BabcockHall

Try drawing the chemical reaction of sodium hydroxide reacting with an amino acid first.

Because we are less than one pH unit away, we are still in the buffering region of the second pKa, which is 9.7. Putting it another way, not all of the weak acid is being consumed by hydroxide. It is actually a nice problem.

One way to describe this is in terms of reduction potentials. The ground state reduction potential of photosystem II is about +1 volts. However, the excited state reduction potential is roughly -1 volt. PS II is the oxygen-evolving photosystem, but a similar idea holds for PS I.

I am going to suggest this bookkeeping as a simple way to make the electrons add up. Six carbon atoms gain a total of 24 electrons. The twelve oxygen atoms in six molecules of carbon dioxide can lose 24 electrons (each one changes from an oxidation number of -2 to 0). Six water molecules are needed to hydrate the six carbon atoms, in order to produce a carbohydrate. This way of thinking about photosynthesis is not intended to be mechanistically accurate; it is only intended to describe the stoichiometry.

The oxidation number of carbon in coal is zero. The average oxidation number of carbon in glucose (and therefore in polymers such as cellulose) is also zero. I am not sure that one is more combusted than the other, at least to the rough approximation given by oxidation numbers. The difference because of boiling off the water is an attractive explanation.

Going on memory here, but I think that the hydration of a nitrile to an amide is done under fairly mild conditions.

We can help you, but we cannot do your work for you. A good place to start would be to look at the specificities of pepsin and trypsin. What are they?

I would use the H-H equation. Which pKa value should you use and why?

I may not be following you. Photosynthesis uses water as a reactant and produces molecular oxygen. I have not looked carefully at the carbon assimilation reactions with respect to whether they are water-producing or water-consuming.

Apparently the answer is yes. Here is a useful page on compatibilities: https://tools.thermofisher.com/content/sfs/brochures/TR0068-Protein-assay-compatibility.pdf

The recipes I have seen for the bicinchoninic acid call for 0.16% disodium tartrate dihydrate (I don't yet have the original 1985 reference). I have sodium potassium tartrate. Using this would produce a concentration of potassium ions of 7 mM. So far I have not seen anything to suggest that potassium interferes with this particular assay. However, the Lowry assay is also based on copper ions, and 30 mM potassium phosphate is listed as the highest acceptable concentration (Bollag et al., Protein Methods, 2nd ed. 1996). On the other hand one recipe I consulted (Ninfa et al.) for the Lowry assay calls for use of sodium potassium tartrate. ThermoFisher's website suggests that sodium potassium tartrate is present in both the Lowry assay and the BCA assay. Their website notes, "The Lowry assay reagent forms precipitates in the presence of detergents or potassium ions. When potassium ions are the cause, the problem can sometimes be overcome by centrifuging the tube and measuring the color in the supernatant." There is also a copper-based method called the Biuret assay, and one recipe (Ninfa et al.) calls for sodium potassium tartrate. https://www.thermofisher.com/us/en/home/life-science/protein-biology/protein-biology-learning-center/protein-biology-resource-library/pierce-protein-methods/chemistry-protein-assays.html Does anyone know if there is likely to be a problem with this concentration of potassium ions?

The initial rate means the rate measured before much (ca. 5%) substrate has been consumed or product produced. If this condition is not fulfilled, the rate measurements are suspect.

I would start with a chemical equation showing what is going on.

Most transcriptional factors increase the rate of transcription, which is opposite to microRNA from what I can gather. The ones that I can think of bind to DNA at a promoter or an enhancer, but I would not be surprised to learn that some bind to other proteins that bind to DNA. General (basal) transcription factors are much more numerous in the eukaryotic world than in the bacterial world. The rate of transcription is not easy for me to define, but I would say that it is related to the number of mRNA transcripts from a given gene in a specified period of time.

I don't think I can give a comprehensive answer, but some proteins are toxic because they have enzymatic or other biological activities; cholera toxin comes to mind in that regard.

Fructose 6-phosphate and glyceraldehyde 3-phosphate may also be formed in one of the reactions catalyzed by transketolase.

What are your thoughts?

It might help to think of reading the template and doing the polymerization as two separate things.

That is a very open-ended question IMO. I might be tempted to answer ATP and NAD(P)H. However, ribose phosphate may be derived from glucose.

One wonders how the hydrogen bonding of the bases is satisfied.

Hemoglobin A has two alpha chains and two beta chains. Hemoglobin F has two alpha chains and two gamma chains. Hemoglobin Barts has four gamma chains. Suppose you had one antibody preparation that reacted solely with the gamma chains and a second antibody preparation that mainly consisted of antibodies which bind to gamma chains but which also had some antibodies that could bind to the alpha chain. Would these two behave differently in an Ouchterlony (double diffusion) experiment involving Hb F and Hb Barts in two adjacent wells? I think that they would. In the first case, you would see a smooth arc of precipitin from anti-HbF antibodies reacting with the gamma chains. In the second case, you would see a smooth arc, but I think you would also see a spur pointing toward the well containing Hb Barts. The spur would be caused by the reaction between the anti-alpha antibodies and the alpha chains found in HbF. The reason for my question is that I am trying to understand the immunochemistry in the Lindy Chamberlain case. In this case the specificity of the anti-HbF antibodies was a very contentious issue.

"Protein. The S-100 brain protein studied in these experiments was purified by Moore (1965) from bovine brain, and was kindly supplied by Dr. Blake Moore. Antiserum. Antibodies to bovine brain S-100 were successfully produced in rabbits after complexing the purified protein with methylated bovine serum albumin according to the method of Plescia et al. (1964) and using this complex as immunogen. The antiserum gave one major band in double-diffusion tests in agar with purified beef brain S-100 protein as antigen and, in addition, a second minor band with crude brain extract as antigen." This is a passage from a 1968 paper (Kessler D, Levine L and Fasman G, Biochemistry 7:758-64). I am trying to understand one aspect of this passage, namely the identity of the second band seen when crude brain extract is being treated with the antibodies. It is regrettable that they did not provide the relative positions of the two bands in the Ouchterlony experiment, which might have been helpful in discriminating among the possibilities. The second band could conceivably be a second protein reacting with the antibodies that bind to S-100. They could also conceivably be a second brain protein reacting with a second antibody in the preparation. Are there other interpretations besides these two? Is there any way to discriminate among these possibilities based solely on this information, or would one need to do further experiments? If anyone has some good textbook or review articles on antibody binding, I would be interested. I have a couple of older textbooks (D Freifelder, Biophysical Chemistry; TG Cooper, The Tools of Biochemistry) that are pretty good, but I would like to have more information.

Ordinary water is not free of ions. Most ionic substances are not volatile; when the water is boiled away, they stay behind.

I have a 1994 textbook on inorganic biochemistry (Lippard and Berg) that shows the electronic configurations (Figure 11.2). They don't provide the hybridization, however.

DeepView is one program that allows you to view a protein structure. There is a good tutorial available.