Things I Should Have Learned in Chem I (but didn’t)

Coastal Carolina Community College, by LouFCD @ Flickr

Coastal Carolina Community College, by LouFCD @ Flickr

I love my school. I don’t think there’s any question about that.

I love the campus (tore up with construction as it is at the moment), I love the size, I love the variety of classes offered (though I wish there were more, of course), I love the high standards, and most of all I love the faculty and staff. I don’t think I’ve ever met a conglomeration of people so dedicated to the purpose of helping a rag-tag, diverse bunch of people and their unique needs as the faculty at Coastal. With one exception (an instructor no longer there, I might add), I’ve spent nearly two years watching instructors fall all over themselves to help students understand the presented material, and inspire us to think about it, evaluate it, expand on it, and run like hell with it. I don’t know if this is the norm for the community college as I’ve never attended another, but it certainly wasn’t my university experience lo, those many years ago. I will sorely miss Coastal when I graduate this Spring and transfer to UNCW this Fall, regardless of how wonderful an experience that might be.

That freedom, I tend to think, has taken a rather extensive toll on this blog (not to mention JanieBelle’s!). I expend a great deal of creative energy going above and beyond, working my ass off to not just pass my classes, but to excel in them, and when I get home, quite frankly, there’s little left for personal projects like blogging or even photography.

So it pains me to level a criticism, valid as it may be, in any shape or form. I have already taken my concern to several of the instructors there, and to The Chair, and I am satisfied that my voice has been heard and the situation is properly addressed. Nevertheless, I thought a bit of explanation for the title and point of this post is in order.

I took CHM 151 (Chem I) online last semester. I didn’t want to, but it was only offered at times when other classes that I needed were offered, and it was the best of a list of unsatisfactory choices for me, near as I could tell with the information I had in hand. Some days will be like that. Coastal can’t possibly tailor their entire schedule to every student, and they do go out of their way to do the best they can with what they have to work with. So with the consolation that at least I’d have a real on-campus lab, I elected to do the online lecture.

Big mistake.

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There Is No Such Thing As Alternative Medicine

Witch Doctor by Felix42 contra la censura @ Flickr

Witch Doctor by Felix42 contra la censura @ Flickr

There is no such thing as alternative medicine. Test it against a placebo. If it works better than the placebo, it’s not alternative – if it doesn’t, it’s not medicine.

At its most basic, the heart of the matter really is that simple.

Think your herb tea cures your cold?

Test it against a placebo. If it works better than the placebo, it’s not alternative – if it doesn’t, it’s not medicine.

The United States federal government has spent $2.5 billion testing alternative medicines.

Ginko biloba helps your memory?

There is no such thing as alternative medicine. Test it against a placebo. If it works better than the placebo, it’s not alternative – if it doesn’t, it’s not medicine.

“Echinacea for colds. Ginkgo biloba for memory. Glucosamine and chondroitin for arthritis. Black cohosh for menopausal hot flashes. Saw palmetto for prostate problems. Shark cartilage for cancer. All proved no better than dummy pills in big studies funded by the National Center for Complementary and Alternative Medicine. The lone exception: ginger capsules may help chemotherapy nausea.”

Shark cartilage cures cancer?

There is no such thing as alternative medicine. Test it against a placebo. If it works better than the placebo, it’s not alternative – if it doesn’t, it’s not medicine.

The board in charge of the testing was artificially loaded with proponents of “alternative medicine”, and still FAILed to find any evidence that these treatments worked any better than placebo.

“The bottom line is that NCCAM is an ideological, not a scientific organization. It exists to validate CAM, not to test whether it works or not. And when it doesn’t produce the results its boosters in the legislature, like Tom Harkin, want to see, there’s serious trouble.”

Guess what? There is no such thing as alternative medicine. Test it against a placebo. If it works better than the placebo, it’s not alternative – if it doesn’t, it’s not medicine.

