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

Blog for 9/10/10 Lecture

On Friday, we talked about functional groups in class.  By adding functional groups, it can change the characteristics or give characteristics to the molecules.  We defined functional groups as groups of atoms with special chemical features that are functionally important.  Some examples of functional groups include:

1) Amino group - NH2 - these can be ionized and participate in electrostatic interaction (ionic bonds) They are anions.

2) Carbonyl - CO - are in lipids, sterioids, waxes, proteins

     a) Ketone - found in the middle of a chain

     b) Aldehyde - found at the end of the chain because Hydrogen can only have one bond and it already has one with the Carbon 

3) Carboxyl - COOH - amino acids, fatty acids, acidic; can be ionized and is involved in electrostatic interaction, amino and carboxyl groups are attracted to each other

4) Hydroxl - OH -  its not an acid, polar covalent bond, found in steroids, alcohol, carbohydrates; participates in hydrogen bonds; target of dehydration reactions

5) Methyl - CH3 - may be attached to DNA, proteins, carbohydrates

There are others as well. 

Isomers are two structures with an identical molecule formula but different structures and characteristics.  Enantiomers are molecules that have mirror images.  However, in order for it to be an enantiomer, it has to have four different attachments.  In order words, Carbon has to bond for four different things.   

Blog for 9/15/10 Lecture

Today the lecture was about the part of the cell that Dr. Weber finds most interesting; proteins! Most molecules of the cell are made up of Carbon, Hydrogen, Oxygen, and Nitrogen.  Proteins are also made up of these elements but they also contain small amounts of other elements, particularly Sulfur.  Amino acids are the monomers or proteins.  They are 20 different amino acids that make up long chains (polymers).  All amino acids have a common structure, but the attached R-group is the variable that gives an amino acid its specific structure and function. 

Amino acids are categorized into three different groups: Nonpolar, Polar (uncharged), and Polar (charged).  In the nonpolar group, the amino acids are hydrophobic and are neutral.  They are slightly branched and are recognizable because they all have a Hydrogen atom.  Tyrosine is part of the nonpolar group but it is an exception because it is slightly charged (has a hydroxyl group - OH )  The polar (uncharged) group is not ionizable.  They have carbonyl functional groups as well as amino groups and hydroxyl groups.  Hydrogen bonds form beacsue partial charges attract each other.  The polar (charged) group has charges and is therefore ionizable.  Carbonyl groups found in these amino acids are positive and acidic.  The amino groups are negative and basic.  Therefore, these two attract one another. 

Peptide bonds are formed between monomers of proteins (the amino acids) by the dehydration reaction (the removal of water). 

Blog of 9/17/10 Lecture (submitted 9/19/10):

Friday's class was different than what our previous classes have been like.  Usually, Dr. Weber shows the students slides and we have a class discussion and incorporate critical thinking into the lesson.  However, on Friday, the entire class was about critical thinking because Dr. Weber put us on the spot in a sense.  It was a good way to keep us thinking, however the pressure made me nervous. 

During class, we discussed more of Chapter 3.  DNA and RNA are information molecules that also participate in protein synthesis.  DNA is made up of genes.  A gene is a discrete unit of DNA that encodes for a functional product such as RNA and proteins.  All cells of an individual have the same DNA.  That is to say that heart cells have the same DNA as liver cells and so on.  Carboxyl and Amino groups participate in stabilizing secondary structures (back bone).  Tertiary Structure, when the protein is in a 3D form, decides the fucntion of the protein and participates in electrostatic interactions for stabilization. 

We looked at and analyzed an experiment in class.  We learned that Nuclease is a protein that cuts up the bonds of RNA and degrades it.  Denaturing a protein means that the protein unfolds due to heat or chemicals and becomes nonfunctional.  Hydrogen bonds and electrostatic interactions have charges (Urea stops charges and therefore denatures a protein).  Size-exclusion columns separate molecules based on their size.  Proteins are the largest macromolecules so the small molecules such as urea molecules stay behind.  This suggests that structure = function. 

Amino acid structure determines protein functioning, this is in the Primary Structure. The Quarternary structure consists of 2 or more polypeptides that form one big protein (ribosomes, hemoglobin, etc.). 

B.  Useful Materials

This website provides information about the drug Thalidomide that was used in the 1960s by many women who had used the drug to treat morning sickness. When the women gave birth, their children had serious birth defects such as shortened or even missing limbs.  Shortly after this observation was made, thalidomide was banned worldwide. However, today it has been proven that thallidomide can help treat diseases such as leprosy and AIDS.  However, the government has put many regulations on the drug so that it is used wisely. 

Thalidomide used during pregnancies (submitted 9/11/10)

Isomers (submitted 9/12/10): 

This video describes Isomers and why they are different.  Isomers have the same molecular formula but differ in their structures and functions.  The video includes a variety of examples to further explain what isomers are.  They use the example of Butanol.  Depending on the structure (placement of Carbons and OH groups), Butanol can have many functions. 

Journal Article:

Effect of Thalidomide and Morphine on Rats (submitted 9/12/10) 

An experiment was performed to see the effects of Thalidomide and Morphine on rats. The rats had neuropathic pain and the scientists wanted to see if using the drugs had any effect on them.  There was a control and the effects on the rats were recorded.   Mechanical stimulus was applied to the paw to measure the withdrawal threshold.  The pain withdrawal thresholds became significantly decreased compared to the baseline.  The results of the experiment are that morphine and thalidomide may be alternative therapeutic approaches to neuropathic pain.  This relates to our most recent lecture because we had discussed Thalidomide and the effects the drug has on people, particularly pregnant women and the baby. 

Protein Structures (submitted 9/19/10):