1. Welcome to Biology (SBI4U) University Preparation
Teacher: Ms. Karellas
Website: karellas.weebly.com

2. Course Outline Unit 1 - Biochemistry
Students will analyse the technological applications used in the food, pharmaceutical, and medical industries that affect biological processes and cellular functions. They will investigate how molecules and their chemical properties affect cellular processes and biochemical reactions. Students will demonstrate an understanding of the important structural and functional roles compounds play in the cells of all living organisms.
Unit 2 - Metabolic Processes
Students will investigate the chemical changes and energy conversions that occur in metabolic processes. They will demonstrate the ways in which an understanding of metabolic processes enables people to make informed choices with respect to a range of personal, societal, and environmental issues.
Unit 3 - Molecular Genetics
Students will demonstrate an understanding that DNA contains all the genetic information for any living organism. They will investigate how proteins control a wide variety of cellular processes. Students will assess the social, legal, and ethical implications of genetic research and biotechnology.
Unit 4 - Homeostasis
Students will demonstrate an understanding of the strict limits on the internal conditions that organisms can tolerate. The will investigate the ways in which organ systems that maintain homeostasis rely on feedback mechanisms. Student will explore the environmental factors that affect homeostasis.
Unit 5 - Population Dynamics
Students will demonstrate an understanding of how population growth follows predictable patterns. They will investigate how increased consumption of resources and production of waste is associated with population growth and results in specific stresses that affect Earth's sustainability. Students will assess technological developments that can contribute to or help offset the ecological footprint associated with population growth and the consumption of natural resources.

3. Unit 1: Biochemistry Introduction to Biochemistry:

4. Prior understanding
Elements are pure substances that cannot be broken down through chemical or physical methods, elements consist of only one type of atom, an atom is the smallest component of an element that retains the properties of that element
A compound is a pure substance composed of two or more elements chemically combined, there is a specific ratio of types of atoms
Atoms contain a nucleus with protons and neutrons, protons are positively charged and neutrons have no charge
The number of protons defines the element i.e. Carbon has 6 protons
Negatively charged electrons travel in orbits (energy levels) around the nucleus, loss or gain of an electron causes the formation of a charged ion, electrons in the outer orbits are referred to as valence electrons, negatively charged ions are anions, positively charged ions are cations
The number of electrons in an uncharged atom is the same as the number of protons
The number of protons and neutrons determines the mass number of the element i.e. Carbon – 12 has 6 protons and 6 neutrons

5. Complete the Diagnostic

6. Lesson 1: Chemistry in Living Systems
What is biochemistry?
BRAINSTORM
Biochemistry: the branch of science dealing with the chemical and physiochemical processes that occur within living organisms.

7. Organic Chemistry
What is the difference between organic and inorganic molecules? Organic molecules – usually contain CARBON and HYDROGEN Inorganic molecules – usually do not contain CARBON
In order to understand biochemistry, we have to have a basic understanding of organic molecules

8. Isotopes
elements that contain atoms with the same number of protons but different numbers of neutrons
the atomic number remains the same, the mass number changes
C-12 has a mass #12, 6 protons and 6 neutrons
C-13 has a mass # 13, 6 protons and 7 neutrons
C-14 has a mass # 14, 6 protons and 8 neutrons

9. C-12 makes up 99% of the carbon in nature, C-14 is a radioisotope that breaks down to release N-14, subatomic particles and energy
Radioisotopes decay in a predictable manner called the half-life (time taken for one half of the nuclei to decay)

11. Organisms take in radioactive carbon dioxide from the environment until the day they die but over time the radioactive carbon will decay but non- radioactive carbon will remain the same so the ratio of radioactive carbon to non-radioactive carbon can be used to date a specimen

12. Organic Elements and Bonding
electrons occupy volumes of space around the nucleus called orbitals or energy levels
2 electrons occupy the first energy level (1s orbital), electrons occupy the second energy level (2 in a 2s orbital, 6 in a 2p orbital)
the outermost s and p orbitals are valence orbitals, and the electrons in them are called valence electrons
the chemical behavior of elements is determined by these valence electrons

13. Organic Elements and Bonding
Atoms combine to make molecules.
The bonds between atoms of the same molecule (i.e. within the molecule) are intramolecular bonds.
DEMO 

14. Organic Elements and Bonding
The three types of intramolecular bonds are:
Non-Polar Covalent Bonds
Polar Covalent Bonds
Ionic Bonds

15. 1. Non-Polar Covalent Bonds
Bond formed by sharing a pair
of valence electrons between
two atoms.