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Blogging My Biology Class 20080924

Biology, Eighth Edition, by Campbell & Reece, et al.

Biology, Eighth Edition, by Campbell & Reece, et al.

My notes and thoughts from Biology 111, for Wednesday, September 24, 2008. The entire series can be found here.

Forgive the delay in this, the next installment of the series. At about this point in the semester, the workload and involvement in school just took off, and I needed to devote as much time as possible to homework and studying.

When last we left off, we had just begun a quick tour of the eukaryotic cell and its structures. We’d gone over the Nucleus and the Ribosomes, and some of the membrane-bound organelles like the Endoplasmic Reticulum (or ER), the Golgi Apparatus (or GA), and the Lysosomes.

We’ll pick it up here with number 7, the Mitochondria (another membrane-bound organelle), and we’ll go into more depth when we get to Chapter 9.

The mitochondria are sites of aerobic respiration. Recall that C:H bonds have a high potential energy because of the maximum distance of electrons from the nuclei of the Carbon and Hydrogen atoms. In other words, the electrons they share equally are midway between the C and the H.

(The lecture notes continue below the fold.)

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Blogging My Biology Class 20080922

Biology, Eighth Edition, by Campbell & Reece, et al.

Biology, Eighth Edition, by Campbell & Reece, et al.

My notes and thoughts from Biology 111, for Monday, September 22, 2008. The entire series can be found here.

Before we get to the actual lecture, there’s something I need to address here.

While taking notes, it is often helpful and even necessary to draw little diagrams and pictures, many of which I reproduce in this series by digital means.

This is often simpler, neater, and more helpful than just scanning pages of notes from my notebook.

Until now, it’s really not made much of a difference, but in this lecture we begin drawing diagrams of cell structure, and while it’s not terribly difficult to do digitally, when drawing them in a notebook it is imperative for accuracy to understand the proper method for drawing a cell. It is a skill which requires a great deal of practice.

Chromosomes and various proteins for example, can be very complicated, and drawing them incorrectly can lead to gross misunderstandings and disaster for the student. To help prevent this, I’ve created a digital animation of the proper method for drawing a chromosome inside a prokaryotic cell. The method employed here can be extended and extrapolations to eukaryotic cell diagramming should not be difficult.

The method, along with this lecture, is below the fold.

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Blogging My Biology Class 20080919

Biology, Eighth Edition, by Campbell & Reece, et al.

Biology, Eighth Edition, by Campbell & Reece, et al.

My notes and thoughts from Biology 111, for Friday, September 19, 2008. The entire series can be found here.

As we took our first exam on Wednesday, September 17, there was no lecture for that day.

We took the first part of class to go over the exam results. I had left the exam feeling very good, figuring I was unsure about and may have missed two or three questions. Turns out, I missed eight.

Damn.

Out of 64 students in 3 sections, the highest score was a 91, the lowest a 29, and the median 67. I scored an 88.

Doc said not to sweat it too much, as the first exam is the one everyone does a little less well on, unfamiliar territory, etc., and he drops the lowest exam score.

I was rather surprised at about 5 of my 8 incorrect answers, thinking to myself, “What the hell were you thinking???? You know better than that!!!” I really pulled some dumb answers from out of my butt to very simple answers.

One of my incorrect answers though, was the molecular formula of maltose (two glucose molecules bonded together). Now, without thinking, I simply answered with double the formula of glucose, stupidly forgetting to subtract the water molecule from the hydrolysis synthesis that is required to form maltose from two glucose molecules (or any disaccharide from two monosaccharides).

Hence the unforgettable graphic I made subsequently. After making that animation, I will never repeat that mistake.

After going over the exam, we moved on to Chapter 6 – A Tour of the Cell.

Notes for that brief lecture are below the fold.

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Blogging My Biology Class 20080915 Lab

Biology, Eighth Edition, by Campbell & Reece, et al.

Biology, Eighth Edition, by Campbell & Reece, et al.

