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Elements & Atoms
Created by G.Baker
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Vocabulary
I can….
10/31 – atom
10/31 – I can name 3 elements.
11/3 – element
11/3 – Name the 3 subatomic particles.
11/5 – describe how to calculate neutrons
11/5 – trace elements
11/6 – ions
11/6 – Explain why it is important to know what
group and element is located.
11/10 – valance
electrons
11/10 - Calculate the charge of an ion of Cl.
11/11 – isotopes
11/13 – explain why compounds form
11/13 – compound
11/14 – activation
energy
11/17 – covalent
bond
11/11 – Explain why atoms even form ions.
11/14 – Name the parts of a chemical reaction.
11/17 – Which type of bond would be stronger
– ionic or covalent?
Review
Relationship atoms and elements
List of elements
Element box
Subatomic particles – location calculate charge
Draw element – bohr’s model
25 elements & symbols
4 main elements in organisms – name 3 trace elements
Valence electrons definiions
Isotopes – definition and number of neutrons
Review
• Why do atoms bond?
• Name and define the 2 types of bonds
• Count atoms in a compound
• Define a compound
• How can you tell if a bond is ionic or covalent
• Draw compounds
Why Study Atoms and Elements
in BIOLOGY??????
Why Study Atoms in Biology?
• Atoms and elements make up our
bodies and those of other organisms
– They make up the physical
environment as well
• The ordering of atoms into molecules
represents the lowest level of biological
organization
– Therefore, to understand life, it is
important to understand the basic
concepts of chemistry
Copyright © 2009 Pearson Education, Inc.
Name the levels of life from the
smallest to the largest!!!
Levels of the Organization of Life
• Subatomic particle
organism
• Atom
populations
• Molecule(compound)
community
• Organelle
ecosystem(biome)
• Cell
biosphere
• Tissue
• Organ
• Organ system
What is this a picture of ? Name
3 facts about this object!
ATOMS
Atoms: smallest unit of matter that still
retains the properties of an element.
.
Atoms consist of protons, neutrons, and
electrons
• An atom is the smallest unit of matter that still
retains the properties of a element
– Atoms are made of over a hundred
subatomic particles, but only three are
important for biological compounds
–Proton—has a single positive electrical
charge
–Electron—has a single negative electrical
charge
–Neutron—is electrically neutral
Copyright © 2009 Pearson Education, Inc.
Protons
Protons are located in the nucleus of the
atom. They are positively charged.
Neutrons
Neutrons are located in
the nucleus.
They have NO charge!
Electrons
Electrons are located in the
shells around the atom.
They are negatively charged.
Parts of an Atom
Protons and neutrons make up the
nucleus and has the most mass.
Electrons do not weigh as
much. SO the atomic mass is only
the Protons + the Neutrons
Atoms make up substances called
elements which are the building
blocks of matter.
There are 110 elements
1. ELEMENTS ARE PURE SUBSTANCES
MADE OF ONLY 1 KIND OF ATOM AND
ARE THE BUILDING BLOCKS OF
MATTER.
2. ELEMENTS CANNOT BE BROKEN DOWN
INTO A SIMPLER SUBSTANCE
3. ELEMENTS HAVE THEIR OWN UNIQUE
SET OF PROPERTIES THAT NO OTHER
ELEMENT HAS.
• ELEMENTS ARE MADE OF ONLY 1 KIND
OF ATOM
• SOME COMMON ELEMENTS
 HYDROGEN (H), HELIUM (He), OXYGEN (0),
 Notice that the first letter is capital and the next
letter is lower case.
Why Do Some Elements Have Differen
Symbols?
They are older elements that
were name
in a different language like
Latin.
Copper – cuprum
Iron – Ferrous
Gold - aurum
Silver - argentum
Elements
•
Weird written in Latin
Rules
1. First letter capital
2. Second letter lower case
Living organisms are composed of
about 25 chemical elements
• Living organisms are composed of
matter, which is anything that occupies
space and has mass (weight)
– Matter is composed of chemical
elements
–Element—a substance that cannot
be broken down to other substances
– same atoms
–There are 92 elements in nature—
only a few exist in a pure state
– Life requires 25 essential elements;
some are called trace elements
Copyright © 2009 Pearson Education, Inc.
Essential Elements of Life
• About 25 of the 92 elements are essential to
life
• Carbon, hydrogen, oxygen, and
nitrogen make up 96% of living
matter
• Most of the remaining 4% consists of calcium,
phosphorus, potassium, and sulfur
• Trace elements – elements required by
organisms in small amounts.
Copyright © 2008 Pearson Education, Inc., publishing as Benjamin Cummings
Elements in Organisms
• 4 elements that make up 96% of human
body: Carbon(C), Hydrogen(H),
Oxygen(O), Nitrogen(N)
2.2 CONNECTION: Trace elements
are common additives to food and
water
• Some trace elements are required to prevent
disease
 Without iron, your body cannot transport
oxygen
 An iodine deficiency prevents production of
thyroid hormones, resulting in goiter
Copyright © 2009 Pearson Education, Inc.
More about Elements..
• Elements are the building
blocks of all matter.
• The periodic table is a list
of all of the elements that
can build matter. It’s a
little like the alphabet of
chemistry.
