1. Honors Biology “The Chemistry of Life” Chapter 2
This material is a quick review from your middle school science curriculum.

2. Important Root Words ROOT WORD MEANING Ad- Co- Hydro- -lysis To, near
Mono-
Di-
Poly-
-mer
Tri-
-saccharide
Iso-
In-
To, near
together
related to water
Split, loosen
one
two
consisting of many units
segment
consisting of three
sugar
Same, equal
Not, without
Important Root Words

3. General Atomic Structure
Proton  + (nucleus) Neutron  0 (nucleus) Electron  - (orbital)
Proton
Neutron
Electron
General Atomic Structure

4. ATOM vs. ELEMENT An atom is the smallest part of all matter.
Matter that contains only one kind of an atom is known as an element.
Examples of Elements:
C, H, O, P, N, Na, Cl
Each element is unique in the number of protons its atoms contain
An atom containing 6 protons is a carbon atom
An atom containing 8 protons is an oxygen atom
ATOM vs. ELEMENT

5. POSITIVE IONS vs. NEGATIVE IONS
When an atom loses or gains an electron it becomes an ion.
POSITIVE IONS vs. NEGATIVE IONS

6. MOLECULE vs. COMPOUND MOLECULES COMPOUNDS NaCl H2O O2 ---- EXAMPLES:
-2 or more atoms -2 or more different
bonded together atoms bonded together
EXAMPLES:
DO YOU SEE A PATTERN BETWEEN A MOLECULE AND A COMPOUND??
MOLECULES
COMPOUNDS
NaCl
H2O O2
----
MOLECULE vs COMPOUND

7. Comprehension Check
What is the difference between a molecule and a compound?
Would 2Fe be a molecule, a compound or neither?
What about O2?

8. Counting # of Atoms in a Compound
# of atoms = subscript # (if there is no # “assume” 1)
Ex: H2O
# Hydrogen atoms = 2 atoms
# Oxygen atoms = 1 atoms
TOTAL = 3 atoms
If there is a BIG number (coefficient) in FRONT of the element or formula, then distribute through all subscripts
Ex: 2H2O
# H atoms 2 x 2 = 4 atoms
# O atoms 2 x 1 = 2 atoms
TOTAL = 6 atoms
Counting # of Atoms in a Compound

9. Understanding Formulas and Equations
Write down everything you know about the following equation (for example: name the compounds involved, # of molecules, # of atoms in each molecule and the products/reactants):
C6H12O6 + O2  CO2 + H20
Understanding Formulas and Equations

10. 1. Compounds Involved 2. # of molecules 3
1. Compounds Involved 2. # of molecules 3. # of atoms in each molecule 4. Products 5. Reactants
Sugar, Carbon Dioxide, Water
1 Sugar, 1 Oxygen, 1 Carbon Dioxide, 1 Water
24 in Sugar, 2 in Oxygen, 3 in Carbon Dioxide, 3 in Water
Carbon Dioxide, Water
Sugar, Oxygen
C6H12O6 + O2  CO2 + H20

11. N2 + H2  NH3 Na + O2  Na2O C6H12O6  C2H5OH + 2CO2
Identify the products and reactants in the chemical equations and then balance each.

12. N2 + 3H2  2NH3 4Na + O2  2Na2O C6H12O6  2C2H5OH + 2CO2 ANSWERS:
REACTANTS  PRODUCTS
N H2  2NH3
4Na + O2  2Na2O
C6H12O6  2C2H5OH + 2CO2

13. Comprehension Check
Can you balance the equation below? C6H12O6 + O2  CO2 + H20 C6H12O6 + O2  6CO2 + H20 C6H12O6 + O2  6CO2 + 6H2O C6H12O6 + 6O2  6CO2 + 6H2O

14. SOLUTIONS (Solvent vs. Solute)
A simple solution is basically two substances that are going to be combined.
A solute is the substance to be dissolved (sugar).
The solvent is the one doing the dissolving (water).
As a rule of thumb, there is usually more solvent than solute.
SOLUTIONS (Solvent vs. Solute)

