1. Essential Chemistry for Biology
CHAPTER 2
Essential Chemistry for Biology

2. Did you know…?

3. Why do we care about Chemistry in Biology?
Take any biological system apart, and you eventually end up at the chemical level.

4. Matter: is anything that occupies space and has mass.
Matter & Elements
Matter: is anything that occupies space and has mass.
Matter is found on the Earth in three physical states:
Solid Liquid Gas
Matter is composed of chemical elements.
Elements are substances that cannot be broken down into other substances.
There are 92 naturally occurring elements on Earth.
All the elements are listed in the periodic table.

5. Reading the Period Table
Note: You have a periodic table in your text in the appendix at the end on page A-3

6. Twenty-five elements are essential to life.
Four of these make up about 96% of the weight of the human body. CHON
Trace elements occur in smaller amounts but are still essential for life!
For example iodine deficiency causes goiter.
This is why we add iodine to salt

7. Amounts of Elements in the Body
What are the major elements in the air?

8. Elements in the Air

9. Key Element Abbreviations – QUIZ!
Carbon –
Hydrogen –
Oxygen –
Nitrogen –
Sulfur –
Phosphorus – 
Magnesium – 
Calcium –
Sodium –
Potassium –
Chlorine –
Chloride Ion –
Iron –
Copper – C H O N S P 
Mg  Ca Na K Cl
Cl- Fe Cu

10. Each element consists of one kind of atom.
Atoms
Each element consists of one kind of atom.
An atom is the smallest unit of matter that still retains the properties of an element.

11. Elements can combine to form compounds.
These are substances that contain two or more elements in a fixed ratio.
Compounds have their own unique properties that are different from those of the contributing elements. +  Na Cl
NaCl

12. Atoms are composed of subatomic particles.
The Structure of Atoms
Atoms are composed of subatomic particles.
A proton is positively charged. p+
An electron is negatively charged. e-
A neutron is electrically neutral. n0

13. Most atoms have protons and neutrons packed tightly into the nucleus.
The Structure of Atoms
Most atoms have protons and neutrons packed tightly into the nucleus.
The nucleus is the atom’s central core.
The electrons orbit the nucleus in a cloud.

14. Elements differ in the number of subatomic particles in their atoms.
The Structure of Atoms
Elements differ in the number of subatomic particles in their atoms.
The number of protons, the atomic number, determines which element it is. The number of protons NEVER changes
An atom’s mass number (atomic mass) is the sum of the number of protons and neutrons.
Mass is a measure of the amount of matter in an object without the effect of gravity. This is DIFFERENT than weight!

15. Reading the Periodic Table: Practice (Periodic Table page A-3 in text)
# of electrons ____
# of protons ____
# of neutrons ____
(Mass #) 23
(Atomic #)11 Na
What is the charge of this atom?_____
# of electrons ____
# of protons ____
# of neutrons ____ C
(Mass #) 23
(Atomic #)11
Na: 11, 11, 12
C: 6, 6, 6
What is the charge of this atom?_____

16. Isotopes are alternate mass forms of an element.
They have the same number of protons and electrons.
But the isotopes have a different number of neutrons.

17. H Isotopes: Practice (Periodic Table page A-3 in text) (Mass #) ____
# of electrons ____
# of protons ____
# of neutrons ____
(Mass #) ____
(Atomic #) ____ 3 H
Al+3: electrons = 10, protons = 13, neutrons = 14
What is the charge of this atom?_____

18. Isotopes: Radioactivity
Radioactive isotopes are unstable: The nucleus decays, giving off particles and energy.
Radioactive isotopes have many uses in research and medicine.
Example: PET scans
Uncontrolled exposure to radioactive isotopes can harm living organisms by damaging DNA.
Example: the 1999 Chernobyl nuclear accident

19. Alzheimer’s disease is a devastating illness.
How a PET scan is used:
Alzheimer’s disease is a devastating illness.
It gradually destroys a person’s memory and ability to think.
Doctors are now using PET scans in an attempt to diagnose Alzheimer’s disease before the onset of symptoms.