• The periodic table tells us
several things…
Created by G.Baker
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Atoms: The Constituents of
Matter
• Each element contains only one
type of atom.
• Information on elements is
arranged in logical order in a table
called the periodic table.
• The periodic table arranges
elements left to right based on
their atomic number, and in
columns based on similarities in
their properties.
Element Info in Each Box
Atomic weight
Atomic Number
Symbol
Name
Information from the periodic table
Atomic Number- Number of Protons
in an atom & electrons
Silver = 47 protons
Atomic Mass - number of
protons + neutron
To find the Atomic Mass:
Round the atomic weight
Krypton's mass number is
84 since its atomic weight,
83.80, rounds up to 84.
Mass Number = (Number of Protons) +
(Number of Neutrons)
84 = 36 + 48
Electrons have special rules….
• You can’t just shove all of the electrons
into the first orbit of an electron.
• Electrons live in something called shells
or energy levels.
• Only so many can be in any certain shell.
Created by G.Baker
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• Valence electrons are those in the
outermost shell, or valence shell
• The chemical behavior of an atom is
mostly determined by the valence
electrons
• Elements with a full valence shell are
chemically inert or do not react
Copyright © 2008 Pearson Education, Inc., publishing as Benjamin Cummings
Atoms: The Constituents of
Matter
• The tendency of atoms to be stable
when they have eight electrons in their
outermost shells is called the rule of
eight, or the octet rule. They want
their outer shell to be FULL!!!!
• This makes them HAPPY!!
• Hydrogen and phosphorus are
exceptions to the octet rule.
Atoms: The Constituents of
Matter
• The outermost shell of an atom
determines how it reacts with other
atoms.
• Generally, if eight electrons are in the
outer shell, the atom is stable and does
not tend to react.
• Atoms which do not have eight electrons
in the outermost shell will share, gain, or
lose electrons to arrive at a stable state.
Bohr Diagrams DRAW AN ATOM
1) Draw a nucleus with the element
symbol inside. Place Protons and
neutrons in the nucleus.
2) The electrons will go in the orbits
around the nucleus. Fill order of
C
shells, 2,8,8,18.
3) Place an X over the atom. This
splits the atom into quarters. Since
electrons are negative and repel
each other place electrons into
different quarters. Clockwise!
4) Place all electrons until gone!
Fig. 2-9
Hydrogen
1H
Atomic mass
First
shell
2
He
4.00
Atomic number
Helium
2He
Element symbol
Electrondistribution
diagram
Lithium
3Li
Beryllium
4Be
Boron
5B
Carbon
6C
Nitrogen
7N
Oxygen
8O
Fluorine
9F
Neon
10Ne
Silicon
14Si
Phosphorus
15P
Sulfur
16S
Chlorine
17Cl
Argon
18Ar
Second
shell
Sodium Magnesium Aluminum
12Mg
11Na
13Al
Third
shell
Hydrogen
Helium
First
shell
Lithium
Beryllium
Boron
Carbon
Nitrogen
Oxygen
Fluorine
Neon
Silicon
Phosphorus
Sulfur
Chlorine
Argon
Second
shell
Sodium
Third
shell
Magnesium Aluminum
PARTS OF PERIODIC TABLE
• Number of electrons in the outermost.
Determines how the element will
bond.
GROUPS or family: Columns
Number of valence electrons.
Group 1 – one valence electron
Group 2 – 2 valence electrons
Periods - ROWS
Rows of elements are called periods. The
period number is the number of energy
level in that element. Number of electron
shells. The number of elements in a period
increases as you move down the periodic
table because there are more sublevels per
level as the energy level of the atom
increases.
IONS
An ion is an atom or molecule with an
electrical charge resulting from gain or
loss of electrons
When an electron is lost, a positive
charge results; when one is gained, a
negative charge results
Two ions with opposite charges attract
each other
Ions Function
• There are nine types of most
essential ions of our body which
plays a role in supporting and
sustaining health and life.
• Out of nine, five are positively
charged ions and four are
negatively charged ions.
Ion (Electrolytes) Function
• The positively charged ions are
called cations ; these are Na+ , K+ ,
Ca++ , Mg++, and H+ .
• The negatively charged ions are
called anions ; these are Cl- , HCO3, PO43- , and OH- .
Electrolytes Functions
• The Sodium (Na+), Chloride (Cl-),
Potassium (K+) and Bicarbonate
(HCO3-) are called principle
electrolytes and are present in the
blood and various body fluids.
• Potassium (K+) is essential for
heart function.
• Our kidneys play a vital role in
maintaining the electrolyte balance.
They filter out excess!! Over work
them!!!
• The osmosis regulates the movement
of water in cells. Theconcentration of
electrolytes or ions to a moves water
from higher concentration of
electrolytes or ions to areas or lower
concentration.
Isotopes
 Atoms with the same number of
protons, but different numbers of
neutrons.
 Atoms of the same element (same
atomic number) with different mass
numbers
Isotopes of chlorine
Atoms consist of protons, neutrons, and
electrons
• Although all atoms of an element have the
same atomic number(protons), some differ in
mass number.
• Atoms with different numbers of neutrons are
isotopes
–One isotope of carbon has 8 neutrons
instead of 6 (written 14C)
–Unlike 12C, 14C is an unstable
(radioactive) isotope that gives off energy
–Many occur naturally but some are man
made
Copyright © 2009 Pearson Education, Inc.
