April 5
This week has been quite eventful to say the least! Students have continued to work on their 3D modeling and poster design for their project on the G-protein transducin. To that end, all the details of the molecular story of the G-protein’s three subunits have been modeled as well as its GTP binding site, and modified side chains associated with its association with the inner cell membrane. With regards to their poster, students have been learning the more complete story of visual processing involving the anatomy and physiology of the eye, its component rod and cones cells, as well as the many layers of neuronal communication that take place to carry the signal through the optic nerve to the primary visual cortex. Students also welcomed Dr. Ken Petersen, researcher from KU Medical Center who spoke on the topic of gene regulation on Monday, and Dr. Randy Nudo, another research at KU Medical Center, who spoke on the topic of neuroplasticity.
March 8
It was nice to finally get back to a full week of school. The students began their explorations of proteins in the laboratory this week. Specifically, they were introduced to a technique for separating proteins using electricity called electrophoresis. In this case, students prepared different concentrations of agarose gels which they then pipetted and ran their sample proteins in. They learned how the technique could be used to determine the molecular weight of a protein relative to a standard curve, as well as how particular aspects of a protein’s electrical properties, shape, etc… could be determined. The proteins they studied included albumin, glutamate dehydrogenase, cytochrome C, and lysozyme, among others. These hands-on activities helped them gain a deeper and more practical understanding of the proteins that we have only been modeling up to this point.
February 15
This week students buckled down in reading and analyzing a review paper on the structure and function of G-proteins, which are important in translating external cellular signals into intracellular actions, and Chaperones, which are important in aiding and maintaining the functional state of proteins. This represents our initial efforts in preparing for our attendance at the annual meeting of the American Society of Biochemistry and Molecular Biology being held in Boston, MA this April. The students have also continued to develop and represent their basic knowledge of protein structure and function. We’d like to wish you a “Happy Valentine’s Day” molecular style! The image on the screen behind the students was generated at the Pep-Fold Server using the amino acid sequence HAPPYVALENTINESDAY.
February 8
This week students have continued their exploration of protein structure through modeling. We have continued to use MolyMods about the peptide bond in the chemical combination of amino acids in the formation of proteins. We also use these models to gain a detailed understanding of how hydrogen bonds form between amino acids in the formation of the alpha-helix and beta-sheet (in the image above). We used flexible toobers to explore these secondary structures while creating a model of a zinc finger. At the end of week they have become JMol experts using the software to manipulate molecules downloaded from the protein data bank.
February 1
At the beginning of the week the students were able to finalize their conclusions on their E. coli challenges. On Tuesday and Wednesday the students helped judge the 100 projects that 6-8th grade students had completed for the Lakewood Middle School Science Fair. The students enjoyed the diversity of projects and applying their recently gained experiences with experimental design in judging and leaving productive comments with their projects. Before we travelled to Lakewood each day, began their exploration into the world of proteins. We began this exploration using MolyMods to model amino acid structure and soon were folding hypothetical proteins using flexible toober models. We will continue our exploration of the coming weeks. To finish the week, Amy presented interesting information on the seasonal flu and is more recent occurrence this year. We also discovered the majority of students had taken the time to get vaccinated for flu this year.
January 25
This week students continued their work on their E. coli challenge. It has taken on a life of its own. The students chose to determine the effectiveness of cinnamon extract as a means of inhibiting bacterial growth. In order to conduct their investigation, students were introduced to standard sterile techniques with the use of laboratory burners and inoculating loops, and to the shaking and standard incubators for preparing the overnight culture that they initially used and for growing their experimental plates, respectively. Their results, though expected based on their background research, were exciting none the less showing that the concentration of cinnamon that was used completely retard the growth. Numerous questions have come to light, and I imagine that we could continue exploring their repercussions the entire semester. On Friday, Mason presented intriguing new research on the engineering of new strains of bacteria that could be adjuvants in the production of new vaccines.
January 18
This week, students were put into the shoes of a microbiologist, and given a challenge to develop a means of inhibiting the growth of E. coli bacteria using a particular spice commonly used in Indian subcontinent. Through the activity they are demonstrating and honing their scientific skills of collecting relevant background information, forming a problem statement and hypothesis, and developing and carrying out a procedure to test their hypothesis. As they have found it necessary to learn to use particular laboratory equipment, it has been introduced.
Students specifically learned to use our autoclave which helps us prepare sterile media for growing our bacterial cultures. They have also become familiar with basic sterile technique in plating Petri dishes and sub-culturing to broth cultures as well. They have also quickly practiced the art of maintaining a laboratory notebook.
January 14
This week was spent getting to know each other with a number of activities promoting learning about each other and what brought them to the CAPS Bioscience Program as well as beginning to learn expectation for working in groups. We completed an activity introducing them to laboratory safety so that we could confidently get to work in the laboratory.