My notes and thoughts from Biology 111 Lab, for Monday, September 15, 2008. The entire series can be found here.

In this lab, we learned to use reagents to test for the presence of proteins, starch, and sugars, using distilled water as a negative control.

Since distilled water should be straight H2O and nothing else, each time we did a test, we could see what the reagent did in solution without the presence of whatever it was we were testing for.

We worked in groups, and our group consisted of four students.

A. In the first experiment, we tested for the presence of proteins with Biuret reagent, a highly corrosive blue/purply substance. Our Lab Manual and Doc each warned us about its potential hazards, safety precautions, and what to do if we got it on our skin.

We marked four test tubes at the 1 cm level.

1) Test tube 1 we filled to the mark with distilled water. We then added about 5 drops of Biuret reagent. The water turned light blue. This was our negative control to which we could compare the other tubes when the Biuret reagent was added.

Lab continues, below the fold.

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Blogging My Biology Class 20080915

Biology, Eighth Edition, by Campbell & Reece, et al.

Biology, Eighth Edition, by Campbell & Reece, et al.

My notes and thoughts from Biology 111, for Monday, September 15, 2008. The entire series can be found here.

The class started with a reminder that the next class period (Wednesday the 17th) would be our first exam.

Then there was a short review of Hydrocarbons generally, and carbohydrates specifically, just to get us back to the place where we had left off.

We picked up this lecture with our discussion of Lipids.

2. Lipids

Triglycerides —> Fats & Oils

glycerol on the left with three fatty acids

Saturated Fat: glycerol on the left with three fatty acids

Glycerol + 3 Fatty Acids

When a glycerol molecule, C3H5(OH)3 (the vertical part on the left of the image), picks up three fatty acids (the long strings of C and H on the right), they combine to form a triglyceride.

Triglycerides are fats and oils. If the long fatty acid chains all remain straight, each carbon bonding with two Hydrogen atoms and its two neighbor Carbon atoms, the triglyceride can pack densely, and thus becomes a solid at room temperature. This is a saturated fat.

Glycerol on the left with three fatty acids. Note the kink in one fatty acid.

Unsaturated Oil: Glycerol on the left with three fatty acids. Note the kink in one fatty acid.

If one or more of the long fatty acids develops a “kink”, ie two Carbons double bond and dump a Hydrogen, the stack can not pack as densely, and thus becomes a liquid at room temperature. This is an unsaturated oil. If there is one kink, it’s a monounsaturated oil, and if more than one, it’s a polyunsaturated oil.

Ta-da. It was kind of cool to suddenly understand the difference between them after having heard the terms for so long in reference to food labels.

We can measure energy in units called calories.

Because of fat’s high percentage of hydrocarbons (all along those fatty acid chains), it has a high caloric content. For comparison, a gram of fat contains 9 calories, while a gram of carbohydrates contains 4 calories. Remember that those Hydrogen – Carbon bonds are high energy content because of the non-polar covalent bond.

(Lecture continues below the fold)

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Blogging My Biology Class 20080912

Biology, Eighth Edition, by Campbell & Reece, et al.

Biology, Eighth Edition, by Campbell & Reece, et al.

My notes and thoughts from Biology 111, for Friday, September 12, 2008. The entire series can be found here.

There are four main classes of organic compounds in living things that Bio 111 is going to cover.

  • Carbohydrates* —> C, H, O
  • Lipids —> C, H, O (sometimes N & P)
  • Proteins* —> C, H, O, N, S
  • Nucleic Acids* —> C, H, O, N, P

* Carbohydrates, Proteins, and Nucleic Acids are Macromolecules, meaning “really honkin’ big”.

1. Carbohydrates – Sugars – all “ose” endings mean “sugar”.

“Carbon Water”

They have a C:H:O ratio of 1:2:1, so the basic carbohydrate formula would be CH2O

a) monosaccharides –> “one sugar” – these are the simple sugars, and contain between 3 – 7 C atoms in them.