Learning Check AT 2
Naturally occurring carbon consists of three
isotopes, 12C, 13C, and 14C. State the number of
protons, neutrons, and electrons in each of
these carbon atoms.
12C
13C
14C
6
6
6
#P _______
_______
_______
#N _______
_______
_______
ISOTOPIC NOTATION
isotopes are atoms with the same number of
protons but different number of neutrons
A
Z
X
A = mass number
(the total number of protons + neutrons)
Z = atomic number
(the total number of protons)
X = element symbol
Figure 2.4 Isotopes Have Different Numbers of Neutrons
Atoms: The Constituents of
Matter
• Some isotopes are radioisotopes,
which emit energy as alpha, beta,
and gamma radiation from their
nuclei.
• Radioactive decay transforms the
original atom into another atom,
usually of another element.
Radioactive isotopes can help or harm us
• Living cells cannot distinguish between
isotopes of the same element
– Therefore, when radioactive
compounds are used in metabolic
processes, they act as tracers
– Radioactivity can be detected by
instruments
• With instruments, the fate of
radioactive tracers can be monitored in
living organisms
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Radioactive isotopes can help or harm us
• Biologists use radioactive tracers
in research
– Radioactive 14C was used to
show the route of 14CO2 in
formation of sugar during plant
photosynthesis
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Healthy brain
Alzheimer’s patient
Compounds
and
Chemical
Reactions
Created by G.Baker
www.thesciencequeen.net
Common Compounds for Life
• CO2
• H2O
• C6H12O6
• NaCl
2.3 Elements can combine to form
compounds
• Compound—a substance consisting of two or more
different elements combined though a chemical reaction!
 There are many compounds that consist of only two
elements
– Table salt (sodium chloride or NaCl) is an example
– Sodium is a metal, and chloride is a poisonous gas
– However, when chemically combined, an edible compound
emerges
Copyright © 2009 Pearson Education, Inc.
How Compounds Form
• FOR A COMPOUND TO FORM, A CHEMICAL CHANGE
MUST TAKE PLACE (A REACTION)
• THE ELEMENTS THAT COMBINE MAKE A NEW
SUBSTANCE WITH NEW PHYSICAL PROPERTIES
• COMPOUNDS CANNOT BE BROKEN DOWN
PHYSICALLY. REQUIRES A CHEMICAL CHANGE
• MORE COMMON THAN ELEMENTS
Why Do Elements Bond to
Form Compounds?
Elements bond to fill their outer
shell and become stable!!!
THEY WANT TO BE HAPPY
+
Sodium
Chlorine
Sodium Chloride
Sodium Chloride
The elements lose their
properties in a compound!
Chemical Changes Through Chemical
Reactions
A chemical reaction – Process in which
the physical and chemical properties of
the original substance change as new
substances with different properties are
formed
http://www.eepybird.com/dc
m1.html
Gummi Bear Exploding!!!!
• Show video of gummi bear and zinc and H gas!!!!
Equation for gummi bear
2KClO3 -- 2KCl + O2 melting
C6H12O6 +6O2 ----- 6CO2 + 6H2O
The energy released is coming from the bonds in the sugar!! This is
where we get our energy!!!
Instantly, a vigorous, even violent chemical reaction takes place. The
oxygen given off by the heated chlorate rapidly attacks the sugars in
the candy, transforming them into carbon dioxide gas and
water. The resultant energy is given off as light - a *lot* of light as
the case turns out. An ex-Army friend of mine compared it to a
magnesium flare. The only other product is harmless potassium
chloride salt. K+ ions create the light!!!!!
Activation energy is the heat which breaks apart the KClO!!
CHEMICAL REACTIONS
!
Reactants: Zn + I2
Product: Zn I2
Molecules VS. Compounds
• Molecules are not compounds
• Molecules are not formed by chemical reaction!
Created by G.Baker
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What is a Chemical Equation?
• A chemical equation is described as
a symbolic representation of a
chemical reaction.
• The reactants of the reaction are
found on the left and the products
on the right, separated by an equal
sign or directional arrows
Fig. 2-UN2
2 H2
O2
Reactants
2 H2O
Reaction
Products
• Photosynthesis is an important
chemical reaction
• Sunlight powers the conversion of
carbon dioxide and water to glucose
and oxygen
6 CO2 + 6 H20 → C6H12O6 + 6 O2
Copyright © 2008 Pearson Education, Inc., publishing as Benjamin Cummings
Fig. 2-19
Chemical Formula
Definition – Short way to write a
compound
using symbols.
Subscript – Small number that is
written
below the element.
Coefficient – The large number in front of
the symbols.
Ba(OH)2 –
.
1) In this compound there are three
different elements (Ba), Oxygen (O) and
Hydrogen (H).
2) In this compound the subscript 2 goes
with the O and H
3) Since Ba is not in the parentheses and it
does not have a subscript there is one Ba.
4. Oxygen is in the parentheses and the
two elements in the paraentheses so there
parentheses are Oxygen (O) and Hydrogen
(H) is 2. Same for Hydrogen.
Coefficients
• In other words a coefficient is used to
display 2 or more of the entire unit it
appears in front of. The coefficient used
in this example shows that, in the left
reactant, there are 4 hydrogen, and in
the product, there are 4 hydrogen and 2
oxygen.
