1. No journal today… Read This!
Turn in the “Properties of Water” white packet right away. It will not be accepted at the end of the hour.
Continue working on the “Molecules: List, Group, Label” activity. It is due tomorrow.
Double-check the directions to make sure that you didn’t skip anything!

2. Biology Journal 10/19/2015
The 4 molecules that IB wants us to be able to draw are glucose, ribose, a fatty acid, and an amino acid. Draw them! Try it from memory first! (look it up if you can’t remember)

3. What is a macromolecule?
Biology Journal 10/5/2015
What is a molecule?
What is a macromolecule?

4. Biology Journal 10/7/2015
On your list, group, label activity, there were several “fatty acids” that looked kind of like this? What are the chemical formulas of these molecules?

5. According to the IB Command Terms, what’s the difference between…
Biology Journal 10/8/2015
According to the IB Command Terms,
what’s the difference between…
label and annotate?
calculate and deduce?
Outline and design?

6. Biology Journal 10/12/2015
What do these prefixes mean? What could be some words that have these prefixes?
Mono-
Poly-
Bi-
Di-

7. Remember your rules for skeletal line drawings? Using those rules…
Biology Journal 10/16/2015
Remember your rules for skeletal line drawings? Using those rules…
what is the chemical formula for these molecules?

8. Biology Journal 10/13/2015
Label each of these molecules with terms we learned yesterday. (such as “disaccharide”, “polyunsaturated fat”…) 5 1 6 2 3 7 8 4

9. Enzymes, transport proteins, keratin,
Biology Journal 10/15/2015
Complete the table!
Molecule Type
Monomer
Dimer
Polymer
Examples
Carbohydrates
Starch…
Proteins
Monopeptide
(one amino acid)
Enzymes, transport proteins, keratin,
Lipids
(aka fats)
CH2
n/a
lipid

10. Monopeptide Dipeptide Polypeptide, Protein CH2 n/a lipid
Biology Journal 10/15/2015
Molecule Type
Monomer
Dimer
Polymer
Examples
Carbohydrates
Monosaccharide
Disaccharide
Polysaccharide, carbohydrate
Starch, lactose, glucose, ribose
Proteins
Monopeptide
(one amino acid)
Dipeptide
Polypeptide, Protein
Enzymes, transport proteins, keratin,
Lipids
(aka fats)
CH2
n/a
lipid
Fatty acids, triglyceride

11. Biology Journal 10/19/2015
The artificial synthesis of urea falsified the theory of “vital principal.” What was this theory? How was is falsified by the artificial synthesis of urea?
“I piss on your theory.”

12. Anabolism Both Catabolism
Biology Journal 10/19/2015
Compare and contrast anabolism and catabolism in a Venn diagram.
Anabolism
Both
Catabolism

13. Anabolism Both Catabolism
Builds polymers from monomers.
AKA synthesis
Biochemical reactions necessary in biology
Breaks down polymers into monomers.
AKA decomposition
Condensation reaction
makes H2O from –H and –OH
Involve the creation or splitting of H2O
Hydrolysis reaction
Splits H2O to replace –H and –OH
Happens when your body makes molecules
Happens when your body digests food you eat

14. → What kind of reaction is shown? Write out the reaction as words:
Biology Journal 8/25/2014
What kind of reaction is shown?
Write out the reaction as words:
Sucrose + _______ → ________ + _______
3. When might this reaction be happing in your life? → +
H2O +

15. Biology Journal 8/25/2014
What kind of reaction is shown? Catabolism (breaking down) through hydrolysis
Write out the reaction as words:
see below
3. When might this reaction be happing in your life? This happens whenever you eat sucrose (sugar)! → +
H2O +
sucrose water → fructose glucose

16. Biology Journal 8/27/2013
What is the name of the monosaccharides shown below? These 2 molecules bond in a condensation reaction to form a disaccharide called lactose. Show this reaction by circling the atoms that are “released” as water, and draw the product.