16. 2. Polar Covalent Bonds
Bond formed by unequal sharing of a pair
of valence electrons between two
atoms.
One atom is slightly negative; one is
slightly positive (dipole)

17. 3. Ionic Bonds
Bond formed by transfer of electrons
from atom to atom.
This results in the formation of positive
cation, and negative anion. Ions are held
together by electrostatic attraction.

18. Ions are important in living systems:
H+ ions are important in cellular respiration
Na+ ions are part of transport mechanisms that enable molecules to enter cells
Ca+ ions are involved in nerve transmission

19. The Role of Electronegativity
Electronegativity is a measure of an atoms ability to attract a shared electron pair in a covalent bond
Each element in the periodic table has an assigned electronegativity number (EN) - the larger the number, the greater the greater the pull on the electron pair
The element with the greater EN has a partial (δ-) charge, the element with the smaller EN has a partial (δ+) charge

20. ∆En is the difference between the electronegativity number between two atoms participating in a covalent bond
Electronegativity values can be found on a periodic table.

21. Electronegativity difference
determines the BOND TYPE:
∆En = 0 is when atoms share electrons equally, nonpolar covalent
 ∆En > 0 < 1.7 – one atom attracts the electrons more than the other, polar covalent bond 
∆En > 1.7 or = 1.7 – electrons are gained by one atom, lost by the other, (anions and cations), ionic bond

22. ∆En ∆En ∆En
> > 4.2
Non-polar polar covalent ionic

23. EXAMPLE:
Bonds in Water (H2O)
Oxygen electronegativity = 3.44
Hydrogen electronegativity = 2.2
Difference – 2.2 = 1.24
Bond Type  Polar covalent
In a water molecule the oxygen is slightly negatively charged because it has a higher electronegativity

24. Learning Check!
Determine the type of bond:
KCl
CH4 H2

25. Learning Check! Determine the type of bond: a) KCl K – 0.9 Cl – 2.9
2.9 – 0.9 = 2.0 ionic bond
b) CH4
C – H – 2.1
2.5 – 2.1 = 0.4 non-polar covalent
c) H2
H – 2.1
2.1 – 2.1 = 0 nonpolar covalent

26. Organic Elements and Bonding
The bonds between molecule intermolecular bonds.
Weaker than intramolecular bonds
DEMO 
Two types of intermolecular interactions are particularly important for biological system: hydrogen bonding and hydrophobic interactions

27. Hydrogen bonding:
water is a polar molecule, attractions between (+) ends and (-) ends are called hydrogen bonds (see role of water)
FON

28. Hydrophobic interactions: non-polar molecules such as cooking oil and motor oil do not form hydrogen bonds, but in the presence of polar molecules such as water, they tend to clump together, extruding water.
These are referred to as hydrophobic (water fearing)
Polar molecules that form hydrogen bonds with water are said to be hydrophilic (water loving)
DEMO 

29. Why is WATER a special molecule?
Greater than 2/3 of body mass is water, lungs 90% water, bones 20% water, fat is 25% water
Controls body temperature, lubricates joints, shock absorber in brain and spinal cord and moisturizes surfaces
Polar covalent bonds and asymmetrical structure creates a highly polar molecule
Polarity of water allows it to form chemical bonds with other molecules (adhesion), itself (cohesion) and ions

30. ∆En ∆En ∆En
> > 4.2
Non-polar polar covalent ionic

31. Learning Check! Determine the type of bond: a) KCl K – 0.9 Cl – 2.9
2.9 – 0.9 = 2.0 ionic bond
b) CH4
C – H – 2.1
2.5 – 2.1 = 0.4 non-polar covalent
c) H2
H – 2.1
2.1 – 2.1 = 0 nonpolar covalent