• The coefficient does not effect the
oxygen in the reactant because it is not a
compound with hydrogen but is
separated by the plus sign.
An ion is an atom, or group of atoms, that has a net positive or
negative charge.
cation – ion with a positive charge
If a neutral atom loses one or more electrons
it becomes a cation.
Na
11 protons
11 electrons
Na+
11 protons
10 electrons
anion – ion with a negative charge
If a neutral atom gains one or more electrons
it becomes an anion.
Cl
17 protons
17 electrons
Cl-
17 protons
18 electrons
2.5
Formation of Sodium Ion
Sodium atom
Na 
2-8-1
– e
Sodium ion

Na +
2-8 ( = Ne)
11 p+
11 p+
11 e-
10 e+
2.5
Why do elements bond?
• Elements bond to fill their outer shells. This
make the element stable. TO BE HAPPY!
• Elements will either gain, lose or share electrons
to fill their outer shell.
2.6 Electron arrangement determines the
chemical properties of an atom
• Atoms want to fill their outer electron
shells
– To accomplish this, the atom can share,
donate, or receive electrons
– This results in attractions between atoms
called chemical bonds
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Types of Chemical Bonds
Chemically combining of two or more
atoms
1. Covalent Bonds
2. Ionic Bonds
These are not all the bonds but all
we are going to cover.
2.7 Ionic bonds are attractions between ions of
opposite charge
• An ion is an atom or molecule with an electrical charge
resulting from gain or loss of electrons
When an electron is lost, a positive charge results;
when one is gained, a negative charge results
• Two ions with opposite charges attract each other
When the attraction holds the ions together, it is
called an ionic bond
Animation: Ionic Bonds
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Ionic Bonds
Ionic Bond – valence electrons are
TRANSFERRED from one ion to
another!!!
METAL IS BONDED TO NONMETAL!!!!
K
F
Drawing an Ionic Compound
1. Draw the Lewis Dot structure
for the atoms.
2. Show the electron(s)
transfering from one atom to
another.
Ionic Bonds: One Big Greedy Thief Dog!
Covalent Bonds
• One or more
pairs of
electrons are
shared by two
atoms
Covalent bonds join atoms into molecules
through electron sharing
• A covalent bond results when atoms
share outer-shell electrons
– A molecule is formed when atoms
are held together by covalent bonds
– EX: H2O, Cl2, H2, CO,
– Notice some are the same elements
and others are not!
Animation: Covalent Bonds
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Covalent Bonds – ARE STRONGER!!
• Sharing electrons causes the bond
to be more stable
• Ionic bonds are weaker: Pulled apart
in water!
• Usually compounds are liquids or
gases!
Created by G.Baker
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NONPOLAR
COVALENT BONDS
when electrons are
shared equally –
SAME ELEMENT
H2 or Cl2
2. Covalent bonds-
Two atoms share one or more pairs of outer-shell
electrons.
Oxygen Atom
Oxygen Atom
Oxygen Molecule (O2)
POLAR COVALENT BONDS
Electrons are shared
but shared unequally.
CHARGED
H2O
Polar Covalent Bonds: Unevenly
matched, but willing to share.
Covalent Bond
• Electronegativity – HOW BAD DO YOU
WANT ELECTRONS. The more you want
them the more you pull.
Unequal electron sharing creates
polar molecules
• Atoms in a covalently bonded molecule
continually compete for shared electrons
– The attraction (pull) for shared electrons
is called electronegativity
– More electronegative atoms pull harder
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- water is a polar molecule because oxygen is more
electronegative than hydrogen, and therefore electrons
are pulled closer to oxygen.
2.9 Unequal electron sharing creates polar
molecules
• Water has atoms with different electronegativities
– Oxygen attracts the shared electrons more strongly than
hydrogen
– So, the shared electrons spend more time near oxygen
– The result is a polar covalent bond
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2.9 Unequal electron sharing creates polar
molecules
• In H2O the oxygen atom has a slight negative charge and
the hydrogens have a slight positive charge
– Molecules with this unequal distribution of charges are called
polar molecules
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(–)
(–)
O
H
(+)
H
(+)
CARBON
SPECIAL – because it has 4 valence
electrons and can form bonds with four other
elements.
BUILDING BLOCKS OF LIFE!!!!!
MACROMOLECULES OF CARBON!!!!!
