we come to hydrogen bonding, which plays an enormously important role in biological processes. It is found in molecules containing an OH group (a hydroxyl group) including water, ethanol, methanol, and numerous other molecules. Like van der Waals interactions, hydrogen bonding is weaker than ionic and covalent bonds. Hydrogen bonds are typically 10–100 times weaker than covalent bonds, depending on the molecules involved.
A hydrogen atom, having one electron, can be covalently bonded to only one atom. However, the hydrogen atom can involve itself in an additional electrostatic bond with a second atom of highly electronegative character, such as fluorine or oxygen. This second bond is a hydrogen bond.
How does hydrogen bonding work? Let's go through the basic points using water:
The charge density in a covalent bond such as an OH bond is highly asymmetric, and the center of charge is much closer to the O atom, as we discovered when discussing the dipole in HCl. For the same reasons, the OH bond also has this dipole character.
This leaves the net positively charged H atom behaving more like a lone, positively charged proton (H+).
Other electrons on the O atom distribute themselves so as to minimize repulsion (Figure 3.15, green lobes). These electrons form lobes of electron density on the opposite side of the O atom to the OH bond.
Another H2O molecule orients itself so that its positively charged H is now close to these negatively charged electrons.
Figure 3.15 Hydrogen bonding in water ice. The dotted lines show the hydrogen bonding. The green lobes are the electrons on oxygen that take part in the interaction with the hydrogen atom on other water molecules.
You can see the result of these interactions much more clearly in Figure 3.15, which shows the hydrogen bonding in water ice depicted in two dimensions.
3.10.1 Hydrogen Bonds and Life
Hydrogen bonding is found in many molecular interactions in life. In the next chapter, we discuss in more detail the structure of the information storage molecule of life: DNA. However, here, one feature of DNA is worth exploring: the role of hydrogen bonding in holding the molecule together. DNA is made up of two complementary strands that bind together to form its characteristic double helix shape. These two strands are held together down their middle by hydrogen bonding.
In the diagram in Figure 3.16 you can see the structure of a DNA double helix that has been flattened into a two-dimensional depiction (from its normal three-dimensional helical structure). Along the two edges of the structure, you can see the pentagonal deoxyribose sugars that make up its backbone linked together with phosphate groups. In the middle are the base pairs. The bases are linked in pairs with dotted lines showing the hydrogen bonding between them. The sequence of individual bases along a DNA strand encodes the genetic information. There are four bases: adenine (A), thymine (T), guanine (G), and cytosine (C). Adenine can only bind with thymine, and cytosine can only bind with guanine. There are two hydrogen bonds for the pairing between adenine and thymine bases, and three hydrogen bonds between guanine and cytosine.
Figure 3.16 Hydrogen bonding in the molecule DNA. (a) The dotted lines in the middle of the flattened two-dimensional molecule on the left are the hydrogen bonds that hold the two strands together. On the right (b) is the three-dimensional double helix.
Source: Reproduced with permission of wikicommons, Michael Ströck.
The hydrogen bonding is just strong enough to hold the strands together so that DNA does not fall apart easily. However, the hydrogen bonds are just weak enough so that the two strands can be unzipped when they need to be pulled apart for replication of the DNA molecule when cells divide, without the requirement for a large amount of energy to be expended. You can imagine that if the two strands were linked at every base pair with covalent bonds, it would require much more energy to pull apart the two DNA strands. In Chapter 4, we investigate the structure and functions of DNA in more detail. For now, let us note how the evolutionary process tends to select bonding types at the atomic level that are optimized to do particular tasks. Hydrogen bonding is ideal for a situation where molecular stability is required, but where the regular opening of molecular bonds means that it is also optimal to have a bonding type where energy requirements to break the bonds are minimized. You might like to ask yourself: Could you imagine a genetic material where two complementary strands are held together using van der Waals interactions that might offer a similar compromise?
3.11 An Astrobiological Perspective
How much of the preceding discussion on bonding types is applicable on a universal scale? We could probably confidently say that the major bonding types we have discussed are universal. They are shaped by fundamental interactions between electrons of different ions, atoms, and molecules. As we have already agreed that fundamental atomic structures are universal, then the bonding types available to construct life are also likely to be universal. However, how much of the detail on how these bonding types are used in different molecular structures is universal? Are we confident that ionic interactions between amino acids to make proteins are universal? Must all life contain proteins? Would all material involved in storing information about life (genetic material or its equivalent) use hydrogen bonding to hold together molecules that need to split in two and replicate? We have already explored some ideas about why life on Earth does not use metallic structures. Are those proposed reasons universal, or could we find aliens with steel bars for bones and skulls made of titanium? (Here I am referring to the process of natural selection, not technological augmentation, which, as we all know, can be used to put steel bars in bones.) As we discuss the major macromolecules of life in Chapter 4, continue to consider the question of the universality of the structure of life.
In the meantime, let us now continue to consider the basic behavior of matter.
Discussion Point: Is the Structure of Life Universal?
Some people say that astrobiologists are narrow-minded and that alien life forms, if they exist, will be constructed in ways unimaginable to us and possibly very differently from life on Earth. Do you agree with this? As you progress through this and later chapters, you might like to consider at what level of hierarchy this statement may or may not be true. Hydrogen bonding, for example, would be expected to be the same anywhere in the Universe, as it is determined by the interactions between atoms in the universal Periodic Table. So too with all the forms of bonding explored in this chapter. Surely, therefore, are we are on safe ground to say that if life exists elsewhere it would use the same types of bonding to hold its atoms, ions, and molecules together? In Chapter 4, we look at how molecules in terrestrial life are put together. Are these molecules universal structures? Would we expect cells to be put together using the same basic molecules? We then progress in Chapter 8 to look at the evolutionary relationships between whole organisms. Are these universal? Consider at what scale in the structure of life from atoms to communities of organisms you would be confident to say that all life in the Universe would share identical characteristics. In other words, at what level of the hierarchy of life's structure is biology deterministic and where can contingency, or chance, play a role? If you could run evolution again, what structures of life could you confidently predict would reappear?
3.12 The Equation of State Describes the Relationship Between Different Types of Matter
Having