1. BIOCHEMISTRY

3. Note: 1) bonds repel each other so that there is the maximum space between them. 2) lone pairs also repel bonds as well as other lone pairs.

5.  Pure water never only contains only H 2 O molecules  Two H 2 O in every 550 million react with each other.

6.  Compounds other than water can increase or decrease [H 3 O+] or [OH-]  ACIDS ◦ Increase the concentration of H 3 O+ ions in a solution. ◦ Acidic solutions: sour taste, ability to conduct electricity. ◦ Contain at least one ionizable hydrogen atom.  BASES ◦ Increase the concentration of OH- ions in a solution. ◦ Basic solutions: bitter taste, slippery feel, conduct electricity. ◦ 2 reactions:  1) Ionic base containing OH- ion dissociate to produce OH-  2) Base not containing OH combines with H+ ions

7.  Pure water contains equal numbers of hydonium and hydroxide ions ◦ [H3O+] = [OH-]  Neutral  Neutralization reaction: ◦ Acid and base mixed

8.  Concentration of a solute in aqueous solution is measured in moles of the solute per litre of solutions  mol/L ◦ A mole is the amount of any substance that contains 6.02 x 10 23 particles of the substance. ◦ A [H 3 O+] of 2.0 mol/L contains __________________________________ H 3 O+ ions. ◦ A neutral solution has [H30+] = 1.0 x 10 -7 mol/L. ◦ The pH of an aqueous solutions is equal to the negative logarithm of the hydronium ion concentration.  Acidic solutions, 0 < pH < 7  Basic solutions, 7 < pH < 14

9.  Carbon ◦ Can form four covalent bonds ◦ Attach to each other to form strait and branched chains and ringed structures.  Hydrocarbons: contain only carbon and hydrogen  non-polar.  Functional groups: reactive clusters of atoms containing hydrogen, oxygen, nitrogen, sulfur, and phosporus. ◦ Attach to the carbon backbone.  Bonding Capacity: number of covalent bonds an atom can form.

12.  FGs are more reactive than the hydrocarbon portions of biological molecules. ◦ Eg. –OH and –COOH are polar due to the electronegative oxygen atom they contain. Therefore, sugars and alcohols are highly soluble in water. ◦ Eg. –COOH makes a molecule acidic. –NH 2 makes a molecule basic.

13. PP, page 27, #1

14. - Complex carbohydrates, proteins, and nucleic acids are polymers. - Lipids (triglycerides and phospholipids) are not polymers but are relatively large molecules composed of several smaller parts.

15.  For carbs, proteins, and Nas, the subunit can also be called a __________________.

16.  Anabolic Reaction: result in the construction of large molecules from smaller subunits. ◦ ‘formation’ ◦ Cells use this process to form proteins (ex//cytoskeleton ( strength), carbohydrates (ex//membrane, glycogen for energy storage), lipids (ex//phospholipid bilayer), etc.  Condensation/Dehydration Synthesis: creates a covalent bond between two subunits, removing (forming) a water molecule in the process. ◦ An –OH group is removed from one subunit, an H is removed from another. OH + H  H 2 O. ◦ Process requires energy.

17.  Catabolic Reactions: reactions that break macromolecules into smaller units. ◦ ‘digestion’ ◦ Cells may use this process to break apart larger unusable macromolecules into their subunits in order to re-build them into functional/required macromolecules. (Lego)  Hydrolysis: water molecule is used to break a covalent bond holding subunits together. ◦ Release of energy

18. Hydrolysis and condensation require the assistance of special protein molecules called enzymes – more on enzymes later.

