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Chapter 3 Blog:  The Chemical Basis of Life II (John T)

Page history last edited by John Tamanas 13 years, 7 months ago

In the first section of this page, you will write a daily summary of that day's class.  For example in  your chapter 2 blog, your first entry should be titled 9/3/10.  You should then write a one or two paragraph summary of that day's lecture, outlining the major points.  In the second section, you are required to add two items (link to a website, video, animation, student-created slide show, student-created PowerPoint presentation) and one journal article pertaining to a topic in this chapter.  A one-paragraph summary must accompany each item describing the main idea and how it applies to the lecture topic.  Please see the PBWorks help guide for assistance embedding video and other items directly in the page.  I will also produce a how-to video on using tables to wrap text around items and other useful tips.  Please see the syllabus for organization and grading details.

 

A.  Daily Blog

9/10/2010: Captain's log. Bio-lecture day 3.  Bio has just been kicked up a notch. We learned the first "new" concept, functional groups. Functional groups are "groups of atoms with special chemical features that are functionally important." Each type of functional group exhibits the same properties in all molecules in which it occurs. We also learned about isomers. Isomers are different molecules with the same molecular formula. We also learned about a few different kinds of isomers, structural and enantiomers. Structural differences are the same atoms, but they have different chemical bonds. Enantiomers, on the other hand, are mirror images of each other. These can only exist if a carbon atom is attached to four different groups. An example of this would be D-Alanine and L-Alanine. Captain out.

 

9/15/2010: Captain's log. Bio-lecture day 4. This lecture started off on a different beat than usual. The super-amazingly-cool-text-your-answers-poll thingy wasn't working! I was so shocked to see the white area remain white after I and other people sent in their answers. I think I may have become a little depressed, but I digress. The lecture was based on the topic of "proteins". We started off class by first discussing the three different categories that the twenty different amino acids are broken into; nonpolar, polar (uncharged), and polar (charged). We then went on to discuss peptide bonds, the bonds that occur between different amino acids. Then came the topic of protein structure and hydrogen bonds (My God they're EVERYWHERE!) There are four different stages of protein folding (The process by which a protein folds to create its functional structure), primary, secondary, tertiary, and quaternary. Primary is just a single strand of amino acids that are in a line. Secondary structure uses the hydrogen bonds of the amino acid back bone to twist into a spiral or fold into a pleated sheet. Then, the tertiary structure is created by the protein folding in a very complex three-dimensional fashion. Lastly, Quaternary structure occurs when a few proteins come together and create an even more complex structure. Captain out.

 

9/17/2010: Captain's log. Bio-lecture day 5. Today's lecture wasn't so much a lecture as much as it was an activity. Commander Dr. Weber began the day with a brief review of the four different types of protein structure and then discussed nucleic acids (The "NA"s). We covered things like genes which are discrete units of DNA that encode for a functional product. Then the activity happened. The commander passed out the notes of the experiment that discovered that some proteins automatically. Here is what happened:

 

1. Incubated ribonucleas with RNA to test its ability to degrade RNA. This is the control.

 

2. Then they added beta-mercaptoethanol with urea to RNA. They did this to denature the protein. The activity dropped a lot.

 

3. Then they filtered out the urea and beta-mercaptoethanol and put the RNA in a separate test tube. The RNA renatured.  

 

Class ended after we had a discussion on the experiment and I ventured off to the lab for our Biology lab class. Captain out.

 

B.  Useful Materials

 

Submitted 9/19/2010http://www.ncbi.nlm.nih.gov/pubmed/20837024

 

Identification and characterisation of a misfolded monomeric serpin formed at physiological temperature.

 

On Wednesday we were discussing protein folding in class. This article discusses how the protein serpin is affected so greatly by physiological temperature and pH. It says that its protein structure changes depending on physiological conditions. 

 

 

Submitted 9/19/2010: http://www.ncbi.nlm.nih.gov/pubmed/20837031

"Abstract

 

AIMS: Thalidomide is thought to prevent TNF-α production, and such mechanism could be useful in a spinally-delivered drug approach for the control of peripheral inflammation. This study aimed to evaluate the effect of intrathecal thalidomide, in comparison with that of intraperitoneal treatment, on articular incapacitation, edema, synovial leukocyte content, and spinal cord glial activation in a model of Escherichia coli lipopolysaccharide (LPS)-induced reactive arthritis in rats.

MAIN METHODS: LPS (30ng) was injected into a knee-joint previously primed with carrageenan (300μg). Systemic (30 and 100mg/kg; intraperitoneal, i.p.) and intrathecal (10 and 100μg; i.t.) thalidomide were given 1 hour or 20min before LPS injection, respectively. Articular incapacitation and edema were evaluated hourly. After 6h, synovial fluid and lumbar spinal cords were collected for subsequent evaluations of cell migration and expression of CD11b/c and GFAP markers, respectively.

KEY FINDINGS: Systemic (30 and 100mg/kg) or intrathecal (10 and 100μg) thalidomide reduced articular incapacitation, edema, and polymorphonuclear migration. In addition, i.p. and i.t. thalidomide reduced the expression of CD11b/c and GFAP markers in the lumbar spinal cord. These results suggest that thalidomide can also produce peripheral anti-inflammatory effects through action in the spinal cord that may involve glia inhibition.

SIGNIFICANCE: This study provides new evidence that the direct spinal delivery of immunomodulators may be an alternative for the treatment of arthritic diseases, which require long systemic treatment with drugs associated with undesirable side-effects."

 

On Wednesday we were talking about isomers and how the difference between D- and L- enantiomers is very important. An example that Dr. Weber gave was the morning sickness pill called thalidomide. Birth defects occurred when the wrong isomer was given to the patient. This new study shows that thalidomide can actually be used for arthritis because of its anti-inflammatory properties. 

 

Submitted 9/19/2010:

YouTube plugin error

This video is a pretty quick review of what we went over in class. It discusses the three different types of amino acids, the three levels of protein folding, and protein denaturing. Oh, and it happens to be in the form of a rap. (I apologize for the horribleness of it, but it's kinda funny.)

 

Comments (2)

Derek Weber said

at 4:44 am on Sep 16, 2010

9/15: Updated.

Derek Weber said

at 11:02 pm on Sep 30, 2010

Well done.

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