15. Hydrogen bond
Figure 2.10 Hydrogen bonds between water molecules.

16. WATER: The Universal Solvent
Water is a polar molecule
This electric charge allows the water molecule to "wiggle" its way between certain atoms in some molecules (salts).
WATER: The Universal Solvent

17. Ion in Salt solution crystal
Figure 2.14 A crystal of salt (NaCl) dissolving in water.
Ion in
solution
Salt
crystal

18. Comprehension Check
Why is water the universal solvent?

19. pH scale Acid: more H+ Neutral : equal amounts of OH- and H+
Oven cleaner
Acid: more H+
Bleach
Ammonia solution
Each step up the scale means that there is 10x more H+ or OH- than the next step.
What type of scale is this????
Soap
Sea water
Human blood
Neutral : equal amounts of OH- and H+
Neutral
Pure water
Milk
Normal
rainfall
Acid rain
Increasingly Acidic
Tomato
juice
Lemon juice
Base: more OH-
Stomach acid

20. ACIDS BASES The more H+ ions, the stronger the acid.
Compounds that break apart in water to form a hydrogen ions (H+).
Compounds that break apart to form a negatively charged hydroxide ions (OH-) in water.
The more H+ ions, the stronger the acid.
The more OH- ions, the stronger the base.
ACIDS BASES

21. The blood of humans is so sensitive to H+ concentration that a small change from your normal pH of 7.4 can result in your death. Buffer systems regulate this using weak acids and weak bases.
Why is pH important?

22. Comprehension Check
How can we test to find if a solution is an acidic or basic?
What can pH tell us about a solution?

23. Activation Energy is the minimum amount of energy needed to start a reaction
A substance known as a catalyst can help lower activation energy
An enzyme is a special kind of catalyst
Starting a Reaction

24. CHEMICAL CHANGE vs. PHYSICAL CHANGE
Chemical Change: a reaction where the products can NOT return to their form as reactants
Example: Log + Fire  Ashes
Physical Change: a reaction where the products can return to their form as reactants
Example: Ice + Heat  Water
ALWAYS ASK YOURSELF “Can I go back to the original?”
CHEMICAL CHANGE vs. PHYSICAL CHANGE

25. Vaporization of Dry ice (physical) Boiling water
Frying an Egg
(chemical)
Vaporization of Dry ice
(physical)
Boiling water
Burning Gasoline
Breaking Glass
(physical)
Souring Milk
(chemical)
Compression of a spring
Determine whether these are physical or chemical changes:

26. Comprehension Check
What is the difference between a physical and a chemical change?
Which reaction has a lower activation energy, the melting of an ice cube or the frying of an egg?

27. Chapter 3 -- Biochemistry
Honors Biology
This is new content that you did not learn in middle school!

28. Compounds Important to Life
Organic Compounds
Compounds derived from living things and containing carbon
Most common organic compounds in living things classified in four groups
Carbohydrates
Fats (Lipids)
Proteins
Nucleic Acids
Inorganic Compounds
Compounds derived from non-living things
Some inorganic compounds are essential for life:
Water
Carbon dioxide
Nitrogen compounds
Minerals
Vitamins

29. Carbon (Organic) Compounds
Carbon links readily with other atoms (it has 4 bonding sites to form covalent bonds), it forms the backbone upon which other atoms can build.
Carbon also bonds to other carbon atoms forming chains, rings or branched chains.
**All of these compounds are isomers because they have the same number of atoms, but different structures!**

30. Comprehension Check Which set of molecules below would be isomers?  

31. Hydrogen Bonds
Hydrogen bond: forms when a hydrogen atom covalently bonded to one electronegative atom is attracted to another electronegative atom
This is a bond BETWEEN molecules (different from polar covalent bond)
Intermolecular forces
FON, DNA, folding in protein H O N
Hydrogen Bonds Video

32. Are inorganic compounds important?
Life first evolved in water and most life on this planet lives in water.
Plants and animals are 70%-90% water.
Pure water is rare
Because of all these facts, water is the most important inorganic compound
Water is polar
Water is the universal solvent
Most cellular activities take place in water
Adhesion/Cohesion
Stabilizing role within living organisms (high specific heat)
Expansion on freezing

33. Comprehension Check   
Assume the arrows in the models below indicate the “pull” of electrons in a particular direction. Using this information, determine which molecules are polar or nonpolar. Using this information, determine which would dissolve in water.   

