1. ORGANIC MOLECULES & FUNCTIONAL GROUPS

2. VITALISM
Anything that was alive possessed a vital spark, while things that weren't
alive...didn’t.
So what is a vital spark?
Well, you can't see it, taste it, feel it, hear it, or smell it.
You can't capture it in a bottle or any other vessel; you can't transfer it from one object to another. You can't measure it or detect it. The only way to determine if an object had one was to determine if it was alive or not.
MECHANISM
Biologists don't believe that there are any substances or materials which are exclusive to living things.
What makes something alive is not what it's made of; it's how it's put together and what activities (i.e, chemistry) go on within its structures.

3. Characteristics of life
Response to the environment
adaptation
order
reproduction
Energy processing
regulation
Growth and development

4. Miller Urey Experiment
Demonstrated that organic compounds can be created by fairly simple physical processes from inorganic substances. The experiment used conditions then thought to provide an approximate representation of those present on the primordial Earth.

5. WHAT’S THE DIFFERENCE BETWEEN ORGANIC COMPOUNDS & INORGANIC COMPOUNDS?
ORGANIC INORGANIC

6. WHY IS CARBON SO SPECIAL?
The versatility of carbon: Makes possible the great diversity of organic molecules

7. Where does the source of carbon for all organic molecules come from?

8. Carbon Chains Form the Skeletons of Most Organic Molecules
What do you notice about these molecules?

9. Hydrocarbons Number of Bonds
(a) Methane
(b) Ethane
(c) Ethene (ethylene)
Molecular Formula
Structural Formula
Ball-and-Stick Model
Space-Filling Model H C
CH4
C2H6
C2H4
Name and Comments
Figure 4.3 A-C
Hydrocarbons
Have suffix –ane if single bonded.
Found in fossil fuels H O N C
Hydrogen
(valence = 1)
Oxygen
(valence = 2)
Nitrogen
(valence = 3)
Carbon
(valence = 4)
Figure 4.4
Number of Bonds
Carbon atoms can form diverse molecules by bonding to four other atoms

10. MOLECULAR SHAPE & FUNCTION
Shapes are determined by the positions of the atoms’ orbital.
Molecular shape is very important in living cells.
It determines how the molecules recognize & respond to each other.
If they are complimentary; they will bond

11. example

12. ISOMERS
COMPOUNDS THAT HAVE THE SAME NUMBERS OF ATOMS OF THE SAME ELEMENTS BUT DIFFERENT STRUCTURES. (THESE MOLECULES THEREFORE HAVE DIFFERENT PROPERTIES)

13. Both of the molecules below are C5H12
Why are there different forms of the same chemical formula?
Because carbon can bond to either hydrogen or another carbon
What would it take to make these molecules identical?
Breaking and reforming a covalent bond
What type of isomer are molecules that have more than 1 structural form?
Structural Isomer

14. LIGHTER FLUID
REFRIGERANT

15. Both of the molecules below are C2H4Cl2
cis
trans
Why are there different forms of the same chemical formula?
Because the H and Cl can bond in any order around the central carbon atoms
What would it take to make these molecules identical?
Rotation around the carbon-carbon double bond
What type of isomer are molecules that have double bonds & more than 1 geometric arrangement?
Cis-trans isomers/ geometric isomers

16. EX: A VISUAL PIGMENT IN OUR EYES CALLED RHODOPSIN
It changes shape when it absorbs light from the cis isomer to the trans isomer.
Process known as
“bleaching”
When you move from a
very bright environment
to a very dark.
There is too little light to stimulate your cones, & it takes a few min. for your bleached rods to become fully responsive again.

17. Both of the molecules below are CHIBrCl
dextro
levo
L isomer
D isomer
In what way are these molecules different from each other?
They are mirror images of each other
What would it take to make these molecules identical?
Breaking and reforming a covalent bond
What do we call these types of isomers?
Enantiomers

19. Functional groups
Are the chemically reactive groups of atoms within an organic molecule
THE COMPONENTS OF ORGANIC MOLECULES THAT ARE MOST COMMONLY INVOLVED IN CHEMICAL REACTIONS

20. NOTICE THE MOLECULES ON THE RIGHT.
THEY DIFFER ONLY IN THE FUNCTIONAL GROUP.
Produce differences in males vs females.

