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

9/10/10: This day's lesson started with carbohydrates, which have a ratio of 1 Carbon : 2 Hydrogen : 1 Oxygen.  Then, the difference between unsaturated and saturated fat was discussed.  Unsaturated fats have "kinks" in the chain, which are caused by double bonds.  They are less organized at room temperature, therefore they tend to stay at liquid form.  Saturated fats are basically the opposite of unsaturated fats.  They have no "kinks."  In addition, they are solid at room temperature since they are organized.  The next subject was functional groups.  Functional groups are groups of atoms with special chemical features that are functionally important.  Each type exhibits the same properties in all molecules in which it occurs.  There are eight functional groups: amino, carbonyl, carboxyl, hydroxyl, methyl, phosphate, sulfate, and sulfhydryl.  The amino group (NH₂) is an organic base found in proteins.  This group can become really ionized, is positively charged, and can act as a cation in electrostatic interactions.  The carbonyl group is found in steroids, waxes, and proteins.  There are two subgroups of the carbonyl functional group: ketone and aldehyde.  The difference is that ketone's C=O are found in the middle of the protein chain while aldehyde's C=O is found at the end of the chain with a Hydrogen atom acting as the terminal end.  The carboxyl group (COOH) is found in amino acids and fatty acids.  It is an acid, can be ionized, and acts as an anion in electrostatic interactions.  The hydroxyl group (OH) is found in steroids, alcohol, carbohydrates, and some amino acids.  They are prevalent in hydrogen bonds and are the target of dehydration synthesis.  The methyl group (CH₃)is found in DNA, proteins, and carbohydrates.  The phosphate group (PO₄^2-) is found in nucleic acids, ATP, and amino acids.  The sulfate group (SO₄^-) is found in carbohydrates, protein, and lipids.  The sulfhydryl group (SH) can form disulfide bonds (a type of covalent bond) when they are in close proximity to one another.  Also, this functional group is found in proteins containing the amino acid cystein.  The next topic covered was isomers.  Isomers are two structures with an identical molecular formula, but different structures.  Structural isomers contain the same atoms but different bonding relationships.  Subsequently, monosaccharides were discussed.  They are the simplest sugars and contain either five or six carbons.  Deoxyribose and ribose are examples of two pentose sugars.  The last topic was glucose isomers.  The structural isomer of glucose is galactose.  Stereoisomers of glucose are alpha and beta glucose, and D- and L-glucose (mirror images). 

 

9/15/10: This lecture was focused on proteins.  Proteins are composed of Carbon, Hydrogen, Oxygen, Nitrogen, and small amounts of other elements (notably sulfur).  The protein's monomer is the amino acid, which have common structure with variable R group.  There are 20 amino acids and the side chain determines the structure and function.  Amino acids have a common structure.  There is one Carbon atom (the alpha carbon) around which an R group, amino group, Hydrogen atom, and CO₂^- are situated about.  To connect amino acids with peptide bonds, dehydration synthesis occurs.  Protein structure is either primary, secondary, tertiary, or quaternary.  Primary structure is characterized by its linear form and peptide bonds.  Secondary structure is characterized by parts of the protein making either an alpha helix or beta sheet.  An alpha helix resembles a piece of string coiled around a pencil.  A beta sheet resembles an accordion.  In addition, this structure is held together by hydrogen bonds.  Tertiary structure is characterized by folding the protein chain into different ways giving the entire three dimensional fold of a protein.  The shape is globular and keeps the non-polar proteins away from water by surrounding it with polar proteins.  The lecture period ended before quaternary structure could be discussed. 

 

9/17/10: The traditional part of this lecture was short-lived.  The prmary structure of amino acid, or amino acid sequence, was discussed.  It is determined by genes which are discreet units of DNA that encodes for functional products like RNA or proteins.  Gene expression is very important.  Subsequently, a discussion of an experiment.  The scientist hypothesized that "within the amino acid sequence, proteins contain all the information needed to old into their correct, 3-dimensional shape."  The materials were purified ribonuclease, RNA, denaturing cemicals, and size exclusion columns.  Based on the data, the scientist was able to conclude that certain proteins can spontaneously fold into their three-dimensional shape without assistance.    

B.  Useful Materials

 

This video briefly explains protein structure.

 

 

Hunting Down Protein Interactions Behind Huntington's Disease http://www.scientificamerican.com/article.cfm?id=protein-interaction-huntingtons-disease

This article is about looking for the protein interactions behind Huntington's disease, a neurodegenerative illness.  The disease is caused by a mutated form of the protein huntingtin which interacts unusually with other cells of the nervous system.  After its typical onset in middle age, dementia, loss of movement control,and eventual death from heart failure choking, or infection occur.  Scientists began a screening process to look for the proteins that caused the huntingtin mutation. It turned out that 234 of 2, 500 proteins ended up being related to the huntingtin mutation.  Then the task was to pinpoint which ones caused the mutation.  Subsequently, the scientists did a random test of 60 of those proteins and 30% acted as either enhancers or suppressors.