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BIO401: Biochemistry

Unit 11: Biochemistry Techniques   Our final unit looks at some common laboratory techniques used to study biochemistry topics. Because much of biochemistry research revolves around protein and nucleic acids, most of the techniques also revolve around these two types of biomolecules. Bioinformatics, the newest of these fields, involves the use of information technology and computing to study large sets of molecules at a time, instead of working with individual molecules in the laboratory.

Unit 11 Time Advisory
This unit should take you 10 hours to complete.

☐    Subunit 11.1: 2 hours

☐    Subunit 11.2: 2 hours

☐    Subunit 11.3: 2 hours

☐    Subunit 11.4: 2 hours

☐    Subunit 11.5: 2 hours

Unit11 Learning Outcomes
Upon successful completion of this unit, students will be able to:

  • List key techniques used in biochemistry.
  • Describe how these techniques define key characteristics of biochemical molecules so as to elucidate their structure and/or function.

11.1 Protein Purification   - Reading: National Center for Biotechnology Information: W.H. Freeman and Co.’s Biochemistry Fifth Ed.: "The purification of proteins is an essential first step in understanding their function" Link: National Center for Biotechnology Information: W.H. Freeman and Co.’s Biochemistry Fifth Ed.: "The purification of proteins is an essential first step in understanding their function" (HTML)
 
Instructions:  Read through the link to learn how proteins can be purified, focusing on the introduction and sections about size-exclusion chromatography (also known as gel-filtration chromatography) and HPLC.  This covers all of section 11.1.
 
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11.1.1 Size-Exclusion Chromatography   11.1.2 HPLC (High-Performance Liquid Chromatography)   11.2 Protein Display   11.2.1 SDS-PAGE (Sodium Dodecyl Sulfate-Polyacrylamide Gel Electrophoresis)   - Web Media: Geneedinc's "SDS-PAGE" Link: Geneedinc's "SDS-PAGE" (YouTube)
 
Instructions:  Watch the video to undertand how SDS-PAGE is used to characterize proteins.
 
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11.2.2 2-D Electrophoresis   - Reading: National Center for Biotechnology Information: W.H. Freeman and Co.’s Biochemistry Fifth Ed.: "The purification of proteins is an essential first step in understanding their function" Link: National Center for Biotechnology Information: W.H. Freeman and Co.’s Biochemistry Fifth Ed.: "The purification of proteins is an essential first step in understanding their function" (HTML)
 
Instructions:  Read the section in the link about 2-D electrophoresis.  This link also has more information about electrophoresis in general, if you would like to review. 
 
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11.2.3 ELISA (Enzyme-Linked Immunosorbent Assay)   - Reading: Davidson College: A. Malcolm Campbell's Genomics: "ELISA" Link:  Davidson College: A. Malcolm Campbell's Genomics:  "ELISA" (HTML)
 
Instructions:  Read through the linked material above to understand the principles of the ELISA method. 
 
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  • Reading: LearnersTV: "Pregnancy Test ELISA" Link: LearnersTV: "Pregnancy Test ELISA" (Adobe Flash)
     
    Instructions: Watch this animation to undertand how the principles of the ELISA method are used in commercial pregnancy tests.
     
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11.2.4 Mass Spectroscopy   - Reading: National Center for Biotechnology Information: W.H. Freeman and Co.’s Biochemistry Fifth Ed.: "The purification of proteins is an essential first step in understanding their function" Link: National Center for Biotechnology Information: W.H. Freeman and Co.’s Biochemistry Fifth Ed.: "The purification of proteins is an essential first step in understanding their function" (HTML)
 
Instructions:  Read the section in the linked material above about mass spectroscopy.
 
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11.3 Nucleic Acid Manipulation   11.3.1 PCR (Polymerase Chain Reaction)   - Interactive Lab: Dolan DNA Learning Center: "Polymerase chain reaction" Link: Dolan DNA Learning Center: "Polymerase chain reaction" (Adobe Flash)
 
Also available in:
YouTube
 
Instructions:  Choose the "amplification" option in the PCR initial slide to start the interactive animation of the PCR reaction.  Be sure you understand how amplification is achieved.
 
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11.3.2 Restriction Digest and Ligation   - Reading: Dolan DNA Learning Center: "Animation 24: The RNA message is sometimes edited" Link: Dolan DNA Learning Center” "Animation 24:  The RNA message is sometimes edited"(Adobe Flash)
 
Instructions:  Click through the animation to understand how restriction enzymes are used in cloning a DNA fragment.
 
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11.4 Nucleic Acid Display   11.4.1 Southern Blot   - Reading: National Center for Biotechnology Information: W.H. Freeman and Co.’s Biochemistry Fifth Ed.: "Detection of Nucleic Acids and Proteins" Link: National Center for Biotechnology Information: W.H. Freeman and Co.’s Biochemistry Fifth Ed.: "Detection of Nucleic Acids and Proteins" (HTML)
 
Instructions:  Read through the introduction and section about nucleic acid hybridization.  Be sure to understand the similarities and differences between northern and southern blots.  This information also covers section 11.4.2.
 
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11.4.2 Northern Blot   11.4.3 DNase Footprinting Assay   - Reading: Wikipedia: "DNase footprinting assay" Link: Wikipedia: "DNase footprinting assay" (PDF)
 
Instructions: Read about the method of DNase footprinting.
 
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11.5 Bioinformatics   11.5.1 Microarrays   - Reading: Dolan DNA Learning Center's "DNA Arrays" Link: Dolan DNA Learning Center's "DNA Arrays" (Adobe Flash)
 
Instructions:  Go through the interactive animation to understand the principles and use of DNA microarrays.
 
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11.5.2 Comparative Studies   - Reading: Wikipedia: "Bioinformatics" Link: Wikipedia: "Bioinformatics" (PDF)
 
Instructions: Read about the field of bioinformatics and how this growing field is contributing to biological research.
 
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11.5.3 Systems Biology   - Reading: Wikipedia: "Systems Biology" Link: Wikipedia: "Systems Biology" (PDF)
 
Instructions: Read about the trend of systems biology.  Click on the picture on the right side of the link page to see an overview regarding the number of fields and technologies that come together to contribute to a Systems Biology approach.
 
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