Chapter 2 - The Chemical Basis of Life
NEW AIM: What’s the matter?
Figure 2.1
Chapter 2 - The Chemical Basis of Life
AIM: What’s the matter?
What is
MATTER
?
- Anything that takes up space and has mass
Chapter 2 - The Chemical Basis of Life
AIM: What’s the matter?
The smallest chemically
unbreakable unit of MATTER
?
An atom
Chapter 2 - The Chemical Basis of Life
AIM: What’s the matter?
Fig. 2.1
Chapter 2 - The Chemical Basis of Life
AIM: What’s the matter?
Fig. 2.1
Chapter 2 - The Chemical Basis of Life
AIM: What’s the matter?
Fig. 2.1
Chapter 2 - The Chemical Basis of Life
AIM: What’s the matter?
Fig. 2.1
Chapter 2 - The Chemical Basis of Life
AIM: What’s the matter?
Elements
- The various types of atoms
Ex. Carbon, Oxygen, Nitrogen, etc…
Chapter 2 - The Chemical Basis of Life
AIM: What’s the matter?
Chapter 2 - The Chemical Basis of Life
AIM: What’s the matter?
Table 2.1
Chapter 2 - The Chemical Basis of Life
AIM: What’s the matter?
Fig 2.3b
Chapter 2 - The Chemical Basis of Life
AIM: What’s the matter?
A lack of iodine in one’s diet can
cause swelling of the thyroid
gland resulting in a GOITER. The
condition is reversible if iodine
is taken. (Don’t worry, we iodize salt)
Fig 2.3b
Iodine is used by thyroid cells to
make hormones (chemicals released by one
cell into the blood and bind to a receptor on another cell,
which is one way cells talk to each other).
Chapter 2 - The Chemical Basis of Life
AIM: What’s the matter?
Element
vs
Compound
(Emergent Properties)
Chapter 2 - The Chemical Basis of Life
AIM: What’s the matter?
Elements – composed of the same types of atoms
Compounds – composed of two or more types of atoms
Chapter 2 - The Chemical Basis of Life
AIM: What’s the matter?
Element
- Any substance composed of only ONE element
Ex) a bar of pure gold, nitrogen gas (N2), oxygen gas (O2)
Compound
- Any substance composed of two or more elements
Ex) Na+Cl- (table salt), H2O, CO2
Chapter 2 - The Chemical Basis of Life
AIM: What’s the matter?
Chapter 2 - The Chemical Basis of Life
AIM: What’s the matter?
Chapter 2 - The Chemical Basis of Life
AIM: What’s the matter?
Chapter 2 - The Chemical Basis of Life
AIM: What’s the matter?
Chapter 2 - The Chemical Basis of Life
AIM: What’s the matter?
Pure sodium (element)
Chlorine (Cl2) gas (element) Na+Cl- Table Salt (Compound)
+
Fig 2.2
=
EMERGENT PROPERTIES (EP’s)
Chapter 2 - The Chemical Basis of Life
AIM: What’s the matter?
What are atoms made of
and how are they organized
Niels Bohr
Danish Physicist
1885-1962
(The Bohr Model)
?
Chapter 2 - The Chemical Basis of Life
AIM: What’s the matter?
Nucleus Organization:
Chapter 2 - The Chemical Basis of Life
AIM: What’s the matter?
Subatomic particles
(sub = below, below the atom level)
proton
neutron
electron
charge mass
+1 1 amu (dalton)
1 amu (dalton)
0
-1
amu = atomic mass unit
1 amu or 1 dalton = 1.67 x 10-27 kg
1/1836th an amu (dalton)
Chapter 2 - The Chemical Basis of Life
AIM: What’s the matter?
How are the electrons “held” to the nucleus? Why
do they not just shoot away?
Electrons are held to the nucleus by the
electromagnetic (EM) force since electrons are
negative and the nucleus is positive – opposite
charges attract / like charges repel.
Chapter 2 - The Chemical Basis of Life
AIM: What’s the matter?
How are the protons “held” together in the nucleus?
