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Lecture 2

Cell Biology - Lecture 2 - Video 1 - Notes

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Boston University
CAS BI 203
Martin Steffen

Lesson 2 – Video 1 [00:00:00.00] 436 [00:00:01.41] Hi, in this video, we will discuss some of the ways that atoms and molecules bond 437 and bind to each other. These topics will be review to many of you, it'll be new to some, but it's 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 bonding, 440 which is a particular type of electrostatic interaction. We'll talk about hydrophobic effects, which 441 is one way that molecules will separate and organize. And we'll sort of drive it home with two 442 rules of thumb, which we'll talk about over and over in this course. One is about electrostatics, 443 opposite charges attract and like charges repel. And the hydrophobic effect, which is basically 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 together, 446 either by covalent bonds, or ionic bonds. In the first case they share electrons, in the second case 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 left, and 449 ionic bonding on the right. The trick is, how do you get to positively charged nuclei to be close 450 to each other? Again, because like charges repel. 13 [00:01:29.15] In the sharing of electrons, you have an excess of 451 electron density in between the 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 nuclei. 454 And that's a stable electrostatic configuration. And that is what we think of as a covalent bond. 455 [00:01:56.47] In the other case, you have the transfer of an electron from one atom to another. 456 Now you have a positively charged atom interacting with the negatively charged atom. And 457 again, this is an ionic bond. This is an attraction between the two, and they will be in close 458 proximity. 459 [00:02:15.61] Now a prototypical ionic bond is one seen between sodium and chlorine. Sodium 460 atoms will donate one of their electrons to chlorine. This gives both ions complete outer valence 461 shells-- eight electrons in the valence shell-- which is a stable atomic configuration. And now 462 sodium and chloride ions can interact with each other. They can, in the absence of solvent, they 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 molecules 465 and energy content in general. We'll start by pointing out that the carbon-carbon bond, a single 466 bond, is about 83 kilocalories at room temperature. And compare that to the average thermal 467 energy available at room temperature, kT, which is about 0.6 kcals. So you can see that at room 468 temperature it's extremely unlikely that a carbon-carbon bond would ever break, due to just 469 average thermal motion. 470 [00:03:27.43] Non-covalent bonds in water, like hydrogen bonds, can be from one to a few-- two 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 oxidation 474 of glucose. 475 [00:04:04.14] On this slide we see the elemental composition of human bodies in red, and that 476 we are comprised primarily of four atoms, hydrogen carbon, oxygen, and nitrogen, with many 477 other atoms contributing small amounts. 478 [00:04:22.96] With covalent bonding there's some different properties between single and double 479 bonds. Single bonds, you're free to rotate around. Double bonds are stronger, but they are 480 constrained. You will not get rotation around this double bond, and these atoms will all be 481 confined in a plane. 482 [00:04:51.70] We are primarily carbon-based creatures. As you can see, our hydrocarbon, 483 carbon, is tetravalent. It's, in this case, bonded to two other carbons and two hydrogens. This can 484 sometimes be drawn like this, without explicitly drawing in the hydrogens. Or like this, where 485 every vertex is a carbon atom, and it's always implied that there are as many hydrogens as there 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 you 488 have four N plus 2 electrons in a cyclic structure that's aromatic. There's extra resonant, extra 14 thermodynamic energy there. And the true benzene structure is 489 a resonance between these two 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 showing a 492 methyl group. Here is a methyl group. If we talked about these two carbons, this would be an 493 ethyl group. If we talked about these three carbons and all the hydrogens, that would be a propyl 494 group. So the different nomenclature is saying something about the number of carbons in this 495 case. 496 [00:06:21.82] In addition to hydrocarbons, you can also have oxygen. In this case, the hydroxyl 497 group, which is an alcohol. A slightly more oxidized version of this carbon is a carboxylic acid, 498 which in solution is a negatively charged molecule, as it will lose a hydrogen ion to water. 499 [00:06:44.24] Some covalent bonds can have partial ionic character. That is the case with water. 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 nucleus. 502 And therefore,
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