Honors Biology Chapter 2
Chemistry
DRY ERASE ATOM ATTITUDE
• Everyone gets a dry erase board, dry
erase pen, and tissue for erasing.
• The teacher will ask you a question about
atomic structure, you will write your
answer and hold up your board.
Are you wondering why we are
learning chemistry in biology class?
• All of our cells are made of chemical
compounds.
• All the activities of our bodies work on
chemical reactions.
• All of our body’s reactions use water.
Such as
neurotransmitters
affecting neurons
MATTER
• Anything that
occupies space
(VOLUME) and has
MASS
• Is air matter?
• Yes
Match as energy (capacity to do
work) or matter (occupies space
and has mass)
•
•
•
•
•
•
•
Water
Electricity
Air
Helium
Sunlight
Iron
Carbon
•
•
•
•
•
•
•
Matter
Energy
Matter
Matter
Energy
Matter
Matter
2.1 ELEMENTS, ATOMS,
COMPOUNDS (are matter)
YOU NEED TO KNOW
• The Names (spelled correctly)
and the Symbols (written
correctly) on p. 18 (Table 2.1)
• “Elements in the Human Body”
• 25 elements (includes trace
elements)
• QUIZ on FRIDAY Sept. 27
ELEMENTS
• Substance that cannot be broken
down to other substances by ordinary
chemical means (heating, adding an
acid…)
• YouTube - ?Tom Lehrer's
The Elements" animated??
****ASAP SCIENCE Periodic Table
In Order
OR YouTube - ?The Elements Animation??
Where can you find an element?
The Periodic Table of the Elements – see
Appendix 2 and get your personal copy
ELEMENTS AND SYMBOLS:
Ca, H, Li, O, C, Mg
• What rules apply to writing the symbols
(abbreviations of the elements)?
• First letter capital, second letter is
lower case
• What are the four most common elements
in the human body? (see chart)
• CHON
• What are trace elements?
• Less than 0.01% of human body weight
Which are elements?
•
•
•
•
•
•
•
Cu
C
CO
N
NO
WHY?
Cu C N only
one kind of matter
Gold - Au
COMPOUNDS
• Substance of two or more different atoms
chemically combined in a fixed ratio
• EXAMPLES: CO2
•
H2SO4
Subscripts (tell how many
atoms there are)
•
H2O
•
CO
• How is a compound written differently than an
element?
• More than one kind of element (more than
one capital letter).
• NOTE: H2 is not a compound – its an element
• (Only one kind of element)
Formula
• Formula is the abbreviation for a
compound.
• CO2
H2SO4
H 2O
• Carbon dioxide sulfuric acid
water
• What rules seem to apply to writing a
formula?
• Capital letters for elements
• Subscript number behind and just
below the line of what element it
represents
Which are compounds?
• Na
N
Why?
H2
NO2 H2O
• NO2
• H2O
• 2 or more different elements
chemically joined (2+ diff. capital
letters)
Which are symbols?
Abbreviations for elements
•C
CO2
Why?
Mn CO
Ni
•C Mn Ni
• Only one capital
letter
What’s the difference?
• Co
CO
co
• Symbol formula nothing
Which are formulas?
Abbreviation for a compound
• H2SO4
Why?
Cl2
H20
Al
H2SO4
H20 abbreviations
for compounds (2 or more
different kinds of elements)
Can you figure out the difference
between a mixture and a
compound?
• A mixture is two or more elements (or
compounds) NOT chemically joined.
• A compound is two or more atoms chemically
joined.
• Do Worksheet: Elements, Compounds, Mixtures
DO WORKSHEET: Elements,
Compounds, Mixtures
• (back of Atomic Mass and Atomic Number
Worksheet)
• Work in groups of three, then we’ll
compare answers.
2.2 What are trace elements?
• Needed in the body in only small
amounts
• Like mg (milligrams)
• WHY IMPORTANT IF WE DON’T
NEED SO MUCH?
• Minerals act as catalysts (speed
up reactions) for many biological
reactions
Trace Elements
Needed by some
organisms but
only in very small
amounts
Like iodine, we
need only 0.15
mg per day
A deficiency will
cause a goiter
Trace Elements
• Fluorine – in drinking water, toothpaste
• (help dental decay) But too much can
cause fluorosis
(white chalky buildup)
Trace Elements
• Iron Rich Foods
• Most important
use is to carry
oxygen in the blood
2.3 Atoms and Molecules
Atoms are made of
protons, neutrons, electrons
• Do you know what these particles are?