Why do they not break apart due to the EM force?
The strong force holds the nucleus together. The strong
force is only “felt” at extremely small distances, which is
why the electrons do not feel it. You would need to be on the
nucleus to feel it. For example, if gravity were like this, you
would only feel it on Earth, but if you jumped up a few feet,
you would no longer be pulled down by it...
Chapter 2 - The Chemical Basis of Life
AIM: What’s the matter?
Electron Organization:
n=1
Electrons are present in shells and move around the
nucleus at a speed of ~2200 km/s. They can only be in
these shells and nowhere else!!
The first shell (n=1) can hold up to 2 electrons. That
means it can have 0, 1 or 2 electrons in it at any time.
The second shell (n=2) can hold up to 8 electrons.
The third shell (not shown, n=3) can also hold up to 8 electrons.
There are many more shells, but you only need to
know the first three for AP Bio.
n=2
Chapter 2 - The Chemical Basis of Life
AIM: What’s the matter?
Electron Organization:
Which shell contains higher energy electrons, shell 1
(n=1) or shell 2 (n=2)? Explain.
n=1
Shell 2. The further from the nucleus the electron, the
further it can fall toward the nucleus and therefore
it has more energy (a greater ability to accelerate
matter) than shell 1 electrons.
n=2
Chapter 2 - The Chemical Basis of Life
AIM: What’s the matter?
Electron Organization:
Electrons can jump between shells (called a quantum leap)
n=1
In order to get an electron to “leap” from n=1 to n=2,
what is required?
n=2
Chapter 2 - The Chemical Basis of Life
AIM: What’s the matter?
Electron Organization:
Electrons can jump between shells (called s quantum leap)
n=3
n=2
n=1
Fig 2.7
The nucleus is charged and therefore is pulling on
the electron. It will take energy to pull the
electron away from the nucleus and move it
further away to shell 2. This is analogous to
picking up a bowling ball. Earth is pulling on the
bowling ball like the nucleus is pulling on the
electron. It takes energy to pick up a bowling ball.
Chapter 2 - The Chemical Basis of Life
AIM: What’s the matter?
Electron Organization:
Electrons can jump between shells (called s quantum leap)
What occurs when an electron leaps in the opposite
direction from n=2 to n=1?
Energy is emitted or lost from the electron (in the
form of light).
n=3
n=2
n=1
Fig 2.7
Chapter 2 - The Chemical Basis of Life
AIM: What’s the matter?
How big are atoms?
1/100,000,000,000th mm
0.62 miles
.
Analogy: If the nucleus were enlarged to the size of a golf ball, the
first electron shell would be over ½ mile away. What does this tell
you about the composition of an atom or matter in general as we
know it on Earth?
Matter as we know it is 99.999999999% empty space and therefore
has an extremely low density.
1/10,000,000th mm
(size)
Chapter 2 - The Chemical Basis of Life
AIM: What’s the matter?
Then what is matter at the
microscopic level?
Mostly empty space with tiny spaced out dots of
matter (protons/neutrons/electrons) held
together by the electromagnetic and strong force.
Chapter 2 - The Chemical Basis of Life
AIM: What’s the matter?
If we are just a collection of
dots, why can’t we pass
through each other? Why don’t
I just fall through the floor?
Chapter 2 - The Chemical Basis of Life
AIM: What’s the matter?
How many water molecules
are in 18ml of water
(size)
?
Chapter 2 - The Chemical Basis of Life
AIM: What’s the matter?
Avogadro’s Number
602,300,000,000,000,000,000,000
or
6.023 x 10
23
(scientific notation)
Chapter 2 - The Chemical Basis of Life
AIM: What’s the matter?
A mole
602,300,000,000,000,000,000,000
or
6.023 x 10
23
Chapter 2 - The Chemical Basis of Life
AIM: What’s the matter?
602,300,000,000,000,000,000,000
or
6.023 x 10
23
(scientific notation)
Chapter 2 - The Chemical Basis of Life
AIM: What’s the matter?