20. Isotopes: Many Applications
Who cares?
Dating of geological strata and fossils
Radiation from certain isotopes can be used to treat cancer
Some can kill bacteria that causes food to spoil
Used as labels or tracers to follow the movements of substances within the organisms. Used in research & disease diagnoses. PET scans
Half life: The time for 50% of radioactive atoms in a sample to decay. C14 has a half life of 5600 years
Radioactive isotopes: are unstable isotopes in which the nucleus spontaneously decats emitting sub-atomic particles and/or energy as radioactivity.

21. Electron Arrangement and the Chemical Properties of Atoms
Electrons determine how an atom behaves when it encounters other atoms.
Electrons orbit the nucleus of an atom in specific electron shells.
The number of electrons in the outermost shell determines the chemical properties of an atom.

22. Figure 2.7

23. Chemical Bonding and Molecules
Chemical reactions enable atoms to give up or acquire electrons in order to complete their outer shells.
These interactions usually result in atoms staying close together.
The atoms are held together by chemical bonds.

24. Ionic Bonds
When an atom loses or gains electrons, it becomes electrically charged.
Charged atoms are called ions.
Ionic bonds are formed between oppositely charged ions.
Note: A positive ion has lost an electron NOT gained a proton!
Ionic Bonds

26. Al+3 Atomic Mass: Practice (Periodic Table page A-3 in text)
# of electrons ____
# of protons ____
# of neutrons ____
(Mass #) ?
(Atomic #)?
Al+3
Al+3: electrons = 10, protons = 13, neutrons = 14
What is the charge of this atom?

27. Covalent Bonds
A covalent bond forms when two atoms share one or more pairs of outer-shell electrons.
Covalent Bonds

28. Hydrogen Bonds
Water is a compound in which the electrons in its covalent bonds are shared unequally.
This causes it to be a polar molecule, one with opposite charges on opposite ends.
The polarity of water results in weak electrical attractions between neighboring water molecules.
These interactions are called hydrogen bonds.

29. Chemical Reactions
Cells constantly rearrange molecules by breaking existing chemical bonds and forming new ones.
Such changes in the chemical composition of matter are called chemical reactions.

30. Chemical reactions include:
Reactants: the starting materials
Products: the end materials
Chemical reactions cannot create or destroy matter
They only rearrange it.
This is the Law of Conservation of Matter
Balancing Equations

31. Life on Earth began in water and evolved there for 3 billion years.
Water and Life
Life on Earth began in water and evolved there for 3 billion years.
Modern life still remains tied to water.
Your cells are composed of 70%–95% water.
The abundance of water is a major reason Earth is habitable.

32. Water’s Life-Supporting Properties
Water is Polar
Water Structure & Polarity

33. Water’s Life-Supporting Properties
The polarity of water molecules and the hydrogen bonding that results explain most of water’s life-supporting properties:
Floating ice
Water’s cohesive / adhesive nature
Versatility of water as a solvent
Water’s ability to moderate temperature

34. Water molecules stick together as a result of hydrogen bonding.
The Cohesion of Water
Water molecules stick together as a result of hydrogen bonding.
This is called cohesion.
Cohesion is vital for water transport in plants.
Water Molecules is also attracted to other molecules and this is known as adhesion. Capillary action is demonstrated by this property.
Water Transport

36. Surface tension is the measure of how difficult it is to stretch or break the surface of a liquid.
Hydrogen bonds give water an unusually high surface tension.

37. How Water Moderates Temperature
Because of hydrogen bonding, water has a strong resistance to temperature change.
Heat and temperature are related, but different.
Heat is the amount of energy associated with the movement of the atoms and molecules in a body of matter.
Temperature measures the intensity of heat.
Water can absorb and store large amounts of heat while only changing a few degrees in temperature.

