2.1 Chemical Elements
Chemistry as it related to biology
QOD: (after quiz)
Read the article and try to answer the
question:
1. Why does the doctor not recommend
the use of external cooling (such as
ice baths, cold water or even air
conditioners) to reduce a fever.
2. Are there any exceptions?
3. What is recommended to treat fever?
Why?
Your should have thorough answers,
including evidence you find in the article.
A. Matter
What is matter?
Biochemistry
Ch 2.1
Write a vocabulary list for yourself: try to define the ones you
remember:
•
•
•
•
•
•
•
•
•
Element
Compound
Protons
Neutrons
Electrons
Atomic number
Atomics Mass
Isotope
Orbital
Matter: “stuff” has mass, takes up space
Made up of elements: substance that cannot be broken down
into other substances by a chem rxn
Compound: consist of 2 or more elements in a fixed ratio
• Six elements:
C, H, N, O, P, S:
make up 98% of
living things.
• C, H, O and N
make up about
96%
“SHNOPS”
B. Atomic Structure
a. Protons (p+): positively
charged particles;
neutrons have no charge;
both have about 1 atomic
mass unit of weight. Both are
found in the nucleus
b. Electrons (e-) are
negatively charged particles
that orbit the nucleus
Periodic Table
(mass)
Atomic number= number of protons
- can’t change or it changes the atom
Atomic mass: about equal to the sum of its
protons and neutrons
All atoms of an element have the same
number of protons, the atom's atomic number
Interactive Periodic Table | Cartoon Periodic Table
Isotopes
Isotopes are atoms with the same number of protons
but differ in number of neutrons; e.g., a carbon atom
has six protons but may have more or less than usual
six neutrons.
Carbon 14 - Break it Down!
Carbon- 12 is the most common form of carbon, it has 6 protons,
6 electrons, and 6 neutrons
It is called Carbon 12 because that is its weight (6 + 6 )
Carbon 14 has 2 extra neutrons, its weight is 14 (6 + 8 ); it is an
isotope of carbon
A carbon with eight rather than six neutrons is unstable; it releases rays
and subatomic particles and is a radioactive isotope.
Sample Question: A 200 g
sample of muskopfonian is
left in a container , the half
life of muskopfonian is 1
hour. How much of the
sample will be left after 4
hours?
Answer:
200 x .5 = 100 (hour 1)
100 x .5 = 50 (hour 2)
50 x .5 = 25 (hour 3)
25 x .5 = 12.5 (hour 4)
or 200 x .54 = 12.5
Low levels of radiation such as radioactive iodine or glucose allow
researchers to trace the location and activity of the atom in living
tissues; therefore these isotopes are called tracers
which are used in CAT scans
High levels of radiation can cause cancerous tissues and destroy
cells; careful use of radiation in turn can sterilize products and kill
cancer cells.
Pick your favorite element from the table. Turn and tell your lab partner
how many protons, electrons and neutrons it has, and what it's atomic
weight is (if you can see it). Have your table partner then name the
element.
E. Electrons and Energy
1. Electrons occupy an orbital at some level near or distant
from the nucleus of the atom.
S orbital:
innermost,
hold 2
elections
P orbital:
after s,
holds 8
elections
Outer elections have more energy and are less stable.
So?
2. Electrons can be used to store and release energy!
3. When atoms absorb energy during photosynthesis, electrons
are boosted to higher energy levels.
4. The innermost shell of an atom is complete with two
electrons; all other shells are complete with eight electrons.
5. The outermost shell is the valance shell, and the number of
valance e- in the outermost shell determine many of the atoms
properties
DRAW IT!
QUICK!!
1. Draw six protons in the nucleus of the atom.
2. Draw six neutrons in the nucleus of the atom.
3. Draw two electrons in the first energy level and label them with
their charge.
4. Draw four electrons in the second energy level and label them with
their charge.
5. What element is it!? __________
(the future of the human race depends on it!)
What can easily be added to carbon to complete it’s valence shell?