34. Comprehension Check Is C02 an organic compound? Why or why not?
Are the hydrogen bonds between water molecules strong enough to make water a substance that is hard to heat?
Name 3 important chemical or molecular characteristics about water.
Which of the picture below is showing adhesion and which is showing cohesion?

35. Carbon Compounds Monomers Basic organic units which make up polymers
Compounds consisting of repeated linked units/monomers
Macromolecules are large polymer units
Example: Carbohydrates include both sugar (simple carbs or monomers) and starch (complex carbs or polymers)

36. Monomers  Polymers
Reactions between organic compounds either build monomers into polymers or break polymers into monomers.
Condensation Reaction (Dehydration Synthesis)
Occurs when two monomers are chemically combined and water is released
Example: 2 Amino Acids  1 Protein + H2O
Hydrolysis Reaction
Occurs when a polymer is broken down with the addition of water
A reversal of condenstaion
Example: 1 Disaccharide + H2O  2 Monosaccharides
Hydrolysis Animation

37. Glucose Glucose Maltose
Figure 3.5 Disaccharide formation by a dehydration reaction.
Maltose

38. Comprehension Check 1. Match the definition with the correct term.
A. Condensation
B. Hydrolysis
C. Monomer
D. Polymer
______ Large molecule that consists of many subunits called monomers
______ Identical or similar subunits of a polymer
______ Process of linking monomers to form a polymer
______ Loss of a water molecule between two monomers to form a covalent bond between the monomers
______ Breaking the covalent bond between monomers by adding a water molecule D. C. A. A. B.

39. Carbohydrates
Organic compounds that contain carbon, hydrogen and oxygen in a set ratio (CH2O: Hydrogen and oxygen are in the same ratio as water)
Monomers = Monosaccharide
Dimer = Disaccharides
Polymers= Polysaccharides
There are two main functions of carbohydrates:
Structure (arthropods-- glycogen and plants-- cellulose)
Energy

40. Carbohydrates Three groups of carbohydrates exist
Monosaccharide (monomers)
Examples: Glucose, Fructose, and
Galactose
General Form: C6H12O6
All three are isomers of one another
Disaccharides (dimer)
Two monosaccharides form in a condensation reaction forming a double sugar (12 Carbon Sugars)
General Form: C12H22O11 (why not exactly CH2O?)
Examples: Sucrose, Maltose, Lactose
Polysaccharides (polymer)
Complex molecule composed of three or more monosaccharides
Examples: Glycogen (Animal), Cellulose (Plant)

41. Comprehension Check
Imagine there were three different solutions on your desk. If you were to taste each solution, how could you decide if you were tasting a monosaccharide, disaccharide, or polysaccharide.
Which would be sweetest, a mono-, di-, or polysaccharide?
Using the concept of molecular structure, explain why polysaccharides taste different than monosaccharides?

42. Testing for Carbohydrates
Monosaccharide (Sugar)  Benedict’s Test
Add equal parts of the solution and benedicts
Heat for a few minutes
Bright Colors = Sugar Present
Polysaccharide (Starch)  Iodine Test
Add equal parts of the solution and iodine
If it turns black/dark purple there is starch present

43. Lipids
Fatty Compounds made up of carbon, hydrogen and oxygen (Fats, Oils and Waxes)
The monomers that make-up most lipids is called a fatty acid
Lipid polymers are a little different than the others, they are Made up of long straight hydrocarbon chain with a carboxyl group attached to one end
Important characteristics of lipids:
Do not dissolve in water
Store energy efficiently
Important functions of lipids:
Cell Membrane (Lipid Bi-layer)
Long term energy storage
Prevent Desiccation

