Class Journal Week 2

Kurt Gosch

1. The biggest discovery I made from these readings was definitely the extent to which bacteria was used to discover and understand the genetic code. It may be a little pretentious of me, but I had always thought as anything DNA related to have been found through studying humans alone. However, it obviously makes perfect sense to use bacteria as the source of study, since they are simpler, easy to reproduce, etc.
2. Most of the Article Deciphering the Genetic Code was difficult for me to understand. There was a large volume of terms that I had no idea what they meant. Some I googled, some I just gave up on. The writing style in general was also not ideal, as the author tended to wander from topic to topic, the information within could have easily been conveyed in perhaps half as many words.
3. From what I could understand, it seemed that it was discovered thought a long and painful process of trial and error. Various combinations of mRNA were mixed together and every time a successful bonding with amino acids took place it was recorded, until all 64 combinations had been found.
4. The genetic code is basically the same as a computer code. The molecules are the 1's and 0's and the way that they combine together as DNA is the language (like Java, C++, or Ruby for a computer). Just like in a computer code, the smallest change in how the words(letters) are put together can have massive impact on what the code does. The best example from the readings is from the last article, when the author states that "errors can mean that embryos fail to develop at all - a fatal flaw in the operating system that causes the human system to crash as it boots up".

Kgosch (talk) 15:45, 7 September 2013 (PDT)

Alina Vreeland

• What is the biggest discovery that I made from these readings?

Before reading the Nirenberg article, I had not been familiar with the idea of cell-free synthesis. Being able to create and manipulate proteins without an actual living cell is quite amazing, and I'm impressed by new technologies in the field that I am constantly learning about.

• What part of the reading did I understand the least?

I didn't understand a lot of the processes described in the Nirenberg reading. I continually had to look up certain compounds or terminology that was used in order to get a feel for what was going on. While the process of discovering how the genetic code worked was interesting, the article itself was tedious to get through.

• How was the genetic code solved experimentally?

First, polynucleotides were synthesized and put into a series of random orders and proportions. After all of them were synthesized, they tested how each would react to one out of twenty tRNA samples, and whether binding would occur. Then the start and stop codon were discovered, which gave way to being able to decipher the genetic code.

• What is the relationship between the genetic code and a computer code?

Genetic code and computer code are very similar in nature. Each have a certain number of inputs that can be paired or strung together in order to achieve a certain output or task. The genetic code has nucleotides that form triplets to code for an end product of proteins, while computer code uses binary, etc, to run a program.

Ajvree (talk) 23:01, 5 September 2013 (PDT) User Page

Miles Malefyt

• What is the biggest discovery that I made from these readings?

The most interesting part of the readings came from the Hayes article where it was determined that only 114 out of a million codes were better than our genetic code already in place. This made me think that over the lifetime of genetic evolution, the code now used in our genes is

• What part of the reading did I understand the least?

The part that I understood the least came from the Moody paper where he compared the four different amino acids as essentially a binary code. I was under the impression that it was pretty important if a nucleotide was either an A or a G and that they couldn't be interchanged

• How was the genetic code solved experimentally?

A scientist named Nirenburg took all the mRNA and observed which amino acids they all translated into

• What is the relationship between genetic code and computer code?

The relationship between the genetic code and a computer code can be viewed as an input-output relationship. A certain code goes in and a specific result comes out. A single codon is like that of a line of code where individually it just makes an amino acid but together and in the right order they form a specific protein, or in coding, a program

Lena Hunt

• What is the biggest discovery that I made from these readings?

The biggest discovery I made from these readings came from the Hayes article. I thought that it would make sense that because DNA has to fit into the nucleus of a cell that it would have to be very information dense, but learning that DNA actually has extra nucleotides to buffer the effect of mutation and mistranslations was a revelation. I knew about introns and exons, but before now I didn't understand why introns existed.

• What part of the readings did I understand the least?

I didn't particularly understand the Nirenberg article. He referred to a lot of organic chemicals that I was unfamiliar with, and the pace of the writing left me glassy-eyed. I think that if I was more familiar with the types of tests he was performing that I would have been more engaged.

• How was the genetic code solved experimentally?

Nirenberg sythesized mRNA and observed which amino acids resulted from a given input.

• What is the relationship between the genetic code and a computer code?

DNA encodes "lines of programming," a message composed of nucleotides that needs to be "run." A section of DNA in transcribed, just as computers transcribe sections of a program on a disk. In both computers and cells, the transcribed pieces are sent to different parts of the system. In cells, mRNA is translated into amino acids which become proteins, while in computers digital data is translated into analog output.

