Chapter 2: The Chemistry of Life

1. Chapter 2: The Chemistry of Life 2.1 Nature of Matter: atom: smallest part/basic unit of matter 3 sub-atomic particles: Proton (+), Neutron (0), Electron(-) Element: pure substance …all the same type of atoms (about 26 elements compose all living things - most abundant are: C, H, O, N ) atomic # : # of protons atomic mass (mass number):protons + neutrons (ie..mass of nucleus)

2. Carbon Hydrogen Oxygen Nitrogen Sulfur Phosphorus Sodium Chlorine Potassium Calcium Manganese Flourine Helium Magnesium Aluminum Iodine Lead Silver Lithium Mercury What are the element symbols for…

3. 2.1 Nature of Matter continued Sodium Chloride Chlorine Sodium Isotopes: elements with different neutron # than a stable atom ex: 14C, 3H, 32P, 34S Radioactive Isotopes: have unstable nuclei – break down at a known rate, give off radioactive particles (gamma rays, etc) * Dangerous AND useful, too * ex: fossil dating, bone scans, GI series, chemotherapy Compound: substance formed by 2 or more elements in a fixed ratio • physical and chemical properties of compound are different than atoms composing the compound • Molecule: smallest unit of most compounds

4. BONDING PATTERNS: Na+ Cl– 0 1. Ionic bonds: attractions between ions of opposite charge • when atoms gain or lose electrons, ions are created 2. Covalent bonds: join atoms into molecules through electron sharing • when two atoms share one or more pairs of outer shell electrons CH4 = ?

5. Polar Covalent/Non-polar Covalent/ H Bonds 0 Non-polar Covalent: When covalently bonded atoms share electrons equally Ex: CO2 Polar Covalent: Electrons are shared unequally between atoms, creating a polar molecule Ex: H20 Hydrogen Bonds: weak bonds important in the chemistry of life • charged regions on water molecules are attracted to the oppositely charged regions on nearby molecules • Ex: water to water (cohesion)

6. 0 Why Water Supports All Life: 1. Cohesion (w+w) and Adhesion (w+other) • allows water to move from rootsleaves • some insects can walk on water due to cohesive surface tension • universal solvent – can dissolve more solutes than any other solvent 2. Moderates temperature (heat capacity): • takes a lot of energy to disrupt hydrogen bonds  water can absorb lots of heat without a large rise in temp • As water cools a slight drop in temp releases a large amount of heat • water molecules take energy with it when it evaporates  evaporative cooling

7. Mixtures: Solutions and Suspensions: Mixture: composed of 2 or more elements or compounds physically mixed, not chemically combined (ex: salt and sugar together) 2 types of Mixtures: a) Solution: where components are evenly distributed (ex: salt water) * water = solvent NaCl = solute * polarity of water allows it to dissolve ionic compounds and polar molecules (ex: salts, sugars, minerals, gases, other solvents like alcohol) b) Suspension: when materials don’t dissolve in water, but break up into tiny pieces which do not settle out (they are suspended by the moving water) * ex: blood (water has dissolved compounds, blood cells and other components (lipids) which remain suspended in mixture)

8. The chemistry of life is sensitive to acidic and basic conditions 0 Acid: a compound that forms H+ ions in solution Base: a compound that produces OH- (hydroxide) ions in solution Acidity or Alkalinity (base) is measured on the pH scale: • From 0 (most acidic) to 14 (most basic) • The pH of most cells is kept close to 7 (neutral) by buffers (substances that resist pH change) • Each step on pH scale is a factor of 10. (ex: pH 5 is 10x more acidic than?) Buffer: weak acid or weak base which can keep a pH stable ex: Bicarbonate: most important buffer in body- maintains homeostasis in blood When the number of H+ is equal to the number of OH-  water H+ + OH-  H20

9. 2.3 Organic Chemistry: The Chemistry of Carbon • “Organic”: must contain at least one carbon. CH4 = simplest organic molecule • Carbon has 4 valence electrons • Therefore, carbon will always make 4 bonds with other atoms • Carbon can bond with other carbons, form chains, rings • Ability to form millions of different compounds with other elements

10. The Four Macromolecules of Life The four main classes of biological molecules: 1. Carbohydrates (sugar, starches, cellulose) 2. Lipids (wax, fats, oils, steroids) 3. Proteins (muscle, hair, hormones, enzymes) 4. Nucleic acids (DNA and RNA) Macromolecule (polymer) made by joining many monomers (single unit) Polymerization: chemical rxn which joins monomers to make polymers

11. 2.3: Carbon CompoundsHow do macromolecules form from monomers? • Polymerization/Dehydration Synthesis - chemical rxn which joins monomers to make polymers • Dehydration - loss of water • Synthesis - creation of

12. 2.3: Carbon CompoundsHow do macromolecules get broken down to release energy? • Condensation/Hydrolysis - chemical rxn which breaks polymers to make monomers (releasing energy) • Hydro - water • Lysis - break

