Biochemistry is the study of chemical reactions in living tissue.
As such, it concerns itself with:
Biochemistry depends primarily on the chemistry of carbon compounds, so it depends on organic chemistry. As Zubay says, the range of organic reactions that occur within biological systems is fairly limited, because
Small molecules other than water make up a small percentage of a cell's mass, but small molecules have significant roles in the cell, both on their own and as building blocks of macromolecules. The classes of small molecules that play significant roles in biology are listed below. In this list, "soluble" means "water-soluble".
Water is a surprisingly complex substance. It is polar, i.e. the charge in the molecule is somewhat unequally shared. The oxygen atom carries a modest partial negative charge and the two hydrogen atoms carry partial positive charges. Thus a single water molecule will orient itself with respect to other water molecules in order to neutralize those partial charges. The oxygen atom will align itself toward one of the hydrogens on a neighboring water molecule, and vice versa. Thus even in liquid water, most of the molecules will align themselves roughly as they would be in crystalline ice. When charged or polar solute molecules appear, they will interrupt the ordered lattice somewhat and participate in the sharing of partial charges. The energetics of solvation involve careful consideration of these effects.
Water in a biochemical setting acts as a medium in which reactions occur, but it also participates in reactions. One of the ways in which enzymes perform catalytic functions (see below) is by enhancing the partial charges on water molecules, so that water can act as a better nucleophile or electrophile. Thus water can be a reactant in biochemical reactions for which the in vitro organic reaction would involve a more potent reactant. The presence of enzymes increases the reactivity of water enough to make it a useful reactant.
Water has some physical properties that are relevant to biochemistry, too. It has a high heat capacity, so it stabilizes the thermal properties of biochemical systems. It also has high surface tension, which can have an impact on some surface-dependent reactions.
Catalysis is the lowering of the activation energy barrier between reactants and products. Typically this is accomplished either by providing a physical substrate that provides a convenient ground on which the reaction can occur, or by providing moieties that can temporarily participate in the reaction, such that the participating species can be restored to their original state at the end of the reaction. Both of these approaches are performed by biological catalysts, which are called enzymes.
Enzymes were first characterized in the late nineteenth century, and Sumner and others advanced the theory in the 1920's that enzymes were proteins. The biochemical community took another fifteen years to fully accept the notion that enzymes were proteins, and the community rested secure in the knowledge that all enzymes were proteins until the 1980's. At that point it became clear that certain RNA molecules could catalyze their own hydrolysis in well-defined ways, so those RNA molecules came to be known as "ribozymes." In 2000 the catalytic activity of RNA evolved from a internal curiosity, mostly of interest to RNA chemists themselves, to a fundamental property of biochemistry. In 2000, Yale /HHMI researchers showed that the catalytic engine of the ribosome, by which each amino acid was to be added to the growing polypeptide change, was a specific adenine nucleotide in the ribosomal RNA. Thus the role of RNA as an enzyme is now part of the core of biochemistry.
We'll discuss thermodynamics in detail in the next chapter. For
now we'll note that the rate of a reaction is related to the activation
energy, and is therefore dramatically increased when the activation energy
is reduced. We'll also note that the equilibrium constant (the ratio of the
concentration of reactants to products at equilibrium) is directly related
to the difference in energy between reactants and products according to
ΔGo = -RT ln KEQ
where T is the Kelvin temperature and R is the gas constant.
Biochemical reactions are regulated in the sense that the degree to which they proceed is influenced by the presence of catalysts--enzymes-- and that the concentration of enzyme in a particular location is subject to control by genetic and developmental mechanisms. They are also regulated in that the enzymes themselves are often subject to inhibition by products of the reactions themselves or by products farther down the reaction path. Suppose an enzyme E catalyzes the conversion of A to B, and B is subsequently converted (with the help of other enzymes) into C and then D and then F. In many instances the molecule F will bind to a noncatalytic site on the enzyme E in such a way as to reduce the rate of conversion of A to B. Thus if too much F is present, then some of the F will bind to E and reduce the rate at which more F is produced, enabling a stabilization of the system.
This subject will be covered in substantial detail later in the semester in the molecular biology section of the course. For now we'll remind you of what you have learned in other courses:
We can define the relatedness of organisms in terms of their functional similarities and differences. This gave rise to charts called phylogenetic trees showing what species were closely related to others. In recent years molecular biologists have begun to compare organisms on more easily quantified basis: by comparing the DNA in regions of the genome that change slowly over time, we can use DNA similarity as a yardstick for overall similarity. Thus researchers are developing evolutionary trees derived from DNA data as an alternative to phenotypic trees.