17. Biology Journal 8/27/2013
What is the name of the monosaccharide below? These 2 molecules bond in a condensation reaction to form a disaccharide called lactose. Show this reaction by circling the atoms that are “released” as water, and draw the product. → +
H2O +

18. What is a monomer? What is a dimer? What is a polymer?
Biology Journal 8/19/2014
What is a monomer? What is a dimer? What is a polymer?
glucose
lactose
starch

19. Biology Journal 8/20/2014
Label each drawing with its name. Annotate the pictures with a description of the elements found in them, and their relative amounts. (you don’t have to draw the pictures in your notebook, just write the names and describe them)
Fatty acid
Has 2 O’s (carboxyl)
Long chain of C’s and H’s
Glucose
General formula = CnH2nOn
Amino acid
Complex C and H structure
Has O’s (carboxyl)
Has N (amino)
R group can be many things
Ribose
General formula = CnH2nOn
Fatty acid (again!)

20. A chemical reaction occurs, synthesizing 5 glucose molecules.
Biology Journal 8/21/2014
A chemical reaction occurs, synthesizing 5 glucose molecules.
What is the name of this chemical reaction?
What is the name of the product?
What is the other product and how many molecules of it are made? H OH H OH H OH H OH
H2O
H2O
H2O
H2O
Condensation anabolism (building up)
starch or cellulose
4 H2O molecules are made

21. Topic 2: Molecular biology (21 hours)
2.1 Molecules to metabolism: Living organisms control their composition by a complex web of chemical reactions.
Nature of science: Falsification of theories—the artificial synthesis of urea helped to falsify vitalism.
Understandings:
Molecular biology explains living processes in terms of the chemical substances involved.
Carbon atoms can form four covalent bonds allowing a diversity of stable compounds to exist.
Life is based on carbon compounds including carbohydrates, lipids, proteins and nucleic acids.
Metabolism is the web of all the enzyme-catalysed reactions in a cell or organism.
Anabolism is the synthesis of complex molecules from simpler molecules including the formation of macromolecules from monomers by condensation reactions.
Catabolism is the breakdown of complex molecules into simpler molecules including the hydrolysis of macromolecules into monomers.
Applications and skills:
Application: Urea as an example of a compound that is produced by living organisms but can also be artificially synthesized.
Skill: Drawing molecular diagrams of (alpha-D and beta-D) glucose, D-ribose, a saturated fatty acid and a generalized amino acid (using R).
Skill: Identification of biochemicals such as sugars (mono- and di-saccharides), lipids (triglycerides and phospholipids, saturated and unsaturated) or amino acids (R groups do not need to be memorized) from molecular diagrams.
Skill: Food tests such as the use of iodine to identify starch or Benedict’s reagent to identify reducing sugars could be carried out.

22. Molecules to Metabolism Section 2.1

23. All of these represent the same substance: glucose
All of these represent the same substance: glucose. There are many ways of expressing the idea of a molecule.
C6H12O6
Chemical Formula
Lewis-stick drawing
Space-filling model
Skeletal-line Drawing
Ball and Stick model

24. Rules for Skeletal Line Drawings:
Skeletal Line Drawings are often used when representing large, complex biological molecules.
Rules for Skeletal Line Drawings:
Lines are covalent bonds
C’s are “corners” or “ends”
H’s attached to C’s are not drawn (remember: C makes 4 bonds)
Other elements, and H’s attached to them, are shown with their symbol
This is nicotine. What’s its chemical formula? H H C C C C H C H C H2 C H C C
C10H14N2 H2 H2

25. Rules for Skeletal Line Drawings:
Lines are covalent bonds
C’s are “corners” or “ends”
H’s attached to C’s are not drawn (remember: C makes 4 bonds)
Other elements, and H’s attached to them, are shown with their symbol
This is Cocaine. It can be turned into crack, with a bit of chemistry. What’s its chemical formula? H H H C C
C10H15N2 C C C C H2 C C H H C H

26. Rules for Skeletal Line Drawings:
Lines are covalent bonds
C’s are “corners” or “ends”
H’s attached to C’s are not drawn (remember: C makes 4 bonds)
Other elements, and H’s attached to them, are shown with their symbol
This is adrenaline, which is stored in your adrenal glands, and released as part of the “fight or flight response.” H C C C C H C H2 C C H C C H H3
C9H13NO3

28. Molecules to Metabolism Section 2.1

29. Molecules can be classified based on the number of repeating “parts.”
Monomer = 1
Dimer = 2
Polymer = 3 or more
glucose
lactose
starch

30. Lipids (aka fats) have repeating CH2 units
Lipids (aka fats) have repeating CH2 units. This gives them lots in energy (calories) in the numerous C-H bonds.
Most mammals (humans included), store their extra energy as the lipid triglyceride, shown below.