What determines the
elemental identity of an atom
?
Chapter 2 - The Chemical Basis of Life
AIM: What’s the matter?
Always has 2 protons
Always has 6 protons
Chapter 2 - The Chemical Basis of Life
AIM: What’s the matter?
Chapter 2 - The Chemical Basis of Life
AIM: What’s the matter?
What determines the
elemental identity of an atom
?
The number of protons (atomic number - Z)
Chapter 2 - The Chemical Basis of Life
AIM: What’s the matter?
Element?
Mass?
Charge?
Chapter 2 - The Chemical Basis of Life
AIM: What’s the matter?
The atomic mass (A) = protons + neutrons
Why do we not add the electrons mass?
Electrons are soooo small relative to
protons and neutrons (1/2000th the
size) that we ignore them.
Chapter 2 - The Chemical Basis of Life
AIM: What’s the matter?
The atomic charge
Compare number of protons to the
number of electrons.
Ex. If there are 10 protons (+10) and 7
electrons (-7) the overall charge is +3
Chapter 2 - The Chemical Basis of Life
AIM: What’s the matter?
Chapter 2 - The Chemical Basis of Life
AIM: What’s the matter?
What happens if we
change the number of protons
?
You change the identity of the atom (becomes a different element)
as well as the mass.
Chapter 2 - The Chemical Basis of Life
AIM: What’s the matter?
What happens if we
change the number of neutrons
You change the mass and perhaps the stability....
?
Chapter 2 - The Chemical Basis of Life
AIM: What’s the matter?
Isotopes are atoms that have the same
elemental identity (same number of
protons/same properties), but
different number of neutrons.
Chapter 2 - The Chemical Basis of Life
AIM: What’s the matter?
stable
stable
unstable
Certain ratios of protons to neutrons are unstable resulting in
breakdown of the nucleus (nuclear radiation).
Ex. 6 protons and 6 neutrons in a nucleus (Carbon-12) is stable, but 6
protons and 8 neutrons (carbon-14) is unstable and will undergo radioactive
decay to become stable. C-14 is called a radioactive isotope.
Chapter 2 - The Chemical Basis of Life
AIM: What’s the matter?
Radioactive decay
Chapter 2 - The Chemical Basis of Life
AIM: What’s the matter?
Radioactive decay
Carbon-14 (radioactive) will decay to Nitrogen-14 (stable). Seven protons and 7
neutrons in a nucleus is stable. An electron is shot out during the decay
making it dangerous and useful.
Chapter 2 - The Chemical Basis of Life
AIM: What’s the matter?
How can we use radioactivity
to our advantage
?
Chapter 2 - The Chemical Basis of Life
AIM: What’s the matter?
Example:
3H (tritium) = radioactive isotope of hydrogen. How
many protons and neutrons?
1 proton, 2 neutrons
1. Add tritiated thymidine (thymidine with 3H hydrogens) to
human cells undergoing mitosis in petri dishes. (tritiated
thymidine will be converted to the nucleotide dTTP and used to
make DNA)
2. Place dishes at different temperatures for a couple hours.
3. Remove dishes, put cells in test tubes and centrifuge down
cells and measure radioactivity.
What would you predict to observe?
Chapter 2 - The Chemical Basis of Life
AIM: What’s the matter?
Example:
3H (tritium) = radioactive isotope of hydrogen. How
many protons and neutrons?
1 proton, 2 neutrons
What would you predict to observe?
Cells growing at 37C performed DNA replication the quickest as
human enzymes typically work best at body temperature.
Therefore these cells with have the greatest amount of
radioactivity. Cell at greater than 50C or less than 20C will have
little to no radioactivity as DNA replication enzymes will not
work at these temps.
Chapter 2 - The Chemical Basis of Life
AIM: What’s the matter?
Tumor (mass of unregulated
dividing cells) with
concentrated radioactive
glucose.
