1. Chapter 6
Chemistry in Biology

2. Chapter 6.1 Atoms, Elements, and Compounds
Matter – anything that occupies space and has a mass.

3. Atoms, Elements, & Compounds
Atoms – the simplest particles of en element; the building block of all matter

4. Structure of Atoms

5. Structure of Atoms 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/shell

6. Structure of Atoms
Electrons constantly move around the atom’s nucleus in energy levels. These energy levels are sometimes referred to as shells or orbitals.
The electrons (-) are attracted to the protons (+).
Atoms contain an equal number of protons and electrons so the overall charge is ZERO

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

8. Elements in Living Things
Hydrogen (H)
Carbon (C)
Oxygen (O)
Nitrogen (N)
Calcium (Ca)
Magnesium (Mg)
Sodium (Na)
Potassium (K)
Phosphorus (P)

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

10. Biology Class Notes - October 3, 2006
The Periodic Table
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 model to the left represents an atom of which element?
How many electrons must be in the electron shells?
= neutron
= proton

11. Biology Class Notes - October 3, 2006
Atomically Speaking…
The Periodic Table
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

12. Practice 19 39 20 What is the atomic number of potassium?
What is the mass number of potassium?
How many protons does potassium contain?
How many neutrons does potassium contain?
(Mass number – Atomic Number = Neutrons)
How many electron does potassium contain? 19 39 20

13. Drawing an Atomic Model
Find the element’s ATOMIC NUMBER. This determines the number of protons and electrons.
Find the MASS NUMBER. Subtract the atomic number from the mass number to determine the number of neutrons.
How many protons, electrons, and neutrons are found in an oxygen atom?

14. Drawing an Atomic Model
Draw the PROTONS and NEUTRONS in the nucleus of the atom.
Place the electrons in the correct shell:
Draw the first shell around the nucleus and place TWO electrons in the first shell.
Draw the next shell and place up to EIGHT electrons in the second shell
If electrons remain, draw the third shell and place up to EIGHTEEN electrons in the third shell
Draw the model for an oxygen atom.

15. Oxygen Example Atomic Number is 8 Mass Number is 16 Protons - 8
Electrons - 8
Mass Number is 16
Neutrons – 8 (16-8 = 8)
8 P
8 N

16. Atomic Models Draw the following atoms in you notebook: Fluorine
Magnesium
Aluminum

17. Bill Nye Atoms Part 1 - http://www.youtube.com/watch?v=zbc85dv3ouk

18. Isotopes
Isotopes are atoms of the same element that have different numbers of neutrons.
Isotopes will have different mass numbers (isotopes have the same atomic number)
Isotopes react the same chemically
= 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.

19. 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.

20. Compounds
Elements combine to form more complex structures called compounds
Compounds are represented by their chemical formula
H2O
CO2
C6H12O6
NaCl
(subscripts show how many atoms of each element are in the compound)

21. Compounds Each compound has a specific ratio of elements
Physically and chemically different from the elements that make up the compounds
Cannot be broken down into smaller elements by physical means (may be broken down chemically)
Held together by chemical bonds

22. Chemical Bonds
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

23. Chemical Bonds
Atoms become more stable by losing electrons or attracting electrons from other atoms
This results in the formation of chemical bonds

24. (electrons are shared)
Two Ways to Bond
Covalent
Bonds
(electrons are shared)
Ionic Bonds
(attraction of a
charged atom)

25. Chemical Bonds Covalent Bond Ionic Bond
A chemical bond that forms when electrons are SHARED
Example: water
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

26. Covalent Bonds

27. Ionic Bond

28. Covalent Bonding Examples
Hydrogen and Chlorine

29. Covalent Bonding Examples
Carbon and Hydrogen
Nitrogen and hydrogen

30. Ionic Bonding Examples
Magnesium and Oxygen

31. Ionic Bonding Examples
Sodium and Oxygen

32. Ionic Bonding Examples
Calcium chloride

33. Chapter 6.2 Chemical Reactions
(until 3:45/8:00)

34. Chemical Reactions 4 Fe + 3 O2 2 Fe2O3
Process by which atoms or groups of atoms in substances reorganize into different substances
Involve the breaking and reforming of chemical bonds.
For example –
4 Fe + 3 O Fe2O3