32. POLAR vs. NON-POLAR BONDS
RECALL: Intramolecular vs. Intermolecular bonds
Electronegativity
Elements have varying electronegativity (EN):
i.e. how strongly an atom can attract electrons
Non-Polar Covalent Bonds: the atoms involved have similar electro negativities, so the electrons are equally shared.
(ex. H-H, O-O, C-H)
Polar Covalent Bonds: the atoms involved have different electro negativities, so there is unequal sharing of electrons. This results in a separation of charge.
(ex. O-H)

33. ∆En ∆En ∆En
> > 4.2
Non-polar polar covalent ionic

34. POLAR vs. NON-POLAR MOLECULES
*Polar bonds ≠ Polar molecule
*Non-polar bonds ≠ Non-polar molecule
Polar Molecules
If the molecule is asymmetrical and has polar covalent bonds, the molecule will also be polar (e.g. glucose)
These molecules are “hydrophilic” (water loving)
Non-Polar Molecules
Non polar molecules occur when a molecule has non-polar covalent bonds (e.g. C-H backbone) OR …
the polar covalent bonds are in a symmetrical arrangement (e.g. CCl4)
These molecules are “hydrophobic” (water hating)

35. Practice Questions:
1.Do the following groups contain polar or non-polar bonds?
-OH
-COOH
-NH2
-PO4
-CH2
2. Are the above groups hydrophobic or hydrophilic?
3. Are the following molecules polar or non-polar?
4. Why is this important for biology?
(e.g. glucose, phospholipids)

36. Practice Questions:
Do the following groups contain polar or non-polar bonds?
-OH (polar) (hydrophilic)
-COOH (polar) (hydrophilic)
-NH2 (polar) (hydrophilic)
-PO4 (polar) (hydrophilic)
-CH2 (non-polar) (hydrophobic)
Are the above functional groups hydrophobic or hydrophilic?
Are the following molecules polar or non-polar?
(polar) (non-polar)
Why is this important for biology?
(e.g. glucose, phospholipids)

37. Functional Groups – (aka reactive clusters)
What are functional groups and why are they important?
All the biological molecules we will be studying have important functional groups which determine their function and interactions in cells

38. With the exception of a few molecules (i. e
With the exception of a few molecules (i.e. carbon dioxide) compounds containing carbon are referred to as organic compounds. The organic molecules of importance to living organisms can be classified into groups – carbohydrates, lipids, proteins and nucleic acids.

39. Carbon
4 valence electrons can form 4 covalent bonds with other elements

40. attach to each other to form linear or branched or ring structures and therefore are the backbone of biological molecules
molecules with only carbon and hydrogen are hydrocarbons, non-polar due to the symmetrical arrangement of their bonds

41. other elements such as hydrogen, oxygen, sulfur, nitrogen and phosphorus may also attach to the carbon backbone to form functional groups

42. Functional Groups Group Chemical Formula Structural Formula Hydroxyl
-OH
Carboxyl
-COOH
Amino
-NH2
Sulfhydryl
-SH
Phosphate
-PO4
Carbonyl
-COH or -CO-
DO ON BOARD
Create Study Cards for each functional group to REVIEW and ASSESS your learning of today’s lesson.

43. Macromolecules of Life

44. MINDS-ON: Macromolecule Sorting Activity!
Get into groups of 4
Go to a station set up around the lab benches
Using your understanding of functional groups, sort the following molecules into the four categories of macromolecules (carbohydrates, lipids, proteins, and nucleic acids) – paste them on the sheet
First group to finish (correctly) gets a prize! 

45. Learning Goals: Understand the structure and function of carbohydrates
Understand that monosaccharides are the smallest structural unit of carbohydrates
List and describe the 4 types of carbohydrates: monosaccharides, disaccharides, oligosaccharides, polysaccharides
Demonstrate condensation and hydrolysis reactions for carbohydrates

46. Macromolecules of Life
What is a macromolecule?
Macromolecules:
A large molecule (polymer) made of many smaller structural units (monomers) linked together
1)Carbohydrates
2)Lipids
3)Proteins
4)Nucleic Acids

47. Macromolecules are assembled and disassembled in the same way:
Monomers  Polymer
(Condensation/Dehydration Synthesis Reaction)
anabolic reaction - large molecules are built from small subunits
energy is required
Water is released

48. Macromolecules are assembled and disassembled in the same way:
Polymer  Monomer
(Hydrolysis Reaction) – hydro -water; lysis -broken
catabolic reaction - large molecules are broken down into small subunits
energy is released
Water is used

