1) Amino acids - If hydrogen bonds between non-adjacent side groups and between the base molecules of the amino acids in a peptide chain contribute to the shape of a protein, and if hydrogen bonds only last a fraction of a second before breaking (which my text book says they do), then the shape of a protein must constantly be in flux. Is this correct?
Partially correct. There are a very large number of hydrogen bonds which hold together a protein. Even if they exist for fractions of a second, enough of the hydrogen bonds (plus other intermolecular forces such as salt bridges, hydrophobic interactions, etc.) are present to keep the protein together. For example, lets say there are 1000 hydrogen bonds in a protein. Even if hydrogen bonds are broken 80% of the time, that still leaves 200 hydrogen bonds keeping the protein together at any one time.
However, you are correct that a protein is constantly in flux. Too many people think of protein structures as static entities. In the past decade or so, people have shown that many proteins contain flexible regions which are dynamic and constantly in flux (an interesting example I can think of off the top of my head is the protein kinase NtrC in bacteria. David Wemmer's group at Berkeley showed using NMR that a large portion of the protein is rapidly sampling two conformations, an inactive conformation and an active conformation. Furthermore, phosphorylation of NtrC stabilizes the active conformation and lowers the rate of exchange between the two conformers).
2a) How is it that peptide bonds act like double rather than single covalent bonds?
Do you know about resonance structures? In one resonance structure, the lone pair from the nitrogen goes to form a double bond between the N and carbonyl carbon while the electron in the double bond between the C and O go onto a lone pair on the O. (see image
here). Since one of the resonance structures has a double bond betwen the N and C, the N-C bond has a partial double bond character.
b) Also, is the rigidity of two amino acids joined by a peptide bond (double bond) analogous to the following?
Two wheels joined by a single axle can rotate freely around that axle independent of one another. If you join the two wheels with a second axle at any location on the two wheels, they can no longer spin freely of one another. Is this the concept that applies to two amino acids not being able to rotate freely when joined by a peptide bond?
Are any two atoms joined by a single bond free to rotate around this bond?
This is basically right. The real reason comes from the fact that double bonds are formed by overlapping p-orbitals. When you rotate the bond, the p-orbitals overlap and you are essentially breaking the pi-bond. Since breaking a pi-bond is very unfavorable, rotation about a double bond occurs at a negligible rate.
3) When an H nucleus spontaneously breaks away from an H2O molecule, resulting in an H+ cation and an OH- anion, the H+ cation tends to bind with a stable H2O molecule making H3O (hydronium).
My question is, is this H+ ion bonded to the H2O molecule through a hydrogen bond or a covalent bond?
If a hydrogen bond, is the H+ ion joined to the O side of the water molecule due to this side being slightly more negative?
Covalent. The proton goes to the O side of water because it has a lone pair which can fill the proton's empty s orbital (remember that H likes to have two electrons around it).
4) What force holds electrons in pairs? Sinc they are both negative, I would think they would repel each other. Also, what is the physical reality of the pairing? Are they closer to one another than any other electrons? Do they travel along the same orbit?
Without going into too much quantum mechanics (partly because I don't fully understand it all myself!), electrons pair up because it results in a lower energy state than if they don't. Remember that electrons are pulled close to the nucleus by their attraction to the protons in the nucleus. But, at the same time, as electrons near the nucleus, they get closer to each other, which causes more repulsion. So, there needs to be a balance between electron-electron repulsion and electron-nucleus attraction.
The physical reality of the pairing is that both electrons occupy similar areas of space. You can't say that electrons travel around an orbit (like planets travel around an orbit around the sun) since the Heisenberg uncertainty principle says that you can't know the exact trajectory of a particle. You can only give a fuzzy sphere where the electron is most likely to be.
I hope these explanations are somewhat clear. Feel free to ask more questions if something is still not clear.
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