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

Page history last edited by Aarti Patel 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

 

September 10, 2010

     Today we learned about organic molecules. Carbon is an organic element. It can create four bonds. It creates nonpolar covalent bonds. To make this bond radioactive, functional groups are attached to it. Functional groups are groups of atoms with special chemical features. They inlude amino (-NH2), cabonyl (-CO), carboxyl (-COOH), hydroxyl (-OH), methyl (-CH3), phosphate (-PO42), sulfate (-SO4), and sulfhydryl (-SH). These groups are bonded to carbon. They make the carbon-hydrogen molecule useful in the world. Isomers are two stuctures with identical molecular formulas but different structures. Carbon containig molecules have various forms. A difference in stucture will completly change properties of the stucture. Structural isomers have the same atoms, but different bonding relationships. Stereoisomers have the same atoms, but the positioning of the atoms are different. There are two types are stereoisomers: cis/trans isomers and enantiomers. Cis/trans isomers have different configurations determined by the positioning of the hydrogen on the carbon double bond. They are called either cis- or trans- depending on whether the hydrogens are on the same side of different. Enantioners are isomer that are mirror images of each other.

     Monomers are single molecules. They link together to form polymers. They are linked together through a proccess of dehydration synthesis (the removal of a water molecule from two molecules). They are broken aparth through hydrolisis (the addition of a water molecule into a polymer). Carbohydrates are composed of carbon, hydrogen, and oxygen (Cn(H2O)n). The simplest sugars are called monosaccharides. Disaccharides are two monosaccharides combinded. Polysaccharides are many monosaccharides linked in a long chain.


 

September 15, 2012

     Today, in class. we discussed protiens.  A protien is composed of carbon, hydrogen, oxygen, and nitrogen.  Protiens are made up of chains of linked amino acids.  Amino acids are the building blocks of protiens.  There are twenty different amino acids.  This are linked together by pepdide bonds to form long chains.  The amino group and carboxyl group are basic in evry amino acid; what changes is the 'R' group.  The R groups differ in being nonpolar, polar (uncharged), and polar (charged).  These changes affect the structure and funtion of the protien.  The nonpolar groups usually have have a methyl group in the R group. The polar uncharged usually have an hydroxyl group.  The polar charged group can include either O- or H+. This characteristic makes those amino acids either acidic or basic.  Due to this, amino acids in that group, are able to form ionic bonds with one another.

     The basic stucture of and amino acid has an alpha carbon (central carbon), attached to an amino group, carboxyl group, hydrogen, and an 'R' group.  There are four different protien structures.  The first is the primary structure.  This is a linear cahin of amino acids attached by peptide bonds.  In the secondary structure, the protien taked either the alpha helix structure or the beta sheet form.  In the alpha helix structure, the protien twists into a helix, held together by hydrogen bonds.  In the beta sheet form, the protien is pleated and also held together by hydrogen bonds.  Protiens fold inorder to keep their hydophobic areas away from the surrounding water.  In the tertiary structure, the protien is folded into a three-demensional shape.  It is held together by several bonds including, hydrogen bonds, covalent bonds, and sulfhydryl bonds. This is the functional unit for a single protien chain.  When two or more protien chains are attached, the quaternary structure is formed.


 

September 17, 2010

     Today we discussed protiens and genes.  Genes are the discrete unit of DNA that encodes for a functional product.  The primary structure of a protien strand is determinded by genes.  We read an experiement that tested whether genes detemined the stucture of the tertiary, or functional unit, as well.  The scientists performing this experiement hypothesised that protiens contain information, within their amino acid sequence, needed to fold into their functional units.  The experiment used the protien ribonuclease. a protien that degrades RNA.  First, the ability of the protien to degrade RNA was tested.  Ribonuclease was 100% functional.  Then, B-mercaptoethanol and urea were added to denature ribonuclease.  B-mercaptoethanol broke the disulfide linkages and urea broke down H bonds and ionic bonds.  The ability of ribonuclease to break down RNA was now again measured.  About only 10% of ribonuclease functioned properly.  Then the mixture was added to a chromatography column.  These beads trapped B-mercaptoethanol and urea due to the large pores of the beads.  Ribonuclease was filtered out and the bonds were formed again.  The ability for ribonuclease to break down RNA was once again measured.  It functioned about 90%.  The scientists concluded that some protiens acan fold into their functional structure, without assistance from anything else.

     This experiement helped me understand how protiens know how to fold into their functional units.  Protiens fold based on the properties of their amino sequence.  How the protien folds is based on how many and where its hydrophobic areas are, the amount of bonds that can be made, etc.


 

B.  Useful Materials

 

  •  http://www.ncbi.nlm.nih.gov/pubmedhealth/PMH0001053 
    • This is an article about the drug Thalidomide.  Thalidomide is a drug used to treat multiple myeloma in people.  The article explains usage and how to recieve this medication.  It also explains the sever side effects and warnings of this medication.  It can cause sever birth defeacts and several other things.  In class, we talked about isomer and how they are two molecules with the same molecular formula, but different structure.  We learned that though the structures are slightly different from one another, the function changes dramatically.  Thalidomide is a molecule which has an isomer.  One isomer, will help treat the disease.  The other form of this molecule and cause sever medical problems.

 

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This is a video of all the functional groups.  It is a song of the functional groups.  It is an easy way to remeber them.  The song is very catchy and easy to learn.  It helps remember the eight functional groups.

 

http://www.youtube.com/watch?v=mAjrnZ-znkY  

 

This video shows the process of protien folding.  There is an interview with a college professor about how protiens fold.  He explained why it folds and how it folds.  He also metioned that there is always trial and error when protiens fold.

This video also talks about the online portein folding cometition on Folding@Home.  It show the different competitors and explains what the program is.

 

http://www.youtube.com/watch?v=EZ1XuOgknuE&NR=1&feature=fvwp 

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Comments (3)

Derek Weber said

at 4:31 am on Sep 16, 2010

9/15: Not updated.

Aarti Patel said

at 6:30 am on Sep 17, 2010

Sorry, my blog was on another Chapter 3 page.

Derek Weber said

at 10:41 pm on Sep 30, 2010

Your 9/17 update is outstanding. You are really doing a great job on this project.

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