49. Carbohydrates (CHO)

50. Carbohydrates (CHO) Used as sources of energy
What is the function of carbohydrates?
Used as sources of energy
-Glucose: primary source of energy
-Sucrose/Lactose: dietary sugars
Building materials
Cell surface markers for cell-to-cell communication

51. Carbohydrates Contain C, H, O in a 1:2:1 ratio
Formula: (CH2O)n (n = # of Carbons)
Sugar names end in –ose
Simple Carbohydrates:
- Monosaccharide and Disaccharide
Complex Carbohydrates
-Polysaccharide and Oligosaccharide

52. Simple Carbohydrates
Monosaccharides: the smallest structural unit (monomer) of a carbohydrate
E.g. C6H12O6 : Glucose, Fructose, Galactose

53. Monosaccharides are characterized by the number of carbons
i.e. ribose has 5 carbons, glucose has 6 carbons and by their functional group i.e. ribose, glucose and galactose have an aldehyde group while fructose has a ketone group
-molecules with 5 or more carbons are linear in dry state but will naturally form a ring structure in water

54. Numbering the Carbons
monosaccharides with the same chemical formula but different arrangement of atoms are called isomers
i.e. C6H12O6 is glucose, galactose and fructose

55. α-Glucose vs. β-Glucose
Hydroxyl group of carbon 1 can exist is alpha or beta form
When a glucose molecule forms a six-carbon ring…
50% chance the -OH will be below the plane (alpha) 50% chance the -OH will be above the plane (beta)

56. Simple Carbohydrates
Disaccharides: composed of two monosaccharides (monomers) joined through a condensation reaction, forming a glycosidic linkage (covalent bonds)
Glucose + Glucose = Maltose
Ex. Infant formula, Beer
Glucose + Fructose = Sucrose
Ex. Sugar cane, Table Sugar
Glucose + Galactose = Lactose
Ex. Milk

58. Disaccharides/Polysaccharides can be broken down through a hydrolysis reaction

59. Complex Carbohydrates
Oligosaccharides
3-10 monosaccharides linked
glucose + galactose + fructose = Raffinose
Found in beans, peas, lentils, broccoli,
asparagus
*Humans lack enzymes to digest oligosaccharides (causes bloating, cramps, gas)

60. Complex Carbohydrates
Polysaccharides
- > 10 monosaccharides linked
- Most are made up of hundreds of monosaccharides bonded together
- Types:
1. Starch: glucose storage in plants
2. Glycogen: glucose storage in animals
3. Dietary Fiber: not used for energy
-Cellulose: structural support in plants
-Chitin: structural support in organisms

61. Starch
A starch molecule contains hundreds of glucose molecules in either
branched chains: Amylopectin or
unbranched (coiled) chains: Amylose
Sources:
grains, dried beans, pasta, bread, potato

63. Glycosidic bonds in Starch
Coiled Branched

64. Glycogen Found in liver and skeletal muscles
Many branch points allows for rapid break down for glucose to be released and used for energy

65. Dietary Fiber
Group of plant polysaccharides that are not digested or absorbed in the human intestine; structural
Fibers: Cellulose, Chitin

66. Cellulose Structural support in plant cell walls
Also used by humans in
wood for lumber and paper, cotton and linen for clothing
Straight chain polymer of β 1-4 glycosidic linkages
Alpha form – starch/glycogen
Beta form – cellulose

67. Chitin
Structure support - exoskeleton of insects, crabs, lobsters, fungi cell wall
Also used in medicine: contact lenses, surgical thread

68. Homework:
Carbohydrates Worksheet
Have a great weekend! 

69. Triglycerides, Phospholipids, Sterols

70. Lipids Lipids: -composed of carbon, hydrogen, and oxygen atoms
-higher proportion of non-polar C-H (high energy) bonds makes lipids hydrophobic
What is the function of lipids?
Provides long-term energy storage, cushions organs, provides cell membrane structure, synthesis of hormones
Four types:
1) Triglycerides (fats)
2) Phospholipids
3) Steroids
4) Waxes