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2.10 Hydrogen bonds are weak bonds
important in the chemistry of life
• Some chemical bonds are weaker than covalent bonds
• Hydrogen, as part of a polar covalent bond, will share
attractions with other electronegative atoms
– Examples are oxygen and nitrogen
• Water molecules are electrically attracted to oppositely
charged regions on neighboring molecules
– Because the positively charged region is always a hydrogen
atom, the bond is called a hydrogen bond
Animation: Water Structure
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WATER’S LIFE-SUPPORTING
PROPERTIES
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Hydrogen bond
2.11 Hydrogen bonds make liquid water
cohesive
• Hydrogen bonding causes molecules to stick together, a
property called cohesion
– Cohesion is much stronger for water than other liquids
– This is useful in plants that depend upon cohesion to help
transport water and nutrients up the plant
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2.11 Hydrogen bonds make liquid water
cohesive
• Cohesion is related to surface tension—a measure of
how difficult it is to break the surface of a liquid
– Hydrogen bonds are responsible for surface tension
Animation: Water Transport
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Adhesion
Water-conducting
cells
Direction
of water
movement
Cohesion
150 µm
2.12 Water’s hydrogen bonds moderate
temperature
• Because of hydrogen bonding, water has a greater ability
to resist temperature change than other liquids
– Heat is the energy associated with movement of atoms and
molecules in matter
– Temperature measures the intensity of heat
• Heat must be absorbed to break hydrogen bonds; heat is
released when hydrogen bonds form
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2.13 Ice is less dense than liquid water
• Water can exist as a gas, liquid, and solid
– Water is less dense as a solid, a property due to hydrogen
bonding
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2.13 Ice is less dense than liquid water
• When water freezes, each molecule forms a stable
hydrogen bond with four neighbors
– A three-dimensional crystal results
– There is space between the water molecules
• Ice is less dense than water, so it floats
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Hydrogen bond
Ice
Hydrogen bonds
are stable
Liquid water
Hydrogen bonds
constantly break and re-form
2.14 Water is the solvent of life
• A solution is a liquid consisting of a uniform mixture of
two or more substances
– The dissolving agent is the solvent
– The substance that is dissolved is the solute
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2.14 Water is the solvent of life
• Water is a versatile solvent that is fundamental to life
processes
– Its versatility results from its polarity
– Table salt is an example of a solute that will go into solution
in water
– Sodium and chloride ions and water are attracted to each other
because of their charges
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Ion in
solution
Salt
crystal
2.15 The chemistry of life is sensitive to acidic
and basic conditions
• A few water molecules can break apart into ions
– Some are hydrogen ions (H+)
– Some are hydroxide ions (OH–)
– Both are extremely reactive
– A balance between the two is critical for chemical processes to
occur in a living organism
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2.15 The chemistry of life is sensitive to acidic
and basic conditions
• Chemicals other than water can contribute H+ to a solution
– They are called acids
– An example is hydrochloric acid (HCl)
– This is the acid in your stomach that aids in digestion
• An acidic solution has a higher concentration of H+ than
OH–
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2.15 The chemistry of life is sensitive to acidic
and basic conditions
• Some chemicals accept hydrogen ions and remove them
from solution
– These chemicals are called bases
– For example, sodium hydroxide (NaOH) provides OH– that
combines with H+ to produce H2O (water)
– This reduces the H+ concentration
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2.15 The chemistry of life is sensitive to acidic
and basic conditions
• A pH scale (pH = potential of hydrogen) is used to
describe whether a solution is acidic or basic
– pH ranges from 0 (most acidic) to 14 (most basic)
– A solution that is neither acidic or basic is neutral
(pH = 7)
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pH scale
0
1
Acidic solution
Increasingly ACIDIC
(Higher concentration of H+)
Battery acid
2 Lemon juice, gastric juice
3 Grapefruit juice, soft drink,
vinegar, beer
4 Tomato juice
5
Rain water
6 Human urine
Saliva
NEUTRAL
[H+]=OH–]
7 Pure water
Human blood,
tears
8
Seawater
Increasingly BASIC
(Lower concentration of H+)
Neutral solution
9
10
Milk of magnesia
11
Household ammonia
12
Household bleach
13
Oven cleaner
Basic solution
14
Acidic solution
Neutral solution
Basic solution
2.16 CONNECTION: Acid precipitation and
ocean acidification threaten the
environment
• When we burn fossil fuels (gasoline and heating oil), airpolluting compounds and CO2 are released into the
atmosphere
– Sulfur and nitrous oxides react with water in the air to form
acids
– These fall to Earth as acid precipitation, which is rain, snow,
or fog with a pH lower than 5.6
– Additional CO2 in the atmosphere contributes to the
“greenhouse” effect and alters ocean chemistry
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2.17 EVOLUTION CONNECTION: The search
for extraterrestrial life centers on the
search for water
• An important question is, has life evolved elsewhere?
– Water is necessary for life as we know it
• The National Aeronautics and Space Administration (NASA)
has evidence that water was once abundant on Mars
– Scientists have proposed that reservoirs of water beneath the
surface of Mars could harbor microbial life
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August 1999
September 2005
New deposit
Atoms: The Constituents of
Matter
• All atoms of an element have the same number
of protons, but not necessarily the same number
of neutrons.
• Atoms of the same element that have different
atomic weights are called isotopes.
Figure 2.4 Isotopes Have Different Numbers of Neutrons
Chemical Bonds: Linking Atoms
Together
• A molecule is two or more atoms bonded
together.
• A chemical bond is an attractive force that links
two atoms together.
Chemical Bonds: Linking Atoms
Together
• A covalent bond is formed by sharing of a pair
of electrons between two atoms.
• In hydrogen molecules (H2), a pair of electrons
share a common orbital and spend equal
amounts of time around each of the two nuclei.
• The nuclei stay some distance from each other
due to mutually repelling positive charges.
Figure 2.8 Electrons Are Shared in Covalent Bonds
Properties of Molecules
Chemical Bonds: Linking Atoms
Together
• Molecules made up of more than one type of
atoms are called compounds.
• Every compound has a molecular weight that is
the sum of all atoms in the molecule.
