Basic Chemistry for Biology (Ch2)
     An understanding of basic chemical principles is necessary to approach the study of cell and molecular biology. In this chapter you will learn, and hopefully to some extent review, these principles. The main focus is on atomic structure, chemical bonds, the chemistry of water as well as the pH concept. We will build on this knowledge as we approach macromolecules as well as cells in the following lectures.
     Chemistry can at times seem abstract and unrelated to the field of biology, but it is an important tool in terms of viewing life on our planet in a different light. Organisms are made of molecules and as a consequence it is crucial to build a foundation in the structures and interactions of such compounds.		 Biochemistry

     As mentioned in class it is extremely important to try to build the skill to visualize these molecules in your mind. Life processes are always brought down to the level of molecules (remember the example of the leaf and photosynthesis in lecture). This skill will build in importance as you continue towards macromolecules and ultimately the biology of cells. The cellular realm is an abstract microscopic world filled with complex processes involving different kinds of molecules and their interactions.  As you learn about them you should never be intimidated by the terminology. We need to label the parts of a structure to be able to talk about them.
     In this section of the class each lecture (and chapter) builds upon the previous one so it is very important that you approach (and try to understand) each chapter each week. Time invested in these chapters pay off as you head towards cell biology, genetics, molecular biology and biotechnology later on in the course. The two latter fields represent the top of a pyramid of knowledge. You will need to understand the foundation of the pyramid as you tackle these more advanced topics.

Review Questions:
  1. Explain how chemical knowledge integrates with other levels in biology. Focus on the example in lecture showing the connection between plants, leaves, plant cells, chloroplasts and chlorophyll.
  2. How does one refer to different kinds of chemical elements? Explain the terminology and the symbols used to represent different elements. How many different kinds of elements are currently known to science?
  3. How do elements differ from each other?
  4. Which are the most common elements in a living organism? The top three? The top six?
  5. Is it surprising to find these elements in an organism? What kind of larger (and smaller) molecules do these elements originate from?
  6. How is a molecule different from an element?
  7. Are molecules always made of the same element or can they be composed of different kinds of elements?
  8. Who is John Dalton? Why did we talk about him in our chemistry lecture?
  9. Explain atomic structure and composition (protons, neutrons, electrons).
  10. Who is Niels Bohr? What was his major contribution to the field of chemistry in 1913?
  11. Describe Mendeleev's contributions to chemistry?
  12. Why is the periodic table a useful tool in chemistry?
  13. Be able to predict the atomic structure of an element with the help of the periodic table if the number of protons is given. E.g. There are six protons in the element carbon (C). Describe its atomic structure. Practice on H, O, N, C, Na and Cl.
  14. What are isotopes? Use carbon (C) to explain the concept of isotopes.
  15. Be able to give examples of how radioactive isotopes can be used.
  16. Explain the use of Carbon 14. How is it possible to date organic remains with the help of carbon 14?
  17. Why do the chemical properties of an element depend on the number of electrons in its outer electron shell?
  18. Explain how ions form as well as the concept of ionic bonds. Use the elements sodium (Na) and Chlorine (Cl) to explain how ions form.
  19. What is the difference between ions and elements?
  20. Why are ions charged?
  21. What is a molecule?
  22. What is the difference between atoms and molecules?
  23. Explain how a covalent bond forms. Distinguish between single, double and triple covalent bonds.
  24. Use an example to demonstrate covalent bond formation.
  25. What is the difference between a polar and nonpolar molecule?
  26. Explain how a hydrogen bond forms. Where can one find hydrogen bonds?
  27. Are hydrogen bonds important in biological systems? Explain.
  28. Explain the basis for surface tension and cohesion.
  29. Water has a high heat capacity due to hydrogen bond formation. What is the biological importance the high heat capacity of water?
  30. Why does ice float?
  31. Why is water often referred to as the universal solvent?
  32. Why is it so important to understand the properties of water as one studies biology?
  33. What are the three major bond types in chemistry?
  34. Which of these bonds is the strongest? Put the bond types in order from the strongest to the weakest.
  35. Define the pH concept.
  36. Why is a highly acidic (or alkaline) solution so corrosive? (i.e. reactive)
  37. Describe the pH scale and give examples of solutions of varying pH.
  38. Why is pH so important in biological systems (e.g. human blood pH)?
  39. What is organic chemistry all about?
  40. What are functional groups? What is their importance in organic chemistry?
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Lecture Outline
Biological function as related to biochemistry (e.g.: leaves to chlorophyll)
Elements
Atomic structure
     protons, neutrons and electrons
orbitals - the Bohr model
chemical characteristics
energy carriers
isotopes
Compounds versus Molecules

Bonds
 formation of bonds


 polar molecule
 hydrogen bonds
 the universal solvent
adhesion and cohesion
 surface tension
 high heat capacity
 high heat of vaporization
 solid water (ice) floats
     consequences in nature
The pH scale
 measurement of acidity/ logarithmic scale 0-14
 role of buffers
Organic Chemistry
 role of carbon in biology
 endless possibilities of combinations
functional groups - importance
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Page created by: Peter Svensson
Updated: February 17,  2010