Answers:
• Do you know what these particles are?
Protons
Neutrons
Electrons
• Basic Atomic Structure Youtube (1:57)
Atom
• Smallest unit of matter that retains the
properties of the element
Li
Na
Which shows one atom?
•C N
Why?
N2
H20
• C and N
• only one in number
• Which are elements?
• C N N2
Molecule
• Two or more atoms held together by
chemical bonds
Which are molecules?
• Co
CO
Why?
CO2
O2
• CO
CO2 O2 two or
more atoms (alike or not
alike, it doesn’t matter)
bonded together
Where is each subatomic particle
located?
• Proton
in the
• Neutron nucleus
Electron-outside the
nucleus
•
Golden Retrievers Show Atomic Structure Youtube
(2:11)
What is the charge of each
subatomic particle?
• Proton
•+
• positive
Neutron
O
none
Electron
_
negative
What is the relative size?
• Proton
• 1 amu
neutron
1 amu
electron
~1/1836 amu
• AMU = atomic mass unit = 1/12 CARBON ATOM
• (standard)
Neutral Atoms (no charge)
(as seen on the periodic table)
• 39
K
• 19
Mass Number
p+n
Symbol
Atomic Number
p
• (electrons = number of protons)
• Neutral if negative charges = positive )
• n=mass no. – at.no.
How can you tell the mass number
and atomic number?
When looking on the periodic
table…
• Atomic Number
• Mass Number
• In order
• Identify element by
its number of
protons
• A decimal (average
of masses of all
isotopes of that
element)
Why is the mass number a
decimal?
Average of the Isotopes of Carbon
• What is the mass
number decimal?
• 12.011
• What would you
round it to?
• 12
What is the atomic number of?
• Silicon
WHY?
fluorine
sodium
• 14
9
11
• Number in succession (not
a decimal)
• Number of protons
What is the mass number of…?
• Carbon
• WHY?
nitrogen
hydrogen
• 12
14
1
• Decimal number on periodic
table
• Not other number in succession
• Number of p + n
How do you find the number of…?
• Protons electrons
neutrons
Atomic
number
atomic
mass number
number
minus atomic no.
(if neutral)
How many?
• Protons electrons neutrons
• Carbon
6
6
6
17
18
• Chlorine
• 17
What is the atomic number?
Mass Number?
• Number of p?
• Number of e-?
• Number of n?
Do Atomic Mass and Atomic
Number WORKSHEET
•Collaborate with your
partner next to you,
then we’ll see what’s
right.
ISOTOPES INTRO
• Isotopes (Virtual School) (2:51)
• Watch the video and list what facts you
learned about isotopes.
• No, not about the Albuquerque Isotopes
Isotope
• Atoms that differ in number of neutrons
• Also differ in mass number(since it is p + n)
• But all have the same number of protons
Isotope Examples
• What are isotopes? (7:56)
Which is the most common
isotope of Li? (check the
periodic table)
Why is the Mass Number a
Decimal?
• Finding the Average Atomic Mass (2:55)
• Watch this and find out how…
How do you write chemical
notation for isotopes?
2.4 Radioactive Isotopes
• An isotope that
decays
spontaneously to emit
(give off) particles or
energy until it is
stable
• Here a radioisotope is
used to examine a
thyroid gland
• Radioactive Tracers
in Medicine (3:57)
Radioactive Decay Examples
Uses of Radioisotopes
• C-14 dating (can date living things up to
6,000 years old) Carbon Dating (2:00 mins)
•
•
•
•
Technetium 99 Radioisotope (2:58)
Nuclear Medicine: What to expect (2:46 mins)
Bozeman Biology Radioactive Dating (9 mins)
PET SCAN: detect tumors,
Carbon-14 Dating (2 mins)
Thyroid tumor
Highlight parts of the
body for diagnosis
weak spots in arteries
Uses of Radioisotopes
• Iodine-131
treat thyroid cancer
PIB molecule to
detect Alzheimers
PET scan
Negative Effects of Nuclear
Radiation
• Chernobyl Nuclear Plant Accident
Negative Effects of Radon
• Radon, a radioactive gas, causes lung
cancer
• Found in regions
containing uranium
2.5-2.7 Chemical Bonds
Ion
• Charged atom
• Differs in number of electrons
• 39
Same mass number
K+
means lost one electron
• 19
Same atomic number
ION
•
•
•
•
Charged atom
Na+ (has lost one electron)
O-2 (has gained two electrons)
Shown with superscript +/- and
number on upper right
• (can omit number if a “1”)
• What's and Ion? Youtube (6:52)
Ions form by gaining or losing
electrons
O-2 has gained two electrons
Na has lost an e- so it is Na+1
Cation
• Positive ion
• Na+
• Mg+2
• Lost
electrons
Anion
•
•
•
•
Negative ion
ClO-2
gained
electrons
If one electron is…
• Lost what
charge will the
ion have?
