1. Chapter 6
Chemistry in Biology

2. Section 6.1 Atoms, Elements, & Compounds

3. Matter! Matter is anything that occupies space and has mass.
Will this astronaut occupy the same space on the moon as he does on Earth?
Will this astronaut weigh the same on the moon as he does on the Earth?
Mass and weight are not the same.

4. The Atom – The Simplest of Particles
The atom is the simplest particle of an element that retains the properties of that element.

5. The Structure of an Atom
Biology Class Notes - October 3, 2006
The Structure of an Atom
Bohr Model – “planetary model”
Proposed by Niels Bohr in 1915
A useful approximation of the structure of an atom.
Consists of two parts:
A central region, or nucleus
Electron cloud – composed of orbitals or three-dimensional regions around a nucleus

6. Subatomic Particles Protons Positively (+) charged particles +
Have mass (1 amu = 1 atomic mass unit)
Located in the nucleus +
Neutrons
Neutral particles (No charge)
Have mass (1 amu)
Also located in the nucleus n
Electrons
Negatively (-) charged particles
Mass is negligible (1/1840 amu)
Remain in constant motion in orbitals

7. Biology Class Notes - October 3, 2006
The Bohr Model
Below is a Bohr Model of a helium (He) atom.
Nucleus
2 protons
2 neutrons n +
Electron cloud
Consists of orbitals where high-energy electrons orbit the nucleus

8. Elements
Elements are substances that cannot be broken down chemically into simpler kinds of matter.

9. The Elemental Body -- The Major Elements
Biology Class Notes - October 3, 2006
The Elemental Body -- The Major Elements
A major element is any element that makes up more than 0.01% of your body mass.
Rank
Chemical Symbol
Element
% of human body* 1 O
Oxygen
62 % 2 C
Carbon
23 % 3 H
Hydrogen
10 % 4 N
Nitrogen
2.6 % 5 Ca
Calcium
1.4 % 6 P
Phosphorus
1.1 % 7 K
Potassium
0.2 % 8 S
Sulfur 9 Na
Sodium
0.1% 10 Cl
Chlorine
0.1 % 11 Mg
Magnesium
0.02 %
* Based on an average 70 kg (154 lbs.) person

10. The Elemental Body -- The Trace Elements
Biology Class Notes - October 3, 2006
The Elemental Body -- The Trace Elements
A trace element is any element that makes up less than 0.01% of your body mass, but is still critical to your health.
Rank
Chemical Symbol
Element 12 Fe
Iron 13 F
Fluorine 14 Zn
Zinc 15 Si
Silicon 16 Cu
Copper 17 I
Iodine 18 Sn
Tin
Rank
Chemical Symbol
Element 19 B
Boron 20 Se
Selenium 21 Cr
Chromium 22 Mn
Manganese 23 Mo
Molybdenum 24 Co
Cobalt 25 V
Vanadium

11. C The Periodic Table 6 12.011 Atomic Number Chemical Symbol
Atomic Mass

12. Biology Class Notes - October 3, 2006
Atomically Speaking…
The number of protons in an atom is called the atomic number.
In an atom, the number of positive protons is balanced by an equal number of negative electrons.
net electrical charge equals zero
The Bohr model to the left represents an atom of which element?
How many electrons must be in the electron cloud?
= neutron
= proton

13. Biology Class Notes - October 3, 2006
Atomically Speaking…
The mass number of an atom is equal to the total number of protons and neutrons of the atom.
What is the mass number of our carbon atom?
= neutron
= proton

14. Isotopes: Not All Atoms are Created Equal
Biology Class Notes - October 3, 2006
Isotopes: Not All Atoms are Created Equal
Isotopes are atoms of the same element that have different numbers of neutrons.
therefore they will have different mass numbers
this is the reason for the average atomic mass in the periodic table
Click here to compare these two atoms.
= neutron
= proton
These two atoms are both carbon atoms. But the atom on the left has 6 neutrons while the atom on the right has 7 neutrons. Because of this, these two atoms are said to be isotopes of one another.
Use this slide to explain why the average atomic mass is not always the same as the mass number. Explain to students that we assumed that the number of neutrons was the same as the protons, but that this is not always the case for all atoms of the same element.
CLOSE

15. Biology Class Notes - October 3, 2006
Radioactive Isotopes
Sometimes having too many neutrons can make the nucleus of an atom unstable.
Unstable nuclei decay, or break apart.
Particles (usually neutrons) and energy in the form of radiation are released.
This radiation can be used to calculate the age of an object or it can be used in medical treatments such as radiation therapy.

16. A Few Words About Electrons
Biology Class Notes - October 3, 2006
A Few Words About Electrons
High energy particles
Are attracted to (+)ve protons in the nucleus – keeps them close together
Constant energy of motion prevents them from collapsing into nucleus
Exact path of travel cannot be known
An electron’s energy confines it to an energy level within the electron cloud
Electrons with higher energy occupy energy levels farther from the nucleus

17. Biology Class Notes - October 3, 2006
Orbitals
Energy levels contain orbitals which can only hold a certain number of electrons.
Energy Level
# of orbitals
Maximum # of electrons 1 2 4 8 3 9 18

18. Expanding the Bohr Model
Biology Class Notes - October 3, 2006
Expanding the Bohr Model
Example: A carbon atom
We know:
From periodic table
atomic number of carbon equals six;
therefore the number of electrons equals six Why?
From previous chart
first energy level holds two electrons maximum
second energy level holds eight electrons maximum