PET scan
We can send molecules like fluorodeoxyglucose (glucose with radioactive
fluorine (F-18) in place of a hydroxyl (-OH) group) containing radioactive
elements into your body. For example, cancer cells use lots of glucose and
therefore the glucose will build up where tumors are found. The radioactive
elements will be shooting out particles (electrons or others) like a billion
microscopic flare guns that we can detect (in this case using PET scanning).
Chapter 2 - The Chemical Basis of Life
AIM: What’s the matter?
Tumor (mass of unregulated
dividing cells) with
concentrated radioactive
glucose.
We can potentially trace (follow) any radioactive molecule we put into you.
Chapter 2 - The Chemical Basis of Life
AIM: What’s the matter?
What if we alter the
?
number of electrons
If you alter the electrons, you simply change the charge of the atom
Chapter 2 - The Chemical Basis of Life
AIM: What’s the matter?
Review:
1. Draw an oxygen atom with a charge of -2 and an atomic
mass of 18
2. What is the atomic number of this atom?
3. Draw a neutral isotope of the above atom.
Chapter 2 - The Chemical Basis of Life
AIM: What’s the matter?
Review:
4. How many protons, neutrons and electrons does the
above element contain?
Chapter 2 - The Chemical Basis of Life
AIM: What’s the matter?
Review:
5. Which of the following models is correct according to
the Bohr model of the atom?
Chapter 2 - The Chemical Basis of Life
AIM: What’s the matter?
Review:
6. You have an atom and determine its mass to be 150 amu
and to have 90 neutrons. The atom has an overall charge
of -3. How many electrons does the atom have?
Chapter 2 - The Chemical Basis of Life
AIM: What’s the matter?
Review:
7. What is a mole? Why is this number important? From
where did it originate?
Chapter 2 - The Chemical Basis of Life
AIM: What’s the matter?
What determines the
?
Chemical reactivity of a given atom
(how an atom will interact with another atom)
The number of electrons in the valence shell (outer shell). This is logical as you would
expect the outer surfaces of atoms to interact with each other. Of course, the number of
protons determines the number of electrons and therefore it boils down to the number of
protons in the nucleus, which is why protons determine the element.
Chapter 2 - The Chemical Basis of Life
AIM: What’s the matter?
Valence shell
Chapter 2 - The Chemical Basis of Life
AIM: What’s the matter?
Climbing the Hierarchy
Chapter 2 - The Chemical Basis of Life
AIM: How do atoms interact with each other?
When are atoms
most happy
?
When their valence shell is full.
Chapter 2 - The Chemical Basis of Life
AIM: How do atoms interact with each other?
To be “happy” (stable) the sodium
atom will need to either get 7
electrons or lose 1. Which is
easier?
The sodium will give away its
outer shell electron.
Chapter 2 - The Chemical Basis of Life
AIM: How do atoms interact with each other?
Chlorine needs one electron for
its outer shell to be full.
Chapter 2 - The Chemical Basis of Life
AIM: How do atoms interact with each other?
Chapter 2 - The Chemical Basis of Life
AIM: How do atoms interact with each other?
Chapter 2 - The Chemical Basis of Life
AIM: How do atoms interact with each other?
Chlorine has a higher AFFINITY
for the electron and therefore
the electron will “fall” from
sodium to chlorine.
Chapter 2 - The Chemical Basis of Life
AIM: How do atoms interact with each other?
When the piece of elemental sodium (countless
numbers of sodium molecules) is placed in the
chlorine gas in the video, all those ridiculous
number of electrons jump to the countless
chlorines. This causes all the molecules to
move around violently (heat up) and electrons
to jump between shells (give off light).
Chapter 2 - The Chemical Basis of Life
AIM: How do atoms interact with each other?
Ionic bond
When sodium loses an electron it becomes
positively charged (a cation). When chlorine picks it
up it becomes negatively charged (a anion). Cations
and Anions are collectively called ions = fully
charged atoms/molecules.
ions
Cation vs Anion
Chapter 2 - The Chemical Basis of Life
AIM: How do atoms interact with each other?