44. Lipids Four kinds of lipid polymers exist: Triglyceride
Macromolecules which are composed of three fatty acid molecules attached to one glycerol molecule
Examples: Oils from plants (peanut, olive, corn), Fats from animals (butter, lard)
Phospholipids
two fatty acids and a phosphate group are attached to glycerol
Waxes
Long fatty acid chain joined to a long alcohol chain
Steroids/Blood Lipids (Cholesterol)
Lipids which are composed of four carbon rings
Considered lipids because they do not dissolve in water

45. Testing for Lipids Lipid (Fat) Test  Brown Paper Towel Test
Add and few drops of the solution to a BROWN paper towel
Wait for the solution to DRY
If it is transparent there is lipid present

46. Proteins
Organic compounds composed of hydrogen, oxygen, carbon and nitrogen
Monomers: Amino Acids
When amino acids link, they share a peptide bond and form a long chain called a protein
Basic Structure of a Protein:
There are two types of proteins
Dipeptide (Two amino acids bonded together)
Polypeptides (Long chain of amino acids)
Proteins can be both fibrous and globular
Examples: Hair, Spider Webs, Hemoglobin
TWO main functions of proteins:
Build body tissues
Form enzymes

47. Functional Groups
A cluster of atoms in a compound that influences the properties of that compound.
Example: hydroxyl group, phosphate group, carboxyl group, R group

48. More on functional groups
The functional groups are
Hydroxyl group—consists of a hydrogen bonded to an oxygen
Carbonyl group—a carbon linked by a double bond to an oxygen atom
Carboxyl group—consists of a carbon double-bonded to both an oxygen and a hydroxyl group
Amino group—composed of a nitrogen bonded to two hydrogen atoms and the carbon skeleton
Phosphate group—consists of a phosphorus atom bonded to four oxygen atoms
You may want to add the methyl group as a functional group because of its importance in methylating certain compounds. For example, a methyl group on DNA may affect expression of genes. Another example is the arrangement of methyl groups in male and female sex hormones to affect their shape and function.
Student Misconceptions and Concerns
1. General biology students might not have previously taken a chemistry course. The concept of molecular building blocks that cannot be seen can be abstract and difficult to comprehend for such students. Concrete examples from our diets and good images will increase comprehension.
Teaching Tips
1. A drill with interchangeable drill bits is a nice analogy to carbon skeletons with different functional groups. The analogy relates the role of different functions to different structures.
Copyright © 2009 Pearson Education, Inc.

49. Table 3.2 Functional Groups of Organic Compounds.

50. Test for Protein Protein Test  Biuret’s Test
Add equal parts solution and biuret
If the solution turns lavender then there is protein present

51. Comprehension Check
What type of organic compounds are these?

52. ENZYMES
Enzymes speed up chemical reactions and lower activation energy
3-Dimensional structure (what type of protein is this?)
Names usually end in –ase
Examples: Maltase, Amylase, Carbonic Anhydrase
Enzyme function can be regulated by temperature and pH
Enzymes can be reused over and over again!

53. Enzyme Activity
-Enzymes are very specific. The substrate must fit into the active site on the enzyme. (Enzyme-Substrate Complex)
-“Lock and Key Model” is often used to describe enzyme function:

54. Coenzymes Help substrates fit into the active site on the enzyme
REMEMBER: Vitamins are NOT proteins!

55. Comprehension Check What do enzymes have to do with activation energy?
Are vitamins an organic compound?

56. Nucleic Acids Nucleotides Three main types of nucleic acids:
Monomer unit of nucleic acids
Made up of phosphate group, five carbon sugar and a ring shaped nitrogen base
Three main types of nucleic acids:
DNA
Polymer that records instructions for the cell and transmits them from generation to generation
RNA
Polymer that reads instructions from DNA and carries them out
ATP
Molecule used to store/release energy in cellular reactions

57. Comprehension Check What is the major function of: Carbohydrates
Lipids
Proteins
Nucleic Acids
What is the advantage for organic compounds to consist of polymers built from smaller monomers?