of the various isotopes of a given
element.
a. see table of elements
b. periodic table
5. protons & neutrons cluster together to form
atomic nucleus
-nucleus has + charge due to protons
-nucleus has almost all of the atomic mass
-due to mass of protons and neutrons
6. electrons move rapidly around nucleus
in specific orbitals
a. orbitals = three dimensional spaces wherein electrons
are statistically likely to be found
-NOTE: orbitals ARE NOT like planetary orbits
b. eg: helium atom (2 protons, 2 neutrons, 2 electrons)
c. helium atom animation (neutrons not shown)
-NOTE: electrons usually found anywhere in a spherical
space centered on the atomic nucleus
-NOTE: this animation is misleading because the
electrons are moving so slowly--electrons actually
move at speeds approaching the speed of light
7. electrons must occupy certain energy levels
a. eg: carbon atom energy levels
- NOTE: this cartoon is misleading relative to the size of components
-if the carbon atom was as big as a baseball field, how big would the nucleus be?
-if the carbon atom was as big as a baseball field, how big would the electrons be?
-lump of solid carbon
-another lump of solid carbon
-conclusion: matter is mostly empty space!
b. most biologically important atoms/molecules use
first, second and third energy levels
c. specific orbitals are associated with
each of the energy levels
-1st energy level
-1S orbital (small spherical orbital)
-2nd energy level
-2S orbital (larger spherical shell orbital)
-2Px orbital (dumbell shaped on X-axis)
-2Py orbital (dumbell shaped on Y-axis)
-2Pz orbital (dumbell shaped on Z axis)
-electrons stay in their orbitals
-animation of e- in S orbital
-animation of e- in P orbital
8. a given orbital can hold 0, 1 or 2 electrons
9. isotopes = atoms of a given element
with different numbers of neutrons
a. examples
b. radioactive isotopes
-additional neutrons MAY make a
nucleus unstable => get nuclear decay
-eg: C12 (stable) (6P+ & 6N)
-eg: C14 (unstable) (6P+ & 8N)
C14 => N14 + beta particle
N14 (stable) (7P+ & 7N)
beta particle = radiation (- charge)
B. Molecular Structure and Bonds
1. molecule = two or more atoms held together
with one or more covalent bonds
2. recall: orbitals hold 0, 1 or 2 electrons
3. atomic orbitals of 2 atoms can merge
to form a "combined orbital" called a bonding orbital
a. bonding orbitals hold 2 electrons
-just like any other orbital
b. the two atoms "share" the 2 electrons
in the bonding orbital
-forms a "covalent bond" between
the two atoms
- covalent bond = the sharing of two electrons
between two atoms in a bonding orbital
c. see animation of covalent bond formation
-note: bonding orbital has unique shape
-note: electrons spend most time between
the two nuclei
4. electrons fill atomic orbitals in a specific
order that depends on energy considerations
a. lower energy levels are filled before
the higher energy levels
b. each orbital of a given energy level gets
at least one electron before any orbital in
the given energy level gets a second
electron
c. no orbital gets more than two electrons
d. see periodic chart
e. can predict of # of bonds possible
-eg: H has one 1 unpaired electron and
H forms 1 bond
-eg: C has 4 unpaired electrons and
C forms 4 bonds
-eg: O has 2 unpaired electrons and
O forms 2 bonds
-eg: Cl has 1 unpaired electron and
Cl forms 1 bond
-possible exam question: Shown to the right is periodic chart.
How many chemical bonds can a XXXXXX atom form?