Ionic bond
The sodium and chloride ions are now attracted to
each other and form an ionic bond.
ionic bond = bond between two oppositely charged ions
ions
Cation vs Anion
Chapter 2 - The Chemical Basis of Life
AIM: How do atoms interact with each other?
Salt crystals
Na+Cl- crystals are repeating arrays of Na+ and Clheld together by the electromagnetic force.
Chapter 2 - The Chemical Basis of Life
AIM: How do atoms interact with each other?
Salt
-general name given to ANY ionic compound (not
just sodium chloride (Na+Cl-) held together in a
lattice structure.
Na+ClK+ClMg2+Cl2Mn2+Cl2Ca2+CO32-
Chapter 2 - The Chemical Basis of Life
AIM: How do atoms interact with each other?
How else can atoms fill their outer shells?
http://www.visionlearning.com/library/flash_viewer.php?oid=1348&mid=55
Chapter 2 - The Chemical Basis of Life
AIM: How do atoms interact with each other?
Single Covalent Bond
H H or H2
In this case, to be stable and fill their outer shells, unlike in an ionic bond, the
atoms will SHARE their electrons to form a covalent bond.
http://www.visionlearning.com/library/flash_viewer.php?oid=1348&mid=55
Chapter 2 - The Chemical Basis of Life
AIM: How do atoms interact with each other?
Chapter 2 - The Chemical Basis of Life
AIM: How do atoms interact with each other?
F F or F2
Chapter 2 - The Chemical Basis of Life
AIM: How do atoms interact with each other?
Chapter 2 - The Chemical Basis of Life
AIM: How do atoms interact with each other?
Double Covalent Bonds (double bond)
=
=
O C O or CO2
Chapter 2 - The Chemical Basis of Life
AIM: How do atoms interact with each other?
Chapter 2 - The Chemical Basis of Life
AIM: How do atoms interact with each other?
Chapter 2 - The Chemical Basis of Life
AIM: How do atoms interact with each other?
Draw :
CH4 or H2O
Chapter 2 - The Chemical Basis of Life
AIM: How do atoms interact with each other?
Why is oxygen gas O2 and
nitrogen gas N2
=
O O and
=
N -N
Covalent bond strengths:
Triple bond > Double bond > Single bond
?
Chapter 2 - The Chemical Basis of Life
AIM: How do atoms interact with each other?
Fig. 2.11
Chapter 2 - The Chemical Basis of Life
AIM: How do atoms interact with each other?
MOLECULE
A molecule is two or more atoms held together by
COVALENT bonds. If you see a covalent bond, it is a
molecule. Period. The End.
Chapter 2 - The Chemical Basis of Life
AIM: How do atoms interact with each other?
C9H8O4 = Molecular formula
Structural formula:
skeletal formula
An aspirin molecule
Displayed formula
Ball-and-stick
You only need to know the difference between a molecular and structural formula, not the
different types of structural formulae.
Chapter 2 - The Chemical Basis of Life
AIM: How do atoms interact with each other?
C9H8O4 = Molecular formula
Why is the molecular formula not usually enough
to tell us what molecule is being indicated?
Because the atoms can be attached in different ways and different structures will give us
different molecules with different functions called structural isomers or constitutional
isomers.
Chapter 2 - The Chemical Basis of Life
AIM: How do atoms interact with each other?
An antibody molecule (a type or
protein) compared to an aspirin
molecule (the smaller one).
Chapter 2 - The Chemical Basis of Life
AIM: What’s the matter?
Drawing molecules
Chapter 2 - The Chemical Basis of Life
AIM: What’s the matter?
Draw the structure of C2H6
HH
HCCH
HH
Draw the structure of H2CO
H-C=O
H
Chapter 2 - The Chemical Basis of Life
AIM: What’s the matter?
Draw the structure of H6C3O
Draw the structure of C6H6
Chapter 2 - The Chemical Basis of Life
AIM: What’s the matter?
