Quiz Me!	Chemicals in the Cell I
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Last revised: Thursday, September 16, 1999
Reading: Ch. 2 in text

Note: These notes are provided as a guide to topics the instructor hopes to cover during lecture. Actual coverage will always differ somewhat from what is printed here. These notes are not a substitute for the actual lecture!

Copyright 1999. Thomas M. Terry

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The premise of Reductionism

Reductionism is an assumption that underlies much of contemporary science. The central premise: To understand a complex system, break the system down into its parts. This has been a very successful program for many areas of biology (though not for all). It can, if applied overly dogmatically, lead to an overly mechanical view of the cell. But it is a useful approach, and one that generates an extraordinary volume of research.

• Hierarchic view of life: to understand life fully, need to study it at different levels
  View hierarchic levels ( protected).
  Note: certain images can be used only if access is limited to students in this class. These images will always be identified by the term "Protected". The first time you link such an image, you will see a dialog box asking for a user ID and a password. The userID is the word "student" (without quotes). The password will be given out in class -- if you forget it, e-mail the instructor or ask a classmate.
• 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

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Elements of Life

1. Definition: element = substance make up of only one kind of atom
2. 92 naturally occurring elements
3. 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)
4. About 25 elements found in cells
5. Can be identified as Macro and Micro-elements

Elements found in Cell's and Earth's Crust

See table 1

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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

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

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Molecular composition of a bacterial cell

See table 2

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Monomers and Polymers

• basic principle of cell; acquire small molecules (monomers); then assemble these into much larger molecules (polymers)

Monomer	Polymer
amino acids	proteins
nucleotides	DNA, RNA
sugars	polysaccharides
fatty acids	complex lipids

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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 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. Example: isotopes of Carbon
   • C¹² = "normal" (99+ %)
   • C¹³ = less common (<1%)
   • C¹⁴ = "unstable" isotope, weakly radioactive; useful in research, in medicine
   
   Compare Carbon isotopes
   

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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

View methane formation
View short movie of covalent bond formation ( protected).

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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

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
   
   View Hydrogen bond formation in Water
   View "water box" in three dimensions
   (Note: to view this interactively on your Web browser, the free Chemscape Chime plug-in viewer must be installed in your browser's plug-in folder. For more information about what plug-ins are and how to install them, click here.)

Polar and Nonpolar molecules

1. Some molecules have electrons asymmetrically distributed = polar molecules.
   View short movie showing polar bond formation ( protected).
2. Example: CH₃CH₂OH (ethanol); the oxygen atom attracts more of the electrons than other atoms
3. Sugars are good examples of very soluble molecules, due to many -OH groups
   Contrast sugar and hydrocarbon ability to form Hydrogen bonds
   
4. Result of polarity: molecule acquires a dipole moment, will orient to one direction when placed in electric field.
5. All polar molecules interact by charge-charge interactions; interact well with water, form good hydrogen bonds.
6. 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.

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