1.  Protons (+), neutrons (0) and electrons (-)  Isotopes – same proton, different neutron number  Ionic bonds vs. covalent bonds (non-polar covalent and polar covalent)  Interaction of electrons determine bonding

3.  Sharing of valence electrons to create molecules  Non-polar covalent – electrons are shared equally  Polar-covalent – not shared equally (water molecule)  Double and triple bonds

5.  Weak bonds between molecules  Water molecules display H-bonding

6. Water and ammoniaWater with Water

7.  Water is cohesive - because of hydrogen bonds – because of polarity  Water has surface tension due to cohesion  Water displays capillary action due to adhesion, which allows it to crawl up tubes.  Ice is less dense than water, therefore it floats  Water heats and cools slowly because of high specific heat.  Water is a biological solvent  Water has high heat of vaporization

8.  pH scale  Acids – H +  Bases – OH- (alkaline)  Tenfold change – pH 3 is ten times more acidic than pH of 4

9.  Polymers - Large molecules made by chains of small molecules  Carbohydrates, Lipids, Proteins, Nucleic Acids are all polymers  Organic – contain carbon  Inorganic – no carbon (except for CO2)  Watch this videovideo  Functional groups – pg. 14

10.  Mono, di, poly saccharides  Glucose and fructose are monosaccharides  Dehydration synthesis yields a disaccharide – glycosidic linkage  Lose water  Hydrolysis breaks the bonds  Gain water  maltose= glucose + glucose  Lactose= glucose + galactose  Sucrose= glucose + fructose

12.  Starches - Carbohydrates stored by plants  Glycogen – Carbohydrates stored by animals in liver and muscle cells. Alpha glucose  Cellulose – forms the cell walls of plants and gives the plant structural support. Beta glucose  Chitin – exoskeletons of arthropods and cell walls of fungi. Beta glucose

14.  Lipids – Fats, oils, phospholipids, steriods  Nonpolar – they do not dissolve in water  Long term energy storage, insulation, and protection  Major component of the cell membrane  Glycerol molecule and 3 fatty acid chains – ester linkage  Unsaturated vs. saturated

16.  Amphipathic – hydrophilic head and hydrophobic tails

18.  Many uses in the cells and are integral in most every process in an organism’s body.

19.  Lose water  Dipeptide then polypeptide  Many polypeptides folded and twisted becomes a functional protein  Primary to tertiary structure  As polypeptide advances in structure, binding sites are formed

21.  Fibrous proteins

22.  Hydrophobic interactions between amino acids with nonpolar side chains cluster in the core of the pleated sheet or alpha helix.  Disulfide bonds between two cysteine amino acids also occur.

23.  Made up of two or more polypeptide chains.  Ex. Collagen and Hemoglobin

25. 1. Structural – keratin, collagen, silk 2. Storage – albumin in eggs 3. Transport proteins on cell membranes 4. Defensive – antibodies 5. Enzymes – regulate all chemical rxns. in the body

26.  Polymers of nucleotides - polynucleotides  Nucleotide – sugar, phosphate group, and nitrogen base  4 nitrogen bases – adenine, guanine, cytosine, thymine  DNA – double helix – deoxyribonucleic acid – deoxyribose sugar  RNA – single strand – ribonucleic acid – ribose sugar

27.  Single ring  Cytosine, thymine and uracil

28.  Adenine and Guanine  Double Ring

31.  Bioenergetics – our cells’ ability to release the energy in glucose, starch, and fat  We do this by chemical reactions catalyzed by enzymes  Exergonic reactions vs. endergonic reactions  Exergonic – nutrients being oxidized in the mitochondria  Endergonic – plants using CO 2 and water to form sugars  Activation energy – energy barrier that must be broken for exergonic rxns to proceed.

