1. Outline Atoms, ions, and isotopes Molecules Chemical bonds
Special properties of water
Acids, bases, and pH
Chemical reactions & energy
Kinds of energy
Laws of energy
Energy quality

2. DHMO
Images

3. THE TOP 10 ELEMENTS FOUND IN YOUR BODY
Why learn chemistry?
THE “BIG 4”
96% of your body is composed of these 4 elements:
Oxygen (65%)
Percentage (%) of body’s composition
Chemical basics are at the root of every biological function
Neural impulse (Na/K pump)
Muscular contraction (Ca ion uptake)
Carbon (18.5%)
Hydrogen (9.5%)
Nitrogen (3%)
OTHER (4%)
Citation: What is Life? A Guide to Biology by Jay Phelan W.H. Freeman and Company
Calcium
Sulfur
Phosphorus
Sodium
Potassium
Chlorine
• Trace amounts (less than 0.1%) of 15 other elements are also found in the body

4. elements are the most abundant elements found in organisms
Figure 2-3
The highlighted
elements are the most abundant elements
found in organisms

5. Atomic Structure The universe is made up of matter
Matter is made up of atoms
Anything that takes up space
and has weight
The smallest piece of gold possible is called an atom. If you divided it into smaller pieces, it would no longer be gold.
Imagine dividing a gold
ring in half, forever
Atom = uncuttable
An atom is the smallest basic unit of matter.
An element is one type of atom.

6. Atomic Structure
So how do you know if you have an atom of copper, gold or silver?
How many protons an atom has determines who it is
Cu = 39
Ag = 47
Au = 79
Atomic number is the number of protons
Cookium diagnostic
A KEY TO THE ELEMENTS
ATOMIC NUMBER
The number of protons found
in the atom’s nucleus
ELEMENT SYMBOL
Abbreviation of the element
ELEMENT NAME
Citation: What is Life? A Guide to Biology by Jay Phelan W.H. Freeman and Company
PERIODIC TABLE HERE
Regardless of where you go – carbon has 6 protons. Find an atom on the surface of Neptune? If it has 6 protons then we know it’s carbon.
We’ll cover in a little bit what happens when you gain or lose neutrons or electrons – but that does not change the element.
ATOMIC MASS
Combined mass of the atom’s protons and neutrons

7. Citation: http://www. chemistmag
Bell ringer here
More on how to read this later (it will be your favorite cheat sheet ever!)
Written in order of atomic number
Talk about mass

8. Terms Atomic number: the number of protons an element possess
What defines an element, every atom of that element has that exact number of protons (or it’s not that element!)
Also indicates the original number of electrons that element has
Atomic mass: the number of protons and neutrons an element possess
The mass of the nucleus (electrons are too tiny to measure)

9. Mass number (number of protons + neutrons) Atomic number
Figure 2-2
Mass number
(number of protons
+ neutrons)
Atomic number
(number of protons)

10. P+N (atomic mass) – P (atomic #) = N
Atomic Structure
So how do you know how many electrons and neutrons there are?
A neutral atom will have equal numbers of protons and electrons
P+ = E-
Element
Atomic Mass
Atomic Number
Protons
Neutrons
Electron Ca 40 20 F 19 9 10 B 11 5 6
The number of neutrons can be determined by subtracting the atomic number from the atomic mass
P+N (atomic mass) – P (atomic #) = N
Atomic Basics Worksheet

11. Except for H and He, a filled layer contains 8 electrons – an octet
Atomic Structure
Atoms are most stable if they have a filled (or empty) outer layer of electrons
Where are the electrons found?
Except for H and He, a filled layer contains 8 electrons – an octet
Citation:
Atoms will gain, lose, or share electrons to make a full or completely empty outer layer

12. ELECTRON SHELLS AND ATOM STABILITY
Electrons move around the nucleus in designated areas called electron shells. An atom can have as many as seven electron shells in total.
First electron shell
(capacity: 2 electrons)
Second electron shell
(capacity: 8 electrons)
Vacancy
The chemical characteristics of an atom depend upon the number of electrons in its outermost shell.
Citation: What is Life? A Guide to Biology by Jay Phelan W.H. Freeman and Company
Emphasize valence electrons
An atom’s electrons determine whether an atom will bond with another atom as well as who it will bond with

13. ELECTRON SHELLS AND ATOM STABILITY ATOM STABILITY
Atoms become stable when their outermost shell is filled to capacity. Stable atoms tend not to react or combine with other atoms.
Unstable atoms
Stable atoms
Hydrogen atom
Helium atom
Nitrogen atom
Neon atom
Citation: What is Life? A Guide to Biology by Jay Phelan W.H. Freeman and Company
Only when atoms have electron vacancies in their outermost shell are they likely to interact with other atoms.

