Class Journal Week 2

Andrew Sandler

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

It is tough to select a biggest discovery I made from the readings. Coming from a high school science background, everything in the reading was stuff I had heard really abstract versions of. Getting to know more really helped me appreciate everything, especially learning the really hard work over numerous years by different scientists that went into everything. If I had to select one single thing I learned, I would say it has to do with the "redundancy" of the genetic code in its coding for proteins. I knew that when you have SNP's or other mutations they could cause major problems and diseases or even death. What I didn't understand was something that comes up in Figure 1 in the article American Scientist.

Figure 1 says: "Consequences of mutations and other errors in transmitting genetic information are ameliorated by the structure of the genetic code." The article goes on to explain how the changes to a single codon can be less drastic than they otherwise would be because of the way the triplets are used to code proteins exist. You can get an SNP in still have the same amino acid produced. Even if you have an error in a spot that doesn't produce the same amino acid, the way it is set up, you still are likely to get either a hydrophilic or hydrophobic resulting compound based on whichever type the original intended molecule was. I think that is so cool! And then going further with what was proposed by "Pierre Béland and T. F. H. Allen of the St. Lawrence National Institute of Ecotoxicology in Montreal" that DNA might have originally been palindromic (read both ways) and the way the math worked out for them on that proposition is so exciting! Basically they found that if DNA was palindromic you could only have it work with the 20 -> 64 scheme that DNA actually uses. (I don't know how RNA fits in since they didn't mention it specifically reference so I added looking into that to my weekend to-do list.)

I also want to mention as a further piece of info to keep in mind that even though this is a very cool idea about the way DNA works and in my opinion (not fact) seems quite likely, not everyone agrees that DNA evolved actively to work this way. This is mentioned in the article as well.

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

To be frank, there was a whole lot I couldn't even read at first. It was like reading spanish. I know some spanish but there are also a lot of words I don't know. It ended up being a process of reading a paragraph. Looking up some words, watching some AP BIO on Khan Academy and reading again. It was super motivating when I didn't understand something and would then have to research and was able to come back and read it again and understand at least somewhat. It's also really motivating to see yourself learning. I think I probably repeated that process for most of the reading, except for the letter by Akira Kaji and Hideko Kaji. That article, even though I couldn't decipher the exact meaning of all of the stuff they were talking about, the overall point was apparent. I do need to mention I still need to read the Historical Review by Marshall Nirenberg because I took almost nothing from it the first time because of all the new terms. I plan doing a more comprehensive read through tomorrow evening after studying for some other courses.

3) What is the relationship between computer and genetic code?

After reading the article Digital Code of Life I would answer like this. There is not a direct relationship between computer code and genetic code. By this I mean they are completely different things. I think it is important to be careful how we talk about this topic. The comparison between computer code and genetic code is definitely a good framework to help people perceive these ideas. That being said one is based off of XAND XOR and other such switches and circuits, while the other has a molecular and atomic underpinning. You could argue both do, but I would argue that so does everything else in existence. I think the reason we compare the two information carrying processes is just because they both have a "digital" aspect to them, and have the ability to read the stored "digital" information. If we wrote information or paper or a rock for example they both store the information but don't have a retrieval process. I think the underlying Idea I am trying to get across is that they are similar really only in the fact that we don't have any other "digital" informational processes that we can really compare them with that have a similar storage capacity. (Even your hard drive and the information on your computer is just physical information written by lasers on a disk, and analog tapes are just another form of the same thing. DNA and RNA are currently in a league of their own, and this is exemplified by the massive push we see by people to figure out how to store computer information on DNA or by using DNA like processes. DNA is just the best way we currently have of storing information. And from my limited knowledge it seems it copies much faster than a computer disk.

Andrew Sandler's References

Acknowledgements

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

- I would have had so much trouble understanding a lot of this if Dr. Dahlquist hadn't given up her time to graciously help explain both the textbook reading assigned and the questions I had on the other readings, especially the reading American Scientist where she helped me understand the 20 amino acids and the way they are coded for. I hope I correctly explained that in my answer to question 1.

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

- I don't have an exact time estimate for when I worked on this, but most of the work on the journal was done at home the night before class from around 9pm. I plan on working until the midnight deadline and really hope to have this done on time.

- Texted with Hailey to discuss the journal entries

- Took the bibliography section directly from the Read section on the Shared Journal Assignment page made by Dr. Dahlquist to save time with making the bibliography.

Bibliography

• Brown, T.A. (2002) Genomes 2, Ch. 3.3.2: The link between the transcriptome and the proteome
• 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)

• Khan Academy Videos on AP Biology

Asandle1 (talk) 21:40, 24 January 2024 (PST)

Hailey Ivanson

Reflection Questions

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

I enjoyed reading Brian Hayes’s “Ode to the Code,” especially the “Code on, Codon” section. While this isn’t a discovery in the readings, it’s more of a relit discovery about myself and the way I think about biology. I don’t usually think of biology as a computational puzzle, but when I read about trying to determine the way that codons are organized, there’s no other way to see it: so many biological concepts can be big, fun computational puzzles. It must be crazy to have lived through a time when something as big as the codon arrangement was being elucidated. Reading about biology as a fun problem to solve makes me realize that that’s why I wanted to major in the life sciences in the first place. I just love it, and there’s no other way of putting it.

What part of the readings did I understand the least?

In Marshall Nirenberg’s paper “Historical review: Deciphering the genetic code – a personal account,” he describes the following advancement that he more or less stumbled on: “Third, the standard method of washing radioactive protein precipitates in trichloracetic acid to remove radioactive amino acids involved repeated centrifugation and resuspension of protein pellets, which was very laborious and time consuming. One evening I compared this standard method with washing protein precipitates by filtration through Millipore filters. The results were identical.” This was glossed over in favor of discussing the deciphering of the genetic code, but seems like a big deal. Though, I completely don’t understand most of the words let alone the methodology of how Nirenberg could’ve come to trying to use Millipore filters over some multi-day standard process. It sounds like the guy is just completely brilliant, and I would like to learn more about him and his accomplishments and discoveries.

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

Moody states that the genetic code, DNA, is itself computer code. Moody draws parallels between DNA and a code-containing software suite, transcribing mRNA running a computer program, ribosomes and wires, mutations and bugs, and other direct genetics:computer parallels. The bottom line is that both DNA and computer code tell a functioning unit what to do. The genetic code for its organism and computer code for its computer. Hivanson (talk) 22:29, 24 January 2024 (PST)

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.

Dean Symonds

1. The biggest discovery I made from these readings is the genetic code is not universal, meaning that certain codons used in RNA translation may be different across organisms. Which seems counter intuitive to me, for I would assume that the reasons for certain codons coding for certain proteins lies deep in their biochemistry and should not change depending on the organism. The reading does point out that this is not very common in genetic codes to see such deviations. However, the fact that they happen at all does come as a surprise to me.
2. What I understood the least about the readings was the article by Marshall Nirenberg, in which he discusses how he was able to decipher the genetic code, and in which he conducted an experiment to determine if protein synthesis was caused by DNA or RNA. I do not understand well what he means when he says he conducted the experiment via cell free synthesis of proteins, and much of the recollection of the experiment also used jargon which was difficult for me to understand.
3. The reading titled digital code of life describes how to represent the genetic code with the computer code known as binary. Because binary is, as the name suggests, a binary code, and DNA is a quaternary code, it requires two units of binary code to represent any nucleotide. The sections of an RNA sequence called introns can also be compared to the segments of code in a program that a computer does not run.

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)