Archive for the ‘Uncategorized’ Category

Rowe (1974)

December 4, 2015

Cognitive research shows that when challenged to answer a question, a person’s response time increases proportionally to the difficulty of the question. Questions regarding a subject on which a student is not well versed requires a bit of brain work, though in many classrooms, this is not observed. In this paper, Mary Budd Rowe summarizes her research resulting in the concept of wait-time. This can be understood as the spaces between vocalization where complex thoughts can form and take on a reasonable shape. This is not familiar research for many of us, so you may want to glance over game theory, cognition, and think about how learning takes place. The rest will be discussed on Monday.

Farman et al. (1985)

December 3, 2015

Farman et al. (1985)

Ozone (O3) is an amazing molecule. In the Stratosphere, it is a vital layer that shields us from harmful UV rays. Near ground level, it is a pollutant that causes acute and long term side effects that are harmful to us. In this famous paper, Farman discovers the “hole” in the ozone layer above Antarctica. He attempts to find the source of this loss of ozone by measurements of [ClOx] and [NOx] and how they interact. Could it be halocarbons caused by freons? Sun spots? NO and NO2 caused by supersonic jets?

Tune in this Friday for the answers!

Age of meteorites and the earth – Claire Patterson (1956)

December 1, 2015

Radiometric dating was started in 1905 and was invented as a method of determining the age of the earth by Ernest Rutherford. In the time since then there has been much interest in definitive dating of the earth using uranium-lead ratio dating, lead-lead ratio dating, potassium-strontium dating, etc. along with a defendable computation. While our discussion will conclude with focus specifically on the 1956 Patterson paper, the radiometric methods used and the error associated with each method, more background discussion on the formation of the solar system, how radiometric dating works, and the characters involved in Patterson’s work will be explored. While reading the paper think about the association between these meteors and the earth, the reasons for using the isotopes used for radiometric dating, and a review of isochrons would be helpful.

Wood (1974)

November 25, 2015

Poisonous chemicals are everywhere in our environment and are synthesized in a variety of ways. Mercury is one of the most well known toxic chemicals in our environment that can be traced back to both industrial production and natural production. In this review article we will analyze the various biological cycles mercury (and other toxic chemicals) take and how their presence impacts humans as well as other species.

While reading this article, here are a couple of questions to ask yourself:

-How does the volatility of elemental mercury affect the biological cycle for mercury toxins?

-Why does methylating a heavy metal result in a more toxic compound?

-Why is Dr Wood writing this review article?

Morel et al. (2008)

November 16, 2015

Carbonic anhydrase is one of the most prevalent enzymes in living organisms and is responsible for catalyzing the reversible hydration of inorganic carbon. It is seen in both vertabrates, where it hydrates carbon dioxide into carbonic acid and plant life, where it converts carbonic acid into carbon dioxide in order to feed into photosynthesis. The enzyme’s discovery was made in the 1930s and since then it had been assumed zinc was the only cofactor that could activate this enzyme. In our discussion on Wednesday we will look at a cousin of carbonic anhydrase that uses another surprising cofactor to catalyze this all too important chemical reaction.

Ferris and Orgel (1965)

November 14, 2015

A couple of weeks back, we discussed the Urey-Miller experiment, where the basic building blocks of life, amino acids, were formed in Early Earth conditions. Continuing with this topic, in a previous paper, Ferris and Orgel discusses the prebiological synthesis of adenine by simple cyanide and ammonia mixtures and/or by irradiation with UV light. As discussed in the current paper, it is determined that the most plausible pathway of adenine synthesis will undergo a photochemical rearrangement by irradiation of the HCN Tetramer (diaminomaleonitrile) to give a more efficient pathway to 4-amino-5-cyanoimidazole, which is essential to synthesize adenine in these specific conditions. 

Structural changes upon oxygenation of an iron(II)(porphyrinato)(imidazole) complex (Ibers 1978)

November 9, 2015

Porphyrins are very important structures found in hemes such as those seen in hemoglobin. Trying to model them can be quite difficult because the protein’s porphyrins are attached to have more function than you would think. When reading this dense but short paper which attempts to explore and model a “T” state of hemoglobin consider the difficulties of preforming this task.

This paper ties in many of the concepts we learned in class such as high spin/ low spin, coordination numbers, and molecular orbits. Be prepared to get picked on so brush up on that material.

Watson and Crick (1953)

November 5, 2015

Awaiting details from Porter…


We’ve seen Pauling and Corey’s competing view for the structure of DNA and now here’s Watson and Crick’s. The double helix model is vastly different in terms of bonding and overall structure from the model presented on Wednesday. While both models incorporate a repeating base/phosphate/sugar unit, they differ in fundamental ways. Why is this? Why is it the case that these two models are so different when they were published around the same time and even used the same technique (x-ray chrystallography)? On Friday we’ll be discussing what makes the double helix model so unique and what data lead Watson and Crick to this groundbreaking conclusion.
Here’s an online version if you prefer that to your packet

Pauling and Corey (1952)

November 3, 2015

December 1952: The understanding of the function and composition of nucleic acid has grown immensely since the turn of the century. However, understanding of the structure of this molecule has so far eluded even the most diligent researcher. In this paper, Linus Pauling descends from Olympus, grabs hold of his thunderbolt (an x-ray crystallographic thunderbolt that is, produced by Astbury as Hephaestus), and puts forward the first structure that fits the various parameters compiled over seventy-some odd years of investigations into this molecular cipher.
What assumptions are made in this prediction? Does the data support the structure? Is the alpha helix a suitable model for understanding the data?

Miller (1953)

November 1, 2015

How do you make organics from simple materials? What begins the process? In a primitive universe of hydrogen and helium we know how we can get to the heavier elements, but how to get to compounds from there?

As we move away from strictly organic chemistry and into biochemistry we should answer the question of where do all these useful starting materials come from.

You should read the wikipedia page and also the original paper (links below).