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)

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.

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?
2. What part of the readings did I understand the least?
3. What is the relationship between the genetic code and a computer code?

Christina Dominguez'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?

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?