35. Physical Change vs. Chemical Change
Physical change affects appearance, not composition. You have the same substance before and after the physical change.
A chemical change affects composition. You have a different substance after the chemical change.
How do you know a chemical change has occurred?
Clues:
Production of heat or light
Formation of a solid, liquid, or gas

36. Chemical Equations C6H12O6 + 6O2  6H2O + 6CO2
Scientists often use chemical equations to show what is happening during a chemical change.
C6H12O6 + 6O2  6H2O + 6CO2
The substances on the left side of the arrow are called the reactants.
They are reacting and are forming the substances on the right side, the products.

37. 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

38. Balanced Equation
According to the principle of conservation of mass, matter cannot be created or destroyed
So the number and types of atoms on each side of the equation must be balanced. (or 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

39. How to Balance an Equation
Step 1: Count the number of atoms of each element on both the product and reactant side. You can create a chart to help you.
Step 2: Determine which atoms are not balanced.
Element
Reactant Side
Product Side O C

40. How to Balance an Equation
Step 3: Balance one atom at a time, using coefficients. Start with atoms that appear only once in the reactants and only once in the products. Usually leave Hydrogen atoms followed by Oxygen atoms until last.
Step 4: After you believe that you have successfully balanced the equation, repeat Step 1, to be certain that mass conservation has been achieved.
Note: DO NOT Change subscripts in a molecular formula (i.e., 2 NaCl Na2Cl2 )

41. Balanced Equation
H2O2 H2 + O2 Na + Cl2 NaCl Zn + HCL ZnCl2 + H2 Fe + Cl2 FeCl2

42. Energy of Reactions
Activation Energy – minimum amount of energy needed to start a chemical reaction; energy needed for reactants to form products

43. Energy of Reactions Endothermic Exothermic Energy-Absorbing Reaction
Energy-Releasing Reaction
Products
Activation energy
Activation
energy
Reactants
Endothermic
Exothermic

44. Enzyme Tutorials Activation Energy and Enzymes - Overview –
Overview –
Sucrose Example -

45. Enzymes
Most chemical reactions proceed slowly since the activation energy is high
A catalyst is a substance that lowers the activation energy needed to start a chemical reaction
Enzymes are biological catalysts; enzymes are proteins

46. Enzymes

47. How Enzymes Work
Reactants, called substrates, bind to specific enzymes; the site where enzymes bind is called the active site
Once the substrate binds to the active site, it changes shape and forms the enzyme-substrate complex
The substrates react to form new products; the enzyme-substrate complex helps to break and form bonds

48. Example of Enzyme Reaction

49. Another View of Enzymes

50. Enzymes Many factors can affect enzyme activity such as: pH
Temperature
Concentration of substrates

51. Chapter 6.3 Water & Solutions

52. Water’s Polarity
Water molecules are formed by covalent bonds between 2 hydrogens and 1 oxygen atom
Since the electrons are more strongly attracted to the oxygen, the electrons spend more time near the oxygen nucleus
The unequal distribution of electrons gives oxygen a slight negative charge
Molecules with an unequal distribution of charges are polar molecules – they have oppositely charged regions
Slight Negative Charge
Slight Positive Charge

53. Water’s Polarity and Hydrogen Bonds
The two water molecules are brought together, their polar ends attract each other
This attraction between water molecules is called hydrogen bonding
It is a weak bond between the hydrogen of one atom and the oxygen of another
A water molecule can hydrogen bond with four other water molecules

54. Hydrogen Bonding in Water

55. Properties of Water
Physical property – properties that describe a substance without changing the identity of the substance.
Physical change – change that does not result in the production of a new substance, only the appearance of the substance
Chemical property – properties that describe how a substance changes into a completely different substance
Chemical change – change that results in the production of another substance

56. Water is COHESIVE and ADHESIVE
Properties of Water
Water is COHESIVE and ADHESIVE
Because of hydrogen bonding,
Water is attracted to other water molecules – this is called COHESION
Water is attracted to other surfaces – this is called ADHESION

57. Cohesion How many paper clips were added before the cup overflowed?
What did the water on the surface of the cup look like just before it overflowed?