31. Saturated fats have the maximum number of H’s.
They are crammed, or “saturated” with H’s
Thus, they have the most calories
Animal fats are usually saturated.

32. Plant fats are usually unsaturated.
Unsaturated fats have one (monounsaturated) or more (polyunsaturated) double bonds.
With double bonds, there is fewer room for H’s
Thus, they have fewer calories, and are generally “healthier.”
Plant fats are usually unsaturated.

34. Condensation is the formation of water
What is condensation?
Condensation is the formation of water

38. Model how fatty acids and glycerol combine to form triglycerides through condensation reactions
OH + H =

39. Build Triglyceride through a condensation reaction!
Cut out the molecules
Label each molecule with a marker
“Chop” off the H and OH from the appropriate molecules, and attach them together.
Put the H and OH on a water drop. It’s H2O! Attach it to the molecule nearby, to show that water was created through this process.

40. Carbohydrates and Sugars
General formula of CnH2nOn
Monomer = sugar or monosaccharide
Polymer = carbohydrate or polysaccharide
Plants often store their extra energy as carbohydrates, rather than lipids.

41. Disaccharides Monosaccharides Polysacchardies
Sucrose = glucose + fructose
Monosaccharides
Lactose = glucose + galactose
Glucose
Polysacchardies
Starch = glucose + glucose +glucose + glucose…
Ribose
Galatose

42. Model how monosaccharides combine to form disaccharides through condensation reactions
OH + H =

43. Build Maltose through a condensation reaction!
Cut out the molecules
Label each molecule with a marker
“Chop” off the H and OH from the appropriate molecules, and attach them together.
Put the H and OH on a water drop. It’s H2O! Attach it to the molecule nearby, to show that water was created through this process.

44. Build Starch through a condensation reaction!
Cut out the molecules
Label each molecule with a marker
“Chop” off the H and OH from the appropriate molecules, and attach them together.
Put the H and OH on a water drop. It’s H2O! Attach it to the molecule nearby, to show that water was created through this process.
Make a starch polymer, consisting of 4 monomers!

45. Protein Long, specifically-shaped chains of amino acids.
Proteins do “almost everything” in living things. Ex: protein channels, receptors, enzymes, structural proteins, motor proteins…

46. Amino Acids
Have amine group (NH2 or NH3+), carboxyl group (COOH, or COO-), alpha carbon, and side chain (R).
Make polymers called polypeptides, or proteins.
Below are a few ways to draw the amino acid tyrosine.

47. There are 20 (or more, depending on how you count) amino acids used in the human body.

48. Generalized Amino Acid
(draw this picture)

49. This is an an amino acid. (this one is called asparagine)
R group
(in this case CH2CONH2)
Amine
(NH2)
Carboxyl
(COOH)
Alpha carbon
(the middle C where the R group is attached)

50. Build a Protein through Condensation!
A maximum of 4 students in a group.
(more than 4 names on a model will result in ½ credit)
Look at your sequence and ID the amino acids you need. Label each amino acid with a marker.
“Chop” off the H and OH from the appropriate molecules, and attach them together, show 1 molecule “drop” of H2O is made and attach it nearby.
Attach all of the amino acids in the correct sequence. Label what sequence number you have is on your model!

52. Molecules to Metabolism Section 2.1

53. Anabolism = building a polymer from monomers. Makes H2O (condensation)
Anabolism = building a polymer from monomers. Makes H2O (condensation). Requires energy. Ex: your body making hair, your body building muscle.
You may have heard of “anabolic steroids.” These are the drugs that athletes can use to increase muscle mass.

54. What does “dehydration” mean.

55. Sometimes condensation reactions are referred to as “dehydration synthesis.” why do you think that is?

56. Catabolism = Breaking down a polymer into monomers
Catabolism = Breaking down a polymer into monomers. Consumes H2O (hydrolysis). Produces energy. Ex: digesting a muffin, breaking down toxins.
Food breaking down is catabolism.
All living things to anabolism and catabolism at the same time; this simultaneous making and breaking down is called metabolism.

