Chapter 6 Lecture Notes—Essential Chemistry for Biology
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 anything that occupies space and has mass
– Matter is composed of chemical elements and compounds
– Elements: substances that cannot be broken down into
other substances
– There are 92 naturally occurring elements on Earth and
20+ more made in a lab
– What are compounds? Examples?
Periodic table of the elements
Location of....
• Metals?
• Nonmetals?
25 Elements are essential to life
• C, H, N, O, P, S: 96% of the weight of the human
body
Some Elements React to Form Compounds
•
Elements can combine chemically to form
compounds
•
Compounds contain two or more elements
chemically combined in a fixed ratio
Examples of Compounds:
1. Table salt (sodium chloride): NaCl
2. Water: H2O
3. Glucose: C6H12O6
Atom: smallest unit of matter that retains the
properties of an element
• Each element consists of one kind of atom
(a) Hydrogen atom
(b) Carbon atom
Proton
Neutron
(c) Oxygen atom
Electron
First
shell
Second
shell
Atomic nucleus
Fig. 2.02
Atomic Structure
• The subatomic particles of an atom
Electron
Proton
 Positive charge
 Determines element
 Negative charge
• Participates in chemical
reactions
• Outer-shell electrons
determine chemical
behavior
Neutron
 No charge
 Determines isotope
Nucleus
• Consists of neutrons
and protons
• Elements
– differ in the number of subatomic particles in
their atoms
• Atomic Number: number of protons
– determines which element it is
• Mass number
– sum of the number of protons and neutrons
Chemical Properties of Atoms
• Electrons
– Located outside the nucleus of an atom in specific
electron shells (energy levels)
• The number of electrons in the outermost shell
determines the chemical properties of an atom
Atoms of the four elements most abundant in life
First
electron shell:
can hold
2 electrons
Outermost
electron shell:
can hold
8 electrons
Electron
Hydrogen (H)
Atomic number = 1
Carbon (C)
Atomic number = 6
Nitrogen (N)
Atomic number = 7
Oxygen (O)
Atomic number = 8
Isotopes
• Isotopes are atoms of the same element that have a
different number of NEUTRONS. Ex. Carbon
Orbital Diagrams of the First 18 Elements
1st
Shell
2
2nd
Shell
8
3rd
Shell
8
Chemical Bonding and Molecules
• Chemical reactions:
– Atoms give up or acquire electrons in order to
complete their outer shells
– Result in atoms staying close together to form
molecules
– Chemical bonds hold molecules together
• Ionic Bonds
• Covalent bonds
Ionic Bonds: form between metals and nonmetals
• When an atom loses or
gains electrons, it
becomes electrically
charged
– Charged atoms are
called ions
– Ionic bonds are
formed between
oppositely charged
ions
Sodium atom (Na)
Chlorine atom (Cl)
Complete
outer shells
Sodium ion (Na)
Chloride ion (Cl)
Sodium chloride (NaCl)
Atoms: electrically neutral
Ions: Electrically charged
(b) Hydrogen ion (H+)
(a) Hydrogen atom (H)
1 electron
No
electron
1 proton
1 proton
No net electrical
charge
(d) Sodium ion (Na+)
(c) Sodium atom (Na)
11
electrons
11 protons
10
electrons
11 protons
No net electrical
charge
Fig. 2.03
Covalent Bonds: form between nonmetallic atoms
• A covalent bond forms when two atoms share one
or more pairs of outer-shell electrons
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
• Cells constantly rearrange molecules by breaking
existing chemical bonds and forming new ones
– Such changes in the chemical composition of matter
are called chemical reactions
Hydrogen gas
Oxygen gas
Reactants
Water
Products
Chemical Equations: symbolize chemical reactions
Reactants: on the left
side of the equation
– the starting materials
Products: on the right side of
the equation
– the ending materials (the stuff
produces)
Law of Conservation of Mass
– Chemical reactions do not create or destroy matter—they only
rearrange it!
WATER AND LIFE
• Life on Earth began in water and evolved there for 3
billion years
• The abundance of water is a major reason Earth is
habitable
– Modern life still remains tied to water
– Your cells are composed of 70%–95% water
The Structure of Water
• The water molecule:
– two hydrogen atoms joined to one oxygen atom by
single covalent bonds
H
H
O
Water: a polar molecule
• The electrons of the covalent bonds are shared unequally
between oxygen and hydrogen
– unequal sharing of electrons makes water a polar molecule
– hydrogen atoms: partially positive (d ) Why?
– oxygen atom: partially negative (d -) Why?
(d )
(d )
(d )
The Structure of Water
• The polarity of
water results in
weak electrical
attractions between
neighboring water
molecules
()
Hydrogen bond
()
()
()
()
– These interactions
are called
hydrogen bonds
()
(b)
()
()
Water’s Life-Supporting Properties
•
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
2. Water’s cohesive nature
3. Water’s ability to moderate temperature
4. Floating ice
Water as the Solvent of Life
• A solution is a liquid consisting of two or more
substances evenly mixed
– The dissolving agent is called the solvent
– The dissolved substance is called the solute
Ion in solution
Salt crystal
Dissolving of
Sodium
Chloride (NaCl)
in Water
Salt
Electrical
attraction
Water molecules dissolve NaCl,
breaking ionic bond
Water
Water
molecules
(H2O)
Hydrogen
bonds
Edge of one
salt crystal
Ionic bond
The Cohesion of Water
• Water molecules
stick together as a
result of hydrogen
bonding
– This is called
cohesion
– Cohesion is vital
for water
transport in
plants
Microscopic tubes
• Surface tension
– 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
Figure 2.13
Water Moderates Temperature
• Because of hydrogen bonding, water has a strong
resistance to temperature change
• 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
• The density of ice is lower than liquid water
– This is why ice floats
Hydrogen bond
Ice
Liquid water
Stable hydrogen bonds
Hydrogen bonds
constantly break and re-form
The Biological Significance of Ice Floating
• When water molecules get cold, they move apart,
forming ice
– A chunk of ice has fewer molecules than an equal
volume of liquid water
• Since ice floats, ponds, lakes, and even the oceans
do not freeze solid
– Marine life could not survive if bodies of water froze
solid
Acids, Bases, and pH
• Acid
– A chemical compound that donates H+ ions to
solutions
• Base
– A compound that accepts H+ ions and removes them
from solution
pH Scale
The pH scale is used to
describe the acidity of a
solution
Oven cleaner
Household bleach
Household ammonia
• Acidic: pH < 7
Basic
solution
Milk of magnesia
-
H+ > OH
Seawater
Human blood
Pure water
• Basic: pH > 7
H+
-
Neutral
solution
< OH
Tomato juice
• Neutral: pH = 7
H+
-
= OH
Urine
Grapefruit juice
Acidic
solution
Lemon juice;
gastric juice
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
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 (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
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 (Fe2O3)
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