58. Surface Tension
Tendency of water molecules on the edges of a water droplet to attract inward toward other water molecules thus producing a “skin”
Predict / Results
What will happen to pepper grains that are sprinkled on a cup of water?
What will happen to the grains when soap is added to the water?

59. Cohesion Causes Surface Tension

60. Adhesion

61. Adhesion (Capillary Action)

62. Temperature Moderation
Temperature is a measure of heat which is a form of energy
Water can absorb large amounts of energy as heat for its molecular size
Water has the highest specific heat of any common substance.
Specific heat is the heat required to raise the temperature of one gram of a substance one degree Celsius.

63. Effects of a High Specific Heat
Water can absorb/release a large quantity of heat without a large change in temperature
Moderates coastal climates
Reduces dramatic day-night temperature fluctuations

64. Evaporative Cooling
As water evaporates, the surface of the water that remains behind cools.
Principle behind sweating to maintain body temperature in land animals

65. Density of Ice
Angle of hydrogen bonds causes ice crystals to have lots of open space
Open space leads to low density
As a result, ice floats!
Ponds & lakes freeze from top to bottom.
Ice insulates deeper water from colder air.
Ice crystal
Liquid water

66. Water Expands When It Freezes
Properties of Water
Water Expands When It Freezes
Because of hydrogen bonding, water molecules separate when freezing and water becomes less dense
Extremely important for marine organisms

67. Solid Water (Ice)
Liquid Water

68. Mixtures
Two or more substances which are combined so that each substance keeps its own chemical identity.
Water combines to form many types of mixtures
Mixtures can be classified as
Homogeneous – a combination of substances that is uniform throughout or
Heterogeneous – a combination of substances that are physically distinct from one another

69. Mixtures Mixtures can be classified as
Homogeneous – a combination of substances that is uniform throughout or
Heterogeneous – a combination of substances that are physically distinct from one another

70. Homogenous Mixtures
Solution – A mixture in which one substance (the solute) is dissolved completely into another substance (the solvent) so that the two cannot be distinguished
Water is the universal solvent
Examples:
Salt in water
Powdered drink mix in water
Saliva

71. Water is the UNIVERSAL SOLVENT
Properties of Water
Water is the UNIVERSAL SOLVENT
Because water is polar, it can dissolve many substances
For example, NaCl

73. Homogenous Mixtures Same uniform appearance
Same composition throughout
Examples
Sugar water
Salt water
Water and vinegar
Air in the atmosphere

74. Homogeneous Mixture Solutions are a homogeneous mixture
There are two components of solution:
Solvent – a substance in which another substance is dissolved
Solute – the substance that is dissolved

75. Heterogeneous Mixtures
Suspension – heterogeneous mixture that contains fine solids or liquids that will settle out spontaneously
Example: sand in water
Colloid – heterogeneous mixture containing particles larger than solutes, but small enough to not settle out spontaneously
Examples: blood, fog, smoke, butter, paint, ink

76. Heterogeneous Mixture
Visibly different substances
Components remain distinct
Examples –
Vinegar and oil
Salad (lettuce, vegetables, croutons, etc.)
Sand and water

77. Acids and Bases WATER H2O ACIDS BASES
Substances that release H+ ions when dissolved in water
WATER H2O
Substances that release OH- ions when dissolved in water
ACIDS
BASES