38. How Water Moderates Temperature
Water can moderate temperatures.
Earth’s giant water supply causes temperatures to stay within limits that permit life.
Evaporative cooling removes heat from the Earth and from organisms.

39. The Biological Significance of Ice Floating
When water molecules get cold, they move apart, forming ice.
A chunk of ice has fewer molecules than an equal volume of liquid water.
The density of ice is lower than liquid water.
This is why ice floats.
Did you know that ice can go from a solid to a gas using a process known as sublimation?

40. Why is the density of ice important?
Since ice floats, ponds, lakes, and even the oceans do not freeze solid.
Marine life could not survive if bodies of water froze solid.

41. Water as the Solvent of Life
A solution is a liquid consisting of two or more substances evenly mixed. It is a type of mixture and therefore is NOT chemically combined!
The dissolving agent is called the solvent.
The dissolved substance is called the solute.
When water is the solvent, the result is an aqueous solution.

42. H2O  H+ (hydrogen ion) + OH- (hydroxide ion)
Acids and Bases
Dissociation of water
Breaking apart of the water molecule into two ions of opposite charge (due to strong attraction of oxygen atom of one molecule for H atom of another water molecule)
H2O  H+ (hydrogen ion) + OH- (hydroxide ion)
H+ + H2O  H3O (hydronium ion)

43. Acids, Bases, and pH
Acid - A chemical compound that donates H+ ions to solutions. In other words an acid is any solution where the number of hydronium ions (H3O) in solutions is greater than the number of hydroxide ions (OH-)
Base - A compound that accepts H+ ions and removes them from solution. In other words a solution is a base if the number of hydroxide ions (OH- ) in solution is greater than the number of hydronium ions
To describe the acidity of a solution, we use the pH scale.

44. pH scale: logarithmic scale for comparing the relative concentrations of hydronium ions and hydroxide ions in a solution ranges from 0 to 14
the lower the pH the stronger the acid
the higher the pH the stronger the base
pH 7.0 is neutral

45. Control of Buffers is CRITICAL for living things
Buffers are substances that resist pH change. Typically they are weak acids and bases that neutralize excess acids and bases in solution
They accept H+ ions when they are in excess.
They donate H+ ions when they are depleted.
Control of Buffers is CRITICAL for living things
Most enzymes in your body only function within a narrow pH range
Buffering is not foolproof.
Example: acid precipitation 

46. Chemical Equations Part 2
How to read and balance chemical equations

47. Chemical Formulas H2SO4 How many atoms of each element is present?
Chemical formulas show the elements & number of atoms of each element in a molecule
In small letters to the right of the elements there is a number that indicates how many atoms of that element are in the molecule. This number is called the subscript. If there is no number assume the number is “1”
H2SO4
How many atoms of each element is present?
Elements
Hydrogen: 2 atoms
Sulfur: 1 atom
Oxygen: 4 atoms
7 atoms total
Subscript

48. A formula may begin with a number.
Coefficients
A formula may begin with a number.
If there is no number, then “1” is understood to be in front of the formula.
This number is called the coefficient.
The coefficient represents the number of molecules of that compound or atom needed in the reaction.
For example:
2H2SO4
The 2 indicates that there are 2 molecules of Sulfuric Acid
Coefficient

49. 2H2SO4 – 2 molecules of Sulfuric Acid
Coefficients
2H2SO4 – 2 molecules of Sulfuric Acid
A coefficient is distributed to ALL elements in a compound
2 – H2 (multiply 2x2) (for a total of 4 H atoms)
2 – S (multiply 1(assume S has 1) x2) (for a total of 2 S atoms)
2 – O4 (multiply 2x4) (for a total of 8 O atoms)

50. WHAT DOES THIS HAVE TO DO WITH BIOLOGY!!?? grrrrrr

51. Chemical Reactions in the Human Body (YAY! Biology!)
Reactions in the human body occur when bonds are formed or broken
Metabolism
All of the chemical reactions that occur within an organism
Anabolism & Catabolism
2H2 + O2 2H2O

52. Chemical Reactions
Catabolism is the metabolic process that breaks down molecules into smaller units. Example: You break down the foods you eat.
Anabolism is the metabolic process that builds larger molecules from smaller ones Example: You builds needed macromolecules such as proteins from smaller molecules in your body that you obtained from catabolism.