19.  Millions of tonnes are produced by plants and algae every year through process of ___________________________.  Functions: ◦ Sources/storage of energy for organisms. ◦ Building materials ◦ Cell surface markers for cell-to-cell identification.  Types (“saccharide”  sugar) ◦ Monosaccharide ◦ Oligosaccharides ◦ Polysaccharides

20.  “mono” + “saccharide”  single sugar.  Contain a single chain of carbon atoms to which hydroxyl groups and a carbonyl group is attached. ◦ Can be distinguished by  the carbonyl group they possess: aldehyde or ketone.  Aldoses: contain aldehyde  Ketoses: contain ketones.  Number of atoms in their backbone.  Pentose: five carbons  Hexose: six carbons.  Etc.

22.  Trioses ◦ Glyceraldehyde (intermediate compound in carbohydrate metabolism) ◦ Dehydroxyacetone (ingredient in sunless tanning products)  Pentoses ◦ Ribose (component of RNA) ◦ Ribulose (used in photosynthesis)  Hexoses ◦ The hexoses are isomers: contain same chemical formula but with a different arrangement of atoms. Possess different shapes and different physical and chemical properties.  Glucose (source of energy in cells)  Galactose (component of lactose, milk sugar)  Fructose (fruit sugar).

23.  Monosaccharides with five or more carbons are linear molecules in the DRY state.  Ring structure: when dissolved in water.  Ex// Glucose: carbons 1 & 5 react. ◦ Hydroxyl group at carbon 1: below plane of ring.  α – glucose ◦ Hydroxyl group at carbon 1: above plane of ring:  β - glucose

24. ◦ Contain two or three simple sugars.  Attached by special condensation rxn: glycosidic linkage.  Disaccharides: contain two monosaccharides.  Important dissacharides  Maltose: α–glucose + α–glucose (α 1-4 glycosidic linkage)  Found in grains – use in the production of beer.  “maltose”  Sucrose: α–glucose + α-fructose (α- 1-2 glycosidic linkage)  Table sugar  Use by many plants to transport glucose from one part of a plant to another.  Found in high concentrations in sugar cane, sugar beet, and sugar maple trees.  Lactose: α-glucose + α-galactose  Sugar found in milk.

26.  ‘complex carbohydrates’  Monosaccharide polymers  several hundred to several thousand monosaccharides. ◦ Energy storage and structural support. ◦ Starch: _________________________(amylose + amylopectin) ◦ Glycogen: _____________________________ ◦ Cellulose: _____________________________ ◦ Chitin: ________________________________

27. Amylose  Unbranched  α-glucose polymer  α 1-4 glycosidic linkages Amylopectin  Branched  α-glucose polymer  Main-chain: α 1-4 linkages  Brances: α 1-6 linkages Angles of glycosidic linkages causes polymers to twist into coils: insoluble in water. AMYLOSE + AMYLOPECTIN = STARCH

28.  Plants store the Sun’s energy mostly in the form of glucose by photosynthesis. ______________________________________________  Glucose is then broken down when energy is needed by the plant: for anabolism, catabolism (formation of proteins, carbs, other processes) ◦ Usually produce more glucose than needed. ◦ Enzymes link together glucose into amylose and amylopectin (polysaccharides), which mix to form starch.  Potato: “starchy”.  Roots in the winter: deciduous trees store energy in roots during the winter so when spring bloom arrives, they are ready to use energy to bud new leaves (beginning photosynthesis!)

30.  Heterotrophs use enzymes to hydrolyze amylose and amylopectin into individual glucose molecules and then respirate to extract energy to glucose: Cellular Respiration: ______________________________________________  Excess glucose molecules are linked to one another to form glycogen. Glycogen  Similar to amylopectin (same linkages and branched), but more branches.  Stored in muscle and liver cells.  Depleted in about a day if not replenished.

32. Cellulose  Primary structural polysaccharide of plants.  Major component of cell walls.  Most abundant organic substance on Earth.  Strait-chain polymer of β-glucose held together by β1–4 glycosidic linkages  Neither coiled nor branched.  Strait shape allows hydroxyl groups of parallel monomers to form many hydrogen bonds, producing microfibrils.