11p+
11 e-
•+1
11p+
10e-
Which are ions?
• Cl
O-2
Why?
Na+1
N2
• O-2
Na+1
• Charged atoms (lost or
gained electrons)
• show charges as superscripts
Valence Electrons
• Outer shell electrons
• Determines the bonding capacity of an
atom
How do electrons arrange
themselves in an atom…
• In the outer electron shells (energy
levels)?
• They are full with 2, 8, 8
• Fill inner shell first,
then go to next shell out
(Outermost shell has the greatest energy)
Can you see any pattern how
the e- arrange themselves?
Get kinda complicated beyond
2,8,8…so that’s all we’ll do for now!
Which electrons determine…
• The chemical
properties of the
atom?
• Outermost shell
If one electron is gained…
• What charge
will the ion
have?
•-1
• If 2 electrons are lost… What
charge will the ion have?
•+2
• If two electrons are gained…
What charge will the ion
have?
•-2
Filled outer e- shells
How many e- fill the first shell (nearest
the nucleus)?
How many e- fill the next two shells?
nucleus
Gain 1 e- or lose 7 e-?
If gains 1 e-, then it becomes -1
Gain 7 e- or lose 1 e-?
If loses 1 e-, the it becomes +1.
Gain or Lose ?
If it could as easily lose or gain e-, then it
will probably share them. It will form a
covalent bond.
Tutorial 2.1 Chemical Bond Formation
Fill in the chart of eElement
carbon
Number First shell Second
of eShell
6
lithium
3
Sodium
11
Oxygen
16
Third
Shell
Fill in the chart of eElement
carbon
Number First shell Second
of eShell
6
2
4
lithium
3
2
1
Sodium
11
2
8
Oxygen
8
2
6
Third
Shell
1
How are ion charges determined?
• Cation = positive (+) ion
• Anion = negative (-) ion
How are ion charges determined?
•
•
•
•
If lose 1 e- = +1 charge
If gain 1 e- = -1 charge
If lose 2 e- = +2 charge
If gain 2 e- = -2 charge
Periodic Table Hint:
• You can tell how many
electrons are in an atom’s
outermost shell by just
looking at its position on the
periodic table!!!!!
Note any pattern of valence
electrons (outer shell) as they
appear in the periodic table?
+1 +2 Ion formed
share
-3 -2 -1 0
e- in outer shells
H
8
e- in outer shell
Full outer eshells
How many electrons in each shell?
(atomic number is given)
• Carbon oxygen fluorine sodium
• 12
16
9
11
• 2,4
2,6
2,7
2,8,1
How many valence electrons?
Will these atoms lose or gain eand how many?
How many valence electrons?
Will these atoms lose or gain eand how many?
Lose 1
lose O
lose 1
share
H+
He
Li+
C
gain 3
lose 1
N-3
Na+
Now let’s do the Drawing Atoms Worksheet
(and next 4 slides)
• How the electrons fill
their shells (link)
• 1st shell – 1 pair
• 2nd shell – e- space
far apart, singles,
then pair
• 3rd shell – e- space
far apart, singles,
then pair
•
Bohr Diagrams
C
1) Draw a nucleus with
the element symbol
inside.
2) Carbon is in the 2nd
period, so it has two
energy levels, or shells.
3) Draw the shells around
the nucleus.