14. THE ATOM: BASIC STRUCTURE
Nucleus
Hydrogen atom
1 Proton
0 Neutrons
1 Electron
Carbon atom
6 Protons
6 Neutrons
6 Electrons
Forces of attraction between positive and negative charges hold the fast-moving electrons (negative) close to the nucleus (positive).
Nucleus:
Citation: What is Life? A Guide to Biology by Jay Phelan W.H. Freeman and Company
Proton
Neutron
Electron

15. Chemical Changes Chemical Change Lab
When atoms exchange or share electrons, a new product (a compound or molecule) is produced. This is called a chemical change.
In a chemical change:
reacting substances form new substances with different compositions and properties.
a chemical reaction takes place.
Change
Chemical
Physical
Melting cheese √
Milk souring
Ripping paper
Bike rusting
Citation:
Citation: Copyright © by Pearson Education, Inc.
Publishing as Benjamin Cummings
Chemical Change Lab

16. A sodium ion being formed
Figure 2-6ab
A sodium ion being formed
Loss of electron
Cation formation
Sodium ion
has positive
charge
A chloride ion being formed
Gain of electron
Anion formation
Chloride ion
has negative
charge

17. Reactants are what you use, products are what you get
Chemical Reactions
The job of a chemical reaction is to depict the kind of reactants and products and the relative amounts in a reaction.
Symbols represent elements, formulas describe compounds, and chemical equations describe a chemical reaction
C + O2 = CO2
If two substances react and the temperature of the mixture decreases, the reaction is endothermic.
If two substances react and the temperature of the mixture increases, the reaction is exothermic.
A chemical reaction involves the breaking of bonds in the reactants and the forming of bonds in the products.
It takes energy to break bonds.
Energy is released when bonds are formed.
If a reaction is endothermic, it takes more energy to break the bonds of the reactants than is released when the bonds of the products are formed.
If a reaction is exothermic, more energy is released when the bonds of the products are formed than it takes to break the bonds of the reactants.
Reactants are what you use, products are what you get

18. Ions form when atoms gain or lose electrons
An ion is an atom that has gained or lost one or more electrons.
positive ions (cation)
negative ions (anion)
Ionic bonds form between oppositely charged ions.
Sodium atom (Na)
Chlorine atom (CI)
Sodium ion (Na+)
Chloride ion (CI-)
Na loses an electron to CI
ionic bond
gained electron
Citation: Biology by Nowicki Holt McDougal Publishers.

19. Ions
Atoms can give up electrons or accept electrons from another atom to become charged ions
Atoms will only do this if it makes them more stable
Rule of Thumb: 8 electrons in the outer (valence) energy level makes an atom stable
Isotopes: different forms of the same element that have different numbers of neutrons

20. Na Cl Sodium ion Chloride ion 11 Protons 10 Electrons 17 Protons
IONS ARE CHARGED ATOMS
An atom that loses one or more electrons becomes positively charged, while an atom that acquires electrons becomes negatively charged. This transfer of electrons is driven by the fact that atoms with full outer electron shells are more stable.
Donated electron Na Cl
Sodium ion
Chloride ion
Citation: What is Life? A Guide to Biology by Jay Phelan W.H. Freeman and Company
11 Protons
10 Electrons
17 Protons
18 Electrons
NET
CHARGE
Positive
Negative

21. Ionic Bonds Formed between ions
Citation: What is Life? A Guide to Biology by Jay Phelan W.H. Freeman and Company
OPPOSITE CHARGES ATTRACT

22. Atoms combine to form compounds
Ionic Compounds
Ions of different charges combine to form ionic compounds (Na+ and Cl- form salt)

