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

Page history last edited by Pankhuri Garg 13 years, 6 months ago

 

A.  Daily Blog

 

9/10/2010 (submitted 9/10/2010)

 

At the beginning of class, for the text-poll question, we had a identify the lipid diagram. We established that lipids are unsaturated and saturated. Unsaturated fats are liquid because of a kink in them cause by a carbon-carbon double bond. This leads to unorganized molecules which cannot stack properly, causing them to be liquid. No matter how large the compound, even one kink in the structure, make the compound unsaturated. We then proceeded to talk about functional groups, which honestly, I do not understand. We discussed there properties and there identification. Its not as hard as it seems, but it will take practice for me to understand them and to be able to name them at first sight. Carbon, a organic molecule, plays a very important role in all our bodily functions and elements. It is a part of many of the functional groups and most organic compounds depend on the number of carbon atoms for there properties and function. The addition of even one extra carbon attracts other groups and atoms; completely changing the compound. One of the most interesting things i learned about today was enantiomers. Enantiomers are basically two compounds with the same molecular formula, same mass, and technically the same structure; except, they are mirror images, causing them to have completely different properties. Just like gloves, the have mirrored structures, and each serves a different purpose. A great example of this was Thalidomide. Thalidomide was a drug given to pregnant women to cure morning sickness. While this drug was distributed in public, there was perhaps a very a important fact unknown about this. The enantiomer of thalidomide, unknowingly distributed to cure morning sickness, actually caused birth defects in new born infants and could have been potentially dangerous to the mother too. Other than that, we quickly went over hydrolysis and dehydration synthesis, and ended class. 

 

9/15/2010 (submitted 9/16/2010)

 

According to me, proteins have always been unnecessarily complicated things at first look (Sorry, Dr. Weber). And functional groups don't make them any more amusing. So ya. Proteins are nasty. There. I said it.  But, then comes today's lecture, which made things a whole lot easier. Now its just a matter of identifying and memorizing. Each amino acid contains a back bone of a carboxyl group, a amino group, and a alpha carbon attached to a H atom. The variable-R group also attaches to the alpha carbon, and is what determines the function of the amino acid. The amino group is the N-terminus and is always to the left, while the carboxyl group is the C-Terminus, and is always to the right. All amino acids are always built around a central carbon atom. The 20 amino acids them selves are split up into 3 groups: non-polar, polar, and charged. Non-polar and polar group amino acids cannot be ionized. Non-polar amino acids are hydrophopic, while polar amino acids are hydrophilic. Charged amino acids are further divided into basic and acidic. An amino acid with a negative charge is basic, while a amino acid with a positive charge is acidic. We then talked about how amino acids bond. The C-terminus end bonds with the N-terminus end. The C-terminus contains a OH molecule, and the N-terminus contains a O molecule. When the two are combines, H2O is released and the bond is formed. The bond is called a peptide bond, and the process is called dehydration synthesis or condensation. The middle row of the polypeptide chains follows the pattern of carbon-carbon-nitrogen-carbon-carbon-nitrogen- and so on. 

     We then proceeded to talk about the actual structure of proteins. Primary structures are linear chains of amino acids. Secondary structures occur when parts of the protein starts to fold up, , forming hydrogen bonds, and becoming more stable than the linear chains. The two types of secondary structures are the alpha-helix, which looks like a spring, and the other type is a beta-sheet, and it looks like a accordion fold. The tertiary structure is the important 3-D complex structure. Hydrophobic amino acids start to fold in towards each other to avoid their aqueous surroundings and more hydrogen bonds fold, putting the protein chain into is most stable form. The tertiary structure is what determines a protein's individual functional unit. One tertiary polypeptide contains several different types of fold. the R groups form H bonds and nonpolar amino acids form bulky rings. The quaternary structure is composed of numerous such polypeptides. 

     To be honest, I don't understand half the stuff I learn in class (no offense to Dr. Weber's amazing teaching skills) and all of it just goes in one ear and out the other, or is automatically tuned-out by my ears. I understand the information when I get home and write this blog; explaining all parts of the lecture for a grade. 

 

9/17/2010 (submitted 9/17/2010)

 

What a great day to come to school and sit in a bio lecture (my birthday). Surprisingly I didn't zone out. We started taking about DNA and nucleotides. Genes are discrete units of DNA that encodes for a functional product. All parts of the body, even if they have different functions, have the same DNA. Its the expression of the gene that gives the part its function. Proteins play an important role in gene expression. We further talked about the structure of proteins. Polar proteins form hydrogen bonds to stabalize structure. Oppisitly charged R groups engage in electrotatic interaction. We were then challenged with the question whether amino acid chains have the ability and the information to fold up by themselves into a certain structure. After reading experiment that tried to test this clause, we learned that certain proteins spontaneously fold into their final, functional shapes without assistance from other cellular structures or factors. In the experiment, ribonuclease, protein that breaks up RNA, was added to a sample of RNA. Urea was added to brake bonds formed by charges i.e. hydrogen bonds and ionic bonds. Beta-mercaptoethanol (BME) was added to break up disulfide linkages. After the protein had denatured, its activity of breaking the RNA had almost stopped. Then, the mixture was filtered, the urea and the BME filtered out. The denatured protein, renatured and its activity was back, close to normal. The bonds that were broken reformed in their original locations. This proves that proteins do not need any other factors to help them regain their original shape, also supporting the hypothesis. Their ability to fold is determined by their primary structure. The order of amino acids in the primary structure is coded in the DNA as that gene. Protein would be nothing without their tertiary structure. Structure = Function of protein. 

 

 

B.  Useful Materials

 

1. Thalidomide: Research Advances in Cancer and other Conditions - I found this particular article very interesting. Dr. Weber mentioned in class how Thalidomide was used as medicine to treat morning sickness in pregnant women. However, th enantiomer of Thalidomide caused defected or undeveloped limbs in newborns. Nearly 10 years after Thalidomide was said to treat morning sickness, the FDA has approved it to be a potential treatment for one type of skin condition, as well as a type of cancer. The drug specifically has been effective in skin lesions cause by leprosy and myeloma - a blood and bone marrow cancer. Thalidomide is now being tested to treat inflammatory disease and HIV. 

 

2. Functional Group Tutorial - This is an interactive web-site about functional groups, something we all struggled with in class. One thing I really like about this is the U-Draw Functional Group activity. Basically, it gives you the diagram of a large molecule. You have to circle all the functional groups in the molecule. Once you are done, you can check it and it tells you if you were right or wrong. Its a great tool to help you recognize Functional groups! 

 

3. Hydrophobic, Hydrophilic, and Charged Amino Acids Networks within Protein - This journal talks about the abundance of non-polar hydrophobic amino acids over the charged amino acids and the polar hydrophilic amino acids. The average degree of hydrophobic networks is larger. The average strength in nodes of hydrophobic articles is close to that of charged amino acids, while the strength of hydrophilic is not even close. 

 

4. Protein Structure - This short animation gives you a crash course on protein structure and denaturing. It uses eggs as its main example to explain the process.

 

5. Amino Acids: This pictures gives a clear view of the 20 different types of amino acids, their composition, and their groups. It also provides you with their symbol and abbreviation. 

 

 

 

Comments (1)

Derek Weber said

at 4:19 am on Sep 16, 2010

9/15: Udpated. I really like the second item on reviewing functional groups. This is what I mean by useful. That should serve as a great study tool.

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