Chemistry of Life (continued)!

1. Chemistry of Life (continued)! • Chapter 4~ Carbon & The Molecular Diversity of Life • Chapter 5~ The Structure & Function of Macromolecules

2. Molecular Biology • Molecular biology explains living processes in terms of the chemical substances involved.

3. Nature of science: Falsification of theories—the artificial synthesis of urea helped to falsify vitalism. • Vitalism is the belief that living organisms possess a non-physical inner force or energy that gives them the property of life. • Thought that organic compounds could NOT be produced without this vital force. • In 1828, urea (an organic compound produced in the liver) was first synthesized artificially. • Since then, many other organic molecules have also been synthesized. urea

4. Organic chemistry • Organic vs. Inorganic • Organic = carbon compounds that are found in living organisms. Almost all carbon compounds are organic. • Inorganic = all compounds that do NOT contain carbon and CO2, carbonates, bicarbonates. • Life is based on carbon compounds (organic molecules) including carbohydrates, lipids, proteins and nucleic acids.

5. Why carbon? • Carbon is tetravalent (can form four covalent bonds) • This allows it to produce a great variety of stable organic compounds.

6. Metabolism • Metabolism is the web of all the enzyme-catalysed reactions in a cell or organism. • Anabolism = the synthesis of complex molecules from simpler molecules. • Catabolism = the breakdown of complex molecules into simpler molecules. • Discuss: when might these occur in an organism?

7. Polymers • Covalent bonding of monomers (subunits) • Condensation reaction (dehydration synthesis): • JOINS MONOMERS One monomer provides a hydroxyl group while the other provides a hydrogen to form a water molecule • Hydrolysis: bonds between monomers are BROKEN by adding water (digestion)

8. 2.3 Carbohydrates and lipids • Essential idea: Compounds of carbon, hydrogen, and oxygen are used to supply and store energy. • Specifically: • Carbohydrates • Lipids (especially fats)

9. Carbohydrates, sugars • MonosaccharidesCH2O = empirical formula • Examples: • Glucose (blood sugar) • Fructose (fruit sugar) • Galactose • Ribose (structural component in RNA) • Importance: • Produced by photosynthesis • Used in cellular respiration (to make energy) • Summary: Energy storage and release. • Note: also used to build structures...

10. Skill: Draw Glucose (alpha-D and beta-D) and Ribose • Ribose

11. Carbohydrates, sugars • Disaccharides • covalent bond between 2 monosaccharides • formula = C12H22O11 (why?) • How is this bond formed? • Examples: • Sucrose= glucose and fructose (transported by phloem in plants) • maltose= glucose and glucose • lactose (milk sugar)= glucose and galactose

12. http://pslc.ws/macrog/kidsmac/starlose.htm Carbohydrates, Polysaccharides • Chitin~ exoskeletons; cell walls of fungi; surgical thread

13. Compare Structures and Relate to Functions

14. Skill: Use of molecular visualization software to compare cellulose, starch and glycogen. • Do this at home! Use page 75 in text book as a guide (answer the questions in your head…) What major structural differences do you see? • http://biomodel.uah.es/en/model3/polisac.htm

15. Lipids • Fats, phospholipids, steroids, waxes • All lipids are Hydrophobic • FATS (Triglycerides) Structure: • 1 Glycerol condensed with 3 fatty acids • Non-polar C-H bonds in fatty acid ‘tails’

16. Types of fatty acids • Saturated – single bonds between all carbons in fatty acid (i.e. saturated with hydrogen). • Unsaturated (oils) – contain double bonds between carbons in fatty acid. • Monounsaturated= have only one double bond • Polyunsaturated = more than one double bond

17. Unsaturated fats continued…Cis vs. Trans Fatty acids • Cis= hydrogen atoms on the same side of the double bond • Typical natural isomer • Bend in fatty acid (Liquid at room temp) • Trans = hydrogen atoms on opposite sides of the double bond. • Produced by artificial partial hydrogenation of oils • No bend in fatty acid (solid at room temp)

18. Skill: Draw a saturated fatty acid O • General formula: • HO C (CH2)n CH3

19. Lipids, II • Purpose of fats • Energy storage • Organ cushioning • Thermal insulation

20. Comparing Carbs and Lipids in Energy Storage • Carbohydrates • Short term storage • Easier to digest (more rapid energy release) • Soluble in water (easier to transport in blood etc.) • Lipids • Long term storage • More energy per gram (lighter energy storage) • Insoluble in water so they do not cause problems with osmosis

21. Theory of knowledge: Fats and Health • There are conflicting views as to the harms and benefits of fats in diets. How do we decide between competing views?