34.  Humans do not have the digestive enzymes able to break linkages between β-glucose subunits. ◦ Therefore, can not digest cellulose.  Animals such as cows, sheep, and rabbits can digest cellulose ◦ Symbiotic bacteria and protists in digestive tract produce enzymes that break the linkages.  Roughage ◦ Cellulose fibres – found in fresh fruit, vegetables, and grains – we are unable to digest. ◦ Pass through our DT undigested  scrape walls of DT  stimulates intestinal cells to secrete mucus  lubricates feces and aids in elimination of solid waste (decreases chance of back-up).

35. Chitin  Exoskeleton of insects and crustaceans and cell walls of many fungi.  Monomer is a glucose molecule with a nigrogen- containing group attached to carbon 2.  Second most abundant organic material found in nature.  Used in contact lenses and biochemical stitches.

38. PPs, page 34. # 2-10

39.  Hydrophobic – composed of H, C and O ◦ Insoluble in water but soluble in other nonpolar substances.  Functions ◦ Long-term storage of energy (more than twice the amount of energy in carbohydrates). ◦ In animals, excess carbohydrates are converted into fat and stored as droplets in the cells of adipose (fat) tissue. ◦ Thermal insulation: layer of fat under skin (penguins, polar bears, walruses, etc). ◦ Plants also store energy in the form of fat: triglyerides.  Main types: ◦ Triglycerides ◦ Phopholipids ◦ Sterols ◦ Waxes

40.  Made of: ◦ A glycerol (3-C molecule with three hydroxyl groups) ◦ Three fatty acids (long H chains containing –COOH)  Usually even number of Cs and around 16-18 C long.  Saturated FAs: all single bonds, max # H  Unsaturated FAs: one or more C=Cs, not max # H.

41.  Condensation reaction between glycerol and fatty acid: ester linkage.

45.  Examples: animal fats: butter and lard. ◦ Contain only saturated fatty acids. ◦ Strait hydrocarbon chains allow for many van der Walls attractions  Dipole-dipoles, dispersion forces  Solid consistency at room temperature.  More difficult to catabolize.

46.  Examples: plant oils: olive oil, corn oil, peanut oil. ◦ Bent at double bonds. ◦ Reduced number of van der Waals attractions. ◦ Liquids at room temperature. ◦ Hydrogenation: process of adding hydrogen atoms to double bonds in unsaturated triglycerides to form semisolid material (margarine).

47.  Glycerol molecule + two Fas + highly polar phosphate group. ◦ Polar head (hydrophillic) ◦ Non-polar tails (hydrophobic).  When added to water, phospholipids form spheres called micelles. ◦ Hydrophyllic heads orient themselves towards the water while the hydrophobic tails orient towards themselves.

48.  Separate two water compartments (extracellular fluid and cell’s cytoplasm/intracellular fluid). ◦ Heads can mix with water and tails can mix with one another in the center of the bilayer. ◦ Water/polar molecules: can not pass through bilayer due to the highly nonpolar center.  Proteins and hydrophillic pores form channels through which charged materials can pass.

50.  Also called steriods  Compact hydrophobic molecules containing four fused hydrocarbon rings and several different functional groups.  Cholesterol: important in cell membrane  aid in fluidity.  Cholesterol in bloodstream and diet rich in saturated fats  artherosclerosis. ◦ Fatty deposits (plaque): line blood vessels and block the flow of blood to tissues  Body tissue dies  Heart tissue: heart attack  Brain: stroke.  Other Sterols: ◦ Sex hormones: testosterone, estrogen, and progesterone.

52.  Long-chain fatty acids linked to alcohols or carbon rings.  Hydrophobic ◦ Waterproof coating on various plant and animal parts ◦ Cutin: wax produced by epidermal cells of plants, forming water-resistant coating on the surfaces of stems, leaves, and fruit  conserve water and barrier to infections. ◦ Birds: secrete waxy material to help keep feathers dry ◦ Bees: produce beeswax to construct honeycombs.

53. Pg. 40 #11-13, 15-18