Welcome to Biology SBI 4 U University Preparation

Welcome to Biology (SBI 4 U) University Preparation Teacher: Email: Website: Ms. Karellas georgia. karellas@yrdsb. ca karellas. weebly. com

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.

Unit 1: Biochemistry Introduction to Biochemistry: https: //www. youtube. com/watch? v=tp. BAmz. Q_ p. UE

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

Complete the Diagnostic

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.

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

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

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)

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 nonradioactive carbon can be used to date a specimen

Organic Elements and Bonding electrons occupy volumes of space around the nucleus called orbitals or energy levels 2 electrons occupy the first energy level (1 s orbital), 8 electrons occupy the second energy level (2 in a 2 s orbital, 6 in a 2 p 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

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

Organic Elements and Bonding The three types of intramolecular bonds are: Non-Polar Covalent Bonds 2) Polar Covalent Bonds 3) Ionic Bonds 1)

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

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)

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.

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

The Role of 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 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

∆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.

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

∆En ∆En 0 ---0. 5 -------> 1. 7 --------> 4. 2 Non-polar covalent ionic

EXAMPLE: Bonds in Water (H 2 O) Oxygen electronegativity = 3. 44 Hydrogen electronegativity = 2. 2 Difference 3. 44 – 2. 2 = 1. 24 Bond Type Polar covalent In a water molecule the oxygen is slightly negatively charged because it has a higher electronegativity

Learning Check! Determine the type of bond: a) KCl b) CH 4 c) H 2

Learning Check! Determine the type of bond: a) KCl K – 0. 9 Cl – 2. 9 – 0. 9 = 2. 0 ionic bond b) CH 4 C – 2. 5 H – 2. 1 2. 5 – 2. 1 = 0. 4 non-polar covalent c) H 2 H – 2. 1 2. 1 – 2. 1 = 0 nonpolar covalent

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

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

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

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

∆En ∆En 0 ---0. 5 -------> 1. 7 --------> 4. 2 Non-polar covalent ionic

Learning Check! Determine the type of bond: a) KCl K – 0. 9 Cl – 2. 9 – 0. 9 = 2. 0 ionic bond b) CH 4 C – 2. 5 H – 2. 1 2. 5 – 2. 1 = 0. 4 non-polar covalent c) H 2 H – 2. 1 2. 1 – 2. 1 = 0 nonpolar covalent

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)

∆En ∆En 0 ---0. 5 -------> 1. 7 --------> 4. 2 Non-polar covalent ionic

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. CCl 4) These molecules are “hydrophobic” (water hating)

Practice Questions: 1. Do the following groups contain polar or non-polar bonds? a) -OH b) -COOH c) -NH 2 d) -PO 4 e) -CH 2 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)

Practice Questions: 1. Do the following groups contain polar or non-polar bonds? a) -OH (polar) (hydrophilic) b) -COOH (polar) (hydrophilic) c) -NH 2 (polar) (hydrophilic) d) -PO 4 (polar) (hydrophilic) e) -CH 2 (non-polar) (hydrophobic) 2. Are the above functional groups hydrophobic or hydrophilic? 3. Are the following molecules polar or non-polar? (polar) 4. (non-polar) Why is this important for biology? (e. g. glucose, phospholipids)

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

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.

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

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

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

Functional Groups Group Chemical Formula Hydroxyl -OH Carboxyl -COOH Amino -NH 2 Sulfhydryl -SH Phosphate -PO 4 Carbonyl -COH or -CO- Structural Formula Create Study Cards for each functional group to REVIEW and ASSESS your learning of today’s lesson.

Macromolecules of Life

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!

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

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

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

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

Carbohydrates (CHO)

Carbohydrates (CHO) 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-tocell communication

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

Simple Carbohydrates Monosaccharides: the smallest structural unit (monomer) of a carbohydrate E. g. C 6 H 12 O 6 : Glucose, Fructose, Galactose

Numbering the Carbons • monosaccharides with the same chemical formula but different arrangement of atoms are called isomers i. e. C 6 H 12 O 6 is glucose, galactose and fructose

α-Glucose vs. β-Glucose 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)

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 -

Disaccharides/Polysaccharides can be broken down through a hydrolysis reaction

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)

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

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

Glycosidic bonds in Starch Coiled Branched

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

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

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

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

Homework: Carbohydrates Worksheet Have a great weekend!

Lipids Triglycerides, Phospholipids, Sterols

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

Fatty Acids The building block (monomer) of lipids Chain of carbon atoms Carboxyl group (-COOH) at alpha (α-) end Methyl group (-CH 3) at omega (ω-) end ω α

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

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)

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

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

Location of double bonds Omega number (where the 1 st double bond is located relative to the methylend) Example: Omega-3 and Omega-6 fatty acids 1 2 3 4 5 6 1 2 3

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+ Hydrogenated (saturated) fatty acid

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

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

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

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

2)Phospholipids 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 1 Glycerol + 2 fatty acids + polar phosphate group + choline group

In water… Phospholipids form micelles Roles: • Plasma membrane • Emulsifiers

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

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!**

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!)

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

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 waterresistant 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)

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)

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)

REVIEW: CARBS and LIPIDS https: //www. youtube. com/watch? v=H 8 W J 2 KENl. K 0 Seatwork/Homework: Lipids Worksheet

Proteins https: //www. youtube. com/watch? v=H 8 WJ 2 KENl. K 0

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

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!

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

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

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

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

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

Levels of Protein Structure Primary Secondary Tertiary Quaternary

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

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: Ø α- helix Ø β-folded sheets

α-helix : 2 3 1 4 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

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: Ø Hydrogen bonds – polar side chains Ø Ionic bonds – charged side chains Ø van der Waals forces – non-polar R groups Ø Proline – natural kink (in α-helix or β-sheet) Ø Disulfide bridge – covalent bond between sulfur containing R groups

Strong stabilizer

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, p. H, temp) Example: Hemoglobin

Protein Folding http: //www. youtube. com/watch? v=Pjt 1 Q 2 ZZVj. A

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

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

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