Atoms, Ions, and Molecules: Structure, Elements, and Bonds

1. Chapter 2 Atoms, Ions, and Molecules

2. About this Chapter • Make up of atoms, ions, & molecules • Bonds combine atoms, form molecules • Concentrations • Biomolecules

3. Atoms and Elements • Structure of an atom • Protons • Electrons • Neutrons • Mass • Charge • Nucleus • Electron orbitals • Elements • Essential & trace elements Figure 2-1: Atomic structure

4. All the Elements Figure 2-2: Periodic table of the elements

5. Elements of the Body

6. Elements other than C, H, O and N in Humans • Primary Elements (3% of all body weight) • Calcium Ca Bones, teeth, muscle and nerve action, blood clotting • Phosphorus P Bones and Teeth, DNA, RNA, ATP. Important in • energy transfer • Trace Elements (Less than 1 % of body weight altogether) • Potassium K Osmotic balance; cell voltage, muscle and nerve • action • Sulfur S Component of proteins (cysteine) and other organic • molecules • Sodium Na Osmotic balance; cell voltage, muscle and nerve • action • Chlorine Cl Osmotic balance; cell voltage, muscle and nerve • action • Magnesium Mg Co-factor for many enzymes • Iron Fe Hemoglobin and many enzymes • Copper Cu Co-factor of many enzymes • Zinc Zn Co-factor of many enzymes • Manganese Mn Co-factor of many enzymes • Cobalt Co Co-factor of many enzymes and vitamin B12 • Chromium Cr Co-factor of many enzymes and potentiates Insulin • Selenium Se Required for normal liver function • Molybdenum Mo Co-factor of many enzymes

7. Ions and Isotopes • Ions have charge • Cations + • Anions - • Isotopes vary mass • Neutrons • Radioisotopes • Unstable nuclei • Emit energy -radiation • Medical uses as tracers

8. Ions and Isotopes Figure 2-3: A map showing the relationship between elements, ions, isotopes, and atoms

9. Molecules and Compounds • Common in biosystems • Carbon (C) • Oxygen (O) • Hydrogen (H) Figure 2-6: Electron configuration of the three most common elements in the body

10. Oxygen • Oxygen is a highly reactive nonmetallic element. As such, it readily forms compounds (notably oxides) with almost all other elements. • Oxygen is a strong oxidizing agent and has the second-highest electronegativity of all reactive elements, second only to fluorine. • Oxygen can be toxic, especially at high partial pressures. The biochemical basis for the toxicity of oxygen is the partial reduction of oxygen by one or two electrons to form reactive oxygen species

14. Bonds and Energy Changes During a chemical reaction: • Bonds in the reactants are broken • New bonds are made in the products • Energy is absorbed to break bonds. Bond-breaking is an endothermic process. • Energy is released when new bonds form. Bond-making is an exothermic process. • Whether a reaction is endothermic or exothermic depends on the difference between the energy needed to break bonds and the energy released when new bonds form. If more heat energy is released when making the bonds than was taken in when they broke, the reaction is exothermic.

15. Catabolic reactions give out energy. They are exergonic. In a catabolic reaction large molecules are broken down into smaller ones. For example, hydrolysis reactions, are catabolic.

16. Metabolism of Glucose • Along metabolic pathways the energy content of the initial substrate (glucose) differs significantly from the energy content of the product (carbon dioxide and water). In thermodynamic terms the change in Gibbs free energy, deltaG, is quite large (negative value). If such a reaction would occur at once, the chemical energy contained in sugar would be converted to heat. Enzymes of metabolic pathways are able to capture this energy in small portions and store it in the form of internal high energy compounds drastically reducing the amount of energy lost as heat. Compare the caloric content of an ounce of bread to burning a small stick of wood (wood and starch contain the same energy-rich stuff - glucose). The heat of the flame represents the released energy. • Converting glucose to carbon dioxide and water in one step has also one other important consequence; the reaction is irreversible due to a prohibitively large activation energy of converting carbon dioxide and water into sugar. Living organisms have evolved metabolic pathways that allow at least partial reversibility of the conversion of such processes by providing many intermediate steps with small Delta G values close to zero, i.e., near their chemical equilibrium.