Chemical Bonds: Linking Atoms
Together
• Covalent bonds are very strong.
• Each covalent bond has a predictable length,
angle, and direction, which makes it possible to
predict the three-dimensional structures of
molecules.
• A double covalent bond occurs when atoms share
two pairs of electrons; in triple covalent bonds
atoms share three electron pairs.
Figure 2.10 Covalent Bonding With Carbon
Properties of Molecules
Chemical Bonds: Linking Atoms
Together
• Electrons are not always shared equally between
covalently bonded atoms.
• The attractive force that an atom exerts on
electrons is called electronegativity.
• When a molecule has nuclei with different
electronegativities, an electron spends most of its
time around the nucleus with the greater
electronegativity.
Chemical Bonds: Linking Atoms
Together
• Unequal sharing of electrons causes a partial
negative charge around the more electronegative
atom, and a partial positive charge around the
less electronegative atom, resulting in a polar
covalent bond.
• Molecules that have polar covalent bonds are
called polar molecules.
Figure 2.11 The Polar Covalent Bond in the Water Molecule
Properties of Molecules
Chemical Bonds: Linking Atoms
Together
• Hydrogen bonds may form within or between
atoms with polar covalent bonds.
• The d– portion of one molecule has a weak
attraction to the d+ portion of another molecule.
Each of these attractions is called a hydrogen
bond.
• Hydrogen bonds do not share electrons.
• Although hydrogen bonds are weak, they tend to
be additive, and they are of profound biological
importance.
Figure 2.12 Hydrogen Bonds Can Form between or within Molecules
Properties of Molecules
Chemical Bonds: Linking Atoms
Together
• Ionic bonds involve a complete transfer of one
or more electrons.
• Ions are formed when an atom loses or gains
electrons.
• Positively charged ions are called cations.
• Negatively charged ions are called anions.
Figure 2.13 Formation of Sodium and Chloride Ions
Properties of Molecules
Chemical Bonds: Linking Atoms
Together
• Ionic bonds are formed by the electrical
attraction between ions with opposite charges.
• Table salt has chloride and sodium ions, held
together by ionic bonds.
• When salt is introduced into water, the partial
charges of the water molecules can easily
interfere with the ionic bonds.
Figure 2.14 Water Molecules Surround Ions
Properties of Molecules
Chemical Bonds: Linking Atoms
Together
• Polar molecules tend to be hydrophilic.
Substances that are ionic or polar often dissolve
in water due to hydrogen bonds.
• Nonpolar molecules are called hydrophobic
because they tend to aggregate with other
nonpolar molecules.
• Nonpolar molecules are also attracted to each
other via relatively weak attractions called van
der Waals forces.
Life and Chemistry: Small
Molecules
• The Mechanistic View of Life
• Atoms: The Constituents of Matter
• Chemical Bonds: Linking Atoms Together
-------------------------------------------------------• Review: Animation – Electron Shells & Reactivity
• Chemical Reactions: Atoms Change Partners
• Water: Structure and Properties
• Acids, Bases, and the pH Scale
• Properties of Molecules
Chemical Reactions: Atoms
Change Partners
• Chemical reactions occur when atoms combine
or change partners.
• In a chemical reaction, reactants are converted
to products.
• A chemical reaction can be written as an
equation. The equation must balance because
matter is neither created nor destroyed.
Structure of Propane
Source: http://kjd.edu-ctr.pref.kanagawa.jp/edb2/chem/models/3d/Propane.jpg
Figure 2.15 Bonding Partners and Energy May Change in a Chemical Reaction
Properties of Molecules
What’s to Come? Metabolic
Pathways
Source: http://www.humboldt.edu/~rap1/BiochSupp/PathwayDiagrams/FolMetPath.gif
Chemical Reactions: Atoms
Change Partners
• Changes in energy usually accompany chemical
reactions. For example, heat and light are
released in the propane reaction.
• In living cells, it is unusual to have reactions that
release light (exceptions: e.g., firefly)
• However, heat is a common product in cellular
reactions. Why does a corpse have a much
lower body temperature than someone who is
living?
• Also common are changes in potential energy!
Potential Energy
• Stored energy, such as that in chemical bonds,
is called potential energy and is available for
future use. For example, the potential energy in
glucose can be used to make ATP.
• We can measure the potential energy of
molecules and express it in units of heat called
calories.
• A calorie is the amount of heat required to
raise the temperature of one gram of pure water
from 14.5°C to 15.5°C.
Figure 2.16 Hydrogen Bonds Hold Water Molecules Together (Part 2)
Properties of Molecules
Water: Structure and Properties
Due to its shape, polarity, and ability to form
hydrogen bonds, water has some unusual
properties.
• Ice floats in liquid water; normally the solid form
of a substance is more dense than the liquid
form.
• Water has a high specific heat.
• Water has a high heat of vaporization.
Figure 2.16 Hydrogen Bonds Hold Water Molecules Together (Part 1)
Properties of Molecules
Water: Specific Heat
• A great deal of heat energy is required to change
the temperature of liquid water because the
hydrogen bonds must be broken.
• Specific heat is the number of calories needed
to raise one gram of a substance 1oC. The
specific heat of liquid water is 1.
• Liquid water has a higher specific heat than most
other small molecules in liquid form.
