Download 3. Chapter 2: Basic Chemistry for Biology

Chapter 2 Lecture Notes—Essential Chemistry for Biology
Biol 100 – K. Marr –2009
Topics Discussed in these notes
•
Matter, Elements and Compounds
•
Periodic Table of the Elements: Metals vs. Nonmetals
•
Atomic Structure
•
Chemical Bonding: Ionic vs. Covalent Bonding
•
Chemical Reactions and Chemical Equations
•
The Structure of Water
•
Water as a Solvent
•
The Importance of Water to Living Things
•
Acids, Bases and pH
•
Self-test/Review Questions
BASIC CHEMISTRY
• Organisms and all other things in the universe
consist of matter
Matter: Elements and Compounds
• Matter is
– Matter is composed of
– Elements are
– There are 92 naturally occurring elements on
Earth
Periodic table of the elements
• 25 Elements are essential to life
Location of....
• Metals?
• Nonmetals?
• C, H, O, N: 96% of the weight of the human body
Elements
Atom:
• Elements
• Each element consists of one kind of atom
• Compounds
(a) Hydrogen atom
(b) Carbon atom
(c) Oxygen atom
Examples of Compounds:
1.
2.
3.
Proton
Neutron
Electron
First
shell
Second
shell
Atomic nucleus
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Atomic Structure
• The subatomic particles of an atom
• Elements
Electron
Proton
 Positive charge
 Determines element
 Negative charge
• Atomic Number: number
• Participates in chemical
reactions
– Determines
• Outer-shell electrons
determine chemical
behavior
• Mass number
Neutron
 No charge
 Determines isotope
– sum of the number
Nucleus
• Consists of neutrons
and protons
Chemical Properties of Atoms
• Atoms of the four elements most abundant in life
• Electrons orbit the nucleus of an atom in specific
electron shells
First
electron shell:
can hold
2 electrons
• The number of electrons in the outermost shell
determines
Outermost
electron shell:
can hold
8 electrons
Electron
Hydrogen (H)
Atomic number = 1
Orbital Diagrams of the First 18 Elements
Carbon (C)
Atomic number = 6
Nitrogen (N)
Atomic number = 7
Oxygen (O)
Atomic number = 8
Chemical Bonding and Molecules
• Chemical reactions:
1st
Shell
2
2nd
Shell
8
– Atoms give up or acquire
order to complete their outer shells
in
– Result in atoms staying close together to form
molecules
– Chemical bonds hold molecules together
3rd
Shell
8
• Ionic Bonds
• Covalent bonds
2
Ionic Bonds: form between metals and nonmetals
• When an atom loses or
gains electrons, it
becomes electrically
charged
– Charged atoms are
called
– Ionic bonds are
formed between
oppositely charged
ions
Atoms: electrically neutral
Ions: Electrically charged
(b) Hydrogen ion (H+)
(a) Hydrogen atom (H)
Sodium atom (Na)
No
electron
1 proton
1 proton
No net electrical
charge
Chlorine atom (Cl)
Complete
outer shells
1 electron
(d) Sodium ion (Na+)
(c) Sodium atom (Na)
11
electrons
10
electrons
11 protons
Sodium ion (Na)
11 protons
No net electrical
charge
Chloride ion (Cl)
Sodium chloride (NaCl)
Covalent Bonds: form between nonmetallic atoms
• A covalent bond forms when two atoms
one or more pairs of outer-shell electrons
Fig. 2.03
Covalent bonding in water
Oxygen atom with unfilled
shell
Water molecule (H2O)
Full shell with 8 electrons
– Slightly negative
Covalent
bond
(shared pair
of electron)
+
+Slightly
positive
Full shells with 2 electrons each
Hydrogen atoms with unfilled shells
Fig. 2.04a
Chemical Reactions
Chemical Equations
• Cells constantly rearrange molecules by breaking
existing chemical bonds and forming new ones
– Such changes in the chemical composition of matter
are called
• Chemical Equations: symbolize chemical reactions
• Reactants: on the
side of the equation
– the starting materials
• Products: on the
side of the equation
– the ending materials—the stuff produced
• Law of
– Chemical reactions do not create or destroy matter—
they only rearrange it
Hydrogen gas
Oxygen gas
Reactants
Water
– Chemical Equations must be ―balanced‖ =
Products
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WATER AND LIFE
The Structure of Water
• Life on Earth began in water and evolved there for 3
billion years
• The water molecule:
– two hydrogen atoms joined to one oxygen atom by
single covalent bonds
• The abundance of water is a major reason Earth is
habitable
– Modern life still remains tied to water
H
– Your cells are composed of 70%–95% water
H
O
Water: a polar molecule
Water: a polar molecule
• The electrons of the covalent
bonds are
between oxygen and
hydrogen.