21. Creating your functional group poster
Functional Groups being presented:
-hydroxyl -carbonyl -amino
-carboxyl -sulfhydryl -phosphate
-methyl

22. Create a large visual aid that conveys the following information:
Draw your functional group
Describe the physical properties your functional group adds to a molecule.
Give the chemical naming suffix
List examples
Record any additional information associated with your functional group.
YOU HAVE 15MINUTES TO COMPLETE YOUR POSTER FOR PRESENTING

23. A Few Discussion Questions
Can a molecule have more than one functional group?
Which group(s) would change the pH of a solution? In what way?
Which of the functional groups would hydrogen bond?
Which groups are hydrophillic?
Yes, most do. EX: amino acids have both the amino group and the carboxyl group.
Carboxylic acids & amines (bases)
All of them
All of them…except methyl

24. Macromolecule Group Project

25. Carbohydrates (2 groups)
Monomer
Polymer
Chemical structural differences
Examples of each & why they are important
One group will present simple carbohydrates
One group will present complex carbohydrates
Glycosidic linkage

26. Lipids 3 major types What is different about each of them
Chemical structure differences
Saturated vs unsaturated
Examples of why/how they are important

27. Nucleic acids Monomer Polymer 2 types Chemical structure
Differences between them
Similarities between them
Examples of why/how they are important

28. Proteins Monomer Polymer Basic chemical structure of a monomer
What is different about the different about each type of monomer?
Examples and why/how they are important

29. WHAT IS THE DIFFERENCE BETWEEN A MONOMER & A POLYMER?

31. SYNTHESIS AND BREAKDOWN OF POLYMERS
Enzymes help
Dehydration (Condensation) reaction
To connect monomers together
A water molecule is released
One molecule gives up a hydroxyl group
& the other a hydrogen
Hydrolysis
Polymers are broken apart to monomers
A water molecule is added to split apart
the monomers
EX: Digestion

32. VARIOUS MONOSACCHARIDES
What do all of these sugars have in common?
They are made of one carbonyl group and several hydroxyl groups.
What’s the difference between the top row of sugars compared to the bottom row?
The top sugars have their carbonyl group at the end of the carbon skeleton & the bottom ones have their carbonyl group in the middle
Identify the difference between glucose & galactose.

33. What are the monomers used to form?
Disaccharides and polysaccharides

34. WHAT IS GLYCOSIDIC LINKAGE?
Where does the polysaccharide bond occur and how?
At an oxygen off the 1’ carbon using a dehydration reaction called glycosidic linkage.
WHAT IS GLYCOSIDIC LINKAGE?
Covalent bond between 2 monosaccharides through a dehydration reaction.
A water molecule is released
One molecule gives up a hydroxyl group & the other a hydrogen

35. 2 Different Structures of Glucose
Linear
Ring
Write down how the linear structure becomes a ringed structure. Be as specific as possible.
Why does this happen?
The ketone or aldehyde react with the hydroxyl group in aqueous solution

36. Carbohydrates Also referred to as sugars
Provide building materials and energy storage
Are molecules that contain carbon, hydrogen and oxygen in a 1:2:1 ratio
Are of two main types
Simple carbohydrates
Complex carbohydrates

37. WHICH OF THESE IS A MONOMER OF CARBOHYDRATE?
WHAT DO WE CALL THIS MONOMER?
HOW CAN YOU TELL?
Glucose
Carbohydrate monomers generally have molecular formulas that have some multiple of the unit CnHxOn in ratios of CH2O
WHAT IS THE CHEMICAL SUFFIX USED FOR CARBOHYDRATES?
-ose

38. Formed by a dehydration reaction
Simple Carbohydrates
Monosaccharide
Consist of one subunit
EX: glucose, fructose, galactose
Disaccharide
Consist of two subunits
EX: sucrose, maltose, lactose
Helps secrete lactose
Glucose
Chemical fuel for the body
Formed by a dehydration reaction
Makes fruit sweet
Sucrose
Type of carbohydrate transported from leaves to roots
Chemical formula: C6H12O6
Glycosidic linkage

39. Complex Carbohydrates
Consist of long polymers of sugar subunits
Few hundred to a few thousand
Also termed polysaccharides
Serve as energy storage and/or building material for structure and/or protection

40. Animals store energy in the form of glycogen, glucose polymer, in their liver and muscles.
Plants store energy in the form of starch which are made from many glucose molecules
Starch granules

41. Plants Use Cellulose in their Cell Walls to give them structure & protection
Primary component of plant cell walls. Most animals cannot digest this. Cows can.