57. A chemical reaction occurs, synthesizing 5 monomers.
What could be two terms to describe this reaction?
What is the name of the reactants, and the product?
What is the other product and how many molecules of it are made? H OH H OH H OH H OH
H2O
H2O
H2O
H2O
Condensation or dehydration and anabolism or synthesis
Reactant = glucose (a monosaccharide, or sugar)
Product = starch (a polysaccharide, or carbohydrate)
4 H2O molecules are made

58. H2O H2O A chemical reaction occurs, breaking down a polypeptide.
What could be two terms to describe this reaction?
What are the names of the reactant and the products?
What is the other reactant, and how many are needed?
H2O
H2O
Splits!
Splits!
Hydrolysis (it splits H2O) and catabolism or decomposition
Reactant = polypeptide (or “protein” –though this would be a tiny protein)
Products = 3 monopeptides (or amino acids)
2 H2O molecules are reactants, and will be split (hydrolysis).

59. 2.1 Skill: Food tests such as the use of iodine to identify starch or Benedict’s reagent to identify reducing sugars could be carried out.
An Iodine Solution (yep, the element “I”) can be used to identify if starch is present.
Iodine
Solution +
Starch
Solution →
Positive
Test
Starch Test:

60. 2.1 Skill: Food tests such as the use of iodine to identify starch or Benedict’s reagent to identify reducing sugars could be carried out.
Benedict’s Reagent can be used to identify all monosaccharides, and many disaccharides. It must be mixed, then heated.
Benedict’s Reagent Test:

61. Hey everybody! Look, I made pee!
The theory that the molecules of living things (called “organic molecules”) came only from a special “vital principal” was proven false, when urea was synthesized artificially.
In 1828 Friedrich Wohler synthesized urea!
Urea was discovered in the 1720’s in urine.
Silver isocyanate
It was assumed to be a product of the kidneys.
Ammonium chloride
Hey everybody! Look, I made pee!
At the time, it was thought that these compounds could only be made with the help of a “vital principle”.
This “vital principle” causes the phenomena of life to happen, rather than chemical or physical forces.
If urea had been synthesized without a “vital principle” then other organic compounds could as well.

63. Drawing Molecules

64. Molecules can be represented in lots of different ways
Molecules can be represented in lots of different ways. Look at the following diagrams, they all represent the same thing. How?

65. Molecules can be represented in lots of different ways
Molecules can be represented in lots of different ways. Look at the following diagrams, they all represent the same thing. How?

66. 2.1 Draw a molecular diagram of alpha-D glucose, D-ribose, a saturated fatty acid, and a generalized amino acid (showing R group)
Glucose
C6H12O6

67. Ribose C5H10O5 We put the D in DNA
2.1 Draw a molecular diagram of alpha-D glucose, D-ribose, a saturated fatty acid, and a generalized amino acid (showing R group)
Ribose
C5H10O5
We put the D in DNA
DNA is deoxyribonucleic acid. A form of ribose with one fewer oxygen called “deoxyribose” is part of DNA’s structure.

68. 2.1 Draw a molecular diagram of alpha-D glucose, D-ribose, a saturated fatty acid, and a generalized amino acid (showing R group)
Saturated Fatty Acid

69. Generalized Amino Acid
2.1 Draw a molecular diagram of alpha-D glucose, D-ribose, a saturated fatty acid, and a generalized amino acid (showing R group)
Generalized Amino Acid

70. This is an an amino acid. (this one is called asparagine)
R group
(in this case CH2CONH2)
Amine
(NH2)
Carboxyl
(COOH)
Alpha carbon
(the middle C where the R group is attached)

72. Review Questions (discussion)

73. 1. Which structure represents an amino acid?
Question from Paper 1
Discuss with your partner. Agree on an answer and put it on your sheet.
1. Which structure represents an amino acid?

74. b. Generalized amino acid c. Generalized fatty acid
Question from Paper 1
Discuss with your partner. Agree on an answer and put it on your sheet.
2. Which molecule is:
a. ribose
b. Generalized amino acid
c. Generalized fatty acid
3. Discuss which two molecules are most similar.

75. 4. Which molecule represents ribose?
Question from Paper 1
Discuss with your partner. Agree on an answer and put it on your sheet.
4. Which molecule represents ribose?
5. What is the name of molecule B?
6. What is the name of molecule C?

76. 7. What kind of molecule is this? 8. Draw it and label its parts.
Discuss with your partner. Agree on an answer and put it on your sheet.
7. What kind of molecule is this?
8. Draw it and label its parts.

77. 9. What is the name of this molecule?
Discuss with your partner. Agree on an answer and put it on your sheet.
9. What is the name of this molecule?
10. List its parts (you don’t have to draw it)

78. 11. What kind of molecule is this?
Discuss with your partner. Agree on an answer and put it on your sheet.
11. What kind of molecule is this?