A Few Simple Sugars
C Atoms Molecular Formula Group Name
3 C3H6O3 triose
5 C5H10O5 pentose
6 C6H12O6 hexose

(Lecture continues below the fold)

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Blogging My Biology Class 20080910

Biology, Eighth Edition, by Campbell & Reece, et al.

Biology, Eighth Edition, by Campbell & Reece, et al.

My notes and thoughts from Biology 111, for Wednesday, September 10, 2008. The entire series can be found here.

In the last lecture, we had left off with a discussion of pH and [H+]. We started this lecture by finishing up with pH.

Remember that pH is a negative log scale, so as [H+] goes up, pH goes down.

We came to definitions right off the bat.

Acid –> Any substance that increases [H+] of a solution. This is accomplished by donation of H+ ions (p+, since a Hydrogen without an e is just a p+)

HCl —> H+ + Cl

Hydrochloric acid will break down in solution into its constituent parts, thus directly increasing the [H+] and lowering the pH of the solution.

Base –> Any substance that decreases [H+] of a solution. This can be accomplished in one of two ways:

Donation of OH to combine with H+ already in the solution

NaOH —> Na+ + OH —> OH + H+ —> H2O

Oven or drain cleaner, Sodium Hydroxide, will break down in solution into its constituent parts, one of which is a hydroxide ion. The hydroxide ion combines with H+ in the solution to make water, thus lowering [H+] and raising the pH of the solution.

Sucking up of H+

NH3 + H+ —> NH4+

Ammonia, NH3, will pick up an H+ and become NH4+, thus directly decreasing [H+], and raising the pH of the solution.

Then we moved on to Chapter 4: Carbon and the Molecular Diversity of Life

(The rest of the lecture is below the fold)

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Blogging My Biology Class 20080908

Biology, Eighth Edition, by Campbell & Reece, et al.

Biology, Eighth Edition, by Campbell & Reece, et al.

My notes and thoughts from Biology 111, for Monday, September 8, 2008. The entire series can be found here.

We left off on Friday discussing the second important emergent property of water, the property of temperature moderation.

On Friday, we began with the third emergent property of water that is critical to biology.

3. Solid form of water is less dense than the liquid form

In other words, ice floats. First we took a quick look at what generally defines each state of matter at room temperatures (we didn’t delve into plasmas etc)

States of Matter
Solid Liquid Gas
Constant Shape, Constant Volume Constant Volume, Changing Shape Changing Volume, Changing Shape

So we can say that generally speaking, the state of matter is dependent on its density and the fixity of its bonding. Ordinarily, the solid state of matter is more dense than the liquid state, and this unusual property of water has a very important consequence for life.

(More of this lecture, below the fold)

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Blogging My Biology Class 20080905

Biology, Eighth Edition, by Campbell & Reece, et al.

Biology, Eighth Edition, by Campbell & Reece, et al.

My notes and thoughts from Biology 111, for Friday, September 5, 2008. The entire series can be found here.

On this day, Tropical Storm Hannah was expected to hit, so the college closed at 1 PM. Although that was well after the end of our scheduled lecture, Doc (if I recall correctly) cut the class a bit short to give folks headed home a little extra time.

So in the previous lecture, we had left off discussing Cohesion and Adhesion, the first of the emergent properties of water on the table for discussion. With this lecture, we picked up with the next emergent property on the list.

2. Moderation of Temperature

Water has a relatively high specific heat, which means that water can absorb and release large amounts of heat with little change in temperature.

To discuss this topic, it helps to first have an understanding of the difference between heat and temperature.

(Lecture Continues Below the Fold)

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Blogging My Biology Class 20080903

Biology, Eighth Edition, by Campbell & Reece, et al.

Biology, Eighth Edition, by Campbell & Reece, et al.

My notes and thoughts from Biology 111, for Wednesday, September 3, 2008. The entire series can be found here.

We left off before the Labor Day break with polarity and the ability to form hydrogen bonds.