2.2 Elements and Compounds
A. Compounds: When two or more different elements react
or bond together, they form a compound (e.g., H2O).
Electrons possess energy and bonds that exist between
atoms in molecules contain energy.
Glycine
B. Ionic Bonding
Ionic bonds: when
electrons are transferred
from one atom to another.
- Attraction of oppositely
charged ions holds the
two atoms together in an
ionic bond.
- Losing or gaining
elections gives ions a
filled outer shell, so they
are more stable
Ex: sodium (Na+) and
Chlorine (Cl- ) make NaCl
Cation:
positively charged
ion
anion:
negatively charged
ion
Why and how do ionic bonds form?
C. Covalent Bonding
Covalent bonds: when two atoms
share electrons so each atom has
octet of electrons in the outer shell.
• Hydrogen can give up
an electron to become
a hydrogen ion (H+) or
share an electron with
another atom to
complete its outer
shell of two electrons.
• Strongest
type of bond
Structural formulas represent
shared atom as a line between two
atoms; e.g., single covalent bond
(H-H), double covalent bond (O=O)
Carbon has amazing bonding properties, as we will
learn in the next chapter
Bonds can be
represented using
structural formation,
where a line
represent the
sharing of 2
elections
D. Nonpolar and Polar Covalent Bonds
1. In nonpolar covalent bonds, sharing of electrons is equal = no
charge
2. With polar covalent bonds, the sharing of electrons is unequal. =
charge
Ex: water molecule (H2O), sharing of electrons by oxygen and hydrogen
is not equal; the oxygen atom with more protons dominates the H2O
association.
*The oxygen then assumes a small negative charge *
Hydrogen Bond: weak attractive force between slightly positive
hydrogen atom of one molecule and slightly negative atom in another
or the same molecule.
•
Weakest bond
•
mainly between O, N, F and an atom of hydrogen
•
•
Many hydrogen bonds taken together are relatively strong.
Hydrogen bonds between complex molecules of cells help maintain structure and
function.
Hydrogen bonds
create surface tension.
Notice the e- spend more time around the oxygen molecule: it’s has more
protons to attract the elections
*the shape allows for one side to be more + and the other more -
Van der Waals Interactions
When you have a molecule which is electrically dipolar (equal
but opposite in charge) you have attraction between the
negative pole of one molecule and positive pole of the other
molecule. They are usually weaker than hydrogen bounds but
exist in all matter
Biological
molecules
recognize and
interact with
each other with
specificity based
on their shape
List the 4 main types of bonds from
weakest to strongest:
van der waal
hydrogen
ionic
covalent
Draw these example and Name the type
of bond.
What elements are in each bond?
1
2
Name the type of bond.
What elements are in each bond?
3
4
Title: Properties of water
In your notebook, create a chart listing the
properties of water, and why each property is
important. Include example whenever possible
use pages 29-31
http://vimeo.com/37064053
Examples of charts
Property
Explanation
Importance
Example
1. High Specific
Heat
2. High heat of
vaporization
3. Universal
solvent
4. Cohesive and
Adhesive
water
5. Ice Floats
Property 1
Property 2
Property 3
Property 4
Property 5
Explanation
https://www.youtube.com/watch?v=0eNSnj4ZfZ8
example
Pg 29-31
2.3. Chemistry of Water
A. Facts
1. All living things are 70.90% water.
2. Because water is a polar molecule, water molecules are hydrogen
bonded to each other.
3. With hydrogen bonding, water is liquid between 0 C and 100 C
which is critical for life.
http://www.johnkyrk.com/H2O.html
B. Properties of Water
1. High Specific Heat: The temperature of liquid water rises
and falls more slowly than that of most other liquids.
- Most water stays a liquid
Because water holds more heat, its temperature falls more slowly than
other liquids; this protects organisms from rapid temperature changes,
living things don't freeze or boil easily
Calorie is amount of heat energy required to raise temperature of one
gram of water 1o C.
http://science.howstuffworks.com/enviro
nmental/458-how-water-works-video.htm
2.