42. We (humans) can eat & digest starch but we cannot digest cellulose. WHY???

43. It’s all about the linkage alpha vs beta
The hydroxyl group attached to the number 1 carbon is positioned either below or above the plane of the ring.
GLYCOSYLIC LINKAGE GIVE THESE CARBOHYDRATES DIFFERENT SHAPES:
Starch = helical
Cellulose= straight non branched
It’s all about the linkage alpha vs beta

44. Your body contains enzymes (amylase) that break starch down into glucose to fuel your body. But we humans don't have enzymes that can break down cellulose.
Some animals do:

45. Cellulose is a lot stronger than starch
Cellulose is a lot stronger than starch. cellulose is strong enough to make fibers from, and make rope, clothing, etc.
Cellulose doesn't dissolve in water the way starch will, and doesn't break down as easily.
This is a good thing… since our clothes are made of cellulose, wooden park benches and wooden houses would all dissolve after one good rain.

46. CHITIN Builds exoskeletons used by arthropods.
Fungi use this instead of cellulose for their cell walls.
GLUSOSE (beta) WITH A NITROGEN APPENDAGE

47. Lipids Large nonpolar molecules that are insoluble in water
They are NOT polymers but they are large molecules assembled from smaller molecules.
Three major types
Triglycerides
Phospholipids
Steroids

48. Triglycerides Used for long-term energy storage
Composed of three fatty acid chains (hydrocarbon tails) linked to glycerol
EX: Fats & oils

49. Types of fatty acids Fatty acids can be saturated or unsaturated
Most plant fats
Most animal fats

50. Saturated fats & Trans Fats:
Linked to coronary disease
Trans fats are worse than saturated fats.
Trans fats are produced artificially where saturated fats are natural
Denmark has banned trans fats in restaurants.

51. We need fat in our diet!! Why?
Essential fatty acids – Dietary fats that are essential for growth development and cell functions, but cannot be made by our body’s processes
Proper functioning of nerves and brain- fats are part of myelin- a fatty material which wraps around our nerve cells so that they can send electrical messages. Our brains contain large amounts of essential fats
Maintaining healthy skin and other tissues.  All our body cells need to contain some fats  as essential parts of cell membranes, controlling what goes in and out of our cells
Transporting fat-soluble vitamins A, D, E and K through the bloodstream to where they are needed
Forming steroid hormones needed to regulate many bodily processes

52. A GREAT SOURCE OF HEALTHY FAT TO EAT ARE THE OMEGAS
Prevent coronary heart disease
Prevent stroke
Prevent diabetes
Promote healthy nerve activity
Improve vitamin absorption
Maintain a healthy immune system
Promote cell development
MAIN FUNCTION OF FATS IS ENERGY STORAGE
-lipids store twice as much chemical energy as the carbohydrate.

53. Lipids are needed for thermal insulation

54. Phospholipids A modified fat
One of the three fatty acids is replaced by a phosphate and a small polar functional group
Essential to cells: they make up the cell membrane.

55. Steroids Composed of four carbon rings Examples: Cholesterol
Found in most animal cell membranes & in vertebrates it is synthesized in the liver
Male and female sex hormones
Progesterone, estrogen, & testosterone
The attaching chemical groups to the 4 carbon rings is what gives variety.

56. Nucleic Acids Serve as information storage molecules
Store, transmit and help express hereditary information
Long polymers of repeating subunits termed nucleotides
A nucleotide is composed of three parts
Five-carbon sugar
Nitrogen-containing base
Phosphate

57. The structure of a nucleotide
Nitrogenous bases
Pyrimidines: one 6 membered ring of carbon & nitrogen
Purines: 6 membered ring fused to a 5 membered ring

58. The sugar and the phosphates are covalently bonded.

59. How DNA differs from RNA

60. Nucleic Acids Two varieties Deoxyribonucleic acid (DNA)
Ribonucleic acid (RNA)
DNA
RNA
Sugar = Deoxyribose
Sugar = Ribose
Bases = A, G, C, T
Bases = A, G, C, U
Double-stranded
Single-stranded
Can’t leave the nucleus
Can travel outside the nucleus

61. Look at the ends of the DNA molecule
Space-filling model
Look at the ends of the DNA molecule

62. 5’ –ATTGCAATGGCTAGGGCCAATGC- 3’ 3’ -TAACGTTACCGATCCCGGTTACG- 5’
AMONG THE DNA SEQUENCE ARE GENES WHICH ARE CODES FOR SPECIFIC PROTEINS.
5’ –ATTGCAATGGCTAGGGCCAATGC- 3’
3’ -TAACGTTACCGATCCCGGTTACG- 5’
In the above DNA sequence the code is different
DNA is read in one direction (5’ to 3’)

