Difference between revisions of "Class Journal Week 2"

Revision as of 16:01, 14 September 2015

Nicole Anguiano

1. What is the biggest discovery that I made from these readings?
   • The biggest discovery that I made from these readings was the existence of selenocysteine. Coded by UGA (typically only a termination codon in the majority of organisms), it is only differentiated from the typical termination codon by a hairpin loop in the mRNA. The fact that such a tiny difference in the structure of the codon makes such a dramatic difference was incredible to me, especially considering the fact that in the organisms with the selenocysteine, UGA also codes for a termination codon when it does not have the loop (Brown, pg 14).
2. What part of the readings did I understand the least?
   • Many of the details of Nirenbirg's experiments were very confusing to me. While I understood the overall purpose of the experiments and the results found from them, the exact details of the methods of the experiments were difficult for me to understand.
3. What is the relationship between the genetic code and a computer code?
   • The genetic code can be represented in binary, the language of computers. Each nucleotide can be mapped to a binary sequence (for example, A - 00, C - 01, G - 10, T - 11). With this mapping, the genetic code can be represented equivalently in binary. DNA can be considered like a large computer program that serves not only the purpose of storing data, but also running the functions that determine the actions that a particular cell will take, the proteins that will be created and relatively how much of them should be, and also regulates itself to determine which functions need to be run at any given time (Moody, pg 3).
   • Considering DNA as a program, it can be thought that the DNA is a program written in a higher level language. The RNA is what is created when the program is run - it is the assembly or machine code that is then processed by the computer. The proteins then are the results of the program, for example, an output on the screen or a change in a GUI (Moody, pg 4-5).

Nanguiano (talk) 11:29, 9 September 2015 (PDT)

Emily Simso

1. What was the biggest discovery that I made from these readings?
   • The biggest discovery for me was from the article "Ode to the Code" by Brian Hayes, specifically that the genetic code is so resilient to substitutions. I thought it was interesting that the experimenters arranged the amino acids according to their polar arrangement to judge whether the code dealt with permutations. It seemed incredible that the genetic code could do better than a million other random codes, showing nature's role in creating the code.
2. What part of the readings did I understand the least?
   • There were sections of the Nirenberg reading that were hard to follow, such as when he described the techniques he used to find mRNA "in vitro." While I feel that I understood the general points he made, the details were a little too complex, such as the relationship between C-labeled valine and mRNA. The graphs were somewhat helpful, but I feel like I don't have a full grasp on the experiments.
3. What is the relationship between the genetic code and a computer code?
   • I thought the Moody reading was helpful for this question. He states that genetic code and computer code are "completely equivalent," since a binary can be assigned to the four bases (4). Genetic code and computer code are also similar since they both allow for "programs" to run, which are dependent upon the exact order of the individual units (5). Both types of code allow for a variety of functions as well, but when a mistake occurs in the order of the code, the function either changes or does not run correctly.

Emilysimso (talk) 10:29, 11 September 2015 (PDT)

Kristin Zebrowski

1. What was the biggest discovery that I made from these readings?
   • The biggest discovery I made from these readings was the notion that the antisense strand might have a more significant purpose than just being a placeholder, which was addressed in "Ode to the Code" by Brian Hayes. I found it interesting that the antisense strand creates an antigene that is opposite of the normal gene--I didn't know that before. It also opens up the door for a lot of opportunities for studying the genetic code by showing that it might code for more than just protein synthesis, which is something I hadn't thought of before, although it makes sense now.
2. What part of these readings did I understand the least?
   • While at first I understood Nirenberg's methodology, it was eventually very difficult to follow the techniques he and his colleagues were using to decipher DNA, such as Heppel's synthesis of "trinucleotides and higher homologues" and the significance that the many different experiments had. This made it more difficult to understand the implications of Akira Haji and Hideko Haji's corrections in response to Nirenberg. It was interesting to read about the collaborative effort involved but I feel as though the details of the many trial-and-error experiments conducted in the process made me lose sight of the big picture until the final paragraphs.
3. What is the relationship between the genetic code and the computer code?
   • The genetic code stores information and instructions just like a computer code does and it can be translated into a binary code, despite DNA being encoded by a 4-nucleotide sequence. DNA is a program that runs a cell like a computer code runs a computer and it is capable of being copied. Like all software, DNA can have "bugs" or errors in the form of mutations.

Kzebrows (talk) 21:03, 13 September 2015 (PDT)

Brandon Litvak

1. What is the biggest discovery that I made from these readings?
   • One of the things that really surprised me in the readings was the fact that the genetic code is neither universal nor applicable to all proteins. Section 3.3.2. from Genomes mentions that context-dependent codon reassignment is widespread and applies to a variety of organisms; it was fascinating to learn about the factors (hairpin structures, protein interactions along the mRNA) that further complicate the genetic code. I would say, however, that my biggest discovery was learning that the natural genetic code is the best (or very close to the best) possible code for error minimization. The evolution of this “optimum” genetic code, through the course of billions of years, is really remarkable.
2. What part of the readings did I understand the least?
   • The readings exposed me to a lot of new technical language relating to protein synthesis and its underlying biochemistry and, while it was interesting, it made some of the articles relatively difficult to understand. The article by Marshall Nirenberg employed a lot of unfamiliar terms, which made some of his methods and strategies a bit unclear for me. I don’t feel like I have a good understanding of his cell-free synthesis system (and how exactly he manipulated it). Nirenberg’s descriptions of the experiments/methods of his contemporaries also seemed confusing. Overall, the core message of each article was fairly clear, despite the new language.
3. What is the relationship between the genetic code and a computer code?
   • DNA, essentially, is biological computer code. Like computer code, the genetic code can be executed to perform many (and a variety of) operations. Cells contain ribosomes that are much like the processing units found in computers; the DNA code acts on the ribosomes to cause certain actions that lead to a certain physical output (protein). Like code, DNA can be used, in certain situations, for very specialized purposes (maintaining the “form and properties” of specialized cells) and stay unexecuted in other situations. Being “digital”, DNA can come to have errors or “bugs” which can prove disastrous/harmless.
   • Powerful computers, computer code, and programs, interestingly enough, are the perfect tools for DNA analysis. Computers, via the field of bioinformatics, are being employed to store, search, and compare massive sequences of DNA. Computer code achieves what people cannot: it is able to work with the vast amount of information that is DNA.

Blitvak (talk) 00:45, 14 September 2015 (PDT)

Jake Woodlee

1. What is the biggest discovery that I made from these readings?
2. What part of the readings did I understand the least?
3. What is the relationship between the genetic code and a computer code?

Jwoodlee (talk) 09:01, 14 September 2015 (PDT)