Water has a high heat of vaporization.
a. Hydrogen bonds between water molecules require a large amount of
heat to break.
b. This property moderates earth's surface temperature; permits living
systems to exist here.
c. When animals sweat, evaporation of the sweat takes away body heat,
thus cooling the animal.
Heat of vaporization
Evaporative cooling
Organisms rely on heat of
vaporization to remove body heat
3. Water is universal solvent, and facilitates chemical
reactions both outside of and within living systems..
a. Water is a universal solvent because it dissolves a great number of
solutes.
b. Ionized or polar molecules attracted to water are hydrophilic.
c. Nonionized and nonpolar molecules that cannot attract water are
hydrophobic.
Solvents dissolve other substances
(solutes) and do not lose their own
properties.
If we use a simple and easy example, we can
get a handle on the idea. Take a glass of warm
water, put a teaspoon of table salt in it, and stir
it. The salt will dissolve in the water and
"disappear" from view. The water is
the solvent here, the salt is the solute in this
example, and the resulting salt water is
a solution that we created. It's that simple.
Hydrophobic vs Hydrophilic
4. Liquid water is cohesive & adhesive
Cohesion = H bonds between water molecules; H2O
molecules tend to stick together.
Adhesive= ability of water to cling to other polar molecules
importance= Higher surface tension
Transport H2O against gravity in plants = capillary action
5. Ice floats
 Most (all?) substances are more dense
when they are solid, but
not water… Ice floats!
H bonds form a crystal
 allowing life to survive the winter

Ice!
I could use
more ice!
And this has
made all the
difference!
Create a Venn Diagram Comparing Acids
and Bases
 Substances with hydrogen
• Stomach acid
ions (H+)
• Citrus fruit: orange
 Substances with hydroxide
• Soap
ions (OH–)
• Cleaning products
 Taste sour
• Baking soda
 Taste bitter
• vinegar
 Feel slippery
 pH greater that 7
Neutral
=
pH
of
7
 pH lower that 7
Acid molecules dissociate in water, releasing hydrogen ions
(H+) ions: HCl ¨ H+ + Cl-.
Bases are molecules that take up hydrogen ions or release
hydroxide ions. NaOH ¨ Na+ + OH-.
See also: Acid & Base
Coloring
Acids and Bases
Covalently bonded water molecules ionize; the atoms
dissociate into ions.
• When water ionizes or dissociates, it releases a small
(107 moles/liter) but equal number of H+ and OH ions;
thus, its pH is neutral.
• Water dissociates into hydrogen and hydroxide ions:
The pH scale indicates acidity and basicity (alkalinity) of
a solution.
-Acid is a substance with pH
less than 7; base is a substance
with pH greater than 7.
-As logarithmic scale, each
lower unit has 10 times the
amount of hydrogen ions as next
higher pH unit;
* Buffers keep pH steady and
within normal limits in living
organisms..
http://www.johnkyrk.com/pH.html
Chemistry in Biology
Acids
 Substances that
dissociates into
hydrogen ions (H+)
 Taste sour
 pH lower than 7
Examples
• Stomach acid
• Citrus fruit: orange
• vinegar
Base
 Substances that
dissociated into hydroxide
ions (OH–)
 Taste bitter
 Feel slippery
 pH greater than 7
Examples
• Soap
• Baking soda
• Cleaning
products
H+ Ion
Concentration
pH Scale
pH
Examples of Solutions
100
0
10–1
1
10–2
2
Stomach acid, Lemon juice
10–3
3
Vinegar, cola, beer
10–4
4
Tomatoes
10 times less H+
10–5
5
Black coffee, Rainwater
pH8  pH7
10-8  10-7
10–6
6
Urine, Saliva
10–7
7
Pure water, Blood
10–8
8
Seawater
10–9
9
Baking soda
10–10
10
Great Salt Lake
10–11
11
Household ammonia
10–12
12
Household bleach
10–13
13
Oven cleaner
10–14
14
Sodium hydroxide
tenfold change
in H+ ions
pH1  pH2
10-1  10-2
10 times more
H+
pH10  pH8
10-10  10-8
100 times more
H+
Hydrochloric acid
Buffers & cellular regulation
 pH of cells must be kept ~7 to maintain
homeostasis!
