Tuesday, September 30, 2008

Eukaryotic cell organelles

In preparation for the biology GRE subject test I need to re-learn (or learn) general biology. My upper division work has been focused on evolution and computational techniques, so I am very rusty on most other biological topics.

Today I went over organelle structure and function in eukaryotes (organisms that have membrane enclosed structures within their cells such as animals, plants, protists, and fungi). As well as containing the chromosomes, the nucleus contains the nucleolus which is the production site for ribosomal subunits. These subunits are then shipped out of the nucleolus, then the nucleus and into the cytoplasm. The ribosomal subunits are destined to either float freely in the cytoplasm where they eventually link up over messenger RNA (mRNA) to make proteins destined for the cytoplasm, or they attach to the walls of the endoplasmic reticulum (ER) where they produce proteins that are destined for a membrane or export out of the cell. It is also interesting to note that the mitochondria and chloroplast produce their own set of robosomes that more closely resembles procharyotic(bacteria, archea, etc) ribosomes.

The destination of proteins is determined by their amino acid sequence, structure, and sometimes post-translational modifications. Proteins that are to be secreted out of the cell have a hydrophobic signal sequence called the signal peptide.

Lysosomes are interesting. They have enzymes inside of them which digest proteins, carbohydrates and nucleic acids. These enzymes function well in an acidic environment where the pH is about 5 (a cell's pH is closer to 7 meaning it is neutral). This fact keeps the overall cell safe because the enzymes aren't able to digest the cell in its higher pH environment. However inside the lysosome, the pH is kept at 5 so that the enzymes are able to do their work. That is a very interesting adaptation.

Peroxisomes are similar and break down fats and harmful chemicals like alcohal. These organelles do so through the production and degredation of peroxide, which if allowed to come in contact with DNA would be very dangerous. Thus the reactions are kept within the peroxisome.

The mitochondria and chloroplast are cool. They have their own DNA, and produce many of their own proteins. They are basically like a small unicellular organism that lives within the cell and produces the energy needed for the cellular function. Biologists theorize that these organelles were once seperate organisms that entered into a symbiotic relationship where they exchanged energy production for protection and a stable environment.

Monday, September 29, 2008

Programming languages

We covered some of the basic programming language types today. The imperative type is the most commonly used one. It is characterized by assignments and statements following a sequential order. C and Java are examples of this. The functional type is less common and includes languages such as scheme, lisp, ML, and Haskell. In its purest form the functional language contains no assignments. The entire program is defined by function definitions, and the invocations of those functions. This idea of a language is called lambda calculus. Logic languages seem pretty interesting. The idea of a logic language is that you define logic relations between variables, and then when you implement the program, you can have it solve for any number of variables. The simple example of this we got in class was say you have a function called append. Rather than defining the function like one would in C where you take in two things and spit out the appended result, in a Logic language like Prolog you have the relational function append that has three things as arguments and the function returns true if the three things satisfy the defined requirement of the first two being subsets of the third. If you pass in a variable you want the function to solve for it will do that for you and spit out all of the solutions. For example ?append([1,2],[3,4],X) would spit out [1,2,3,4]. If you give it ?append(X, [3,4], [1,2,3,4]) it would spit out [1,2]. It seems like logic languages could, in theory, simplify programming.

Artificial Intelligence

This is the first post of what I plan on being many posts about what I learn from day to day in my classes. Yes, this may be a good time to unsubscribe from email updates.

AI is extremely prevalent. More so than I previously thought. When I think of AI I typically think of humanoid robots like Kizmet. Examples that I wouldn't have thought of include the intelligent agents in computer games, wall street trading robots and risk management systems, Google web search, the mars rover... There are tons of examples out there. In fact every computer utalizes concepts that were first thought of in AI research. For example the idea of hard coding expert information into computers was an active area of research in the 80's; today searchable dictionaries, computer diagnostic programs, and online sites like webmd are commonplace.

I am very excited to continue on with this class. I plan on posting a few things that I find the most interesting from each lecture.