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)

Highlighting Carbons four unpaired valence electrons

Highlighting Carbon's four unpaired valence electrons

Organic Compounds —> Carbon based compounds

Hydrocarbons —> Hydrogen and Carbon, joined together in non polar covalent bonds. There is a lot of potential energy in these bonds due to the maximum distance from the nucleus of the shared valence e pairs. These bonds also make for hydrophobic molecules, due to the non-polarity.

Carbon Can Form Four Bonds

Carbon Can Form Four Bonds

Hydrocarbons are built on a skeleton of these Hydrogen and Carbon bonds, with other stuff added on. Remember that Carbon has four unpaired valence electrons, so it can form four covalent bonds. Hydrogen has one unpaired valence electron, so it can form one covalent bond.

This makes for a very nice set-up between Carbon and Hydrogen, where the carbon atom can form bonds with four Hydrogens, or three Hydrogens and another carbon, or two Hydrogens and two other Carbon atoms. Using this technique, nature can and does form chains of Carbon atoms surrounded by Hydrogens. These are called hydrocarbons, and form a skeleton upon which nature can build almost infinitely complex molecules. We can even think of the surrounding Hydrogens as plug covers for interchangeable parts.

Hydrocarbon Skeletons are like Legos

Hydrocarbon Skeletons are like Legos

Hydrocarbons form non-polar covalent bonds, and since the shared e are equally far from each of the nuclei of the two atoms, that gives the bond its high potential energy. That’s why Hydrocarbons are so attractive as fuels. There’s lots of bang for the buck.

Of course, the big problem is that it takes about 300,000,000 years to make Hydrocarbons, due to the fact that they’re made from decayed organic material (i.e. dead plants and animals). As a species, we’re using the planet’s available Hydrocarbons much faster than they are being made. It doesn’t take a genius to work out the math 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

Functional Groups

1. Hydroxyl Group

A Hydroxyl Group, is just an OH that replaces a Hydrogen atom as in this Hydrocarbon.

Makin some juice.

Makin' some juice.

Ethane is a Hydrocarbon molecule, and by exchanging one Hydrogen for an OH, we change it to ethanol. Ethanol is better known as “grain alcohol” or “ethyl alcohol”. Note that the ending “ol” always denotes an alchol. Note too that we keep the Hydrogen in the OH portion of the molecule separate from the other Hydrogens in the molecular formula, to point out that it’s not just another Hydrogen hanging off the main skeleton, but is associated with the Oxygen.

2. Carboxyl Group

A Carboxyl Group donates a Proton

A Carboxyl Group donates a Proton

A Carboxyl Group is made up of a Carbon, two Oxygens, and a Hydrogen, in the form COOH.

When latching onto a Hydrocarbon skeleton, it will ditch the H+, leaving it with a Carbon single bonded to a negatively charged Oxygen, and double bonded to another Oxygen. Because it donates that H+, it is an acid (lowers pH of a solution), and the negative charge makes it very attractive to water (hydrophilic).

3. Amino Group

Amino Group

Amino Group

An amino group is NH2, a Nitrogen and two Hydrogens. It will pick up an H+ from a solution, making it a base, and also hydrophilic.

4. Phospate Group

A Phosphate Group is a Phosphorus bonded with two negatively charged Oxygen atoms, one regular Oxygen atom, and double bonded with one Oxygen atom. It’s molecular formula is PO42- or sometimes OPO32-, to separate the double bonded Oxygen.

Phosphate Group

Phosphate Group

Here is where the lecture ended. Although I asked in a later lecture about the odd bondings here that seem to break the rules that we earlier set forth, Doc basically said, “It’s complicated, and you don’t need to know that for this class, though you’ll learn about it in a Chemistry class if you take one.” Ok, fair enough.

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.

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