24. COVALENT BONDS
1 Hydrogen atoms are most stable when their outer electron shell is filled to capacity. They can achieve this by sharing electrons in a covalent bond.
Hydrogen
atom
Hydrogen
atom
2 The nuclei come closer together and the two electrons begin to circle around both of them. The new H2 molecule is very stable.
Citation: What is Life? A Guide to Biology by Jay Phelan W.H. Freeman and Company
One way to help you remember the types of bonding is to think about similar words.
A coworker is someone who shares work with you. A covalent bond is a bond that
shares valence electrons.
H2 molecule
Covalent bonds form electrically neutral molecules. Covalent bond are very strong bonds, common in most organic molecules

25. Covalent Bonds carbon dioxide (CO2) water (H2O)
A molecule is made of atoms sharing electrons
water (H2O)
carbon dioxide (CO2)
Citation: Biology by Nowicki Holt McDougal Publishers.

26. A chemical structure held together by covalent bonds
Citation: Biology by Nowicki Holt McDougal Publishers.
Molecule
A chemical structure held together by covalent bonds
The chemical structure shows the number of each element forming the molecule (CH4) 26

27. Ions (charged atoms) follow the rule that opposites attract
Balloon Buddy
Simulation
Ions (charged atoms) follow the rule that opposites attract
Citation:
Static electricity is the imbalance of positive and negative ions. An accumulation of an electric charge on something will discharge onto something with a positive charge. It is frequently encountered as a type of electricity produced by friction.
When a person walks across carpet, dragging his feet, he pulls electrons from the carpet to himself, giving himself a negative charge. When he approaches a metal object which has a neutral charge, he attracts the protons and repels the electrons from the metal. When the attraction between the electrons on the person and the protons on the metal is strong enough, they are pulled together, from his body to the metal object. When this happens, the person feels the static shock of electricity.
Static electricity is a reflection of the difference in charges between objects

28. Covalent compounds
Often the atoms share the electrons unequally so the molecule (or compound) has an area of positive charge as well as an area of negative charge.
Charged
molecules
are called
polar molecules.

29. An attraction between two oppositely charged ions, forming a compound.
1 COVALENT BOND
A strong bond formed when atoms share electrons in order to become more stable, forming a molecule.
SUMMARY: THREE TYPES OF BONDS
Strongest
2 IONIC BOND
An attraction between two oppositely charged ions, forming a compound.
H2 molecule
Bond Strength
3 HYDROGEN BOND
An attraction between the slightly positively charged hydrogen atom of one molecule and the slightly negatively charged atom of another.
NaCl compound
Citation: What is Life? A Guide to Biology by Jay Phelan W.H. Freeman and Company
Weakest
H2O
H2O
Chemical Bonds Rap
Chemical Bond

30. Concept map Build a concept map to show connections. Atom Element
Compound
Ion
Ionic bond
covalent bond
molecule

31. Hydrogen Bonds

32. Polar molecules Polar molecules can be attracted to one another.
The bond that holds these molecules together is called a hydrogen bond.
Hydrogen bonds are very weak; heat and changes in pH can break these bonds.

36. Elixir of Life Special properties of water cohesion & adhesion
surface tension, capillary action
good solvent
many molecules dissolve in H2O
hydrophilic vs. hydrophobic
lower density as a solid
ice floats!
high specific heat
water stores heat
high heat of vaporization
heats & cools slowly

37. Can you suck sugar up a straw?
Cohesion & Adhesion
H bonding between H2O molecules is cohesion
water is “sticky”
surface tension
drinking straw
H bonding between H2O & other substances is adhesion
capillary action
meniscus
water climbs up paper towel or cloth
Can you suck sugar up a straw?

38. How does H2O get to top of trees?
Transpiration built on cohesion & adhesion
APBio/TOPICS/04Biochemistry/MoviesAP/03_03WaterTransport_A.swf

39. Water is the solvent of life
Polarity makes H2O a good solvent
polar H2O molecules surround + & – ions
solvents dissolve solutes creating solutions
What dissolves in water easily?
polar or non-polar molecules?
How about Oxygen? Does that dissolve in H2O?

