• Received after fifth class, Jan 8
-- From Walter Allen
Your page got me interested in reviewing glycolysis and the Krebs cycle. Sal Kahn does a great overview that should not be too hard for our classmates explaining what it is all about, HERE.
Listening to Sal brought back the cycle. I had it memorized in the 60s on my way to an MS in biochem.
-- From Elizabeth Housewright
I have all of my mimeographed exams from my yearlong Biochem class at Cal State Fullerton (would have been 1974 or so) and was remembering Dr. Weber’s sense of humor. Each exam started with a quote (example: “This is a long story, which shouldn’t be long, but it will take a long time to make it short” Henry David Thoreau) and often had a story to go along with some of the questions.
Example: "In addition to being a wizard of some repute, Gandalf was a biochemist who published regularly in the Journal of the Middle Earth Biochemical Society (JMEBS). A soil bacterium found only in the Shire (B. Gandalfi) was studied by Gandalf and he observed that in addition to the twenty usual amino acids there was a new one, which he named tolkeinine (tol) which has the following structure ….”
He goes on to describe various mutants and their properties, asks a variety of questions— what amino acid accumulates for mutant1? write the reaction for the biosynthesis of tolkeinine, deduce the overall pathway for tol and thr biosynthesis, predict the pattern of regulation for the pathway in part c, defend your prediction.
I got 24 of 30 possible points for my answers on that set of questions, but got 138 of 150 on the exam. It was an amazing class— 8 AM, typically everyone would stay up all night the evening before an exam, then go have breakfast when class was over at 9, with sore hands from so much writing!
Chemists (and biochemists) are not what many might predict!
And if you still have exams from 1974, I'm wondering if you ever throw anything away. Do you have a ship container out back? I taught biochemistry for nigh onto 40 years, and I don't have a single exam to show for it. My motto was, "When in doubt, throw it out,"
-- From Risa McDade
In the respiration equation, (aq) appears after the sugar molecule and the oxygen molecule. Does this represent water? The sugar molecule, at least, would be solid, wouldn't it?
The symbol "(aq)" means "in water"; it does not mean that the substance in the equation is a liquid. If a substance in a chemical equation is itself a liquid, its formula would be followed by (l). The equation you refer to says that the both the sugar and the oxygen reactant are dissolved in water.
And, in the Map of Chemistry video, the narrator says "Hydrogen and Helium made all the elements and exploded them all over the universe." I don't understand how this would work (i.e. 2 elements making all the ones in the periodic table). Is the narrator referring to the Big Bang theory (of which I know little)?
Well, yes, two elements DID indeed make all the elements in the periodic table, but not during the Big Bang. Only H and He, were made then (and a bit of element 3, lithium). Gas clouds of these elements then condensed to form stars, which, during their "lives" and during the smoldering or violent ends of their lives made all the other elements. Remember the periodic table of origins of elements in which each element is color-coded to shown what proportions of it were made in various processes the make up the lives of stars. So it all came from H and He, but it took some millions of years at least, and a generation of stars that started out with nothing but the two lightest elements.
-- From Steve Schiffman
Here’s what prompted my in-class question: “do you need to do chemistry experiments any longer or can AI now (or in future) answer everything”:
I am struck by the contrast between Faraday’s lectures and the materials that you (Gale) show us subsequently in class. Faraday's chemical world was a “physical” world - of glass beakers, tubes, liquids, gasses, heat, bits of marble, etc. Modern in-class materials are: software simulations of molecular structure, movement of gasses, etc. The bit of chemistry I took in college (1960’s) was more like Faraday’s world. Is chemistry still taught that way in college today? Or is it more like “here is a software simulation of X, do your lab experiments about X using that platform”?
In the classroom, when I retired (2008), college chemistry was still taught much like in the sixties, and included discussion of basic methods like those Faraday might have used, and in addition, discussion of modern methods like those I have added to this class. A typical textbook contains some historical discussions, often laying groundwork for modern ideas. (Gradually, more sophisticated teaching tools have come in -- slides, simulations, and other high-tech instructional tool -- but old-fashioned lecture is probably still the default.)
As for labs, when I retired, first-year labs still included many "Faraday world" methods, because nothing replaces hands-on experience with chemicals and kitchen-like hardware. Notice how many times in the Commentary videos they say something like, "We still used this demonstration [or lab method] today."
As for AI answering everything, AI can only process things already known (from the training data) and can sometimes find surprising connections in what we know, but to my knowledge, has not made any real surprise discoveries. For example, in a field of great interest to me, AI has predicted 3-D structure of proteins from only the sequences of building blocks (amino acids) within each protein, with surprising accuracy, but only if given thousands of structures determined manually and laboriously. So it is finding correlations that are more complex than humans can discern, but it is not teaching us any principles of protein folding; that is, it does mot reveal the mechanisms and forces that fold the random shapes that protein chains can form into the organized shapes of functional proteins.