71. Fatty Acids ω α The building block (monomer) of lipids
Chain of carbon atoms
Carboxyl group (-COOH) at alpha (α-) end
Methyl group (-CH3) at omega (ω-) end ω α
Lipids yield double the amount of energy as carbohydrates per gram
Glycogen is more accessible to break down; carbs are used up before lipids are broken down

72. How are fatty acids characterized?
Based on:
Length of carbon chain
Saturation
Degree of Saturation
Location of double bonds
Hydrogenation
Orientation of hydrogen around double bond

73. Length of Carbon Chain Length of carbon chain:
- Short-chain fatty acids (<8 carbons)
- Medium chain fatty acids (8-12 carbons)
- Long chain fatty acids (>12 carbons)

74. Saturation Saturated fatty acids:
have only single bonds between C atoms
- contain maximum # of H atoms possible
Unsaturated fatty acids:
have one or more C-C double bonds
- fewer than maximum # of H atoms possible
- formed by removing H atoms from molecule
Example BECEL

75. Degree of Saturation Saturated fatty acid Monounsaturated fatty acid
Single carbon-carbon atoms
Solid at room temperature
Examples?
Monounsaturated fatty acid
1 double bond
Thick liquid at room temperature
Polyunsaturated fatty acid (must be obtained through diet)
> 2 double bonds
Liquid at room temperature

76. Location of double bonds
Omega number (where the 1st double bond is located relative to the methyl-end)
Example: Omega-3 and Omega-6 fatty acids

77. Hydrogenation
Double bonds carry a slightly negative charge, and can accept positively charged hydrogen atoms to create a saturated fatty acid
Polyunsaturated fatty acid
H+ H+ H+ H+
Example: Margarine……
Hydrogenated (saturated) fatty acid

78. Orientation of Hydrogen around Double Bond
Cis- double bond
Hydrogen atoms are on the same side of
the double bond
Trans - double bond
Hydrogen atoms are on opposite sides of double bond
Trans fats are used to extend the shelf life of processed foods, typically cookies, cakes, fries and donuts. Any item that contains “hydrogenated oil” or “partially hydrogenated oil” likely contains trans fats. Hydrogenation is the chemical process that changes liquid oils into solid fats. The tide is turning against trans fats. Since January 2006, all food manufacturers are required to list trans fat content on food labels.

79. Fatty acid deficiencies
Irritated & flaky skin
Gastrointestinal problems
Compromised immune system
Slow growth in children
Reproductive failure
Neurological and visual problems

80. 1)Triglycerides
Made up of 1 Glycerol and 3 Fatty Acids
ESTER BOND

81. Triglyceride Saturated fatty acid Mono-unsaturated fatty acid
Poly-unsaturated fatty acid

82. 2)Phospholipids In FOOD: Stabilizers in food Mayo and ice cream
Head is polar (hydrophilic) – glycerol, phosphate, choline
Tail is non-polar (hydrophobic) – fatty acids
In FOOD:
Stabilizers in food
Mayo and ice cream
Phosphatidylcholine = lecithin
Soy products
Polar Head; Non-polar Tails
1 Glycerol + 2 fatty acids + polar phosphate group + choline group

83. In water… Phospholipids form micelles Roles: Plasma membrane
Emulsifiers

84. 3)Sterols/Steroids
Four fused carbon rings with many different functional groups

85. Steroids can be synthesized in the body
Steroids can be obtained through diet
from plants and animals
only animals have cholesterol
(meat, eggs, fish, dairy products)
**NOT all sterols are cholesterol!**

86. Important Roles of Steroids
Bile acids
Precursor for the production of hormones
Cholesterol – found in cellular membranes (provides support and fluidity)
In medicine – used to reduce inflammation, skin ointments, found in inhalers to treat asthma
Anabolic Steroids (synthetic) – build muscle mass in people who have cancer or AIDS (misused by athletes!)