Buffers: solutions used to stabilize
the pH of a solution
 Control pH by using buffers

reservoir of H+
9
8
 donate H+ when [H+] falls
7
 absorb H+ when [H+] rises
pH
6
Buffering
range
5
4
3
2
1
0
AP Biology
0
1
2
3
4
Amount of base added
5
BICARBONATE BUFFER SYSTEM:
H2O + CO2  H2CO3  HCO3 -+ H+
HCO3- = Bicarbonate (weak base)
H2CO3 = Carbonic acid (weak acid)
Major buffer system in blood
Maintains blood pH between 7.38 and
7.42
AP Biology
He’s gonna
earn a
Darwin Award!
Any
Questions?
2009-2010
1. The only atom that has a nucleus with no
neutrons is _________.
A) argon
B) carbon
C) oxygen
D) hydrogen
2. Which of the following elements is NOT
one of the six that make up 98% of most
organisms' body weight?
A) hydrogen
B) nitrogen
C) carbon
D) iron
Which of the following statements is true?
A) All isotopes give off subatomic
particles.
B) All isotopes are radioactive.
C) All isotopes have the same number of
protons.
D) All isotopes have the same number of
neutrons.
What type of bond is formed when atoms share
electrons?
A) ionic
B) covalent
C) hydrogen
If an atom has an atomic number of 17 and an
atomic mass of 35, the number of neutrons in
its nucleus equals _____.
A) 17
B) 18
C) 52
Which bond is most easily broken?
A) a hydrogen bond
B) a triple covalent bond
C) a single covalent bond
Hydrophobic molecules tend to be
_________.
A) nonpolar
B) inorganic minerals
C) ionic
D) water soluble
The calcium ion (Ca2+) _____.
A) has accepted two protons
B) has given away two electrons
C) will form a covalent bond with the
chlorine ion (Cl-)
D) All of these
The three isotopes of carbon 12C, 13C and 14C
have different numbers of _______?
A) electrons
B) protons
C) neutrons
The combined number of ___________ will
determine the number of electrons in orbital(s)
around a neutral atom.
A) orbitals
B) neutrons
C) bonds
D) protons
Which of the following statements is true?
A) There are two polar covalent bonds in
water.
B) There are two ionic bonds in water.
C) There is one ionic and one covalent
bond in water.
D) Electrons are less attracted to oxygen
than hydrogen.
The two parallel strands of DNA are held together by
_______ bonds.
A) nonpolar
B) hydrogen
C) ionic
D) covalent
The calcium ion (Ca2+) _____.
A)
has accepted two protons
B)
has given away two electrons
C)
will form a covalent bond with the
chlorine ion (Cl-)
D)
All of these
Hydrogen bonds form when ___________.
A)
atoms share electrons
B)
a slightly negative atom is attracted to a
slightly positive atom
C)
atoms gain electrons
D)
atoms lose protons
Which of the following has a basic pH?
A) lemon juice
B) milk of magnesia
C) tomatoes
D) hydrochloric acid
Aquatic living things are able to survive the winter
thanks to which property of water?
A) It is less dense as a solid than as a
liquid.
B) It is cohesive and adhesive.
C) It is the universal solvent.
D) It resists changes of state (from liquid
to ice or liquid to steam).
QOD:
In a group of 4, each pick one paragraph
of the article to read. (note: paragraph 2
is the hardest one, the back page will be
more helpful)
When you are done reading, discuss as a
group and try to answer the question:
1. Why does the doctor not recommend
the use of external cooling (such as
ice baths, cold water or even air
conditioners) to reduce a fever.
2. Why do movie theaters put so much
salt on popcorn?