40. Do you dissolve in water?
Hydrophilic
substances have attraction to H2O
polar or non-polar?
What dissolves in water easily?
polar or non-polar molecules?
How about Oxygen? Does that dissolve in H2O?

41. Or don’t you? Hydrophobic
substances that don’t have an attraction to H2O
polar or non-polar?
What dissolves in water easily?
polar or non-polar molecules?
How about Oxygen? Does that dissolve in H2O?
fat (triglycerol)

42. The special case of ice
Most (all?) substances are more dense when they are solid
H bonds form a crystal in water

43. Why is “ice floats” important?
Oceans & lakes don’t freeze solid
surface ice insulates water below
allowing life to survive the winter
if ice sank…
ponds, lakes & even oceans would freeze solid
in summer, only upper few inches would thaw
seasonal turnover of lakes
cycling nutrients in autumn

44. Heat of vaporization Evaporative cooling
Organisms rely on heat of vaporization to remove body heat

45. Ionization of water & pH
Water ionizes
H+ splits off from H2O, leaving OH–
if [H+] = [-OH], water is neutral
if [H+] > [-OH], water is acidic
if [H+] < [-OH], water is basic
pH scale
how acid or basic solution is
1  7  14
H2O  H+ + OH–

46. pH Scale H+ Ion Concentration Examples of Solutions pH 10–1
Stomach acid, Lemon juice 1 pH
100
Hydrochloric acid
10–2 2
10–3
Vinegar, cola, beer 3
10–4
Tomatoes 4
10–5
Black coffee, Rainwater 5
10–6
Urine, Saliva 6
10–7
Pure water, Blood 7
10–8
Seawater 8
10–9
Baking soda 9
10–10
Great Salt Lake 10
10–11
Household ammonia 11
10–12
Household bleach 12
10–13
Oven cleaner 13
10–14
Sodium hydroxide 14
In pure water only 1 water molecule in every 554 million is dissociated

47. Buffers & cellular regulation
pH of cells must be kept ~7
pH affects shape of molecules
shape of molecules affect function
pH affects cellular function
Control pH by buffers
reservoir of H+
donate H+ when [H+] falls
absorb H+ when [H+] rises 1 2 3 4 5 6 7 8 9
Amount of base added
Buffering
range pH
Exercise = acidic in muscles
CO2 = carbonic acid
lactic acid
body uses buffers to counter act this

48. Chemical Symbols
The subscripts tell you how many atoms of a particular element are in a compound. The coefficient tells you about the number of molecules of the compound.
Citation:

49. Remember?
Physical change: no change in chemical composition (cutting matter does not alter it chemically)
Chemical change: composition of the elements or atoms are altered
Shorthand equations are used to illustrate a chemical reaction
C6H12O6 + O2  CO2 + H2O

50. Balancing Reactions
Due to the Law of Conservation of Mass: matter cannot be created nor destroyed.
An equation must be balanced (it must have the same number and kinds of atoms both before and after a reaction.
Reaction Rate Demo
Collisions must have enough energy to produce the reaction: must equal or exceed the “activation energy”, which is the minimum energy needed to react.
Will a AA battery start a car?
Think of clay clumps thrown together gently – they don’t stick, but if thrown together forcefully, they stick tightly to each other.
When balancing a chemical reaction you may add coefficients in front of the compounds to balance the reaction, but you may not change the subscripts.
Changing the subscripts changes the compound. Subscripts are determined by the valence electrons (charges for ionic or sharing for covalent)
Think of a recipe without any measurements
Reaction Rate Demo

51. Laws of Thermodynamics
1st Law: Energy cannot be created nor destroyed, only converted
You can’t get something from nothing
We make think that since we can’t destroy energy, we will always have enough
2nd Law: Energy is always lost to the environment during any energy change
Usually in the form of heat or light
Prevents a 100% efficient or perpetual motion machine

52. 2nd Law of Thermodynamics

53. Elements & their valence shells
Elements in the same column have the same valence & similar chemical properties
Oxygen has medium electronegativity so doesn’t pull electrons all the way off hydrogen whereas chlorine would.
So oxygen forms a polar covalent bond.
Carbon has only a weak electronegativity so forms a nonpolar covalent bond

