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

Page history last edited by Siddarth Santhebennur 13 years, 2 months ago

n 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

September 10, 2010: Today's lecture had to be very interesting and confusing as well. When Dr. Weber said "Once you memorize these functional groups, you will be able to identify all kinds of structures!" I had to say I was confused at first, but I guess it is the matter of repeating and understanding the concepts. So in today's lecture we discussed about Organic Molecules (specifically carbon). Carbon is considered to be an organic compound because of its four valence electrons. We also discussed Functional Groups. Functional Groups are considered to be what helps carbon toughen up or when attached to. For most of the class we discussed about different functional groups as well as examples of them and most importantly: How To Identify Them! Some of the groups that we discussed were amino, carbonyl (ketone), aldehyde, hydroxyl, carboxyl, methyl, phosphate, sulfate and sulfhydry. We were able to look at their structures and what kind of bonds that they form between each other. 

     What I found really interesting during class was the discussion about enantiomers. They are basically mirror images of two stereoisomers. Their structures may seem the same, however their properties can be completely different. An example of this would be Thalidomide. This drug was mentioned in class and is a very good example of why the structure of certain substances can make a very big difference. As explained in class, one enantiomer of Thalidomide was known as a drug that could help with insomnia, colds, coughs and headaches. The other (which was also distributed without knowledge) caused defects to new born's.  Another thing we mentioned in class was carbohydrates and lipids. These are both organic molecules. We also mentioned about macromolecules which are large molecules made up from smaller molecules into carbohydrates. We ended the lecture with a brief definition of disaccharides. I will definitely have to continue looking over the functional groups and trying to recognize them!


September 15, 2010: Macromolecules are pretty cool things if you think about it. They are tiny in our eyes, but do so much to help humans and other creatures survive. I have to agree with Dr. Weber when he said: "Proteins are my favorite organic molecule". The first reason I agree with him is because I understand this lesson much more easier to understand and remember rather those functional groups (however functional groups some how came back to this lesson when trying to differentiate amino acids). The second reason is because after studying a small amount of information, I have learned many ways that proteins can be used. We would be lost without proteins! Moving onto what we focused in class, we kicked off the discussion of proteins by talking about the basic structure and components found in proteins. Proteins are the only organic molecule that has small traces of sulfur. This is useful when trying to find proteins since sulfur can be used a radioisotope to track them down. Like other organic molecules, proteins are made up of monomers. These monomers are called amino acids and there are 20 different kinds of amino acids. We also observed a chart that differentiated different kinds of amino acids. This chart broke them up into three groups which were: Nonpolar, Polar and Polar (with charges). The group with charges had two groups further into it which were acids and bases. The nonpolar groups are also called the hydrophobic (water fearing) group and can not be exposed to water otherwise the linear chain of amino acids can end up in a contorted shape resulting in a "bad protein". The polar amino acids are hydrophilic (water loving) and can be exposed to water. 

     This later made sense when started to talk about the different structure levels of proteins. We talked about how amino acid's link together (peptide bond through dehydration synthesis) and grow larger as they join with others. On a chain there are 2 ends: N terminus and C terminus. The C terminus is where amino acids continue to attach where as the N does not attach to anything. I think of it as N =e"N"d and C= "C"ontinue. Towards the end of the lecture we discussed about the different structures of proteins and how they can be folded or twisted (ex. b sheet & a Helix respectively). Their are four different structure levels starting from primary, secondary, tertiary and quaternary. The primary is very basic linear structure and is where peptide bonds are formed. In secondary, the structure either folds or twists in a way that hydrogen bonds are being able to form between Carboxyl and Amino groups. We concluded the lecture by briefly mentioning the tertiary structures in proteins. What a great lecture right?!


September 17, 2010: So today we kicked the lecture by talking about nucleic acids. We mentioned two very common examples of nucleic acids that we find inside of a cell which are RNA and DNA. Nucleic acids contain information for different purposes that are required in the cell. The information contained in these nucleic acids can be anything from the making proteins to instructions to carry out functions in the cell. In DNA, there are discrete parts of DNA that encodes for a functional product. So there are different genes in DNA that encode for different functions. "All cells within the same structure have the same DNA in their nucleus". I have heard about that in previous lessons in other courses, but I still can't figure why do they all have the SAME DNA in their nucleus. When Dr. Weber (btw thank you Dr. Weber) explained that each cell may have the same DNA, but it is the way they express their genes which makes them unique from other cells. For the remainder of lecture, we looked at an experiment that was conducted a while back and basically studied the different components of this experiment. Patrick and I went to discuss the materials used in this experiment thinking that we would just read off the materials. We did more than just read a list. Even though we were lost when we were asked certain questions, it made sense after our wonderful classmates explained to us the answers and helped us get a better understanding. Well moving on, the experiment was created in order to prove that amino acids have proteins that have all the information needed to fold. Each step was discussed by different groups of people. We broke up the experiment and took it in one by one by just like eating baby bites! At the end of class we briefly talked about the quaternary structure and what it is composed of. I can tell that when Dr. Weber said he loves proteins...he really meant it ! : ) 


B.  Useful Materials

   Useful Article

Mapping Protein-Protein Interactions by Quantitative Proteomics 


This is a very short article that I found on PubMed that talks briefly about how important proteins are in a cellular structure. There is now a way to track certain protein-protein interactions by using a method known as Quantitative Mass Spectrometry. This has been used to detect different protein-protein interactions that occur in a cell or even during events that occur in a cell. 


   Useful Video
Carbohydrates!  YouTube plugin error  

This video is a basic overview of Carbohydrates and what they are made up of.

It discusses how carbohydrates are made and what make up large chains.

They also mention how large chains can be broken down into smaller chains.

This video has no audio lecture, however a basic visual lecture on Carbohydrates

which I found very helpful.




   Useful Link
Lipids  http://www2.chemistry.msu.edu/faculty/reusch/VirtTxtJml/lipids.htm   This is a very useful link on information for Lipids. As seen in the e-book, there are many kinds of lipids and they carry many different characteristics. The link that I have posted breaks down the information into simpler terms and provides diagrams that go along with the explanations. On this link you will find information from Fatty Acids to Steroids. I have used this link in our freshman Biology class to have a better understanding of Lipids.





Comments (2)

Derek Weber said

at 4:41 am on Sep 16, 2010

9/15: Updated. Great job expressing yourself in the daily update. For your journal article, try to find the original paper cited in that summary and link to that as well.

Siddarth Santhebennur said

at 7:37 am on Sep 16, 2010

Once again..Yes Sir : )

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