Class Journal Week 2

Katie Miller

Reflection Questions

1. What is the biggest discovery I made from these readings? The biggest discovery I made from these readings is that there is so much about the genetic code that I still don't know. Although it may seem easy to understand, as there is only four nucleotides, there is actually countless details that must be accounted for. For example, some scientists believe the genetic code used to be read from the two strands of DNA at the same time. This is supported by the discovery that in the genetic code, there is often an antigene opposite a normal gene. The example provided in the American Scientist reading is that when a strand has a hydrophilic amino acid, there is often a hydrophobic amino acid in the opposite strand. I didn't know that there may be antigenes for a normal gene, and had just assumed that the strands are completely complementary and will always code for the same thing.
2. What part of the readings did I understand the least? I didn't understand how synonymous codons could not have identical roles in the cell. This was also from the American Scientist, where it is said there is growing recognition that codons may have more of a role than just coding for a specific amino acid, meaning that codons that seemingly do the same thing may actually be more different than we know. There are different rates of which codons are used depending on the organism, and I don't understand how an organism determines which codon to use if they both result in the same amino acid being added to a sequence.
3. What is the relationship between the genetic code and a computer code? In the Digital Code of Life reading, it is said that DNA itself is digital. DNA stores information through its nucleotides, which is compared to a protein whose function is determined by its physical properties. Genetic code and computer code both use basic units to store information that can later be expressed. While DNA is a quaternary system of A, C, G, and T units, computer code is binary with 0 and 1 units. The reading also explains why a digital copy like DNA is necessary, as it reduces the rate of error. By always going back to a digital copy to recreate something, rather than making copies from copies, the digital source is always perfect and the recreation should have a low rate of error. Because DNA is present in all cells, its program is always running, like in computer code where certain code must always run for proper computer function.

References

Brown, T.A. (2002) Genomes 2, Ch. 3.3.2: The link between the transcriptome and the proteome (freely available on NCBI Bookshelf)

Nirenberg, M. (2004) Deciphering the Genetic Code—a Personal Account. Trends in Biochemical Sciences 29: 46-54. DOI: 10.1016/j.tibs.2003.11.009 (also on Brightspace)

Kaji, A., Kaji, H. (2004) The history of deciphering the genetic code: setting the record straight.

Trends in Biochemical Sciences 29: 293. DOI: 10.1016/j.tibs.2004.04.005 (also on Brightspace)

Moody, G. (2004) Digital Code of Life, Chapter 1, Hoboken, New Jersey: John Wiley & Sons, pp. 1-9. (on Brightspace)

Hayes, B. (2004) Ode to the Code, American Scientist 92: 494-498. (on Brightspace)

Kmill104 (talk) 12:33, 24 January 2024 (PST)

Charlotte Kaplan

Reflection Questions

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

The major discovery from these readings is the author's confirmation that messenger RNA is essential for protein synthesis within cells. Through experiments utilizing bacterial extracts and ribosomes, the author investigated the role of RNA and DNA in protein production. Using a more sensitive test, they determined that only RNA from ribosomes, not DNA, played a key role in facilitating protein synthesis. This finding significantly advanced our understanding of cellular processes. The author also highlighted methodological enhancements, including the freezing of extracts and process optimization, which contributed to the overall effectiveness of their research (https://www.sciencedirect.com/science/article/pii/S0968000403003025)

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

The confusing aspects to me in the reading came from the details surrounding the chemical diversity of proteins. The focus on amino acids, with their varied structures and unique side chains R groups is challenging to grasp, especially considering the many sizes and complexities involved. The introduction of the additional amino acid selenocysteine and its role during protein synthesis guided by a modified genetic code interpretation adds a layer of complexity. The discussion of modifications during protein processing, including acetylation, phosphorylation, and the attachment of large side chains with sugar units, was confusing to me. https://www.ncbi.nlm.nih.gov/books/NBK21121/#A5818

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

The connection between the genetic code and a computer code both have sets of instructions, but they work in different areas. The genetic code is a set of rules in biology that tells cells how to make proteins from DNA. On the other hand, a computer code is a set of instructions in a language computers understand. It tells computers what to do, like processing data or performing tasks. Both involve giving instructions for specific outcomes.

References

Brown, T.A. (2002) Genomes 2, Ch. 3.3.2: The link between the transcriptome and the proteome (freely available on NCBI Bookshelf)

Nirenberg, M. (2004) Deciphering the Genetic Code—a Personal Account. Trends in Biochemical Sciences 29: 46-54. DOI: 10.1016/j.tibs.2003.11.009 (also on Brightspace)

Kaji, A., Kaji, H. (2004) The history of deciphering the genetic code: setting the record straight.

Trends in Biochemical Sciences 29: 293. DOI: 10.1016/j.tibs.2004.04.005 (also on Brightspace)

Moody, G. (2004) Digital Code of Life, Chapter 1, Hoboken, New Jersey: John Wiley & Sons, pp. 1-9. (on Brightspace)

Hayes, B. (2004) Ode to the Code, American Scientist 92: 494-498. (on Brightspace)

Ckapla12 (talk) 17:33, 24 January 2024 (PST)

Andrew Sandler's Entry

Andrew Sandler's References

Acknowledgements

- Used the first week's template with Dean to base this week's template on.

- All work is my own except where acknowledged otherwise Asandle1 (talk) 21:32, 24 January 2024 (PST)

- Was inspired by Charlotte and Katie to add the line with my name in the underlined format they used with two equals signs and a space.