53. So what is a chemical equation?
A chemical equation is a symbolic representation of a chemical reaction.
Putting chemical changes into words and symbols

54. The burning of methane gas in oxygen is represented as follows:
Equation Example:
The burning of methane gas in oxygen is represented as follows:
CH4 + 2 O2 → CO2 + 2 H2O
Note: The arrow stands for “yields”. So if you put this into words you would say that one molecule of methane added to two molecules of oxygen gas reacts and yields one molecule of carbon dioxide and two molecules of water.

55. Reading Chemical Equations
Each side of an equation represents a combination of chemicals.
The combination is written as a set of chemical formulas, separated by + symbols.
CH4 + 2 O2 → CO2 + 2 H2O
Coefficient

56. Reading Chemical Equations
The two sides of the equation are separated by an arrow.
Reactants: The combination of chemicals before the reaction are on the left side of the arrow
Products: The right side indicates the combination of chemicals after the reaction.
CH4 + 2 O2 → CO2 + 2 H2O
Reactants
Products

57. For Example:
Na + O2 → Na2O
In this reaction, sodium (Na) and oxygen (O2) react to make a single molecule, Na2O

58. Balancing Equations
The Law of Conservation of Matter states that in a chemical reaction, the quantity or amount of each element does not change.
This means that each side of the equation must represent the same quantity of each element; in other words have the same number of each kind of atom.
The law of conservation of mass (the Lomonosov-Lavoisier law) states that mass cannot be created or destroyed, but can change its form.

59. Example: Na + O2 → Na2O Balancing Equations
In order for this equation to be balanced, there must be an equal amount of Na on the left hand side and on the right hand side. Right now, there is 1 Na atom on the left but 2 Na atoms on the right. We solve this problem by putting a 2 in front of the Na on the left hand side, Like this:
2Na + O2 → Na2O

60. 2Na + O2 → Na2O Balancing Equations
There are now 2 Na's on the left and 2 Na's on the right. But what about the O? We now must check to see if the O's are balanced on both sides of the equation. On the left hand side there are 2 O's and the right hand side only has one. This is still an unbalanced equation. To fix this we must put a 2 in front of the Na2O on the right hand side. Now our equation reads:
2Na + O2 → 2Na2O

61. 2Na + O2 → 2Na2O Balancing Equations
Notice that the 2 on the right hand side is "distributed" to both the Na2 and the O. Currently the left hand side of the equation has 2 Na's and 2O's. The right hand side has 4 Na's total and 2 O's. Again, this is a problem, there must be an equal amount of each chemical on both sides. To fix this let's add 2 more Na's on the left side. The equation will now look like this:
4Na + O2 → 2Na2O

62. Balancing Equations: Practice In Class
Balance the following equations with a partner:
H2 + O2 => H2O
Cs + N2 => Cs3N
CH4 + O2 => CO2 + H2O
C + SO2 => CS2 + CO
Na + Cl2 => NaCl
N2 + H2 => NH3

63. Check your Answers
2 H2 + O2 => 2 H2O
6 Cs + N2 => 2 Cs3N
CH4 + 2 O2 => CO2 + 2 H2O
5 C + 2 SO2 =>  CS2 + 4 CO
2 Na + Cl2 => 2 NaCl
N2 + 3 H2 => 2 NH3

64. Balancing Equations
Please work on the balancing equations worksheet. You should work INDIVIDUALLY and quietly. You may listen to your ipods if you are staying focused. Work will be collected at the end of class.