Water: Structure and Properties
• The heat of vaporization is the amount of heat
needed to change a substance from its liquid
state to its gaseous state.
• A lot of heat is required to change water to a
gaseous state because the hydrogen bonds of
the liquid water must be broken.
• Evaporation has a cooling effect by absorbing
calories. (Role of sweating and panting.)
• Condensing has the opposite effect, releasing
heat.
Cohesion and Surface Tension
•
Source: http://www.npl.co.uk/acoustics/techguides/wetting/images/insect.jpg
Water: Structure and Properties
• Water has a cohesive strength because of
hydrogen bonds.
• The cohesive strength of water molecules allows
the transport of water from the roots to the tops
of trees.
• Water has high surface tension, which means
that the surface of liquid water is relatively
difficult to puncture.
Water as a Solvent
•
Source: http://www.uccs.edu/~rmelamed/MicroFall2002/Chapter%202/water%20solvent.jpg
Water: Structure and Properties
• Water is the solvent of life.
• Living organisms are over 70 percent water by
weight and many reactions take place in this
watery environment.
• A solution is a substance (the solute) dissolved
in a liquid (the solvent).
Water: Structure and Properties
• The mole concept is fundamental to quantitative
analysis, which deals with concentrations or the
amount of a substance in a solution.
• A mole is the amount of a substance in grams
whose weight is equal to its molecular weight.
For example, methane (CH4) has a mw = 16.04
• One mole of any given compound contains
approximately 6.02 x 1023 molecules of that
compound (Avogadro’s number).
Water: Structure and Properties
• A 1 molar (1 M) solution is one mole of a
compound dissolved in water to make one liter.
• Example: One mole of NaCl is the atomic weight
of Na (23) plus the atomic weight of Cl (35.5), or
58.5, in grams. When 58.5 grams of NaCl are
dissolved in water to make one liter, the solution
is 1 molar.
Acids & Bases
Source: http://dbhs.wvusd.k12.ca.us/webdocs/AcidBase/Lab-AcidBaseTitration/BottleHCl&NaOH.JPG
Acids, Bases, and the pH Scale
• Some substances dissolve in water and release
hydrogen ions (H+); these are called acids. Their
release is called ionization.
• Other substances dissolve in water and release
hydroxide ions (OH–); these are called bases.
• Acids donate H+; bases accept H+.
Acids, Bases, and the pH Scale
• Acids release H+ ions in solution.
• If the reaction is complete, it is a strong acid,
such as HCl.
• The carboxyl group (—COOH) is common in
biological compounds (e.g., amino acids). It
functions as an acid because
 —COOH  —COO– + H+
Acids, Bases, and the pH Scale
• Bases accept H+ in solution.
• NaOH ionizes completely to Na+ and OH–. The
OH– absorbs H+ to form water. It is a strong
base.
• The amino group (—NH2) is an important part of
many biological compounds; it functions as a
weak base by accepting H+:
 —NH2 + H+  —(NH3)+
Acids, Bases, and the pH Scale
• pH is the measure of hydrogen ion
concentration.
• It is defined as the negative logarithm of the
hydrogen ion concentration in moles per liter.
• The pH scale indicates the strength of a solution
of an acid or base. The scale values range from
1 through 14.
• A pH 7 means the concentration of hydrogen
ions is 1 x 10–7 moles per liter of water.
Figure 2.18 pH Values of Some Familiar Substances
Properties of Molecules
Acids, Bases, and the pH Scale
• A buffer is a mixture of a weak acid and its
corresponding base.
• Because buffers can react with both added
bases and acids, they make the overall solution
resistant to pH change.
• Buffers illustrate the law of mass action:
 Addition of reactants to one side of a reaction
drives the reaction in the direction that uses that
component.
Figure 2.19 Buffers Minimize Changes in pH
Properties of Molecules
Properties of Molecules
• Chemists use the characteristics of composition,
structure, reactivity, and solubility to help classify
molecules.
• Two other properties that influence the behavior
of molecules are the presence of recognizable
functional groups, and the existence of isomers
of molecules.
Properties of Molecules
• Functional groups give specific properties to
molecules.
• Functional groups are covalently bonded to
organic molecules.
• Amino acids are biological molecules that contain
both a carboxyl group and an amino group.
