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BIO401: Biochemistry

Unit 1: Basic Chemistry and Biology Concepts   In our first unit of biochemistry, we will review some general chemistry and organic chemistry concepts, as well as a few biology concepts.  As this course uses both branches of science, it is important to be familiar with these topics before continuing on.  These topics can be found in the BIO101, CHEM101, and CHEM102 courses.

Unit 1 Time Advisory
This unit should take you 6 hours to complete.

☐    Subunit 1.1: 2 hours

☐    Subunit 1.2: 2 hours

☐    Subunit 1.3: 2 hours

Unit1 Learning Outcomes
Upon successful completion of this unit, students will be able to:

  • Discuss and apply the basic concepts of general chemistry, including chemical bonding, intermolecular forces, pH, and thermodynamics.
  • Discuss and apply the basic concepts of organic chemistry, including organic groups and organic reactions.
  • Discuss and apply the basic concepts of general biology, including the central dogma of biology, cellular structure and respiration, and DNA replication.

1.1 General Chemistry Principles   1.1.1 Covalent Bonds   - Reading: Wikibooks: Stuctural Biochemisty: "Chemical Bonding" Link: Wikibooks: Stuctural Biochemistry: "Chemical Bonding" (PDF)
 
Instructions: Read the section to review chemical bonding properties relevant to biological molecules.
 
Terms of Use: The article above is released under a Creative Commons Attribution-Share-Alike License 3.0 (HTML).  You can find the original Wikibooks version of this article here (HTML).

1.1.2 Non-Covalent Bonds   - Reading: National Center for Biotechnology Information: W.H. Freeman and Co.’s Biochemistry Fifth Ed.: "Chemical Bonds in Biochemistry" Link: National Center for Biotechnology Information: W.H. Freeman and Co.’s Biochemistry Fifth Ed.: "Chemical Bonds in Biochemistry" (HTML)
 
Instructions: This page discusses various types of bonds and intermolecular forces.  It covers sections 1.1.2 and 1.1.3.
 
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1.1.3 Intermolecular Forces   1.1.4 Association and Disassociation Constants   - Reading: University of Akron: James K Hardy's General, Organic and Biochemistry: "Reaction Rates and Equilibrium" Link: University of Akron: James K Hardy's General, Organic and Biochemistry: "Reaction Rates and Equilibrium" (PDF)
 
Instructions: Click on the link and select the "Reaction Rates and Equilibrium" link on the left side of the page to connect with the relevant set of slides.
 
Terms of Use: Please respect the copyright and terms of use displayed on the webpage above.

1.1.5 pH   - Reading: Carnegie Mellon Carnegie Mellon Open Learning Initiative:: Biochemistry Spring 2010: "Acid Base Behavior" Link: Carnegie Mellon Carnegie Mellon Open Learning Initiative: Biochemistry Spring 2010: "Acid Base Behavior" (HTML)

 Instuctions: This reading reviews the principles of pH, acids,
bases, and buffers.  Perform the included assessemnts if you would
like to test yourself.  Click on the link and choose "Enter Course"
to view the relevant material.  
    
 Terms of Use: Please respect the copyright and terms of use
displayed on the webpage above.

1.1.6 Thermodynamic Principles   - Reading: National Center for Biotechnology Information: W.H. Freeman and Co.’s Biochemistry Fifth Ed.: "Chemical Bonds in Biochemistry" Link: National Center for Biotechnology Information: W.H. Freeman and Co.’s Biochemistry Fifth Ed.: "Chemical Bonds in Biochemistry" (HTML)
 
Instructions: This webpage discusses the principles of thermodynamics.  Focus on the section "1.3.3.  Entropy and the Laws of Thermodynamics."
 
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1.2 Organic Chemistry Principles   1.2.1 Oxygen Containing Organic Groups   - Reading: University of Akron: James K Hardy's General, Organic and Biochemistry: "Alcohols Phenols and Ethers" Link: University of Akron: James K Hardy's General, Organic and Biochemistry: "Alcohols Phenols and Ethers" (PDF)
 
Instructions: Click on the link and select the "Alcohols Phenols and Ethers" link on the left side of the page to connect with the relevant set of slides.  This reading covers subunits 1.2.1 and 1.2.2.
 
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1.2.2 Sulfur Containing Organic Groups   1.2.3 Common Organic Reactions   - Reading: University of Akron: James K Hardy's General, Organic and Biochemistry: "Chemical Reactions" Link: University of Akron: James K Hardy's General, Organic and Biochemistry: "Chemical Reactions" (PDF)
 
Instructions: Click on the link and select the “Chemical Reactions” link on the left side of the page to connect with the relevant set of slides.
 
Terms of Use: Please respect the copyright and terms of use displayed on the webpage above.

1.3 Biology Principles   Note: Much of biochemistry looks in detail at these following biology principles, so it is especially important that you have a good grasp of these before moving on! 

1.3.1 Eukaryotic Cell Organelles   - Web Media: CellsAlive.com: “Animal Cell” Link: CellsAlive.com: “Animal Cell” (Adobe Flash)
 
Instructions: Click on the link to view an interctive picture of a eukaryotic animal cell.  Be sure to scroll down and review the different components of a eukaryotic cell.
 
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1.3.2 Central Dogma of Biology   - Reading: National Center for Biotechnology Information: W.H. Freeman and Co.’s Biochemistry Fifth Ed.: "DNA Illustrates the Relation between Form and Function" Link: National Center for Biotechnology Information: W.H. Freeman and Co.’s Biochemistry Fifth Ed.: "DNA Illustrates the Relation between Form and Function" (HTML)
 
Instructions: This webpage discusses the "central dogma of biology," which describes the flow of information in a cell: from DNA to RNA to protein.
 
Note: Much of biochemistry looks at these biology principles; it is especially important that you have a good grasp of them before moving on!
 
Terms of Use: Please respect the copyright and terms of use displayed on the webpage above.

1.3.3 Glycolysis and Cellular Respiration   - Reading: University of Cincinnati-Clermont College: J. L. Stein Carter's Biology 104: "Cellular Respiration and Fermentation" Link: University of Cincinnati-Clermont College: J. L. Stein Carter's Biology 104: "Cellular Respiration and Fermentation" (HTML)
 
Instructions: Review the concenpts of glycolysis and cellular respiration.
 
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1.3.4 DNA Replication   - Reading: National Center for Biotechnology Information: W.H. Freeman and Co.’s Biochemistry Fifth Ed.: "DNA Replication fo Both Strand Proceeds Rapidly from Specific Start Sites" Link: National Center for Biotechnology Information: W.H. Freeman and Co.’s Biochemistry Fifth Ed.: "DNA Replication of Both Strand Proceeds Rapidly from Specific Start Sites" (HTML)
 
Instructions: This webpage discusses many aspects of DNA strucutre and replication.  Focus on the section entitled, " DNA Replication fo Both Strand Proceeds Rapidly from Specific Start Sites."
 
Terms of Use: Please respect the copyright and terms of use displayed on the webpage above.