17. Molecules and Compounds • Bonds capture energy • Bonds link atoms • Molecules • Molecular weight • Chemical formula Figure 2-7b: Chemical structures and formulas of some biological molecules

18. Types of Chemical Bonds • Covalent bonds • Common in biosystems • Share a pair of electrons • Ionic Bonds • Transfer an electron • Opposite charges attract

19. Ionic Bonds and Ions • Ionic Bonds and Ions • Gain 1 positive charge for each electron lost • Gain 1 negative charge for each electron gained • Dissolve and disassociate in polar solutions • Important ions of the body Figure 2-9a : Ions and ionic bonds

20. Polarity of Molecules • Partial charges on regions of molecule • Soluble in polar solvents ( i. e. H2O) • Non polar molecules • No regional partial charges • Do not dissolve easily in water (i.e. lipids) Figure 2-8: Water is a polar molecule

21. Hydrogen Bonds (H-bonds) • Strong polarity • Attracts to self • Surface tension • Form droplets • Thin films

22. Types of Chemical Bonds • Hydrogen bonds • Weak partial bonds • Water surface tension • Van der Waals forces - weak Figure 10a: Hydrogen bonds of water

23. Hydrogen Bonds (H-bonds) Figure 2-10: Hydrogen bonds of water

25. Solutions: Water is the main Solvent in Biosystems • Solutes dissolve in liquids • Solvents dissolve solutes • Solution: solute dissolves in solvent • Solubility , ease of dissolving • Hydrophobic • Hydrophilic Figure 2-11: Sodium chloride dissolves in water

26. Ionic Bonds and Ions Table 2-2: Important Ions of the Body

28. Functional Groups • Direct reactivity of a molecule • Common examples in biosystems Table 2-1: Common Functional Groups

29. Concentrations • Mole defined- 6.02 × 1023 atoms, ions or molecules of a substance • Molarity–# of moles solute dissolved per liter of solution 1M NaCl = 58g NaCl + H2O up to 1 liter • Molality–# of moles of solute dissolved in 1 Kg of solvent 1m NaCl = 58g NaCl + 1 Kg of H20 • Equivalents of an ion– equal to the molarity of ion times the number of charge of the ion • Concentrations: Amount of Solute in a Solution • Weight/volume- Milligrams or Grams solute/(ml, dL or Liter) solution , i.e. (mg/ml, mg/dL or grams/Liter) • Volume/volume- 0.1% HCl= Add 0.1 ml of conc. Acid to water to give final volume of 100 ml. • Percent solution- 5% glucose = 5 parts of solute (glucose) per 100 parts of total solution

30. Hydrogen Ion Concentration (pH) in Biosystems • Acid - contributes H+to solution(CO2 + H2O <=> H2CO3 <=> H+ + HCO3- ) • Base - decreases H+ in solution( NH3 + H2O <=> NH4+ OH-) • Buffer minimizes changes of pH

31. Hydrogen Ion Concentration (pH) in Biosystems Figure 2-12: pH scale

35. Carbohydrate Biomolecules: Carbon, Hydrogen & Oxygen • Complex carbohydrates: polymers (polysaccharides) • "Simple sugars" monosaccharides (glucose, ribose)

36. Carbohydrate Biomolecules: Carbon, Hydrogen & Oxygen Figure 2-13-1: Carbohydrates

37. Carbohydrate Biomolecules: Carbon, Hydrogen & Oxygen Figure 2-13-2: Carbohydrates

38. Lipids: Mostly Carbon and Hydrogen; little Oxygen • Triglycerides: Glycerol,Fatty acid chains • Eicosanoids, Steroids & Phospholipids

39. Lipids: Mostly Carbon and Hydrogen; little Oxygen Figure 2-14: Lipids and lipid-related molecules

41. The importance of selectively permeable membranes • Membranes are physical barriers of cells and subcellular compartments controlling material exchange between the internal environment and the extracellular environment • A membrane is essentially a hydrophobic permeability barrier consisting of phospholipids, glycolipids, and membrane proteins • Membranes contain amphipathic molecules such as phosphatidyl ethanolamine, an example of phosphoglycerides, the major class of membrane phospholipids in most cells. Polar head Nonpolar tail

42. Omega 3 Fatty Acids Omega-3 fatty acids that are important in human physiology are α-linolenic acid (18:3, n-3; ALA), eicosapentaenoic acid (20:5, n-3; EPA), and docosahexaenoic acid (22:6, n-3; DHA). These three polyunsaturates have either 3, 5, or 6 double bonds in a carbon chain of 18, 20, or 22 carbon atoms, respectively. As with most naturally-produced fatty acids, all double bonds are in the cis-configuration,

44. Pathways in biosynthesis of eicosanoids from arachidonic acid: there are parallel paths from EPA & DGLA.

45. Proteins: Amino acid polymers • Amino Acids: essential, amino group, acid group • Protein structure: polypeptides, primary -quaternary Figure 2-15: Amino acid structure

46. Combination Biomolecules • Lipoproteins (blood transport molecules) • Glycoproteins (membrane structure) • Glycolipids (membrane receptors) Figure 2-19: Chemistry summary

48. Nucleotides, DNA and RNA • Composition • Base • Sugar • Phosphate • Transmit and store • Information (genetic code) • Energy transfer molecules • ATP • Cyclic AMP • NAD & FAD