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Chapter 2

Chapter 2. Atoms, Ions, and Molecules. About this Chapter. Make up of atoms, ions, & molecules Bonds combine atoms, form molecules Concentrations Biomolecules. Atoms and Elements. Structure of an atom Protons Electrons Neutrons Mass Charge Nucleus Electron orbitals Elements

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Chapter 2

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  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. 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

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

  12. 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

  13. 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

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

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

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

  17. 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

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

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

  20. 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

  21. 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

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

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

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

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

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

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

  28. Omega 3 Fatty Acids Omega-3 fatty acids that are important in human physiologyare 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,

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

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

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

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

  33. Nucleotides, DNA, and RNA Figure 2-18: RNA and DNA

  34. Visualization of DNA Double Helix

  35. Summary • Atoms: structure, mass, charge & orbitals • Bonds: covalent, ionic, hydrogen • Solutions: solutes, solvents, concentrations • pH: hydrogen ions, acids, bases & buffering • Biomolecules: carbohydrates, lipids, proteins & nucleic acids

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