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

Page history last edited by KimberleyHausheer 13 years, 9 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


9/10/10- On Friday the main topic of the lecture was functional groups. In the reading there had only been a few paragraphs on them and a table so I was surprised when we spent the majority of the class going over them. Functional groups by definition are group 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. There are eight different functional groups amino, carbonyl, carboxyl, hydroxyl, methyl, phosphate, sulfate, and sulfhydryl. Each one consists of different atoms arranged and bonded differently. After, isomers were covered briefly which is when one molecular formula can form two different structures that have different characteristics. Structural isomers contain the same atoms but in different bonding relationships. There are also stereoisomer   have identical bonding relationships, but the spatial positioning of the atoms differs in the two isomers. There are two types of stereoisomers; cis/trans and eneantiomers. Cis/trans Isomers are Organic molecules with the same chemical composition but existing in two different configurations determined by the positions of hydrogen atoms on the two carbons of a double bond. When the hydrogen atoms are on the same side of the double bond, it is called a cis isomer; when on the opposite sides of the double bond, it is a trans isomer. Enantiomers are when a pair of molecules are mirror images of each other. We also quickly reviewed hydrolysis which is a way to break a bond in cells. Hydrolysis is when a water molecule breaks up a larger molecule into smaller molecules.


9/15/10-Wednesday's lecture was on proteins. In the beginning of class we went over functional groups again and how they affect the molecule that they are a part of. Then we went over protein structure there are four different levels of protein structure. Primary structure is when amino acids are connected through peptide bonds. Secondary structure is when parts of the protein starts to fold. There are two different types helix, and sheet. Secondary structures are held together by hydrogen bonds. Tertiary structure is the entire three-dimensional fold of a protein. The structure stays together with different kinds of bonds. Quaternary is when all the structures are together in one strand of protein.



9/17/10-During lecture on Friday we talked about proteins and the four different factors that help hold it together;hydrogen bonds, ionic bonds, hydrophobic effects, Van der Waals forces, and disulfide bridges. We examined an experiment done by the scientist Anfinsen that showed that the bonds of a protein are determined by its primary structure.  In the experiment, first he measured the amount of RNA ribonuclease degraded in its normal state. Then he added two chemicals,  BME and urea that would break up the bonds in the protein into its primary structure. Then he put the solution through a chromatography tube to separate the protein and the chemicals. Then, without the chemicals, the protein renatured itself. This experiment proved that certain proteins can fold into their final, functional state without the help of cell organelles or other cell forces.


B.  Useful Materials

YouTube plugin error This is a short video about protein structure. In the beginning it has a few interesting facts about how complex proteins are. The image I thought also helps to show the different structures and how they look all together. The second half of the video is not as helpful. It states that proteins live in a complex environment and how it survives.


YouTube plugin error This is a video of a teacher going over the different functional groups. He shows you how you can identify each. He also explains how to draw them.


 Flubbed Folding Can Make Prtoeins Lethal  is a short article found at Scientifc American that explains how delicate proteins are. It mentions two studies. The first done by Christopher Dobson and published in the journal Nature explains that even normal proteins when coaxed into misfolding can become very dangerous. The second study is done by Dennis Selkoe stating that by reducing the amount or production of amyloid beta oligomers might be a way to treat Alzheimer's. This relates to the material we are covering in class because we were discussing how one little difference in a protein could be a drastic change in its function.


Gaming the System: Video Gamers Help Researchers Untangle Protein Folding Problem

is the article in Scientific American that talks about the online website called Fold it!. The article briefly gives a background of proteins. Stating they are the "workhorses of the body."It even has a video about the game.



Comments (2)

Derek Weber said

at 4:24 am on Sep 16, 2010

9/15: Updated. Please insert the youtube videos direclty using the insert video button in the editor. Just paste the URL to embed. You raised a good point about the functional groups and the time spent in the text. The reason I devote a bit more time was apparent as we discussed the R-groups of amino acids today.

Derek Weber said

at 10:37 pm on Sep 28, 2010

You need to link to the actual journal article and not the summary from SA.

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