63. Proteins Made up of subunits called amino acids
Nearly every dynamic function of a living being depends on proteins.
They are instrumental in almost everything we do.
Proteins
R Group
Made up of subunits called amino acids
There are 20 common amino acids, and they fall into one of four general groups
Six amino acids
Six amino acids
hydrophobic
hydrophillic
Five amino acids
Three amino acids

64. Polar and non-polar amino acids
Amino acids with non-polar chains are found in regions of proteins that are linked to the hydrophobic area of the cell membrane.
Amino acids with polar side chains are found in regions of proteins that are exposed to water.
Membrane proteins: create a hydrophillic channel in proteins through which polar substances can move.

65. Proteins Amino acids are linked together by peptide bonds
Amino group
Carboxyl group
Long chains of amino acids are called polypeptides

66. Protein Function Hemoglobin Actin & myosin insulin immunoglobulins
Contains iron that transports oxygen from the lungs to all parts of the body in vertebrates
Actin & myosin
Interact to bring about muscle movement
insulin
Hormone secreted by the pancreas that aids in maintaining blood glucose level
immunoglobulins
group of proteins that act as antibodies to fight bacteria & viruses
amylase
Digestive enzyme that catalyses the hydrolysis of starch

67. Types of Protein

68. Other Types of Protein

69. Protein Structure Determined by the sequence of its amino acids
There are four general levels
Primary
Secondary
Tertiary
Quaternary

70. Building a Protein
Go to the back and grab a blue toober and a bag of thumb tacks
Make sure your bag of thumb tacks have the following:
2 blue
2 red
2 green
3 white
6 yellow

71. Building a Protein
Take your 15 tacks and place them in any order along the toober. Just make sure they are equal distance from each other and they are on the same side.
Fold your protein so that all of the hydrophobic sidechains (yellow tacks) are buried on the
inside of your protein, where they will be hidden from polar water molecules.

72. Fold your protein so the acidic and basic (charged)
sidechains are on the outside surface of the protein and pair one negative sidechain (red tack) with one positive sidechain (blue tack) so that they come within one inch of each other and neutralize each other. This positive-negative pairing
helps stabilize your protein.

73. Continue to fold your protein making sure that your polar side-chains (white tacks) are also on the outside surface of your protein where they can hydrogen bond with water.
Last, fold your protein so that the two cysteine side-chains (green tacks) are positioned opposite each other on the inside of the protein where they can form a covalent disulfide bond that helps stabilize your protein.

74. Every toober had a different random sequence of tacks & therefore each toober folded into a different structure.
Some sequences were more easily folded than others.
The 30,000 proteins encoded by the human genome have been selected from an enormous number of possible amino acid sequences based on their ability to spontaneously fold into a stable structure that simultaneously satisfies these basic laws of chemistry.

75. Protein Structure Primary structure Secondary structure
The specific amino acid sequence of a protein
Secondary structure
The initial folding of the amino acid chain by hydrogen bonding
Tertiary structure
The final three-dimensional shape of the protein
Quaternary structure
The spatial arrangement of polypeptides in a multi-component protein

76. Protein Structure
Changes in a protein’s environment can cause a protein to denature
It loses its three-dimensional structure
And becomes inactive

77. Chaperonins aka Chaperone Proteins
Help newly-produced proteins to fold properly
Chaperone protein deficiencies may play a role in certain diseases
Cystic fibrosis and Alzheimer’s disease , Parkinson’s disease & mad cow disease

78. Protein Structure Proteins can be divided into two classes
1. Structural
Long cables
Provide shape/strength
2. Globular
Grooves and depressions
Enzymes
Fibrin
Silk
Keratin

79. ENZYMES
ORGANIC MOLECULES WHICH ACT AS CATALYSTS

80. Enzymes
Are proteins
So they are made up of ?
Somewhere in this protein is an area that’s designed to match a specific molecule = active site.
The molecule that matches the active site is called the enzyme’s substrate.

81. Enzymes Influence the rate of reaction
A set of reactants present with enzymes will form products at a faster rate than without enzymes.
Enzymes cannot force reactions to occur that would not normally occur
The enzymes role is to lower the energy level needed to start the reaction.
Enzymes lower the activation energy of reactions
Enzymes are not used up during the reaction

82. WHAT FACTORS MIGHT AFFECT ENZYME CATALYST REACTIONS?
ENZYME LAB TIME!!!