We're going to spend a large portion of this course discussing the functional roles that proteins play in biochemistry. This discussion is an attempt to introduce those roles in a general way. Proteins perform a large number of tasks in cells, and it would be useful to start with an overview of those tasks.
It's worth considering why cells employ proteins for so many tasks. At one level, cells use proteins to perform tasks because the reproductive machinery is geared to produce proteins, not something else. But that simply moves the question back: why is the reproductive machinery set up that way? The answer is that proteins are chemically nimble. The chemistry of proteins is flexible: protein side chains can participate in a large number of interesting reactions, and even main-chain atoms can play roles in certain circumstances. The wide range of hydrophobicity available (from highly water-hating to highly water-loving) within and around proteins gives them versatility that a more unambiguously hydrophilic species (like RNA) or a distinctly hydrophobic species (like a triglyceride) would not be able to acquire. Proteins can act as catalysts, transporters, scaffolds, signals, or fuel in watery or greasy environments, and can move back and forth between hydrophilic and hydrophobic situations. Furthermore, proteins can operate either in solution, where their locations are undefined within a cell, or anchored to a membrane. Many proteins have membrane-attachment domains (see our discussion of domains in the previous lecture) that keep them in a fixed location in a cell or on the outside surface of a cell; the portion of the protein that actively participates in some chemical change may operate in the membrane or in solution, but the anchoring keeps the protein from moving around. We will summarize some of the specific functions that proteins perform in the sections below.
It is easy to sound profound if you're studying proteins: just repeat the mantra, structure-function. The point here is that we can gain an understanding of a protein's function by knowing something about its structure. This point could potentially be overemphasized. In some instances we can discern a great deal about a protein's function without knowing anything about its structure, and there are proteins whose structure is well-understood but for which we have no clear knowledge of their function. But it is characteristic of the modern approach to biochemistry that we either obtain or deepen our knowledge of function by learning something about structure.
Traditionally, biochemists have used structural information to
clarify and deepen their understanding of a protein's function after
having determined that function in some other way. In this traditional
approach, an enzyme is first identified in terms of the reaction it
catalyzes: we recognize that a yeast cell is capable of enzymatically
interconverting ethanol and acetaldehyde, using NAD as the oxidizing
agent:
CH3CH2OH + NAD+ <-->
CH3CH=O + NADH + H+
We will discuss what NAD is in a later lecture, but you're welcome
to look up its structure now: structure matters for small molecules
too!
We assert, then, that that cell must contain an enzyme, known as
alcohol dehydrogenase or acetaldehyde reductase,
that can catalyze this reaction. By convention we use the
first of these two names, although biochemists are not
entirely consistent about that: the enzyme that interconverts
dihydrofolate and NADPH with tetrahydrofolate and NADP is
known as dihydrofolate reductase, not tetrahydrofolate dehydrogenase.
We would then seek to purify the protein responsible for this
enzymatic activity and characterize it in terms of its overall
properties: we would find, in this instance, that yeast
alcohol dehydrogenase is a soluble tetrameric protein
(i.e., it has four subunits) with a total molecular mass of
140 kilodaltons. We would find that the four subunits are
identical, so since we can do arithmetic, we recognize that the
molecular mass of each subunit is 35 kDa.
We might do careful analysis of the proteins produced by our
strain of yeast and find that there are actually two slightly
different alcohol dehydrogenases, one of which is employed
primarily in converting ethanol to acetaldehyde and the other
of which is primarily used in the reverse reaction.
But we would at that point be left with some chemical questions:
how does this enzyme actually catalyze this reaction?
Do the individual subunits of the tetramer interact with one
another during catalysis? Are there binding sites on the protein
where the presence or absence of effector molecules would influence
the enzyme's ability to bind its substrates or its ability
to catalyze the reaction? These are questions that a detailed
structural analysis could help to resolve.
I picked this particular protein for an odd reason: the structure of yeast alcohol dehydrogenase is still unknown, although the enzymes from horse liver, Drosophila, and some other organisms are known. We expect the two forms of the yeast enzyme to be similar to the known structures, but we would like to understand the differences. So we would examine the known structures, like the horse liver structure shown below, and think about how the differences in sequence between the yeast enzyme and the horse liver enyzme might affect their properties.
The first, and conceptually simplest, class of proteins we'll
discuss are structural proteins. Structural proteins perform
mechanical or scaffolding roles in organisms; they do not participate
in chemical reactions, unless you consider
(human being standing upright) -> (human being huddled in a lump on the floor)
to be a chemical reaction.
Structural proteins tend to be simple in terms of their three-dimensional
structures and even their primary sequence. We have already discussed
collagen, a structural protein that is composed primarily of sequences
of the form gly-X-Y, where X is often proline and Y is often hydroxyproline.