54. Elements & their valence shells
Elements in the same row have the same number of shells
Moving from left to right, each element has a sequential addition of electrons (& protons)

55. Periodic Trends Alkali Metals Alkaline Earth Metals Boron Family
Carbon Family
Nitrogen Family
Oxygen Family
Halides
Noble Gases

56. Periodic Trends Periodic Table
In ascending atomic number (mass usually follows trend)
Valence electrons can be determined by what group the atom is in
Periods (horizontal)
Groups (vertical)
The total number of energy levels can be determined by the period
Trend doesn’t work well for the transition elements

57. Energy Defined as the capacity to do work Potential: stored energy
Kinetic: the energy of motion
Radiation: the transmission of energy through space
Electromagnetic radiation: different types based on wavelength
X ray, gamma ray, microwaves, etc

58. High-quality matter vs. low-quality matter
High-quality matter is:
Organized
Concentrated
Found near the earth’s surface
Has great potential for use

60. Energy Quality Fig. 2-10, p. 31 Source of Energy Relative
(usefulness)
Energy Tasks
Electricity
Very high temperature heat
(greater than 2,500°C)
Nuclear fission (uranium)
Nuclear fusion (deuterium)
Concentrated sunlight
High-velocity wind
Very high-temperature heat
(greater than 2,500°C)
for industrial processes
and producing electricity to
run electrical devices
(lights, motors)
Very high
High-temperature heat
(1,000–2,500°C)
Hydrogen gas
Natural gas
Gasoline
Coal
Food
Mechanical motion (to move
vehicles and other things)
High-temperature heat
(1,000–2,500°C) for
industrial processes and
producing electricity
High
Normal sunlight
Moderate-velocity wind
High-velocity water flow
Concentrated geothermal energy
Moderate-temperature heat
(100–1,000°C)
Wood and crop wastes
Moderate-temperature heat
(100–1,000°C) for industrial
processes, cooking,
producing steam,
electricity, and hot water
Moderate
Dispersed geothermal energy
Low-temperature heat
(100°C or lower)
Low-temperature heat
(100°C or less) for
space heating
Low
Fig. 2-10, p. 31

61. Figure 04_09

62. Figure 04_10

63. Laws of Conservation
The only time matter is converted to energy or visa versa is during a nuclear reaction (which do not occur spontaneously here on earth)
When there is a transfer of protons, the element changes into a different type of atom (a new element)
This occurs with unstable isotopes
Emit gamma rays, alpha or beta particles

64. Isotopes
Going back to those neutrons…
Citation:
Elements with the same number of protons but different number of neutrons are called isotopes

65. Isotopes
Nucleus
Neutron
Proton +
Electrons
Nucleus
Nucleus
Neutron
Proton +
Carbon-12
Neutrons 6
Protons 6
Electrons 6
Electrons
The chemistry of each element is determined by its number of protons and electrons.
In a neutral atom, the number of electrons equals the number of protons.
Symbols for elements are derived directly from the element’s name.
Nuclei of atoms contain neutrons as well as protons.
The number of neutrons is not fixed for most elements, unlike protons.
Atoms that have the same number of protons, and hence the same atomic number, but different numbers of neutrons are called isotopes.
As istopes decay, the release nuclear particles at a rate called a half life
Carbon-14
Neutrons 8
Protons 6
Electrons 6
Nucleus

66. Isotopes
Knowing an atoms half life allows us to determine the age of organic items based on their relative amounts of isotopes
Citation:

67. Radioactive Decay
Each type of radioisotope decays at a characteristic rate to a different isotope (this is it’s half-life)
Half life: time it takes for ½ of a sample to decay, continues through many different isotopes until a nonradioactive isotope is formed
An isotope’s ½ life cannot be changed by temp, pressure, or chemical rxns

68. Nuclear Fission
Large nuclei of isotopes are split into 2 lighter nuclei when struck by neutrons
Each collision (fission) releases more neutrons which can then strike more nuclei = chain reaction
Enormous amounts of energy are released (power of nuclear plants, atomic bombs)

70. Nuclear Fusion
Two small nuclei from different isotopes collide under extreme temps to form a second, larger isotope
Not as well understood
Occurs at temperatures not practical on earth
Source of energy for the sun