Lena (talk) 23:00, 3 September 2013 (PDT)

Kevin McGee

1. What is the biggest discovery that I made from these readings?

• I thought it was extremely interesting how Moody compared computer hackers to Nirenberg’s experiment. He would construct his own mRNA codons and watch what amino acids they would make as he imputed them. This is similar to computer hackers, who learn about knew computer systems by imputing information and watch what happens.

1. What part of the readings did I understand the least?

• I found the Nirenberg article to be very confusing. It was very heavy in its science and involved many procedures and language that I was unfamiliar with. I was able to grasp the big picture of the article, but I had trouble following the details

1. How was the genetic code solved experimentally?

• Nirenberg synthesized all 64 RNA codons, and looked at what amino acids were given from the codons.

1. What is the relationship between the genetic code and a computer code?

• The genetic code holds an extremely large amount of information and it is encoded through 4 nucleotides. A computer code tells a computer a large amount of information through the use of 2 numbers, 1’s and 0’s. The nucleotides tell the code for the cells, and the numbers tell the code for computer commands.

Kevinmcgee (talk) 19:38, 4 September 2013 (PDT)

Lauren Magee

Reading Reflection Questions

1. The biggest discovery that I made from these readings was how extensive the process was in initially solving of the genetic code. Now that the genetic code has been established, I think in modern day research of genetics, we take it for granted, because we are constantly moving on to the next discovery. As someone how has been involved in genetics research and plans on going into the field of genetics, I wasn't aware of who solved the genetic code and of all the work that lead to it.
2. I've always had trouble understand the molecular processes of genetics. The central dogma is easy enough to understand, but beyond that is always difficult for me to picture. This includes identifying the important areas before the start codon or after the stop codon and determining which strand is the template. I think it'll just take some practice, because I find cell functions much harder to comprehend and retain compared to the other aspect of genetics.
3. The genetic code was solved by Marshall Nirenberg as he translated the 64 possible messenger RNA codons (mRNA) into the appropriate amino acid they code for.
4. The genetic code is similar to a computer code in that it is the informational ground work for a whole system. A computer code allows for the greater machine that is a computer to function in a proper and efficient manner, just as a genetic code allows for a cell to function in the same way for the greater machine that is our bodies.

Genetic Code

• 5'-CGTATGCTAATACCATGTTCCGCGTATAACCCAGCCGCCAGTTCCGCTGGCGGCATTTTA-3' -template strand
• 3'-GCATACGATTATGGTACAAGGCGCATATTGGGTCGGCGGTCAAGGCGACCGCCGTAAAAT-5' -complementary strand
• 1st reading frame (+1): R-M (start)-L-I-P-C-S-Y-N-P-A-A-S-S-A-G-G-I-L: open reading frame (no stop codon included)
• 2nd reading frame (+2): V-C-(stop)-Y-H-V-P-R-I-T-Q-P-P-V-P-L-A-A-F: stop codon included
• 3rd reading frame (+3): Y-A-N-T-M (start)-F-R-V-(stop)-P-S-R-Q-F-R-W-P-H-F: stop codon included
• 4th reading frame (-1): (stop)-N-A-A-S-G-T-G-G-W-V-I-R-G-T-W-Y-(stop)-H-T: stop codon included
• 5th reading frame (-2): K-(start)-P-P-A-E-L-A-G-L-Y-A-E-H-G-I-S-I: open reading frame (no stop codon included)
• 6th reading frame (-3): K-C-R-Q-R-N-W-L-G-Y-T-R-N-(start)-V-L-A-Y: open reading frame (no stop codon included)

Laurmagee (talk) 23:49, 5 September 2013 (PDT)

Gabriel Leis

1. The biggest discovery that I made from these readings was the concentration of protein in a cell as described by Brown in the NCBI article. As a biochemistry student I focus my attention on these molecules on the atomic level so often that I lose scope of the number of these molecules in organisms.
2. I understood sections of the Nirenberg article the least. A lot of topic specific information was needed to fully understand the article.
3. The Genetic Code was developed in two primary ways. The first was through analysis of the protein products derived from known sequences of artificial mRNA using cell free protein synthesizing systems. The second method involved the evaluation of a sensitive ribosome assay to see which amino acids associated with which RNA sequences.
4. The genetic code is essentially is essentially the link between mRNA (program lines) and amino acids (the output). The ribosome acts like the CPU as machinery to translate the program lines into an output but the Genetic Code is what guides the translation machinery.

