Final Entry (for now)

The three things that bound this class together were as follows:
1. DNA. Everything in some way relates to DNA. its structure, its components and function, and how things interact with it.
2. Gel electrophoresis. It seems that every lab, we ran a gel. due to this fact, I feel like gel electrophoresis is an important component to understanding the concepts in this course, and in this way binds everything together.
3. Computers have it out for me. Every assignment has been plagued with computer issues, from things not loading, to things not posting, to the final and utter obliteration of computer components due to a freak lightning strike about a week ago, I have learned that computers, while very important to this course, cannot be trusted. I have since learned to back up all my important school documents in multiple formats in multiple devices to prevent such horrific things from happening.

They are intertwined as gel electrophoresis can be used to analyze DNA and PCR reactions, which failed for me, though I hate to think of how they might have failed should a computer have been involved in the PCR process.

Edit: when posting this blog entry, I recieved an error message and had to retype everything! hooray! new lesson learned; use word to write entries for web-based submission.

Glucose

Glycolysis is not a simple process. While one might think glucose would be a main energy source for the cell, it isn't. It is, however, a great way to generate the main energy source of cells, ATP. Glucose must first be broken down into pyruvate. In this process,some ATP is used, but there is a net gain of 2 ATP molecules. Pyruvate can then go on to fuel the citric acid cycle, which causes the build up of NADH, and 2 FADH molecules. these molecules go on to create many more ATP molecules in the electron transport chain. One glucose molecule can eventually become 32 molecules of ATP via these three processes. That's a lot of energy.

Connections with past knowledge

Thus far, not much has changed since my last post on this topic. Thermodynamics was covered extensively in organic chemistry. Transcription, translation and nucleic acid structures have been extensively covered in Biology 1. Mention was made in biology 1 of glycolysis but he details were not fully revealed until now.

Cool Biochem website

Check this out!
Science Daily is all about the research, and while not an accredited source for research papers, it tends to pull up some of the coolest research being done currently. Science Daily has a dedicated biochemistry section full of the most interesting stories from recent research. A great way to remind yourself how truly exciting research can be.

What knowledge have you connected with past knowledge?

This course has been a recurring source of flashbacks to organic chemistry. Between chemical kinetics, chemical structures and the importance of functional groups, there has been a lot of review on the subject of organic chemistry. In ties with the name of the field, chemistry isn’t the only knowledge to bear connections with biochemistry, there have also been numerous times where the knowledge overlap between biology and biochemistry have become apparent. Most recently with the discussion of how enzymes work, although when I first learned it, I had know the “lock and key” variant of the process, and knew nothing of the induced fit model. Other previously known information includes: amino acids, primary, secondary, tertiary and quaternary structures of proteins and formation of polypeptide chains. No information so far has been “new” so to speak, but it has gone more in depth into ideas discussed in previous classes.

Find a protein using PDB explorer–describe your protein, including what disease state or other real-world application it has.

My protein, lymphoid tyrosine phosphatase (LYP) is composed of alpha helixes and beta pleated sheets. Having only one unit, and no subunits, this protein has no quaternary structure. An important protein in the function of the human autoimmune system, LYP is a target for modern drugs and possesses a large risk factor. Recent studies of the structure of this protein have revealed a rather unusual disulfide bond between the catalytic CYS and a local non-catalytic CYS. This disulfide bond is important to the regulatory function of LYP. The study also found a phosphate ion bonded in the active center of LYP which, upon dephosphorylation but before the actual release of the phosphate, the protein will take on an intermediate conformation. These finds help us understand more about the regulation of this protein, which in turn helps us find out more about the human immune system.

What is biochemistry, and how does it differ from the fields of genetics, biology, chemistry, and molecular biology?

Biochemistry is the study of chemicals within organisms, and an amalgam of the other sciences to be mentioned in this post. Using bits and pieces of genetics, biology, chemistry and molecular biology to describe the chemicals within organisms and their function within that organism. Genetics is the study of DNA and gene expression in organisms, focusing both on the genotypic expression (microscopic level) and the phenotypic expression (macroscopic level) of genetic traits. Biology is the study of organisms (on a macro scale mostly) and their interactions with other organisms. Molecular biology focuses on the molecular processes that occur within cells, it is very closely related to biochemistry.