Class Journal Week 2

Naomi Tesfaiohannes's Response

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

The Brown, T.A. (2002) reading explained transcriptome and Proteome. Transcriptome is a collection of RNA molecules from protein-coding genes. These molecules are in charge of the synthesis of the product of genome expression. The proteome specifies the biochemical reactions a cell is able to produce. Both transcriptome and Proteome are a part of the what makes gene expression.

The Nirenburg, M. (2004) reading explained the steps that led to the breaking of the genetic code and how it was understood. This was done in a 5 year span (1961-1966). First the base composition was deciphered by directing cell-free protein. Second, nucleotide sequences of RNA codons were deciphered.

The Kaji, A (2004) reading explained how their work helped decipher the genetic code by providing a method (binding of tRNA to programmed ribosomes). It touched on how other researchers examined amino acid contributions to polypeptides while using heteropolymers but that the results from these studies were not consistent.

The Moody, G (2004) reading explained the "Digital Code of Life" and said how DNA is a computer code. To understand the DNA message we must also understand how the cell interprets the DNA. What purpose does DNA have? It also touched on Gregor Mendel and his discovery of heredity. He stated that traits come from parents. However, instead of mixing there was one dominant factor over the other (one from each parents). With these understandings, scientists are most equipped with understanding DNA.

The Hayes, B (2004) reading explained how although the genetic code was discovered, it is not fully understood. It also explained how a change in nucleotides, such as a single nucleotide change, will not make the same amino acid but can produce a similar one. The triplet genetic code "the diamond code" was discovered in 1955. The discovery of genetic code was made with the help of multiple researchers adding to the recognition of the genetic code.

Overall, all the reading had to do with genetic coding and how it has been discovered, but is still not completely understood today. The components of how it was discovered was touched on by each author listed above, however some being more in detail. Being that these articles are relatively recent, the latest being 17 years ago, the information presented was constructed based on previous research and discoveries, such as the breaking of the genetic code in 1961-1966 (Nirenburg, M 2004).

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

In the Hayes, B. (2004) reading ribosome- recycling factors (RRF) were discovered to bind to the ribosome and share tRNA-binding sites. Even with its near-perfect structure to tRNA and its ability to bind to tRNA sites why is it that it has a different function? Can it replace tRNA in any way or mimic its function?

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

This was briefly addressed in the Moody, G. (2004) article. DNA was described as being a digital code by Watson & Crick. Similar to a computer code, DNA holds a large amount of information that is deciphered by the cell. The use of mRNA is essential, and although it is closely related to DNA it comes as a single strand. It too had a coding that is to be transcribed from the DNA sequence. Similar to a computer code, the genetic code has information that opens and processes more information. Without it, mRNA does not have the information it needs to transcribe. The ribosomes get the message carried by mRNA and use it to make protein. It takes the computer-like information and makes it into a product, protein. Similar to how a computer can take data points for example and make a table. Both genetic codes and computer codes work to bring about a certain product, that is only capable of being done by instilling proper function of its key parts.

John Nimmers-Minor's Response

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

Emma Young's Response

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?

Michael Armas' Response

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

• Chapter 1: Most of this reading was review, as I have plenty of biology and biochemistry experience. However, I found it very interesting that the human genome project is limited by current technology, making what is still considered as a scientific frontier even though it has be studied since the 70s.
• Chapter 3: Once, again, the chapter is mostly review, but I was refreshed on the function of the transcriptome and proteome. I forgot about these collections of biological structures that make up these different "-omes". Intuitively, these are similar to the genome in such that they are a collection of RNA and proteins for the transcriptome and proteome, respectively.
• Nirenberg 2004: This paper was somewhat complex to understand the exact steps taken to deduce the genetic code. I feel as if this is the greatest discovery I made. Of course, I assumed that breaking the genetic code would be no easy matter, but reading through the steps that these scientists took to achieve one of the most important biochemical marvels and the progression of difficulty is fascinating.
• Kaji 2004: In this letter, I discovered the inconsistencies of the Nirenburg paper with that Kaji and Kaji actually discovered. While reading the Nirenberg paper, this section regarding the 'poly(U) binding of the polyphenylalanine was somewhat confusing. However, this letter describes how the findings described by Kaji and Kaji do not support "that 'poly(U) stimulated the binding of radioactive polyphenylalanine-tRNA to ribosomes."
• Moody 2004: In this reading, I discovered the early stages of the digital age and its relation to genetics (what is now considered bioinformatics). On page 6, Moody introduces the skepticism of the viability of computing power in relation to a genome. Today, the world of bioinformatics has expanded so much that so many discoveries were made only with the power of computing and computer science.
• Hayes 2004: A discovery that I found very intriguing was the effiency of the amino acid codons. Specifically, Hayes talks about the codons of similar amino acids are similar enough that, in some mutative cases, a mutation in the codon will still result in the same amino acid. He states how the table of amino acids is not just random, and that its similarities are organized and represent the viability of how multiple codons can code for one amino acid.

What part of the readings did I understand the least?