Gleis (talk) 21:33, 4 September 2013 (PDT)

Tauras

1. I was most interested in the comparison between DNA and computer code made in the Moody article and how the quaternary of the genetic code could be converted to two digit binary code. I've always heard DNA referred to as the genetic code, but had not thought before about the possibility of converting it into computer code.
2. Like many of my classmates, I understood the Nirenburg article the least. He included a lot of technical language that did not make much sense to me, especially about his earlier research and the terms he used to describe his research.
3. The genetic code was solved as Nirenburg (and Martin) synthesized trinucleotides and then determined what amino acid each trinucleotide added to a protein chain.
4. The genetic code can be translated into computer code by using a di-digit binary system to represent the four amino acids. Like computer code, genetic code gives the instructions for specialized program output which is translated by different cells (computer equivalents) to produce proteins and working machinery.

-Taur.vil (talk) 23:16, 4 September 2013 (PDT)

Stephen Louie

1. I was intrigued at the relationship shared between computer code and DNA. For the most part, I was relatively familiar with the biological aspect of DNA. However, I never considered the possibility of DNA being translated into something that can be input as a program. I am sincerely intrigued at the aspect of using digital technology to research and modify the human genome in the form of a code.
2. The historical review article was slightly confusing to me. From prior knowledge, I had a good idea at the type of work the author was performing. However, I was unfamiliar with several parts of the article when he went into greater detail. I feel that I would have a better understanding of this article, if I had taken more upper division biology courses.
3. The 64 trinucleotides of known sequences were used to determine what nucleotide input created what amino acid.
4. Genetic code is similar to computer code in that they are both command instructions that determine the actions of a machine, whether it is a organism or a computer program. Genetic code can also be translated into a binary sequence with A being 00, C being 01, G being 10, and T being 11.

Slouie (talk) 05:46, 5 September 2013 (PDT)

Mitchell Petredis

1. The biggest discovery I made from the assigned readings for this week was how complex and time consuming it was for Nirenberg and his colleagues to properly decipher the genetic code. Most textbooks I've seen gloss over the history of a research project, but being able to hear this story from a personal account made the reading more insightful.
2. Nirenberg's account was also the most difficult to understand since the many organic chemicals and procedures involved in the research were unfamiliar to me.
3. Nirenberg and his colleagues spent a year synthesizing all 64 trinucleotides and tested each one to see what amino acids were produced.
4. According to Glyn Moody, the four letters of the genetic code (A, C, G, T) can be read in terms of binary code found in computers by swapping "A" with "00", "C" with "01", "G" with "10", and "T" with "11" (Moody 3).

Mpetredi (talk) 14:40, 5 September 2013 (PDT)Mitchell Petredis

Kevin Meilak

1. The biggest discovery I made from these readings was how the genetic code was cracked experimentally. I had previously learned about how it was thought at the time that protein was the genetic material, not DNA, but never imagined how long the experiments took or how difficult it was to demonstrate that mRNA caused the incorporation of amino acids into protein.
2. The most difficult part of the readings was some of the experimental procedures in the Nirenberg reading. Despite a background in biology, experimental procedure from a biochemistry perspective was discussed little, even for processes as significant in biology as replication, transcription, and translation.
3. The genetic code was cracked in several steps. After it was discovered that DNA, not protein, was the genetic material, the next logical step was to discover how it translated itself into protein and RNA. First, it was discovered that mRNA was the molecule that served as an intermediate between DNA and protein. The existence of this intermediate demonstrated that DNA did not, or could not, directly translate itself into protein. Then it was discovered that the code was read in triplets “by the amounts of radioactive histidine, threonine, asparagine, glutamine, lysine and proline that were incorporated into protein by five poly(A-C) preparations that contained different ratios of A and C” (Nirenberg, 50). Then, each possible trinucleotide combination was mixed with the 20 different tRNAs to determine which amino acid was coded for by each trinucleotide.
4. The genetic code is like a computer code in that both at digital; the base pairs adenine, guanine, thymine, and cytosine do not code for protein because of inherent chemical properties but rather in how they relate to each other. The Moody reading demonstrated that substituting 00, 01, 10, and 11 for each nucleotide produced the same effect as A, T, C, G. The importance is how they are read, not what they are.