The polarity of the water molecule, having an oxygen to one side and the two hydrogen atoms to the other, gives the molecules a slight attraction to charged molecules, since the oxygen end is going to have a slight negative charge and the hydrogen end is going to have a slight positive charge. This is caused by the unequal sharing of valence e- between the oxygen and the two hydrogens. Because the oxygen pulls harder on the shared e-, they are going to spend more time toward the oxygen, increasing its negative charge a little, and away from the hydrogens, increasing their positive charge a little (actually decreasing their negative charge a little, to be accurate).

That little bit of polarity will cause the oxygen end of one water molecule to be attracted to the hydrogen end of another water molecule (or any other positively charged molecule), and though the effect is small in one pair of molecules, it adds up with millions of molecules.

(More below the fold)

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RTFB

Biology, Eighth Edition, by Campbell & Reece, et al.

Biology, Eighth Edition, by Campbell & Reece, et al.

For those of you unfamiliar, RTFB stands for “READ THE FUCKING BOOK”. We had a Biology quiz today, and I totally blew two questions because I didn’t RTFB.

The first question, and how I answered it:

This Molecule Doesnt Make Sense

This Molecule Doesn't Make Sense

I recognized that there was a problem, and couldn’t work it out. Looking at it, obviously the H atom is making too many bonds here, winding up with too many e- in its valence shell. What I didn’t do was read the instructions for the problem thoroughly, which offered the option of saying the molecule didn’t make sense. I could SEE it didn’t make sense, and why, but didn’t write down that this was the case.

Those instructions appeared in the book, from whence the problem came, but not on the quiz sheet which said something like “Draw the Lewis Dot Diagrams for problem 9 on page 36” or whatever.

There was a similarly nonsensical molecule, that I also did not label as such.

Damnit, Damnit, Damnit.

RTFB.

drekshunz

From whence came the art:

The first image is of our textbook, Biology, Eighth Edition, by Campbell & Reese et al.

Other images by me and are licensed under the Creative Commons Attribution- NonCommercial- Share Alike 3.0 License.

Blogging My Biology Class 20080829

Biology, Eighth Edition, by Campbell & Reece, et al.

Biology, Eighth Edition, by Campbell & Reece, et al.

My notes and thoughts from Biology 111, for Friday, August 29, 2008. The entire series can be found here.

Forgive the delay, but I’ve had a ton of stuff to work on.

On Friday, we started out with a review of covalent bonding. Doc re-stressed that in covalent bonding, atoms are sharing one or more pairs of electrons.

Let’s take another look at our covalent bonding notation:

Bonding Notation for Oxygen and Nitrogen

Bonding Notation for Oxygen and Nitrogen

Now note that the two Oxygens share two pairs of e- and the two Nitrogens share three pairs of e-, as noted by the lines and by the dots between them. Also note that in the Lewis Dot diagram, all valence e- are depicted, regardless of whether they are involved in the bonding.

(Continued below the fold)

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Blogging My Biology Class 20080827

Biology, Eighth Edition, by Campbell & Reece, et al.

Biology, Eighth Edition, by Campbell & Reece, et al.

My notes and thoughts from Biology 111, for Wednesday, August 27, 2008. The entire series can be found here.

Wednesday’s lecture began with a review of atomic structure, including a reminder that our e * diagrams are 2D representations of 3D space.

Then we moved on to some more basic chemistry.

We focused mostly on electrons, and will continue to, as electrons are what determines reactivity of an atom, and reactivity is what’s really vital to biology.

e orbits are called e shells or energy levels. Each e orbital can hold up to 2 e.

The first energy level has one orbital, because it’s so small, and electrons, having all the same negative electrical charge, repel each other.

The second and third energy levels each contain 4 orbitals, each energy level then is capable of holding 8 e (2 e in each orbital).

Then doc talked about how electrons fill from the innermost energy level, out.

(Continued below the fold)

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