Figure 2.20 Some Functional Groups Important to Living Systems (Part 1)
Properties of Molecules
Figure 2.20 Some Functional Groups Important to Living Systems (Part 2)
Properties of Molecules
Figure 2.20 Some Functional Groups Important to Living Systems (Part 3)
Properties of Molecules
Concept 2.3: The formation and function
of molecules depend on chemical bonding
between atoms
• Atoms with incomplete valence shells can
share or transfer valence electrons with
certain other atoms
• These interactions usually result in atoms
staying close together, held by attractions
called chemical bonds
Copyright © 2008 Pearson Education, Inc., publishing as Benjamin Cummings
Covalent Bonds
• A covalent bond is the sharing of a pair of valence
electrons by two atoms
• In a covalent bond, the shared electrons count as part of
each atom’s valence shell
Copyright © 2008 Pearson Education, Inc., publishing as Benjamin Cummings
Fig. 2-11
Hydrogen
atoms (2 H)
Hydrogen
molecule (H2)
• A molecule consists of two or more atoms held together
by covalent bonds
• A single covalent bond, or single bond, is the sharing of
one pair of valence electrons
• A double covalent bond, or double bond, is the sharing of
two pairs of valence electrons
Copyright © 2008 Pearson Education, Inc., publishing as Benjamin Cummings
• The notation used to represent atoms and bonding is
called a structural formula
 For example, H–H
• This can be abbreviated further with a molecular
formula
 For example, H2
Animation: Covalent Bonds
Copyright © 2008 Pearson Education, Inc., publishing as Benjamin Cummings
Fig. 2-12
Name and
Molecular
Formula
(a) Hydrogen (H2)
(b) Oxygen (O2)
(c) Water (H2O)
(d) Methane (CH4)
ElectronLewis Dot
Spacedistribution Structure and filling
Model
Diagram
Structural
Formula
Fig. 2-12a
Name and
Molecular
Formula
(a) Hydrogen (H2)
ElectronLewis Dot
distribution Structure and
Diagram
Structural
Formula
Spacefilling
Model
Fig. 2-12b
Name and
Molecular
Formula
(b) Oxygen (O2)
ElectronLewis Dot
distribution Structure and
Diagram
Structural
Formula
Spacefilling
Model
Fig. 2-12c
Name and
Molecular
Formula
(c) Water (H2O)
Lewis Dot
Electrondistribution Structure and
Structural
Diagram
Formula
Spacefilling
Model
Fig. 2-12d
Name and
Molecular
Formula
(d) Methane
(CH4)
ElectronLewis Dot
distribution Structure and
Diagram
Structural
Formula
Spacefilling
Model
• Covalent bonds can form between atoms of the same
element or atoms of different elements
• A compound is a combination of two or more different
elements
• Bonding capacity is called the atom’s valence
Copyright © 2008 Pearson Education, Inc., publishing as Benjamin Cummings
• Electronegativity is an atom’s attraction for the electrons
in a covalent bond
• The more electronegative an atom, the more strongly it
pulls shared electrons toward itself
Copyright © 2008 Pearson Education, Inc., publishing as Benjamin Cummings
• In a nonpolar covalent bond, the atoms share the
electron equally
• In a polar covalent bond, one atom is more
electronegative, and the atoms do not share the
electron equally
• Unequal sharing of electrons causes a partial positive
or negative charge for each atom or molecule
Copyright © 2008 Pearson Education, Inc., publishing as Benjamin Cummings
Fig. 2-13
d–
O
d+
H
H
H2O
d+
Ionic Bonds
• Atoms sometimes strip electrons from their bonding
partners
• An example is the transfer of an electron from sodium
to chlorine
• After the transfer of an electron, both atoms have
charges
• A charged atom (or molecule) is called an ion
Copyright © 2008 Pearson Education, Inc., publishing as Benjamin Cummings
Fig. 2-14-1
Na
Cl
Na
Sodium atom
Cl
Chlorine atom
Fig. 2-14-2
Na
Cl
Na
Cl
Na
Sodium atom
Cl
Chlorine atom
Na+
Sodium ion
(a cation)
Cl–
Chloride ion
(an anion)
Sodium chloride (NaCl)
• A cation is a positively charged ion
• An anion is a negatively charged ion
• An ionic bond is an attraction between an anion and a
cation
Animation: Ionic Bonds
Copyright © 2008 Pearson Education, Inc., publishing as Benjamin Cummings
• Compounds formed by ionic bonds are called ionic
compounds, or salts
• Salts, such as sodium chloride (table salt), are often found
in nature as crystals
Copyright © 2008 Pearson Education, Inc., publishing as Benjamin Cummings
Fig. 2-15
Na+
Cl–
Weak Chemical Bonds
• Most of the strongest bonds in organisms are
covalent bonds that form a cell’s molecules
• Weak chemical bonds, such as ionic bonds and
hydrogen bonds, are also important
• Weak chemical bonds reinforce shapes of large
molecules and help molecules adhere to each other
Copyright © 2008 Pearson Education, Inc., publishing as Benjamin Cummings
Hydrogen Bonds
• A hydrogen bond forms when a hydrogen atom
covalently bonded to one electronegative atom is
also attracted to another electronegative atom
• In living cells, the electronegative partners are
usually oxygen or nitrogen atoms
Copyright © 2008 Pearson Education, Inc., publishing as Benjamin Cummings
Fig. 2-16
d
d+
Water (H2O)
d+
Hydrogen bond
d
Ammonia (NH3)
d+
d+
d+
Van der Waals Interactions
• If electrons are distributed asymmetrically in molecules or
atoms, they can result in “hot spots” of positive or negative
charge
• Van der Waals interactions are attractions between
molecules that are close together as a result of these
charges
Copyright © 2008 Pearson Education, Inc., publishing as Benjamin Cummings
• Collectively, such interactions can be strong, as between
molecules of a gecko’s toe hairs and a wall surface
Copyright © 2008 Pearson Education, Inc., publishing as Benjamin Cummings
Fig. 2-UN1
Concept 2.4: Chemical reactions make
and break chemical bonds
• Chemical reactions are the making and
breaking of chemical bonds
• The starting molecules of a chemical
reaction are called reactants
• The final molecules of a chemical reaction
are called products
Copyright © 2008 Pearson Education, Inc., publishing as Benjamin Cummings