22. Do this for homework: Read pages 83-86 and outline important points regarding the following in your notes: • Application: Scientific evidence for health risks of trans fats and saturated fatty acids. • Application: Evaluation of evidence and the methods used to obtain the evidence for health claims made about lipids. • Read this article (printed) • http://www.health.harvard.edu/staying-healthy/the-truth-about-fats-bad-and-good

23. Body Mass Index: Calculate • Units: kg m-2

24. BMI Nomogram

25. Practice Calculation of BMI • Calculate BMI for an individual with the following measurements • Height: 1.68 m • Weight: 86 kg • Answer: about 30 kg/m2 • Imagine what this individual might look like

26. BMI isn’t perfect • Darren Sproles

27. Other lipids…

28. Phospholipids • Structure is same as fat except 2 fatty acids and a phosphate group attached to glycerol

29. Steroids • Lipids with 4 fused carbon rings • Ex: cholesterol: • Used in cell membranes; • precursor for other steroids (sex hormones); • atherosclerosis

30. Thought question: • Describe how the hormone estrogen will enter cells to have its effect on cell function.

31. Proteins • Importance: • Have a very wide range of functions! • each one has a complex three-dimensional shape (conformation) • Monomer: amino acids (there are 20) ~ • 4 PARTS surrounding a central carbon: 1) amino group (NH2) 2) carboxyl group (-COOH) 3) H atom 4) variable group (R) • Variable group characteristics: Determine the amino acid properties. Ex. polar (hydrophilic), nonpolar (hydrophobic), acid or base

32. Skill: Draw a generalized amino acid

33. The 20 amino acids

34. Proteins (Forming Polypeptides) • Polypeptides (formed by condensation reaction) • peptide bonds~ covalent bond; carboxyl group to amino group • Skill: Be able to draw peptide bond formation!

35. Primary Structure • = The order of Amino Acids • Each type of protein has a unique primary structure of amino acids • This sequence will determine the 3-D conformation • Amino acid substitution: hemoglobin; sickle-cell anemia

36. Secondary Structure • Coils & folds (due to hydrogen bonds at regular intervals along molecule) • Alpha Helix: coiling; ex. keratin • Pleated Sheet: parallel; ex. silk

37. Tertiary Structure • Overall 3-D Shape (Conformation) of polypeptide. • contortions from R group bonding due to… • Hydrophobic interactions (nonpolar side chains) • disulfide bridges (strong covalent bonds between sulfhydryls of cysteine) • hydrogen bonds (between polar side chains) • ionic bonds (charged side chains)

38. Quaternary Structure • 2 or more polypeptide chains aggregated into 1 macromolecule • Ex. collagen • May involve binding of a prosthetic group to form a conjugated protein ( a protein with attached non-protein parts) • Ex. hemoglobin, glycoproteins etc. Note: • Chaperone proteins involved in helping other proteins to fold correctly.

39. Polar vs. Nonpolar Amino Acids • Review: What is the significance of polar and non-polar amino acids to protein structure and placement within membranes?

40. Functions of Proteins (incredibly diverse!) • General Functions of proteins: • Structural • Transport • Muscle contraction • Defense • Cell Adhesion • Tensile strengthening • DNA packaging • Hormones • Receptors • Catalysis (enzymes) • Etc.

41. Application: Functions of specific Proteins • Know these as examples: • Rubisco = carbon fixation during photosynthesis • Insulin = hormone that regulates blood sugar by signaling glucose uptake by cells • Immunoglobulins = Antibodies – specific immunity • Rhodopsin = pigment that absorbs light in rod cells of retina • Collagen = forms a strong mesh of fibers in body (in skin, blood vessel walls, ligaments, bones etc.) In humans makes up about ¼ of the protein in the body. • Spider silk = strong fibers for forming webs

42. Proteome • Proteome = all the proteins produced by a cell, tissue or organism at a given time. • Every individual has a unique proteome • One possible exception… make your hypothesis. • Identical twins (but even they can become different as they age)

43. Skip…not in new syllabus: Types of Proteins • Fibrous • Usually structural proteins • Usually insoluble • Shape (elongated) • Ex. Keratin, collagen, elastin • Globular • Variety of uses: transport, hormones, enzymes etc. • Often soluble • Shape (spheroidal) • Ex. Hemoglobin, insulin, immunoglobulins (antibodies)

44. Proteins continued: Enzymes • Enzymes=Catalytic proteins that change the rate of reactions w/o being consumed. Enzymes lower activation energy. • Activation Energy: The amount of energy necessary to start a reaction. (the E required to break bonds in reactants) • Substrate: enzyme reactant • Active site: pocket or groove on an enzyme that binds to substrate. (i.e. the spot on the enzyme where the reaction occurs) • Induced fit model: enzyme and substrate fit together, but enzyme conforms to substrate.

45. Enzymes control metabolic pathways: • chains and cycles of enzyme-catalyzed reactions! • Ex. Cellular respiration (glycolysis= a chain, Krebs cycle= a cycle…)

46. Effects on Enzyme Activity • Temperature • pH • Substrate concentration • Cofactors: inorganic, nonprotein helpers; ex.: zinc, iron, copper • Coenzymes: organic helpers; ex.: vitamins • Denaturation: a structural change in a protein that results in the loss (usually permanent) of its biological properties.

47. Enzyme Inhibition • Competitive: competes for active site, mimics the substrate • Ex. Penicillin and enzyme for cell wall synthesis in bacteria. • Noncompetitive: bind to another part of enzyme (allosteric site) altering its conformation (shape) • Ex. Heavy metal poisoning (heavy metals bind to allosteric sites on enzymes) • End product inhibition (akaFeedback Inhibition) • The end product of a pathway acts as an inhibitor for an enzyme in the pathway, thus slowing it down. • Can control metabolic pathways • Not required: Irreversible (covalent); reversible (weak bonds)

48. Application: End-Product Inhibition: • Threonine to Isoleucine Pathway:

49. Distinguish types of inhibition on a Graph

50. Utilization: Enzyme inhibition in medicine • Example: Ethanol has been used as a competitive inhibitor for alcohol dehydrogenase to treat antifreeze poisoning.