19. Expanding the Bohr Model
Biology Class Notes - October 3, 2006
Expanding the Bohr Model
Putting it all together:
Two of carbon’s electrons will be found in the first energy level of the electron cloud.
The remaining four electrons will be found in the second energy level of the electron cloud.
The second energy level of a carbon atom is not full. It can still accommodate four more electrons.
= neutron
= proton
= electron

20. Compounds
Compound – substance formed when two or more different elements combine
Form a specific combination of elements in a fixed ratio
Chemically and physically different from the elements that comprise them
Cannot be broken down into simpler compounds or elements by physical means (can be broken down chemically)

21. Why Combine?
Compounds form because most atoms are not stable in their natural state.
A partially-filled outermost energy level is not as stable as an energy level that is completely filled with the maximum number of electrons it can hold.
Is this carbon atom stable?
= neutron
= proton
= electron

22. Two Ways to Bond
Ionic Bonds
Covalent
Bonds

23. Chemical Bonds Ionic Bond Covalent Bond
An atom can gain or lose an electron to make a stable energy level. This atom is called an ion and is now charged.
An ionic bond is electrical attraction between two oppositely charged atoms.
Example: sodium chloride
A chemical bond that forms when electrons are SHARED
Example: water

24. Achieving Stability
Atoms become stable by attaining at least one of the following:
They fill their outermost, or valence, energy level with the maximum amount of electrons that it will hold. OR
They fill their outermost energy level with eight electrons.
The ‘Rule of Eight’

25. There IS Another Way
Atoms can also share one or more pairs of electrons.
When two atoms share electrons, the shared electrons occupy orbitals around both of the atoms.
The electrons move so quickly that it is difficult to predict which atom they are orbiting at any given time.
So far we have investigated how atoms react when they have one or two electrons in their outermost energy levels. We have also discussed how atoms react when they have six or seven electrons in their outermost energy levels. But what happens when atoms have three, four, or even five electons in their outermost energy levels.

26. Water – A Model of Covalent Bonding
Oxygen 8p 8n
Hydrogen
1 p
0 n
Hydrogen atom (atomic #: 1)
Oxygen atom (atomic #: 8)
How many valence electrons does each atom have?
How many more electrons does each atom need to fill its outermost energy level?

27. Water – A Model of Covalent Bonding
This is a molecule of water. It can also be referred to by its chemical formula, H2O.
A shared pair of electrons can be considered to be part of the outermost energy level of both atoms that share them.
How might each of these atoms fill its outermost energy level?
Oxygen 8p 8n
Oxygen 8p 8n
Hydrogen
1 p
0 n
Hydrogen
1 p
0 n
Hydrogen
1 p
0 n
If each hydrogen atom shares a pair of electrons with oxygen, how many valence electrons does each atom have?

28. Covalent Bond
A covalent bond forms when two atoms share one or more pairs of electrons.
A molecule is the simplest part of a substance that retains all the properties of that substance

29. Modeling Ionic Bonds Activity
In your notes, draw a Bohr model of a sodium atom (atomic number 11). Next to the sodium atom draw a Bohr model of a chlorine atom (atomic number 17).

30. Activity
1. On the left, draw a neutral sodium atom with a mass number of 23 (atomic number 11).
2. On the right, draw a neutral chlorine atom with a mass number of 35 (atomic number 17).

31. The Sodium-Chlorine Ionic Bond
17 p
18 n
Sodium
11 p
12 n
Sodium atom (atomic #: 11)
Chlorine atom (atomic #: 17)
How many electrons does each atom have now?
How does this affect the total charge of each atom?

32. The Sodium-Chlorine Ionic Bond
These atoms are no longer electrically neutral.
How many protons does sodium (Na) have?
How many electrons does Na have now?
What is the total charge of this atom of sodium?
Chlorine
17 p
18 n
Sodium
11 p
12 n
These atoms are stable, but because of their opposite charges they now attract one another.
Protons +11
Electrons -10
Charge +1
Protons +17
Electrons -18
Charge -1

33. The Sodium-Chlorine Ionic Bond
An atom with an electrical charge is called an ion.
As a result of their opposite charges, sodium ions and chlorine ions attract each other.
Chlorine
17 p
18 n
Sodium
11 p
12 n
Chlorine ion -1
This new substance is a compound called sodium chloride.
Sodium ion +1
An ionic bond is the chemical bond formed between ions with opposite charges.

34. Chapter 6.2 Chemical Reactions

35. Chemical Reactions
Process by which atoms or groups of atoms in substances reorganize into different substances
Chemical bonds are broken or formed
For example –
4 Fe + 3 O Fe2O3

36. Reactants and Products
Chemical Equation: C6H12O6 + O2 CO2 + H20 (Glucose and oxygen react to form carbon dioxide and water) Reactants (starting substances): C6H12O6 + O2 Products (substances formed): CO2 + H20

37. Balanced Equation
According to the principle of conservation of mass, matter cannot be created or destroyed
The number of atoms of each element on the reactant side must equal the number of atoms of the same element on the product side
For example:
2 H2O2 2 H20 + O2
C6H12O O2 6 CO H20

38. Energy-Absorbing Reaction Energy-Releasing Reaction
Products
Activation energy
Activation
energy
Reactants