An interesting Biochemistry website I found is The Journal of Biological Chemistry (JBC).
The JBC website is fascinating, and filled with more information than any one person could ever absorb! Unlike other journals I have looked through, this website is very user friendly; you do not have to have a PhD to understand the resources, let alone navigate them.
Aside from the usual search features, articles, reviews, and archives, there a number of interesting features worth noting. The JBC has links to "Affinity Groups" which lead you to pages tailored for specific disciplines such as enzymology, gene regulation, RNA, or signal transduction.
The website also offers downloads of podcasts which is extremely helpful. We might not always have enough time to read every article of interest, so it is helpful to be able to download and listen to discussions in the car or wherever and whenever we want. The podcasts I have listened to were interviews with the authors of various papers; it also was helpful to hear authors discuss their work and findings in their own voice and answering questions, rather than just reading a standard article.
On top of the podcasts, the JBC actually offers an iPhone and iPad app to keep up to date with the journal. Overall, there is a vast array of information and resources available on the JBC website which help connect Biochem to medicine, research, and so much more. Making these connections helps me better understand the topics we study by keeping up to date with their real world implications.
Friday, March 2, 2012
Connections With Past Knowledge
When friends and family have asked me how my Biochemistry class is going, most are a bit shocked at my emphatic response: I love it. I love this class precisely because of the connections it has created for me between the other areas of science I previously studied.
I knew right away in our first class that this would be the case. We were asked to look at a titration curve and give our best guess interpretation of the information in front of us. Prior to this summer, I would have been clueless. Yet, as I studied for the MCAT exam last year, I found that I was teaching myself a great number of concepts; titration curves were one of these. So my interest was piqued during that first lecture when I realized this class will strengthen my knowledge of previous concepts, as well as tie them together across the multiple disciplines from which they were first introduced.
Since then I have continued to connect our lessons in this class with previously encountered information. Most strikingly, Biochemistry has thus far seemed to provide a comprehensible bridge between lessons learned in Biology and those learned in Organic Chemistry. Biology was the study of life. Orgo was the study of chemistry related to carbon and its importance. More specifically, Orgo began to show how so much of our biological processes are dictated by the chemical rules and mechanisms covered in that course. I studied polarities, acids, bases, hydrolysis reactions, kinetics, activation energies, isoelectric points, peptide formations, and so much more. While many of the terms and molecules occasionally rang familiar bells from Biology class, the context in which they were discussed felt somewhat detached from their real world applications in living organisms.
Yet in Biochemistry thus far, many of these concepts and molecules are being readdressed in ways which connect their Organic properties with the biological functions I had simply accepted at face value. Now, Biochem seems to be allowing me to connect dots between how things happen and why they happen, biologically and chemically speaking. For example, instead of simply memorizing curved arrow mechanisms, I have now seen how hydrolysis and saponification are used to break down triacyglycerols. Or for instance, instead of learning to recognize bonds with generic R groups, I have now seen that I am able to recognize bonds like phosphodiester linkages within essential DNA molecules.
Learning how chemical properties dictate the biological functions which enable life to exist, has thus far fostered connections between my prior studies. Building these bridges between disciplines has furthered my comprehension of each topic. Synthesizing various disciplines into a cohesive understanding of biological systems has left me eager to discover what connections I will make next.
I knew right away in our first class that this would be the case. We were asked to look at a titration curve and give our best guess interpretation of the information in front of us. Prior to this summer, I would have been clueless. Yet, as I studied for the MCAT exam last year, I found that I was teaching myself a great number of concepts; titration curves were one of these. So my interest was piqued during that first lecture when I realized this class will strengthen my knowledge of previous concepts, as well as tie them together across the multiple disciplines from which they were first introduced.
Since then I have continued to connect our lessons in this class with previously encountered information. Most strikingly, Biochemistry has thus far seemed to provide a comprehensible bridge between lessons learned in Biology and those learned in Organic Chemistry. Biology was the study of life. Orgo was the study of chemistry related to carbon and its importance. More specifically, Orgo began to show how so much of our biological processes are dictated by the chemical rules and mechanisms covered in that course. I studied polarities, acids, bases, hydrolysis reactions, kinetics, activation energies, isoelectric points, peptide formations, and so much more. While many of the terms and molecules occasionally rang familiar bells from Biology class, the context in which they were discussed felt somewhat detached from their real world applications in living organisms.
Yet in Biochemistry thus far, many of these concepts and molecules are being readdressed in ways which connect their Organic properties with the biological functions I had simply accepted at face value. Now, Biochem seems to be allowing me to connect dots between how things happen and why they happen, biologically and chemically speaking. For example, instead of simply memorizing curved arrow mechanisms, I have now seen how hydrolysis and saponification are used to break down triacyglycerols. Or for instance, instead of learning to recognize bonds with generic R groups, I have now seen that I am able to recognize bonds like phosphodiester linkages within essential DNA molecules.
Learning how chemical properties dictate the biological functions which enable life to exist, has thus far fostered connections between my prior studies. Building these bridges between disciplines has furthered my comprehension of each topic. Synthesizing various disciplines into a cohesive understanding of biological systems has left me eager to discover what connections I will make next.
Thursday, March 1, 2012
PDB Molecule: Amyloid-beta precursor protein
The Amyloid-beta precursor protein (APP) is a rather large transmembrane protein, comprised of a sequence of 770 amino acids. APP is found on the surface of cells throughout the body and is responsible for many different physiological functions. Researchers believe APP has a central role in various processes, though the exact details of the protein's numerous functions are still being discovered. It is comprised of multiple domains which make the molecule flexible, and thus challenging to examine as a single intact protein. APP's fragmented form, however, garners the most attention as it is seen as a pivotal role player in Alzheimer's and other neurodegenerative disorders.
A healthy intact APP acts as a receptor on the surface of cells, capable of binding to various extracellular molecules. However, the protein is also subject to cleavage by secretases, a specific class of proteases. When APP is cleaved, peptide fragments are released. Release of one of these small peptides, known as the amyloid-beta peptide, is highly problematic. When amyloid-beta peptide is released, it changes shape and aggregates into long fibrils which then accumulate and form dangerous plaques. A buildup of these dense plaques on the surface of nerve cells leads to a disruption of normal function. The accumulation of plaque can slow nervous functions, lead to memory loss, dementia, and the onset of Alzheimer's Disease.
Though much has yet to be learned about the specifics of APP and it's fragmented peptides, they are the focus of current research. Scientists hope to target this protein and it's peptide fragments as possible sources of curing or treating debilitating neurodegenerative disorders such as Alzheimer's.
A healthy intact APP acts as a receptor on the surface of cells, capable of binding to various extracellular molecules. However, the protein is also subject to cleavage by secretases, a specific class of proteases. When APP is cleaved, peptide fragments are released. Release of one of these small peptides, known as the amyloid-beta peptide, is highly problematic. When amyloid-beta peptide is released, it changes shape and aggregates into long fibrils which then accumulate and form dangerous plaques. A buildup of these dense plaques on the surface of nerve cells leads to a disruption of normal function. The accumulation of plaque can slow nervous functions, lead to memory loss, dementia, and the onset of Alzheimer's Disease.
Though much has yet to be learned about the specifics of APP and it's fragmented peptides, they are the focus of current research. Scientists hope to target this protein and it's peptide fragments as possible sources of curing or treating debilitating neurodegenerative disorders such as Alzheimer's.
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