5. sometimes atoms share electrons unequally
a. atoms are very stable (tend not to react)
when their outer energy level is complete
-see He, Ne, Ar, etc
b. atoms tend to gain, lose or share electrons when
their outer energy level has unpaired e- such that
their outer energy level becomes complete
c. some atoms have a high affinity for electrons
-high affinity for electrons = (electronegativity)
-eg: oxygen, chlorine, fluorine, sulfur
-these atoms have high electronegativity
-tend to "gain" extra electrons to complete
their outer energy level
-eg: F gains 1 electron to complete
second energy level
-forms the F- ion
-F- is very stable
-eg: S gains 2 electrons to complete
third energy level
-forms the S-2 ion
-S-2 is very stable
d. some atoms have low affinity for electrons
-eg: Li, Na, Mg, Be
-these atoms have lower electronegativity
-tend to "lose" electrons such that they have
a complete energy level
-eg: Li loses 1 electron to complete
the first energy level
-forms the Li+ ion
-Li+ is very stable
-eg: Mg loses 2 electrons to complete
the second energy level
-forms the Mg+2 ion
-Mg+2 is very stable
e. ionic bonds form when atoms with high
electronegativity react with atoms of low
electronegativity
-eg: Na reacts with Cl
-Cl has high electronegativity
-Na has low electronegativity
-Cl "takes" electron from Na
-Cl becomes Cl- ion
-Na becomes Na+ ion
-both ions (Na+ and Cl-) have complete outer shell
-Na+ is electrostatically attracted to Cl-
-ionic bonds = the electrostatic attraction
between ions of opposite charge
-ionic bonds are very important in biology
f. polar covalent bonds form when the
electronegativity difference between
atoms is smaller
-eg: H and O differ in electronegativity
-O has a larger electronegativity
-H has a smaller electronegativity
-H and O share electrons, but unequally
-electrons in bonding orbital spend
more time closer to the
O nucleus than to the H nucleus
-see animation of a O-H bond
-polar covalent bonds have unequal
electron density
-eg: H-O bond is polar covalent
-has a partial + charge
(due to the reduced electron density)
surrounding the H nucleus
-the + charge of the H nucleus
"shows through" the thinner
electron density of the bonding
orbital around the H nucleus
-has a partial - charge
(due to the extra electron density)
surrounding the O nucleus
-polar covalents bonds are very
important in biology
-help explain solubility in water
-some examples (in red) of polar covalent bonds
-O-H, -S-H, -N-H, -C=O
6. weak bonds
a. hydrogen bonds
-H forms polar covalent bonds with O, S, N etc
-the H takes on a delta +
(a partial + charge)
-the O or S or N takes on a delta -
(a partial - charge)
-when a H of a polar covalent bond is close
to a O, S or N in a different polar bond, there
is a weak attraction between the delta + of the H
and the delta - of the more electronegative species
-the weak attraction between the delta + of a H
and the delta - of another atom = a hydrogen bond
-see an illustration of a H-bond
-H-bonds are very important in biology
-see H-bonds in the structure of DNA (Jmol)
-How many H-bonds hold together a human chromosome?
-How likely is it that the two strands of DNA will fall apart?
-see H-bonds in the structure of proteins Jmol
b. Van der Waals interactions
-very weak interactions between
closely adjacent molecules
-physical basis explained in chem class
-single Van der Waals interactions much weaker than H-bonds
-huge numbers of Van der Waals interactions can be very significant
-very important in explaining "lipophilic" behaviors
-eg: hydrocarbon tails of
phospholipids self-associate due to
Van der Waals interactions
-Van der Waals interactions are very important in biology
-important in forming lipid bilayer membranes
-important in making lipid bilayers
impermeable to hydrophilic molecules
-discussed later in membranes
-important in protein structure
-"oil drop" structure of globular proteins
-discussed later in biochemistry
C. biological function comes from
molecular structure (shape)
1. central theme of this course
2. will repeatedly relate molecular structure
to function
a. What is the function of this molecule?
-another view as gif file
-another view plus membrane lipids
b. What is the function of this molecule?
D. chemical reactions = making and
breaking of chemical bonds
1. central theme of chemistry
2. biology IS chemistry
- recall our definition of "life":
Life = a set of energy driven,
self replicating, changeable, chemical reactions
3. will look at many chemical reactions
orbitals
x orbitals
y orbitals
z orbitals
xyz orbitals
periodic chart
H2
H2O
Hydrogen Molecule
++++++++++++
Define: Biology = the study of life
Back to the outline
Back to the outline
Most Abundant Elements in Mammalian Tissue
| Symbol | Element | Atomic Number | Atomic Mass | % of Mass |
| O | Oxygen | 8 | 16 | 65 |
| C | Carbon | 6 | 12 | 18.5 |
| H | Hydrogen | 1 | 1 | 9.5 |
| N | Nitrogen | 7 | 14 | 3.3 |
| Ca | Calcium | 20 | 40 | 1.5 |
| P | Phosphorous | 15 | 31 | 1.0 |
| K | Potassium | 19 | 39 | 0.4 |
| S | Sulfur | 16 | 32 | 0.3 |
| Na | Sodium | 11 | 23 | 0.2 |
| Cl | Chlorine | 17 | 35.4 | 0.2 |
| Mg | Magnesium | 12 | 24.3 | 0.1 |
Back to the Lecture Outline
Back to the Lecture Outline
Some Isotopes of Carbon and Nitrogen
| Symbol | # of Protons | # of Neutrons | # of Electrons | Atomic Mass |
| C-12 | 6 | 6 | 6 | 12 |
| C-13 | 6 | 7 | 6 | 13 |
| C-14 | 6 | 8 | 6 | 14 |
| N-14 | 7 | 7 | 7 | 14 |
| N-15 | 7 | 8 | 7 | 15 |
Back to the Lecture Outline
Matter = anything that takes up space and has mass
Back to the Lecture Outline
Examples of matter = rocks, air, butterflies, bacteria, plants, dirt, chairs, books, etc
Back to the Lecture Outline