(The hype and fears surrounding AI make it hard to judge what it might do, and even what it's doing now. Among its future limitations is the amount of energy consumed [and consequent environmental damage] in carrying out AI calculations (same problem with cryptocurrencies).
••••••
• Received after fourth class, Jan 31
-- From Walter Allan
I was stimulated by this lecture to look up the burning of hydrocarbons and found this page which compares the amount of CO2 produced by various sources. Helps explain the problem with burning coal.
https://energyeducation.ca/encyclopedia/Hydrocarbon_combustion
-- From Risa McDade
When "Faraday" (Bill Hammack) demonstrates air compressibility, he fills a balloon with air, puts it in a tank and takes the pressure off. The yellow balloon expands. How is the air getting into the balloon? Is the surface of the balloon permeable? (I don't think so.) This experiment stymies me.
No air is getting into the balloon. The balloon's size is stable in the outside air because the air pressure inside the balloon is the same as that outside. When the balloon is inside the closed, transparent container, the pump removes air from the container, but not from the balloon. So the air pressure outside the balloon goes down over time, and allows the air inside the balloon to expand until its internal pressure matches the lower pressure outside the balloon. (At the molecular level, as the pump removes air from the container, fewer molecules of air are hitting the outside of the balloon than are hitting the inside.)
And my other question is about the moving the egg from one cup to another. The commentary reveals that the egg is a plastic one. So it's very light. Would this experiment work with a heavier boiled egg?
The experiment should work, but you would have to blow harder. I've never tried this; I have no egg cups. You would need ones that spread out at the top. If the top fits the egg snugly, it might not allow any air to get underneath the egg.
Also, if we're demonstrating that air has weight and it can move an object, why not just blow a piece of paper that would skitter across a table?
Faraday might have thought the jumping egg would be more dramatic than something everyone has already seen.
• Received after third class, Jan 24
-- From Risa McDade
These are some questions from Lecture 2, the Brightness of a Flame.
What are the different elements that make up a flame? The lecture refers to solid carbon particles that make a flame very bright. And hydrogen which makes the flame blue. Are these elements creating new compounds that impart different colors?
A flame is really not a substance at all, not an element or compound. It's the visible manifestation of certain kinds of chemical change. So it's the elements that produce the colors, depending on what conditions the elements experience. In a candle flame, the main thing producing the colors is heat. See next question.
There is a comment that electrons impact light. Electrons go from a higher energy level to a lower one. I presume that a higher energy level produces a brighter flame and a lower one, a dimmer flame. How does this actually work?
Brightness of flame does not depend on what energy levels electrons are moving between, but only on how many are moving. So brightness has to do with quantity of atoms taking part. The colors depend on the distance between energy levels between which electrons are dropping. Large drops produce bluer colors in the color spectrum (larger energy changes produce bluer light); short drops (small energy changes) produce redder colors.
Can you make an unlimited number of compounds from the periodic table, even ones that are unstable?
The number of compounds is very large, but not unlimited. If a compound is not stable at all, you can't make it, or will never know if you made it or not.
A similar question would be [ Can stars make an unlimited number of elements, even ones that are unstable? ]
In theory, yes, but ones that are unstable might decay so quickly they cannot be detected. You might say that all combinations of protons and neutrons are possible, but many so unstable that they will never be detected. The ones that can be detected in some manner make up the periodic table.
And in lecture 3, where you assigned reading about molecules (a group of atoms stuck together which can also come apart), I was thinking about the Twin Towers in NY on 911. Did chemical changes occur in the building materials that caused the collapse or were other forces at work?
No simple chemical answers. Collisions by the airplanes broke or weakened many supporting structures, released many gases (heating cooling systems, and started lots of fires . Flammable things burned, metals melted, all weakening the structures. The weight of the buildings on supports that were broken, softened, or consumed by fire did the rest.
NOTE TO STUDENTS: These questions helped me a lot in making decisions about how to present subsequent materials. I get little sense of your level of understanding if you don't ask questions in class and by mail.
• Received after second class, Jan 17
--
From Lee Ivy:
Yes, but could Mendeleev carry a tune?
https://youtu.be/AcS3NOQnsQM?si=GU141oEgoqQqGE8f
Thanks, Lee. I'm sure this song will go down in history.
--
From Risa McDade:
Two questions for you:
1) On a TV news show, there was a segment about wine tasting. The vinyard owner said if you slurp wine, you are splitting the molecules so you can taste the different components. Is this true?
No. Slurping is a physical process, not a chemical one, and will not break chemical bonds nor separate different molecules in solution from each other. "Wine-speak" (like most food-speak) is full of such nonsense.
2) Back to the first lecture about how does a candle burn, I tried to summarize an answer. Is it accurate to say that the wick, through capillary action, draws the wax to the top of the candle. The liquid wax forms the fuel source for the flame? The other piece of information I took from the lecture is that the wick must be porous, so the fuel adheres to the cotton fibers.
This is an accurate summary of the ideas you are summarizing.
Thanks, Risa
--