13. 1. CARBOHYDRATES: Monomer = Monosaccharide • Contain C, H, and O in a 1:2:1 ratio • Most end with “ose” • An animal’s main energy source • Carbs are burned first in the body • Monosaccharides: (C6H12O6): glucose, fructose, galactose • Disaccharides: (C12H22O11) sucrose, lactose, maltose • Polysaccharides: (complex carbohydrates) • A) glycogen (carb storage animal liver) • B) starch (carb storage in plants) • C) cellulose (cell walls, cotton) “roughage” • D) chitin (exoskeletons of arthropods)

14. 2. LIPIDS: Monomer = Fatty Acids * Mostly C and H atoms linked by nonpolar covalent bonds * Reserve energy-storage molecules (burned after carbs are gone) * Insoluble in water (polar) * Soluble in nonpolar solvents (ether) * More energy in lipids than in carbs - 9 cal/g Lipid vs. 4 cal/g Carb * Examples: triglycerides, phospholipids, steroids (cholesterol), waxes, oils, fats * Triglyceride = 3 fatty acids + 1 glycerol * Saturated Fats: all single bonds in chain - solid at room temp (ex: butter, lard) * Unsaturated fats: one or more C=C bond in chain - liquid at room temp (ex: all oils)

15. 3. NUCLEIC ACIDS: Monomer = Nucleotide • Nucleic acids (DNA and RNA) store and transmit genetic information • DNA = Deoxyribonucleic acid • RNA = Ribonucleic acid • Large macromolecules containing C, H, O, N, P • One nucleotide = 5-carbon sugar, phosphate (PO4-), nitrogenous base The sugars and phosphates are the backbone for the nucleic acid DNA’s sugar = deoxyribose RNA’s sugar = ribose

16. 4. PROTEINS: Monomer = Amino Acid • Essential to the structures and activities of life • Contain C, H, O, N (S, P) • 50% of your dry weight • examples of groups of proteins: 1. enzymes (amylase, sucrase, maltase, lactase) –ase ending 2. structural (collagen, elastin) 3. contractile (actin, myosin) 4. transport (hemoglobin, protein channels) 5. hormones (insulin)

17. AMINO ACID: Structure 0 Each amino acid has: • An amino group (-NH2) • A carboxyl group (COOH) • An R group, which distinguishes each of the 20 different amino acids * Each amino acid has specific properties based on the R-group * Peptide bonds link amino acids together  polypeptide (protein)

18. PROTEINS: 4 Levels of Organization Primary Structure: the sequence of amino acids in its polypeptide chain Amino acids are assembled into polypeptide chains according to instructions coded in the DNA. Secondary structure: the coiling or folding of the chain Tertiary Structure: the overall three-dimensional shape of a polypeptide – created when R-groups bond Quaternary Structure: the association of two or more polypeptide chains

19. 2.4 Chemical Reactions and Enzymes • Chemical reaction: process that changes or transforms one set of chemicals into another • Those chemicals that enter into a reaction are the “reactants”, those that are made are the “products” • Chemical reactions change the bonding patterns in the reactants • Energy is released or absorbed when chemical bonds are formed or broken during a reaction • Rxns releasing energy generally happen spontaneously • Rxns which absorb energy need energy to start them • Some energy releasing rxns need activation (input of )energy to get started

20. Enzymes are vital proteins that run biochemical rxns • Lower the activation energy (EA) of chemical reactions (they are catalysts) • The reactants they “work” on are called “substrates” • Most enzymes are named for their substrates with an “-ase” ending Ex: sucrase digests sucrose lactase digests lactose • VERY shape specific (“lock and key”) reaction with active site on enzyme (where substrate and enzyme join) One Enzyme : One Substrate • Enzymes have unique three-dimensional shapes so they can fit onto their specific substrate • Shapes determine function and which chemical reactions they can perform • All related to their 3-D folding pattern born from?

21. Factors Which Affect Enzyme Activity: • Temperature, salt concentration, pH, inhibitors • Enzyme inhibitors can alter enzyme function: • Competitive inhibitor: blocks active site, substrate can’t attach and remains unchanged • Non-competitive inhibitor: alters enzyme’s function by changing its shape • Many poisons, pesticides, and drugs are enzyme inhibitors Some food for thought: • Why do we put lemon juice on apples? • What is the purpose of a fever? • What happens when a raw egg hits a hot fry pan? • Why do we put produce/perishables in the fridge? • How does a Siamese cat get it’s color pattern?

22. GENES = Sequences of DNA 0 • DNA sequences spell out the amino acid sequences of proteins • Mutations in the DNA sequence  wrong amino acid sequence  wrong protein shape  no function • Ex: Lactose Intolerance : Mutations in lactase gene mutations in lactase amino acid chain sequence  defective lactase shape enzyme can’t fit onto lactose substrate  lactose does not get digested. Q: Why is it a big deal? A: If YOU don’t digest the lactose in your digestive tract, all the E.coli will…all of their waste made from eating all this food will leave you with cramps, bloating, and diarrhea…not fun! Lactase enzyme