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BIO401: Biochemistry

Unit 2: Amino Acids   We begin our study of biochemistry with a look at amino acids. They are the primary building blocks of proteins, the diverse set of biomolecules that make up much of what we are from the keratin in our hair to the enzymes that aid digestion. There are twenty standard amino acids from the Central Dogma theory, although there are many more that we encounter in biochemistry. We begin by looking at stereochemistry and organic chemistry aspects to gain a good understanding of the chemical nature of these molecules. Next, we will classify amino acids according to their organic residues. Most amino acids fall into one of these categories, and we often refer to amino acids in these groups rather than specific ones. Finally, we will look at the life cycle of amino acids, from synthesis and degradation to nitrogen cycling. Most importantly, nitrogen homeostasis from amino acids is the main reason we produce urine. Failure to recycle amino acids is lethal!

Unit 2 Time Advisory
This unit should take you 12 hours to complete.

☐    Subunit 2.1: 1 hour, 30 minutes

☐    Video Lecture: 45 minutes

☐    Review: 45 minutes

☐    Subunit 2.2: 2 hours

☐    Subunit 2.3: 2.5 hours

☐    Subunit 2.4: 3 hours

☐    Subunit 2.5: 3 hours

Unit2 Learning Outcomes
Upon successful completion of this unit, students will be able to:

  • Identify amino acids based on their structure.
  • Explain how the various side chains of amino acids influence their chemical properties.
  • Describe how amino acids are synthesized and broken down.

2.1 Amino Acid Structure   - Lecture: Appalachian State University: Dr. Eric Allain's "Amino Acids Part 1"  Link:  Appalachian State University: Dr. Eric Allain's "Amino Acids Part 1"

 Instructions: This lecture covers information for sections
2.1.1-2.1.4.  Take notes while you watch.  
    
 Note: Amino acids are found in either L or D configurations,
although almost all of the amino acids that we encounter are in the
L configuration.  Be sure to know this fact and the main exceptions
to this rule.  
    
 Terms of Use: The material above has been reposted by the kind
permission of Eric Allain from Appalachian State University, and can
be viewed in its original form [here](http://vimeo.com/3296558).
 Please note that this material is under copyright and cannot be
reproduced in any capacity without explicit permission from the
copyright holder.

2.1.1 Organic Composition   2.1.2 Residues   2.1.3 Zwitterion   2.1.4 Chirality   2.2 Essential vs. Nonessential Amino Acids   - Reading: NCBI Bookshelf’s version of W.H. Freeman(publisher), Berg, Tymoczko, and Stryer (authors) Biochemistry 5th Edition: “Section 24.2 Amino Acids Are Made from Intermediates of the Citric Acid Cycle and Other Major Pathways”

Link: Reading: NCBI Bookshelf’s version of W.H. Freeman(publisher),
Berg, Tymoczko, and Stryer (authors) Biochemistry 5<sup>th</sup>
Edition: “[Section 24.2 Amino Acids Are Made from Intermediates of
the Citric Acid Cycle and Other Major
Pathways](http://www.ncbi.nlm.nih.gov/books/NBK22459/)” (HTML)  

 Instructions: Read the first section of this webpage and the
section titled “24.2.1 Human Beings Can Synthesize Some Amino Acids
but Must Obtain Others from the Diet”  
  

Terms of Use: Please respect the copyright and terms of use
displayed on the webpage above.

2.3 Amino Acid Types   - Reading: University of Akron: James K Hardy's General, Organic and Biochemistry: "Amino Acids and Proteins" Link: University of Akron: James K Hardy's General, Organic and Biochemistry: "Proteins" (PDF)
 
Instructions: Click on the link and select the "Proteins"
link on the left side of the page to connect with the relevant set of slides.  This link covers subsections 2.3.1-2.3.5.
 
Terms of Use: Please respect the copyright and terms of use displayed on the webpage above.

2.3.1 Hydrophobic   2.3.2 Polar   2.3.3 Acidic and Basic   2.3.4 Proline   2.3.5 Cysteine   2.4 Synthesis of Amino Acids   2.4.1 Aminoacyl-tRNA synthesis   - Reading: NCBI Bookshelf’s version of W.H. Freeman(publisher), Berg, Tymoczko, and Stryer (authors) Biochemistry 5th Edition: “Section 24.2 Amino Acids Are Made from Intermediates of the Citric Acid Cycle and Other Major Pathways”

Link: NCBI Bookshelf’s version of W.H. Freeman (publisher), Berg,
Tymoczko, and Stryer (authors) Biochemistry 5<sup>th</sup> Edition:
“[Section 29.2 Aminocayle-Transfer RNA Synthetases Read the Genetic
Code](http://www.ncbi.nlm.nih.gov/books/NBK22356/)” (HTML)  
    
 Instructions: Read the entire webpage.  
    
 Terms of Use: Please respect the copyright and terms of use
displayed on the webpage above.

2.4.2 Metabolic Precursor Groups   - Reading: NCBI Bookshelf’s version of W.H. Freeman(publisher), Berg, Tymoczko, and Stryer (authors) Biochemistry 5th Edition: “Section 24.2 Amino Acids Are Made from Intermediates of the Citric Acid Cycle and Other Major Pathways”

Link: NCBI Bookshelf’s version of W.H. Freeman(publisher), Berg,
Tymoczko, and Stryer (authors) Biochemistry 5<sup>th</sup> Edition:
“[Section 24.2 Amino Acids Are Made from Intermediates of the Citric
Acid Cycle and Other Major
Pathways](http://www.ncbi.nlm.nih.gov/books/NBK22459/)”  (HTML)  

 Instructions: Read the first section of this webpage, paying
special attention to Figure 24.7.  

 Terms of Use: Please respect the copyright and terms of use
displayed on the webpage above.

2.5 Amino Acids and Nitrogen Homeostasis   - Reading: University of Albany: Biology366: "Amino Acid Metabolism" Link: University of Albany: Biology366: "Amino Acid Metabolism" (PDF)
 
Instructions: Click on the link and then select "L08_AminoAcidMetab1.pdf" and "L09_AminoAcidMetab2.pdf" to view the set of slides entitled "Amino Acid Metabolism."  Information in these slides covers sections 2.5.1-2.5.3.
 
Terms of Use: Please respect the copyright and terms of use displayed on the webpage above.

2.5.1 Fates of Amino Groups   2.5.2 Deamination of Amino Acids   2.5.3 Urea Cycle