The premise of Reductionism

• Hierarchic view of life: to understand life fully, need to study it at different levels
  View hierarchic levels (protected)
  
• The cell is a chemical machine; its parts and its language are chemical
• Need sophisticated tools to analyze the components: chromatography,electrophoresis, etc.
• Biochemistry = study of these parts

Elements of Life

• Definition: element = substance make up of only one kind of atom
• 92 naturally occurring elements
• Note: abundance on earth's crust is not mirrored in living tissue.
  • Some of earth's major elements are not found in cells (e.g. Aluminum)
  • some major elements in cells are not abundant on earth's crust (e.g. Carbon)
• About 25 elements found in cells
• Can be identified as Macro and Micro-elements

Elements found in Cell's and Earth's Crust

CHNOPS (Macro elements)

• These 6 elements are the predominant elements in all cells.
  1. C = Carbon
  2. H = Hydrogen
  3. N = Nitrogen
  4. O = Oxygen
  5. P = Phosphorus
  6. S = Sulfur
• Some organisms have extra abundance of other elements (e.g.,vertebrates have lots of Calcium, mostly in bone)

Micro-elements and trace minerals

• Remaining elements are used in a variety of ways; many minerals are critical for function of certain enzymes (e.g. Copper, Molybenum, Zinc)
• others required for certain functions:
  • Calcium for bone
    
  • Silicon for glassy shell in certain protists
    
  • Potassium and Sodium for nerve conduction in animals
• Considerable variation in amounts needed; generally very small amounts relative to CHNOPS

Atoms & Isotopes

1. Atom: smallest units of matter. Contains electrons (- charge), protons (+ charge), neutrons (no charge)
   Different atoms compared
   View a model of a hydrogen atom with electron represented dynamically as "electron cloud"
   
2. number of protons & electrons is the same, unique for each element
3. Example: H = 1 proton; C = 6 protons; O = 8 protons. This is also called the atomic number.
4. Electrons fit into specific geometrical patterns, called orbitals (not described further here -- learn about this in chemistry). Each orbital holds 2 only electrons.
5. As orbitals closest to nucleus become filled, additional electrons must occupy orbitals further from nucleus.
6. Groups of orbitals can be approximated as electron shells.
   View electron arrangement in different elements (Campbell website activity)
   View periodic table, showing electron shells for some common elements ( protected).
   
7. Some atoms lose or gain electrons, become charged ions. Examples: Na Na⁺; Cl Cl^-
8. Isotopes differ in neutron number.
9. Example 1: isotopes of Hydrogen
10. Example 2: isotopes of Carbon
• C¹² = "normal" (99+ %)
• C¹³ = less common (<1%)
• C¹⁴ = "unstable" isotope, weakly radioactive; useful in research, in medicine
  Compare Carbon isotopes
  

Molecules

1. Elements adjacent to Noble Gases tend to ionize
2. Elements further removed from noble gases tend to form covalent bonds, become stably connected into molecules.
3. Each atom in a molecule tries to complete outer electron shell by sharing electrons
   
4. Number of electrons shared is called valence
5. Valences of C, O, N, H, S, P:
   1. H = 1
   2. O = 2
   3. N = 3
   4. C = 4
   5. P = 5
   6. S = 2
6. Some examples of molecules:
   • 2H + O = H₂O
   • C + 4H = CH₄

Strong and weak Chemical Bonds

Covalent Bonds

1. Due to shared electron pairs
2. Formed by elements such as C, H, N, O, P, S; usually not found in the periodic table columns immediately adjacent to noble gases
3. View covalent bond formation of methane (Campbell website activity)
   

Polar and Nonpolar molecules

1. Some molecules have electrons asymmetrically distributed = polar molecules.
   
2. View animation of polarity in water (Campbell website activity)
3. What is electronegativity?
4. Example: CH₃CH₂OH (ethanol); the oxygen atom attracts more of the electrons than other atoms
5. View graph comparing electronegativity of different bonds (Note: values of "0" on the x-axis mean that electrons are shared absolutely equally. Moving to the right means the difference in electron distribution becomes more prononunced; e.g., C=O bonds (value 1) are much more assymetric than C-H bonds (value 0.3)
6. Sugars are good examples of very soluble molecules, due to many -OH groups
   Contrast sugar and hydrocarbon ability to form Hydrogen bonds
   
7. Result of polarity: molecule acquires a dipole moment, will orient to one direction when placed in electric field.
8. All polar molecules interact by charge-charge interactions; interact well with water, form good hydrogen bonds.
9. By contrast, non-polar molecules, such as hydrocarbons, do not dissolve in water, because to do so would have to break hydrogen bonds already present in water. Instead, will form layer separate from water (e.g. oil film on surface) or will form globules of fatty material inside water.

Hydrogen Bonds

1. if electrons are not evenly distributed, result is polarity
2. H₂O; H carries fraction of + charge, O fraction of - charge
3. Result: Hydrogen bond (weak bond); stable only for short periods of time. Typical bond strength ~ 3-5 kcal/mole
   
4. View Hydrogen bond formation in Water
5. View "water box" in three dimensions (Requires CHIME plugin).

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