(d )
(d )
• The electrons of the covalent bonds are shared
_____________ between oxygen and hydrogen
– __________________________makes water a polar molecule
– hydrogen atoms: partially positive (d )
makes
– oxygen atom: partially negative (d -)
water a polar molecule
(d )
• hydrogen atoms: partially
positive (d )
(d )
(d )
• oxygen atom: partially negative
(d -)
(d )
Water’s Life-Supporting Properties
The Structure of Water
•
• The polarity of water
results in weak
electrical attractions
between neighboring
water molecules
()
Hydrogen bond
The polarity of water molecules and the hydrogen
bonding that results explain most of water’s lifesupporting properties
()
1. Versatility of water as a solvent
()
– These interactions are
called
()
()
()
2. Water’s cohesive nature
()
()
3. Water’s ability to moderate temperature
4. Floating ice
(b)
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Water as the Solvent of Life
Dissolving of Sodium Chloride, NaCl, in Water
• A solution is a liquid consisting of two or more
substances evenly mixed
Salt
– The dissolving agent is called the _______________
Electrical
attraction
Water molecules dissolve NaCl,
breaking ionic bond
Water
– The dissolved substance is called the _____________
Ion in solution
Water
molecules
(H2O)
Salt crystal
Hydrogen
bonds
Edge of one
salt crystal
Fig. 2.05a
• Surface tension
The Cohesion of Water
• Water molecules
stick together as a
result of hydrogen
bonding
– This is called
cohesion
Ionic bond
– is the measure of how difficult it is to stretch or break
the surface of a liquid
– Hydrogen bonds give water an unusually high
surface tension
Microscopic tubes
– Cohesion is vital
for water
transport in
plants
Figure 2.13
Water Moderates Temperature
• Because of hydrogen bonding, water has a strong
resistance to temperature change
• The density of ice is lower than liquid water
– This is why ice floats
Hydrogen bond
• Water can absorb and store large amounts of heat
while only changing a few degrees in temperature
– Earth’s Oceans cause temperatures to stay within
limits that permit life
Ice
Liquid water
Stable hydrogen bonds
Hydrogen bonds
constantly break and re-form
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The Biological Significance of Ice Floating
Acids, Bases, and pH
• When water molecules get cold, they move apart,
forming ice
• Acid
– A chunk of ice has fewer molecules than an equal
volume of liquid water
– A chemical compound that
to solutions
• Base
• Since ice floats, ponds, lakes, and even the oceans
do not freeze solid
– A compound that
removes them from solution
and
– Marine life could not survive if bodies of water froze
solid
pH Scale
pH scale—used to
describe the acidity of
a solution
• ____________: pH < 7
Oven cleaner
Household bleach
Household ammonia
Basic
solution
Seawater
H+ > OH-
•
Human blood
Pure water
: pH > 7
H+ < OH
Milk of magnesia
Neutral
solution
-
Urine
Tomato juice
Grapefruit juice
•
: pH = 7
H+ = OH
-
Acidic
solution
Lemon juice;
gastric juice
Self-test/Review Questions
6. A carbon atom has 6 protons, and the most common isotope
of carbon has 6 neutrons. A radioactive isotope of carbon
has 8 neutrons. What are the atomic numbers and the mass
numbers of the of the stable and radioactive forms of
carbon?