In the Nirenberg (2004) paper, I was very confused about the steps taken to finally break the genetic code. The deductions made through advanced experimentation were difficult to comprehend. It is interesting to me that all of this highly advanced research resulted in making the simple codon table we all know today.

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

Moody regards genetic code and computer code very similar in the single character code. He relates the binary language of computers to the quaternary language of the genome. Binary consists of the characters 1 and 0, while the genetic code consists of the characters A, C, T, and G.

Kaitlyn Nguyen's Response

Reflection

1. What is the biggest discovery that I made from these readings?
   • -
2. What part of the readings did I understand the least?
   • - In regards to readings Ch.1 Genome 2 and Ch.2 Genome 2, most of the studies on the human genome I have previously studied in Genetics; such as, transcription, reverse transcription, Watson and Crick's experiments, etc. What I understood the least were pseudogenes. I have learned that mutations would have an effect on gene expression, whether it be minor or major, but my question is if a gene is no longer useful, would it be considered a pseudogene and degrade or be inactive, or is it expressed and cause similar effects as those born with extra/fewer chromosomes?
3. What is the relationship between the genetic code and a computer code?
   • -

Iliana Crespin's Response

1. What is the biggest discovery that I made from these readings?
   • After looking over all the assigned readings, the biggest discovery was about the autobiographical description regarding genetic code. It was fascinating to know that there were two stages involved in this process and how such information known today was a very tricky thing to discover. In General Biology, many students are being taught about genetic code in a broad aspect. There are discussions about RNA and codons, but there isn't much discussion on how the whole process came to be. Going over different readings, there are different viewpoints and narratives on this. It kind of shows every person's take on the information. It is pretty amazing how each person interprets this topic.
2. What part of the readings did I understand the least?
   • The part of the readings that was understood the least was from Marshall Nirenberg (2004) regarding the article, "Historical review: Deciphering the genetic code - a personal account". It was very confusing how this article is placed in a first person point-of-view and discussing on how they discuss genetic code. It kind of diverges to a whole other thing about the life of an author and not what genetic code actually is about.
3. What is the relationship between the genetic code and a computer code?
   • The relationship between the genetic code and a computer code is that they both play a key role in the functioning aspect of a system/organism. The genetic code defines the organism. The computer code defines a system (a computer). They both consist of their own "rules" to transfer information or translate it. Without these codes, there wouldn't be anything telling an organism or system how to function properly.

Icrespin (talk) 15:19, 11 September 2019 (PDT)

Christina Dominguez's Response

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

The biggest discovery I made is switching from emphasizing the part of DNA that is physical/chemical to the information that it stores. It can almost be seen more simplistic by seeing it as a type of computer code. I was able to see many more connections between computer science and DNA in Moody’s Digital Code of Life- such as DNA components as computer software.

What part of the readings did I understand the least?

In Nirenberg’s Deciphering the Genetic Code, it was difficult to follow what exactly he was doing in his experimentation and research. I also found Kaji’s explanation of further and more detailed experimentation to be confusing. It became more clear when it was explained in simpler terms in Moody’s Digital Code of Life.

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

The genetic code devises a type of language that can be applied to every living thing as stated by Nirenberg: “These results had a profound philosophical impact on me because they indicate that all forms of life on this planet use essentially the same language” (53). I like to think of computer code as a type of language as well. This language can be used universally to give a certain output. It follows a logical set of information that apply and will give the same outcome or command. In this way, the genetic code and computer code are similar in their set of code or language that are able to dictate a certain outcome that is universal.

Cdomin12 (talk) 00:06, 11 September 2019 (PDT)

DeLisa Madere's Response

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?

Marcus Avila's Response

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

The biggest discovery that I made from these readings was that the genetic code can be compared to computer binary code. This is interesting because it makes me think of the difficulty in creating artificial intelligence based on binary code and various if then statements.

What part of the readings did I understand the least?

I did not understand how binary was able to give identical information as the DNA nucleotides.

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

Both genetic code and computer code give information based on the arrangement of symbols. Genetic code uses nucleotides abbreviated to A T/U G C, while computer code uses numerical binary of 1 and 0. The arrangement of each coding stands for information that is used to carry out actions.

Ivy Macaraeg's Response

1. What is the biggest discovery that I made from these readings?
   • The biggest discovery I made was how the genetic code was figured out by binding tRNA bound to complexes of polyalanine-ribosomes instead of polyphenylalanine-ribosomes. I think this is also interesting because it reminds us of how little changes in what we already know as biologists are still happening, and the field is always evolving to know more.
2. What part of the readings did I understand the least?
   • The part of the readings that I understood the least was Nirenberg's article. I thought the jargon was very specialized. Also, to read this kind of biology paper told in a narrative, historical way was unusual, and not something that I was practiced in reading.
3. What is the relationship between the genetic code and a computer code?
   • The genetic and computer codes are very similar. They each use digitalized language (in DNA, it is letters A,G,C,T, and in computers, it is binary code 01) to convey a certain message in order to enact a certain function. The codes for both are usually complex and expansive, while being contained in such a small space.