79. pH Scale
H2O H+ + OH-
pH scale – measurement system used to indicate the concentration of H+ ions in a solution
pH scale ranges from 0-14
pH 7 is neutral and the concentration of H+ ions and OH- ions is equal
Acids – any compound that forms H+ ions in solution; contain pH values less than 7 (the lower the pH values, the higher the acidity)
Bases – a compound that produces hydroxide ions (OH-) in solution; contain lower concentrations of H+ ions than water and have pH value greater than 7
Buffers
weak acids or bases that can react with strong acid or bases to prevent sudden changes in pH
For example, to buffer a strong acid, you would add a weak base

80. The Building Blocks of Life
Chapter 6.4
The Building Blocks of Life

81. Organic Chemistry Organic compounds are those containing CARBON
Life forms are carbon-based and therefore considered organic

82. Organic Chemistry Carbon has FOUR electrons in its outermost shell
Therefore, carbon can form up to FOUR covalent bonds with other atoms

83. Macromolecules CARBOHYDRATES LIPIDS PROTEINS NUCLEIC ACIDS
Macromolecules – large molecules that form from joining smaller molecules together
The smaller molecules are called monomer
The larger molecules are called polymers
Four biologically important macromolecules:
CARBOHYDRATES
LIPIDS
PROTEINS
NUCLEIC ACIDS

84. Macromolecules Monomer – smaller molecule
Polymer – larger molecule formed by joining together smaller molecules

85. Biological Macromolecules
Group
Function
Carbohydrates
Store Energy
Provide structural support (cell wall)
Lipids
- Store energy
- Provide cellular barriers
Proteins
- Transport substances
- Speed up reactions
Provide structural support
Make hormones
Nucleic Acids
Store and communicate genetic information

86. Carbohydrates Chemical Composition
Made of Carbon, Hydrogen , and Oxygen
Ratio of 1:2:1
(# of C atoms: # of H atoms: # of O atoms) Or
(CH2O)2
Functions in Living Things
ENERGY!
Structural support (cellulose in plant cell walls or chitin in animal shells)
Structure
Monomers may be small carbohydrates like glucose or sucrose. These monomers are called monosaccharide
The monomers join to form large polymer called polysaccharides
Examples
Sucrose – table sugar
Cellulose – support of plant cell walls
Chitin – rigid support for animal shells (ex. lobster)

87. Carbohydrates Polymer
Monosaccharaides linked together to form larger molecules
2 linked together in a chain are called disaccharides
3 or more are called polysaccharides (starches)
Monomer - 3 – 7 CH2O molecules linked in a ring structure are a simple sugar or monosaccharide

88. Lipids Chemical Composition Made of Carbon, Hydrogen, and Oxygen
Higher ratio of Hydrogen to Carbon
Functions in Living Things
ENERGY storage
Provide barriers for cell (cell membranes)
Protective layers
Structure
Composed of several fatty acids attached to glycerol
Examples
Fats
Waxes – protective coating on leaves
Oils
Biological steroids

89. Lipids
Lipids have fatty acid tails that are made of carbon and hydrogen by single or double covalent bonds
Single Bond = Saturated Fat
Double Bond = Unsaturated Fat
More than one double bond is called a polyunsaturated fat

90. Proteins Chemical Composition
Composed of Carbon, Hydrogen, Oxygen, Nitrogen, and sometimes Sulfur
Functions in Living Things
Transport substances
Speed up chemical reactions
Hormones
Structural support
Structure
Monomers of proteins are amino acids
The monomers, amino acids, join to form long chains of proteins
Examples
Enzymes – speed up chemical reactions

91. Proteins Monomer is the amino acid
Polymer is the Protein – several amino acids are joined together by covalent bonds called a peptide bond

92. Nucleic Acids Chemical Composition
Composed of Carbon, Hydrogen, Oxygen, Nitrogen, and Phosphorus
Functions in Living Things
Store genetic information
Structure
Smaller monomers, called nucleotides, join together to form long polymers, DNA and RNA
Examples
DNA – stores genetic information
RNA – copies and transmit genetic information; help to make proteins

93. Nucleic Acids Monomer is the nucleotide Polymer is the nucleic acid
Nucleotide with 3 phosphate group is ATP
6 major nucleotides
Polymer is the nucleic acid
DNA and RNA