7. Explain the difference between an ionic and covalent bond
in terms of what happens to the electrons in the outer shell of
the participating atoms.
8. Sodium fluoride, NaF, is often added to toothpaste to both
kill bacteria that cause cavities. It also helps to harden the
enamel of teeth thus helping it resist cavities. Is sodium
fluoride an ionic or covalent compound? How do you know?
Explain your reasoning.
9. Is carbon dioxide an ionic or covalent compound? How do
you know? Explain your reasoning.
Self-test/Review Questions
Use these questions as a self test and then discuss your responses with
your study group/classmates—your responses will not be collected.
1. Why is carbon dioxide gas, CO2, classified as a compound
but nitrogen gas, N2, is not?
2. Which of the following are compounds? Elements?:
C6H12O6, CH4, O2, Cl2, HCl, MgCl2, Fe, Ca, Ne, NaI, I
3. What is the difference between an atom and an ion? Give
examples of each to support your response.
4. Which subatomic particle determines the identity of an
atom?
5. Which subatomic particle determines the chemical
properties of an atom?
Self-test/Review Questions (cont.)
10. Why are the following incorrect structures for the substances
below? Rewrite their structures with the correct number of chemical
bonds.
a.
Carbon dioxide gas: O—C—O
b. Oxygen gas: O—O
c.
Nitrogen gas: N—N
11. Explain how water’s versatility as a solvent results from the fact
that water is polar molecule.
12. A bottle of Pepsi consists mostly of sugar dissolved in water,
with some carbon dioxide gas that makes fizzy and makes the pH
less than 7. Describe Pepsi using the following terms: solute,
solvent, acidic, aqueous solution
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Self-test/Review Questions (cont.)
13. Which of the following are chemical changes? Physical changes? If
possible, write the balanced chemical equation for those that are a
chemical change.
a.
The alcoholic fermentation in Yeast in which yeast produce
ethanol, C2H5OH, and carbon dioxide, CO2, from the sugar
glucose, C6H12O6
b. Water boils to form steam
c.
The healing of a cut finger
d. Cutting a piece of wood with a saw
e.
Potassium metal, K, and chlorine gas (Cl2) combine to form
potassium chloride.
f.
The rusting of iron, Fe, to produce rust, iron (III) oxide (Fe 2O3)
Self-test/Review Questions (cont.)
14. Which of these is not a subatomic particle? a) proton; b) ion; c)
neutron; d) electron
15. The outermost electron shell of every Noble Gas element
(except Helium) has ___ electrons. a) 1; b) 2; c) 4; d) 6; e) 8
16. An organic molecule is likely to contain all of these elements
except ___. a) C; b) H; c) O; d) Ne; e) N
17. The chemical bond between water molecules is a ___ bond. a)
ionic; b) polar covalent; c) nonpolar covalent; d) hydrogen
18. A solution with a pH of 7 has ___ times more H ions than a
solution of pH 9. a) 2; b) 100; c) 1000; d) 9; e) 90
19. The type of chemical bond formed when electrons are shared
between atoms is a ___ bond. a) ionic; b) covalent; c)
hydrogen
Self-test/Review Questions (cont.)
20. The type of chemical bond formed when oppositely charged
particles are attached to each other is a ___ bond. a) ionic; b)
covalent; c) hydrogen
21. Carbon has an atomic number of 6. This means it has ___. a)
six protons; b) six neutrons; c) six protons plus six neutrons; d)
six neutrons and six electrons
22. Each of the isotopes of hydrogen has ___ proton(s). a) 3; b) 1;
c) 2; d) 92; e) 1/2
23. A molecule is ___. a) a mixture of various components that can
vary; b) a combination of many atoms that will have different
ratios; c) a combination of one or more atoms that will have a
fixed ratio of its components; d) more important in a chemistry
class than in a biology class
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