Bohr Diagram
Let’s do carbon (6 electrons)
Get
worksheet
C
• 1. Draw a nucleus.
• 2. Draw the number of
rings needed.
• 3. Start in the first shellonly 2 e-, paired (put
next to each other)
Bohr Diagrams
1
2
4
C
3
1) Since you have 2
electrons already
drawn, you need to
add 4 more.
2) These go in the 2nd
shell.
3) Add one at a time starting on the top and
going counter clockwise.
Bohr Diagrams
1
1
5
5
2
4
4
2
6
6
3
3
If you were to have more
electrons, start pairing
them in the same
clockwise order.
Bohr model electron filling order
2
Are these correct Bohr models?
Are these correct Bohr models?
• What errors are at the
?
Now do on the Atomic Structure
Worksheet
See the trend of how electrons
fill the valence shells
• Lewis dot structures
• Octet Rule – electrons fill a shell until it’s
full with 8 electrons
• Atoms are most stable with a filled outer
electron shell
What do we call the forces that…
• Hold atoms
together in a
molecule?
• Chemical
bonds
• …not to be
confused with
James Bond
Why do atoms bond?
•To have filled
outer electron
shells!
• Atom
Heaven
ATOM
What is a chemical bond?
• Attraction between two or more atoms
YouTube - ?Ionic and covalent bonding
animation??
Get Bonding Handouts
• Electronegativities
• Intermolecular Forces
• Bonding Reference Sheet
Types of Bonds
Intramolecular
• Within the molecule
Intermolecular
• Between different
molecules
• -Ionic
• -Covalent
•
Polar
•
Nonpolar
• Van der Waals
•
London forces
•
Dipoles
• Hydrogen Bonds
Bonding
• Covalent
• share
electrons
• Ionic
• transfer of
electrons
• (lose or gain)
IONIC BOND
• lose one or more electrons become (+)
• gain one or more electrons become (-)
• The (+) and (-) ions formed now attract
each other and form an ionic bond.
Covalent Bonds
• Polar Covalent
• Nonpolar Covalent
• Unequal sharing • Equal sharing of eof e-
Covalent Bonds
Click HERE: Polar Covalent
Bonding (3 animations)
•Electrons are shared
•Usually if near the
same number of e- in
outer shells
Covalent bonding can be shown
as:
• Bohr model
• Electron-dot
• Structural Formula
How can covalent bonds be
written?
• Single bond
•
•
•
C-C
C:C
2 e-
double bond
C=C
C::C
4 e-
triple bond
C=C
C:::C
6 e-
•
•
Writing Bonds
Each “ –” is equal to
“ : “ or
• “two electrons”
Single C – C or C:C
Double C = C or C::C
Triple C≡C or C:::C
Different Ways to Represent Four
Common Molecules
butane
Making ionic bond in NaCl
• YouTube - ?Ionic and covalent bonding example??
• YouTube - ?Reaction of Sodium & Chlorine (with subtitles)??
SALT =
• Synonym for an ionic compound
• Not just NaCl
Sodium
chloride
Copper
Sulfate
Iron Sulfide
LET’S REVIEW: Which atoms
combine…
• with other atoms?
• Ones that do not have filled
outer electron shells
REVIEW: What is the driving
force to make atoms join with
other atoms to form compounds?
• TO HAVE FILLED OUTER
ELECTRON SHELLS
REVIEW: How does an atom…
• Get a filled outer electron
shell?
• Gaining, losing, or sharing
electrons
What do you notice about the
ion charge and the subscripts?
Do the Flip-Flop
• So you can cancel out the (+) and (-)
If there is only one atom, you do
not need to write a “1”
You can reduce the subscripts if
they are the same:
Fe+2
O-2
reduce to
Fe2O2
FeO
Electronegativity
•Get
Electronegativities
handout
Electronegativity
Tendency of an atom to attract
electrons towards itself and thus
the tendency to form negative ions.
Electronegativity
• The more electronegative
atom pulls shared electrons
toward its nucleus.
• NONPOLAR – equal
sharing of electrons
• POLAR – unequal sharing
of electrons
Electronegativities
• H = 2.1
O=3.5
C=2.5
• H-H = 0.0 bond pure covalent
• O-H bond = 1.4 polar
• (3.5-2.1)
• covalent
• NaCl = 2.1 ionic
Molecule
• A group of two
or more atoms
held together
by covalent
bonds
What’s the difference
between Intramolecular
and Intermolecular
Forces?
