Physiology: The Integrated Science of Life and Chemistry Basics

1. Physiology is an Integrated Science • biology • molecular • cellular • organ and organism • physics • chemistry • we are made of stuff of universe • we follow rules of the universe

2. chemistry basics • element substance with unique identity • atom single unit of element • molecule 2 + atoms • compound molecules of different atoms

3. elements – table 2.1 H2O

4. more elements

5. atom = protons + electrons chargemass + 1 none 1 - none

6. Periodic table • # protons identity atomic number • # electrons behavior

7. electrons electron shells can hold: 1st 2 2nd 8 3rd 8 4th 8 outer electrons = valence electrons

8. only the outer shell matters electron shells can hold: 1st 2 2nd 8 3rd 8 4th 8 outer electrons = valence electrons

9. Nature’s rules • nature is lazy entropy • nature wants equilibrium • equal concentrations • equal electric charges opposites attract • equal pressure • nature wants a full outer shell octet rule

10. Biology’s rule of living things • You can break nature’s 3 rules , if: • you supply energy • it aids survival • breaking the rules requires energy : • molecules are organized • gradients require work • these store energy

11. what is life ? • Living things take energy from the environment • Living things use energy to break nature’s rules. • build molecules • change molecules • maintain gradients

12. what is energy ? • it is the stuff that does work • holds molecules and atoms together • prevents equilibrium • maintains concentration gradients • maintains electrical gradients • breaks chemical bonds

13. electron shells hold Energy

14. Ions • ion = charged atom or molecule • cation = + charged • anion = - charged • nature wants a full outer shell octet rule • atoms gain/lose electron

15. common ions • Sodium Na+ • Potassium K+ • Calcium Ca++ • Chlorine Cl- • Phosphates PO4--- • Iron Fe++ • Copper Cu++ • Bicarbonate HCO3- • see table 2.1

16. which atoms form ions # electron shells  # electrons (valence) in outer shell  1 2 3 4 5 6 7 8 + -

17. ions and physiology • many physiologic functions are merely molecules seeking to have equal charges : • molecules will move toward opposite charge • molecules will move away from like charge • molecules will change their shape to get equal charge

18. Nature’s rules - bonding • Chemical bonds depend on nature’s desire for : • a full outer shell • equal charges • chemical bonds store energy decreases entropy

19. types of chemical bonds • ionic • covalent • di-sulfide • hydrogen

20. ionic bonds • ions with full outer shell nature happy? • ions with + / - charge nature happy? • opposites attract = ionic bond ions ionic bond

21. covalent bond • too many electrons to gain or lose • nature still wants ? • shared electrons • neutral atoms

22. octet rule? is nature happy? • neutral charge? is nature happy?

23. What element can form the most covalent bonds ? # electron shells  # electrons (valence) in outer shell  1 2 3 4 5 6 7 8

24. polar covalent • nonpolar • electrons shared equally • polar • electrons shared unequally • have + and - ends

25. hydrogen bonds • H tends to be + • attracted to - end of other molecules (eg . O ) • water • 3D shape of proteins

26. hydrogen bonds - Water

27. Polarity - ions in water • universal solvent ions (salts) dissolve in water

28. acid – base • pH = parts Hydrogen • acidity • increase H+pH < 7 • neutral pH =7 • alkalinity • decrease H+pH > 7 Figure 2.13

29. Biochemistry • biomolecules molecules of life • based on Carbon • specific functions • store energy • carbohydrates • lipids • nucleic acids • proteins

30. carbohydrates • Carbon + hydrates (water) CHO • C + H2O  C H2O C2 H4O2 C6 H12O6 • functions: • energy source glucose • store energy glycogen • DNA • antigens

31. Figure 2.14a, b

32. Figure 2.14a, b

33. lipids • fats • mostly C and H (little O) • functions: energy storage triglycerides insulation “ cell membranes phospholipids hormones cholesterol • hydrophobic

34. triglycerides • glycerol + 3 fatty acids • unsaturated FA • saturated FA • trans fats

35. phospholipids • 2 fatty acids + phosphate group • cell membranes hydrophilic hydrophobic

36. steroids • made from Cholesterol • cell membranes • hormones • Vitamin D • bile

37. Cholesterol, other Steroids also: Estrogen ; Progesterone

38. Nucleic Acids • DNA genetic code • RNA protein synthesis • gene code for protein code for AA order

39. other nucleic Acids • ATP adenosine triphosphate • ADP adenosine diphosphate • cAMP cyclic adenosine monophosphate • NAD nicotinamide adenine dinucleotide • FAD flavin adenine dinucleotide • GTP

40. amino acids • building blocks of proteins

41. Proteins • polymers of amino acids 20 diff AA • diverse molecules • different order of AA - different protein • genes control AA order

42. Protein functions Table 2.3.1

43. Protein functions Table 2.3.2

44. Proteins and 3D shape • 3D shape based on AA order • di-S bonds • H bonds in molecule in water • functions based on • 3D structure • change in 3D structure

45. H-Bonds

46. Fig. 2.27 tertiary

47. 3D shape dictates function

48. what changes 3D ? • other molecules covers some AA • ions change charge • ATP phosphorylation • change AA order genes damage • heat • pH

49. Physiology and protein shape • function ~ CHANGE PROTEIN 3D SHAPE • examples: • open / close channels • receptors • hormone actions • transcription factors • enzyme functions and activation • immunity

50. chemical reactions • anabolic make bonds = synthesis • A + B  AB • builds large biochemicals • require energy = endergonic • catabolic break bonds = decomposition • AB  A + B • breaks apart biochemicals • release energy = exergonic