32. (a) Exergonic reaction: energy released, spontaneous (b) Endergonic reaction: energy required, nonspontaneous Reactants Energy Products Progress of the reaction Amount of energy released (  G  0) Reactants Energy Products Amount of energy required (  G  0) Progress of the reaction Free energy

33. Figure 8.8b Adenosine triphosphate (ATP) Energy Inorganic phosphate Adenosine diphosphate (ADP) (b) The hydrolysis of ATP

34. How the Hydrolysis of ATP Performs Work The three types of cellular work (mechanical, transport, and chemical) are powered by the hydrolysis of ATP In the cell, the energy from the exergonic reaction of ATP hydrolysis can be used to drive an endergonic reaction Overall, the coupled reactions are exergonic © 2011 Pearson Education, Inc.

35. Figure 8.9 Glutamic acid Ammonia Glutamine (b) Conversion reaction coupled with ATP hydrolysis Glutamic acid conversion to glutamine (a) (c) Free-energy change for coupled reaction Glutamic acid Glutamine Phosphorylated intermediate Glu NH 3 NH 2 Glu  G Glu = +3.4 kcal/mol ATP ADP NH 3 Glu P P i ADP Glu NH 2  G Glu = +3.4 kcal/mol Glu NH 3 NH 2 ATP  G ATP =  7.3 kcal/mol  G Glu = +3.4 kcal/mol +  G ATP =  7.3 kcal/mol Net  G =  3.9 kcal/mol 1 2

36.  Lower activation energy  Specificity  Active site binds substrate in lock and key fit – enzyme/substrate complex  Induced fit – when enzyme changes its shape to accommodate substrate  Enzymes are not used up in the reaction  Do not work alone – need co-enzymes like vitamins, iron, and magnesium

37. Figure 8.13 Course of reaction without enzyme E A without enzyme E A with enzyme is lower Course of reaction with enzyme Reactants Products  G is unaffected by enzyme Progress of the reaction Free energy

38. Figure 8.14 Substrate Active site Enzyme Enzyme-substrate complex (a) (b)

39. Figure 8.15-3 Substrates Substrates enter active site. Enzyme-substrate complex Enzyme Products Substrates are held in active site by weak interactions. Active site can lower E A and speed up a reaction. Active site is available for two new substrate molecules. Products are released. Substrates are converted to products. 1 2 3 4 5 6

40. 1. Temperature  Increasing temp. increasing rxn rate  Too much heat can damage the enzyme – denature  most human enzymes work at 37 degrees Celsius 2. pH 3. Enzyme concentration 4. Substrate concentration

41. Figure 8.16 Optimal temperature for typical human enzyme (37°C) Optimal temperature for enzyme of thermophilic (heat-tolerant) bacteria (77°C) Temperature (°C) (a) Optimal temperature for two enzymes Rate of reaction 120 100 80 60 40200 0 12 3 4 5 6 78910 pH (b) Optimal pH for two enzymes Optimal pH for pepsin (stomach enzyme) Optimal pH for trypsin (intestinal enzyme)

42.  Allosteric regions on an enzyme can be bound by inhibitors or activators  Allosteric sites are subject to feedback inhibition – where the product inhibits the rxn.  Competitive inhibition – when the allosteric inhibitor binds the active site of the enzyme  Non-competitive inhibition – when the inhibitor binds another site on the enzyme leading to a conformational change in the active site

43. Figure 8.17 (a) Normal binding(b) Competitive inhibition (c) Noncompetitive inhibition Substrate Active site Enzyme Competitive inhibitor Noncompetitive inhibitor

44. Figure 8.19 Regulatory site (one of four) (a) Allosteric activators and inhibitors Allosteric enzyme with four subunits Active site (one of four) Active form Activator Stabilized active form Oscillation Non- functional active site Inactive form Inhibitor Stabilized inactive form Inactive form Substrate Stabilized active form (b) Cooperativity: another type of allosteric activation

45. Figure 8.21 Active site available Isoleucine used up by cell Feedback inhibition Active site of enzyme 1 is no longer able to catalyze the conversion of threonine to intermediate A; pathway is switched off. Isoleucine binds to allosteric site. Initial substrate (threonine) Threonine in active site Enzyme 1 (threonine deaminase) Intermediate A Intermediate B Intermediate C Intermediate D Enzyme 2 Enzyme 3 Enzyme 4 Enzyme 5 End product (isoleucine)

46. Video on Enzymes Watch this videovideo