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

Page history last edited by Derek Weber 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

Lecture on 9/10/10

In this lecture, we discussed the various types of organic molecules. We learned about the different type of functional groups, such as amino acids, ketones and aldehydes, carboxyl groups, hydroxyl groups, methyl groups, phosphate groups, sulfates, and suflhydryls. We discussed their properties and what they make up on a larger level. We also discussed how the structure of a molecule has a big effect on the molecule, just as the different atoms affect the molecule. We talked about different types of isomers, such as structural isomers and enantiomers. Structural isomers are molecules that contain the same atoms but have different bondings. Enantiomers are mirror images of molecules that need 4 covalent bonds to different groups combined to a carbon.


Lecture on 9/15/10

Today's lecture focused on proteins. We learned about how amino acid chains are formed by peptide bonds, and how proteins are grouped into three categories based on their "R" group, polar, nonpolar, and polar uncharged. Polar proteins are acidic or basic, and have modified amino groups to make them bases, and carboxyl groups that make them acidic. The acidic groups are negatively charged, and the basic groups are positively charged. Ionic bongs in amino acids come this electrostatic attraction. Nonpolar proteins have no charge and all have hydrocarbons. They are hydrophobic and have hydrogen bonds. The core of the amino acid can interact with other molecules because of the hydrogen bonds. Polar uncharged groups contain hydroxyl groups. We learned about the four structures of proteins. The primary structure is a linear chain of amino acids. The secondary structure is where parts of the protein begin to fold into helical structure and pleated sheets. Hydrogen bonds keep the structure of the protein together. 


Lecture on 9/17/10

In class on Friday, we learned about the factors that cause protein folding and stability. These factors are hydrogen bonds, ionic bonds and other polar interactions, the hydrophobic effect, van der Waals forces, and disulfide bridges. There are a large number of weak hydrogen bonds within a polypeptide and between polypeptides. These add up to a collectively strong force that stabilizes the protein structure. Ionic bonds and other polar interactions cause bonding between differently charged proteins. Negatively charged proteins are attracted to positively charged proteins, and this attraction brings them together, which can fold the protein. Uncharged polar side chains may bind to ionic amino acids. This effect is particularly important in tertiary and quaternary structure. The hydrophobic effect occurs from hydrophobic amino acids being in the center of the protein, as they try to minimize the contact with water. Some proteins have stretches of nonpolar amino acids that attach them to hydrophobic sections of membranes. Van der Waals forces are attractions that form from atoms within molecules being at an optimal distance apart, generating the van der Waals force. If atoms are too close together, then their electron clouds repel each other. But at a great enough distance, the van der Waals force diminishes. Disulfide bridges occur from sulfhydrl groups reacting with each other. These bonds are covalent, and help stabilize the tertiary structure of the protein.

B.  Useful Materials

Interactive and In-depth Animation explaining the folding of proteins! YAY!

If you don't understand the process of protein folding, then click on the link above. The animation takes you through the process, carefully detailing all aspects of protein folding. Proteins form from amino acids. Within these amino acids there are different types of groups that characterize the amino acid. The way that these groups interact with each other forms different types of bonds, which cause folding and stability within a protein.


In the above video (I tried an embed code, so I don't know how well it will show up, and if not the URL is below), the structure and functions of carbohydrates are explained. Carbohydrates are what provides us with the energy to do everyday tasks, and non-everyday tasks. Carbohydrates can be built up from single molecules called monosaccharides. Monosaccharides are simple sugars. Monosaccharides form with other monosaccharides to form disaccharides and polysaccharides.



Abstract on Article about Heat Shock Proteins and the Aging of Flies

This abstract talks about heat shock proteins and their effect on the aging of Drosophila. Heat shock proteins regulate stress-resistance and life-span. The aging process comes from abnormal proteins being produced. Because of abnormal protein production, the gene expression of heat shock proteins is activated, and heat shock proteins come into play. The heat shock proteins act by refolding abnormal proteins, thereby fighting their toxicity. The way they are expressed can actually predict the life-span of an organism. 

This article kind of tricked me, because a) I'd have to pay to read the article (as usual, cause people love to make money off of EVERYTHING) and b) I thought heat shock proteins were some kind of super protein (like heat/electric shock super powers, but not really). While I was disappointed by the lack of super powers, the idea that the aging process can be determined and facilitated by proteins was quite interesting, especially the fact that they fix abnormal proteins by refolding them.

Comments (2)

Derek Weber said

at 4:26 am on Sep 16, 2010

9/15: I assume there will be a bit more coming from the 9/15 lecture.

Derek Weber said

at 10:54 pm on Sep 28, 2010

I fixed the video. Great article. If you go through the library to get to PubMed we may have rights as a college.

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