Kmeilak (talk) 17:22, 5 September 2013 (PDT)

Dillon Williams

1. The biggest discovery that I made from these readings was the particular process in which the genetic code was solved. I had never actually read the process of how the code was cracked before this article.
2. I found the Nirenburg article to be very confusing based on the language that he was using as well as the multiple references to things that I didn't have any previous knowledge of, as a result it was fairly difficult to follow.
3. The genetic code was solved by Nirenburg, who synthesized trinucleotides and then determined which amino acid each trinucleotide added to a given protein chain.
4. Much like computer code, genetic code can be translated into a formulaic system using binary. This code is then read based on how the nucleotide sequences are read, allowing the body to respond to the function in the code.

-Dwilliams (talk) 20:05, 5 September 2013 (PDT)

Katrina Sherbina

1. In going through the assigned readings, I was most intrigued by Hayes's discussion at the end of his paper about the different conjectures that scientists have as to why 64 codons evolved to code for 20 amino acids. As the hypothesis diverges significantly from what I have been taught, I was struck by the idea that this may be a result of an ancient mechanism of translation by which both strands of DNA were read simultaneously.
2. I had some difficulty reading through the paper by Nirenberg. I found myself pausing several times to look up unfamiliar terms and reread sections in order to understand the different types of experiments that Nirenberg discussed in the paper. In contrast, the other readings were less technical and, thus, easier to read.
3. By performing cell-free protein synthesis using randomly ordered polynucleotides composed of different ratios of nucleotides, Nirenberg, with the help of other scientists, deduced that the genetic code consists of codons composed of three nucleotides. This led to the idea that there are 64 possible codons. The sequence of each of the possible codons was matched to an amino acid by synthesizing each of the 64 codons and testing each one against 20 different radioactive amino-acyl tRNAs.
4. The genetic code, like computer code, is essentially a set of instructions that is processed to produce a specific output. As mentioned in the paper by Moody, both codes consist of discrete signals: the four nucleotides make up the genetic code and sequences of 1's and 0's form computer code. The genetic code can be written in binary by assigning one of the four binary digits 00, 01, 10, or 11 to each one of the nucleotides.

Ksherbina (talk) 22:18, 5 September 2013 (PDT)

Hilda Delgadillo

What is the biggest discovery that I made from these readings?

• The biggest discovery I made from these readings was the fact that tRNA was discovered before mRNA as read in Nirenberg’s personal account, so in a way we approached the synthesis of proteins in reverse, from translation to transcription.

What part of the readings did I understand the least?

• I couldn't really understand why there was so much importance to the almost insoluble polyphenylalanine which as Nirenberg mentions, is soluble in 15% hydrobromic acid dissolved in concentrated acetic acid, and why was it necessary (Nirenberg, 49)?

How was the genetic code solved experimentally?

• Nirenberg and his colleagues were able to make different combinations of polynucleotides and were able to see the results of their matches with what the polynucleotides yielded in terms of amino acids.

What is the relationship between the genetic code and a computer code?

• The genetic code is like a computer code due to its ability of handling all types of “programs” within the body. The genetic code is crucial for the function of the human being, so it is the software of the body as computers are in need of operating system software to continue their function.

HDelgadi (talk) 10:38, 12 September 2013 (PDT)

Viktoria Kuehn

• What is the biggest discovery that I made from these readings?

The thing that I found surprising about the readings is the way Mendel's work was so under appreciated and ignored when they were in search of answers to genetic and hereditary questions. His work is taught to everyone studying biology today and was so methodical and accurate that it is surprising that people did not pay more attention to it when it was published.

• What part of the readings did I understand the least?

I had the most trouble understanding the details in the Nirenberg reading. It was very dense with biochemical details of the experiment and this made it hard to follow, there were a lot of specifics that it referenced about the processes that made it difficult. It was interesting to read about an on hand account of what happened though, even if I did not understand all the details fully.

• How was the genetic code solved experimentally?

After deciding that DNA was responsible for the genetic code, not proteins, Nirenberg used a way of trial and error by experimenting with the base compostions of RNA codons by combining different polynucleotides with different proportions of nucleotides to see what amino acids resulted.

• What is the relationship between the genetic code and a computer code?

I think that the most fundamental like between the genetic code and a computer code is the way that they transmit information. So many proccesses in the body are driven by biological factors through physical or chemical signals, but genes are encoded in a very unique way. They are in the form of a code that other parts of the cell can regognize and respond to in a specific way. This is also the case for computer code; there is a set of guidelines that the computer always carries out when presented with a code that it recognizes.

Vkuehn (talk) 23:43, 5 September 2013 (PDT)