87. **Important for us because we build our steroid hormones out of cholesterol**

88. 4)Waxes
Lipids that contain long-chain fatty-acids linked to alcohols or carbon rings; solid at room temperature
Produced in plants and animals
Roles:
Cutin: produced by plants to form a water-resistant coating of the surfaces of stems, leaves and fruit; helps the plant conserve water
Birds: produce waxy material (to keep their feathers dry)
Bees: make beeswax to make honeycombs
Humans: earwax (protects the ear canal)

89. Negative Health Effects of Lipids
Heart disease
Cholesterol plaque deposits in the arteries of the heart (narrowed arteries)
Cancer
Breast cancer and Prostate cancer
Association not as strong as between fat intake and heart disease
Dietary fat may promote cancer once it has arisen (does not initiate it)
Obesity
- High fat food vs. high energy food (kcal from carbs)

91. Positive Health Effects of Lipids
Omega-3 Fats:
- Prevent blood clots
- Protect against irregular heartbeats
- Lowers blood pressure (especially for people with hypertension and atherosclerosis)

92. REVIEW: CARBS and LIPIDS
NlK0
Seatwork/Homework: Lipids Worksheet

93. Proteins

94. Learning Goals Understand the function of proteins
Identify and describe the structural units of proteins (amino acids)
Describe and draw condensation and hydrolysis reactions
Describe the four levels of protein structure
Apply understanding of protein structure to explain the process of denaturation

95. Proteins What is the function of proteins?
Speed up chemical reactions (catalysts), transport specific substances, provide structure, carry cellular messages, fight infection…and many more!

96. Proteins Amino acids: the building blocks (monomers) of proteins
The body uses 20 different types of amino acids to make proteins
Consist of:
Central carbon bonded to hydrogen
Amino group
Carboxylic group
R-group
***The R group determines the FUNCTION of the protein***

97. Types of Amino Acids
Polar – prefer an aqueous (water) environment; usually exposed on the surface of the protein
Non-polar – do not prefer aqueous environment; usually make up the core of the protein
Electrically Charged – positively or negatively charged; hydrophilic

99. Amino Acids Classification of Amino Acids in Nutrition:
8 Essential a.a.
- the body can NOT synthesize these
- must be obtained through diet
12 Non-essential a.a.
- The body can synthesize these from
other sources
TOTAL: 20 a.a.

101. Proteins – The peptide bond
Proteins are formed when amino acid (monomers) are linked together by peptide bonds
Proteins are broken down into amino acids by the addition of water to break peptide bonds

102. Proteins Dipeptide – 2 amino acids linked by a peptide bond
Tripeptide – 3 amino acids linked by 2 peptide bonds

103. Levels of Protein Structure
Primary
Secondary
Tertiary
Quaternary

104. Primary (1˚)Structure - Polypeptide
sequence of amino acids (aa) = polypeptide chain
Critical to final protein structure and function
Determines the chemical and physical characteristics of the protein
Sickle cell anemia – single error in aa sequence  affects folding  rigid, sticky, sickle-shaped red blood cells

105. Secondary (2˚) Structure – coils and folds
As amino acids are added to the polypeptide chain, it starts to fold along its length and hydrogen bonds form between elements of the amino acid backbone
Common patterns:
α- helix
β-folded sheets

106. 2 1 3 4 α-helix : Ex. Fibrous proteins such as α-keratin in hair
β-sheet: two parts of polypeptide lie parallel to one another
Ex. Proteins in silk used
by spiders to make webs 1 2 3 4

107. Tertiary (3˚) Structure
Strong forces of attraction and repulsion between the polypeptide & its environment force further folding into a tertiary structure
Interactions involve the R-groups:
Hydrogen bonds – polar side chains
Ionic bonds – charged side chains
van der Waals forces – non-polar R groups
Proline – natural kink (in α-helix or β-sheet)
Disulfide bridge – covalent bond between sulfur containing R groups

108. Strong stabilizer

109. Quaternary (4˚) Structure – the final shape
Two or more folded polypeptide subunits come together to make a functional protein
Physical and chemical environmental factors play a role (aq, pH, temp)
Example: Hemoglobin

110. Protein Folding
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111. Changes in 3D shape of protein
Caused by changes in :
Temperature pH
Ionic concentration
Protein Denaturation
Useful: Gastrin digestive enzyme works in stomach (low pH) and inactive in small intestine (high pH)
Dangerous: Prolonged fever above 39C can denature critical enzymes in brain  death

113. The body burns Carbohydrates Fat Protein
Not exclusive. All burned at the same time but in different amounts, in that order.

114. Seatwork/Homework
Macromolecule Chart
(complete – carbs, lipids, proteins)
Quiz on TUES: Carbs, Lipids, Proteins