Lesson 2 – Video 1
436 [00:00:01.41] Hi, in this video, we will discuss some of the ways that atoms and
437 and bind to each other. These topics will be review to many of you, it'll be new to some,
438 important that we're all get on the same page, so we can have more discussions.
439 [00:00:18.72] We'll talk about covalent and ionic bonds, and we'll talk about hydrogen
440 which is a particular type of electrostatic interaction. We'll talk about hydrophobic effects,
441 is one way that molecules will separate and organize. And we'll sort of drive it home with
442 rules of thumb, which we'll talk about over and over in this course. One is about
443 opposite charges attract and like charges repel. And the hydrophobic effect, which is
444 saying that oil and water don't mix.
445 [00:00:55.85] To start the discussion, we want to talk about how atoms can be held
446 either by covalent bonds, or ionic bonds. In the first case they share electrons, in the
447 they will transfer electrons to each other.
448 [00:01:12.18] In this slide we have very simple schematics of covalent bonding on the
449 ionic bonding on the right. The trick is, how do you get to positively charged nuclei to be
450 to each other? Again, because like charges repel.
[00:01:29.15] In the sharing of electrons, you have an excess of 451 electron density in
452 two positive charges. So whereas before, you have a spherical distribution, now you will
have a 453 distribution of the electrons which are concentrated between the two positively charged
454 And that's a stable electrostatic configuration. And that is what we think of as a covalent
455 [00:01:56.47] In the other case, you have the transfer of an electron from one atom to
456 Now you have a positively charged atom interacting with the negatively charged atom.
457 again, this is an ionic bond. This is an attraction between the two, and they will be in
459 [00:02:15.61] Now a prototypical ionic bond is one seen between sodium and chlorine.
460 atoms will donate one of their electrons to chlorine. This gives both ions complete outer
461 shells-- eight electrons in the valence shell-- which is a stable atomic configuration. And
462 sodium and chloride ions can interact with each other. They can, in the absence of
463 can form regular grids, which are visible here as salt crystals, when being evaporated.
464 [00:02:54.34] On this slide, we'll talk about some of the strengths of interactions of
465 and energy content in general. We'll start by pointing out that the carbon-carbon bond, a
466 bond, is about 83 kilocalories at room temperature. And compare that to the average
467 energy available at room temperature, kT, which is about 0.6 kcals. So you can see that
468 temperature it's extremely unlikely that a carbon-carbon bond would ever break, due to
469 average thermal motion.
470 [00:03:27.43] Non-covalent bonds in water, like hydrogen bonds, can be from one to a
471 or three-- kilocalories. And average thermal motions are large enough to disrupt those
on 472 occasion. When we hydrolyze a molecule of ATP in the cell, we will get about 11 to 12
473 kilocalories per mole from that, verses approximately 673 kilocalories for the complete
474 of glucose.
475 [00:04:04.14] On this slide we see the elemental composition of human bodies in red,
476 we are comprised primarily of four atoms, hydrogen carbon, oxygen, and nitrogen, with
477 other atoms contributing small amounts.
478 [00:04:22.96] With covalent bonding there's some different properties between single
479 bonds. Single bonds, you're free to rotate around. Double bonds are stronger, but they
480 constrained. You will not get rotation around this double bond, and these atoms will all
481 confined in a plane.
482 [00:04:51.70] We are primarily carbon-based creatures. As you can see, our
483 carbon, is tetravalent. It's, in this case, bonded to two other carbons and two hydrogens.
484 sometimes be drawn like this, without explicitly drawing in the hydrogens. Or like this,
485 every vertex is a carbon atom, and it's always implied that there are as many hydrogens
486 need to be to make each atom tetravalent.
487 [00:05:27.04] Aromatic compounds, such as benzene, it's more than double bonds when
488 have four N plus 2 electrons in a cyclic structure that's aromatic. There's extra resonant,
thermodynamic energy there. And the true benzene structure is 489 a resonance between
490 structures. And it's often written as a circle. 491 [00:05:56.32] We have certain words for different groups. As you can see here, it's
492 methyl group. Here is a methyl group. If we talked about these two carbons, this would
493 ethyl group. If we talked about these three carbons and all the hydrogens, that would be
494 group. So the different nomenclature is saying something about the number of carbons
496 [00:06:21.82] In addition to hydrocarbons, you can also have oxygen. In this case, the
497 group, which is an alcohol. A slightly more oxidized version of this carbon is a carboxylic
498 which in solution is a negatively charged molecule, as it will lose a hydrogen ion to
499 [00:06:44.24] Some covalent bonds can have partial ionic character. That is the case
500 There's covalent bonds here between oxygen and hydrogen, but since oxygen is more
501 electronegative than hydrogen, it will attract more of the electron density closer to its
502 And therefore,