79. 13. Describe it’s structure in as much detail as you can.
Discuss with your partner. Agree on an answer and put it on your sheet.
12. Name this molecule.
13. Describe it’s structure in as much detail as you can.

80. → + + 14. What kind of reaction is shown?
Discuss with your partner. Agree on an answer and put it on your sheet. → +
H2O +
14. What kind of reaction is shown?
15. Write out the reaction as words:
Sucrose + _______ → ________ + _______
16. When might this reaction be happing in your body?

81. → A chemical reaction is shown below.
Discuss with your partner. Agree on an answer and put it on your sheet. →
A chemical reaction is shown below.
17. Name each reactant and product.
18. What kind of reaction is this?
19. Where should water be present in the reaction? How many molecules of water?

82. A chemical reaction occurs, synthesizing 5 monomers.
Discuss with your partner. Agree on an answer and put it on your sheet.
A chemical reaction occurs, synthesizing 5 monomers.
20. What could be two terms to describe this reaction?
21. What is the name of the product?
22. What is the other product and how many molecules of it are made?

84. Review Questions (Answers)

85. 1. Which structure represents an amino acid?
Question from Paper 1
1. Which structure represents an amino acid?

86. Generalized Fatty Acid
Question from Paper 1
Ribose
Generalized Fatty Acid
Generalized Amino Acid
2. Which molecule is:
a. ribose
b. Generalized amino acid
c. Generalized fatty acid
3. Discuss which two molecules are most similar in structure.
Ribose (II) and Glucose (III) are most similar because they are both monosaccharides.

87. Amino Acid Ribose Glycerol 4. Which molecule represents ribose?
Question from Paper 1
Amino Acid
Ribose
Glycerol
4. Which molecule represents ribose?
5. What is the name of molecule B?
6. What is the name of molecule C?

88. It’s an amino acid! 7. What kind of molecule is this?
R group
(in this case CH2CONH2)
Amine
(NH2)
Carboxyl
(COOH)
Alpha carbon
7. What kind of molecule is this?
8. Label its parts.

89. 9. What is the name of this molecule? 10. Label its parts
a. triglyceride
Carboxyl groups
3 Fatty acids
Glycerol
9. What is the name of this molecule?
10. Label its parts

90. 11. What kind of molecule is this?
It’s a lipid! Specifically, a phospholipid.
11. What kind of molecule is this?

91. 13. Describe it’s structure in as much detail as you can.
12. Fatty acid (monounsaturated)
13. It is a lipid, it has a carboxyl group (COOH), and it is monounsaturated (it has 1 double bond), which makes it have fewer calories than a saturated version.
12. Name this molecule.
13. Describe it’s structure in as much detail as you can.

92. → + + 14. What kind of reaction is shown?
15. Write out the reaction as words:
Sucrose + _______ → ________ + _______
16. When might this reaction be happing in your body?

93. Catabolic Hydrolysis → + + 14. What kind of reaction is shown?
sucrose water → ribose glucose
14. What kind of reaction is shown?
15. Write out the reaction as words.
16. When might this reaction be happing in your body?
This happens whenever you eat sucrose (white sugar)!

94. → A chemical reaction is shown below.
17. Name each reactant and product.
18. What kind of reaction is this?
19. Where should water be present in the reaction? How many molecules of water?

95. Catabolic Hydrolysis → 17. Name each reactant and product.
Monopeptide
(amino acid)
Monopeptide
(amino acid)
Dipeptide → +
H2O
Hydrolysis (1 H2O is split)
It “fills in” both monomers’ bonds
17. Name each reactant and product.
18. What kind of reaction is this?
19. Where should water be present in the reaction? How many molecules of water?

96. 20. Condensation anabolism (building up) 21. starch or cellulose OH H OH H OH H OH
H2O
H2O
H2O
H2O
20. Condensation anabolism (building up)
21. starch or cellulose
22. 4 H2O molecules are made
A chemical reaction occurs, synthesizing 5 monomers.
20. What could be two terms to describe this reaction?
21. What is the name of the product?
22. What is the other product and how many molecules of it are made?

98. Saturated Fatty Acid
Glucose
C6H12O6
Amino Acid
Glucose
Ribose
Glucose
Amino Acid
Saturated Fatty Acid