What’s the difference?
• Intermolecular
attractions are
between one
molecule and a
neighboring
molecule
• (Van der Waals,
hydrogen bonds)
• USUALLY WEAKER
• Intramolecular
attractions are the
forces which hold an
individual molecule
together (for example,
the covalent bonds or
ionic bonds).
• USUALLY STRONG
WHAT IS THE STRENGTH
COMPARISON?
• STRONGEST BOND • Covalent
• Ionic
intramolecular
• Hydrogen
• WEAKEST BOND
• Van der Waals
•
(dipole-dipole
•
London forces)
INTERMOLECULAR
FORCES
• A. H-bonds (H to F, O, or N)
• B. van der Waals- temporary “dispersion”
London (nonpolar) and dipole-dipole
forces (polar)
• C. Disulfide bridges (-S-S-)
• Intermolecular Forces Youtube (9:11-if ya got time)
•
• Intermolecular Forces
video and worksheet
• What three types of intermolecular forces are
there?
• What does dipole mean? Why do those
molecules attract each other?
• London forces are in molecules that are not
dipoles. What do they do to their e- to cause an
attraction?
• What three possible atoms can make a
hydrogen bond with hydrogen?
• List the forces in order of strength.
Hydrogen Bonds: Intermolecular
between H and F, O, or N
Where Might you find
Hydrogen Bonds?
• In Water –
between O- and H+
• In DNA –
between bases
Intramolecular: Van der Waals
• Van der Waals on Gecko Feet (8:22)
• Is the sum of the attractive forces between
molecules (but not H-bonds or covalent
bonds)
van der Waals
Van der Waals Dispersion Forces
•
Temporary dispersion of electrons
make temporary charges
Where might you find van der
Waals?
• crystal structures (e. g. the shapes of
snowflakes),
• DNA shape
Intramolecular: (Van der Waal
type) Dipole-dipole
• exists between neutral polar
molecules only when they are close
together
• Dipole Forces Bozeman youtube (7:32)
• Temporary shift of the electrons to make a
partial + and a partial - end
Weakest van der Waals:
London Dispersion Forces
• Temporary polarity between nonpolar
atoms or molecules
• All molecules have them at some time
• Bozeman London Dispersion Forces (5:02)
London Dispersion Force
London Dispersion Force Animation
Disulfide Bonds:
Protein Tertiary Structure
• Disulfide Bond in Tertiary Protein
Disulfide Bonds
• formed between
the side chains of
cysteine in a
protein SH) to
form a disulfide
bond (S-S)
• (Will learn about this in
Chapter 3)
THEME OF EMERGENT
PROPERTIES
• New properties that arise with each step
upward in the hierarchy or life, owing to
the arrangement and interactions of parts
as complexity increases.
• WHOLE IS GREATER THAN THE PARTS
How is the emergent property idea
apply to a compound and atoms?
• HINT:
2.9 Chemical Reactions
• The making and breaking of chemical
bonds, leading to changes in the
composition of matter.
Chemical Reactions
•
•
•
•
•
•
Reactants on the left of the arrow
Products on the right of the arrow
IDENTIFY:
2Mg(s) + O2(g) → 2MgO(s)
MgO(s) + H2O(l) → Mg(OH)2(s)
N2(g) + 3H2(g) → 2NH3(g)
Same number of each element on
left side as on the right side
• CH4 (g) + 2O2 (g) CO2 (g) + 2H2O (g)
Reactants
Products
C=1
H=4
O=4
C=1
H=4
O=4
Signs of a Chemical Reaction
• Precipitate forms
• Color Change
• Gas Forms
• Temperature change
Chemical Reaction Videos
• Na and Cl Chemical Rx (52 secs.)
• Genie in a Bottle Reaction - Steve
Spangler (3:36)
• Weirdest Chem. Rx in the World (2:52)
Mercury(II) thiocyanate Hg(SCN)2
• The Naked Scientists Videos (MP3)
Chemical Reaction Example
• An iron bar rusts. The iron reacts with oxygen
in the air to make rust.
4 Fe + 3 O2 2 Fe2O3