Number of bonds formed by each element:
Element
Number of Covalent
Bonds it will form to be
“happy” (stable)
Hydrogen
1
Oxygen
2
Nitrogen
3
Carbon
4
The element will form as many bonds as it needs electrons in its valence shell. For example,
carbon needs four electrons and therefore it will make four covalent bonds (it will share 4
electrons) with other elements.
Chapter 2 - The Chemical Basis of Life
AIM: What’s the matter?
Using the terms element, compound
and/or molecule, characterize the
following:
C6H6
This is certainly a molecule because there will be covalent bonds. It is also a compound
because there is more than one type of element.
Chapter 2 - The Chemical Basis of Life
AIM: What’s the matter?
Using the terms element, compound
and/or molecule, characterize the
following:
+
Na Cl
This is not a molecule since there are no covalent bonds present. It is a compound since
there is more than one type of atom present.
Chapter 2 - The Chemical Basis of Life
AIM: What’s the matter?
Using the terms element, compound
and/or molecule, characterize the
following:
O2
This is a molecule because there is a covalent bond (a double covalent bond in this case). It
is not a compound since there is only oxygen, which would make it an element.
Chapter 2 - The Chemical Basis of Life
AIM: What’s the matter?
Another structure/function example:
The structure of a molecules
determines its function...
Opium poppy fruit that has
been cut revealing the fluid
containing morphine.
In the example to the right, endorphin (a
naturally occuring chemical in your brain that
reduces the sensation of pain) has its
structure mimicked by morphine (a chemical
found in opium poppy).
This allows morphine to bind the endorphin
receptor main it a very popular painkiller.
Fig. 2.17
Chapter 2 - The Chemical Basis of Life
AIM: What’s the matter?
Another structure/function example:
The structure of a molecules
determines its function...
The structure of hemoglobin allows it to
carry four oxygen (O2) molecules.
Fig. 2.17
Chapter 2 - The Chemical Basis of Life
AIM: What’s the matter?
Another structure/function example:
The structure of a molecules
determines its function...
Lovastatin treats hypercholesterolemia
(high cholesterol level).
It was first isolated in 1978 from the
fungus Asperfillus terreus.
Chapter 2 - The Chemical Basis of Life
AIM: What’s the matter?
Another structure/function example:
The structure of a molecules
determines its function...
Cholesterol Biosynthesis – you don’t need
to eat cholesterol. Your enzymes make it.
**Enzymes are in blue.
**Substrates/Products are in black with final
products in GREEN.
Lovastatin binds to and inhibits HMG-CoA
reductase – remember that enzyme
names will usually end in –ase.
Chapter 2 - The Chemical Basis of Life
AIM: What’s the matter?
Another structure/function example:
The structure of a molecules
determines its function...
HMG-CoA reductase with lovastatin bound:
Lovastatin has a structure that allows it
to bind to the active site of this enzyme
thereby giving it its function as an
inhibitor and in turn reducer of blood
cholesterol.
Alpha helices are in blue.
Beta sheets in purple.
Loops in yellow.
Chapter 2 - The Chemical Basis of Life
AIM: What’s the matter?
Another structure/function example:
The structure of a molecules
determines its function...
This is the reaction normally catalyzed by this enzyme.
Compare the natural substrate (HMG CoA) to Lovastatin. Could
you guess that this molecule would bind to this protein?
Chapter 2 - The Chemical Basis of Life
AIM: What’s the matter?
Chemical Reactions and Chemical Equilibrium
Some reactions proceed to completion (irreversible reaction) indicated by the
single arrow:
CaCO3 + 2HCl → CaCl2 + H2O + CO2
However, many proceed in both directions (reversible reaction) as indicated by
the double arrow in the reaction diagram reaching an equilibrium.
or
Chapter 2 - The Chemical Basis of Life
AIM: What’s the matter?
Chemical Reactions and Chemical Equilibrium
Biological Example:
Glycolysis is shown to the right. The
circled numbers are enzymes.
Which reactions are reversible?
Those catalyzed by enzymes 3, 4, 6, 7, 8, 9, 10, and 11
Which reactions are irreversible?
Those catalyzed by enzymes 1, 2, 5 and 12