Biochemistry and Molecular Biology: How Life Works

Book Preface

Biochemistry: A Young Science
Biochemistry is new, as the sciences go. Separately, the subjects of chemistry and biology have been around since the time of the ancient Greeks and Egyptians. But the idea of combining them is much more recent. About 200 years ago, there was no evidence that a science of biochemistry was even possible. Even 100 years ago, the word biochemistry was barely coming into use, and the field had scarcely begun.

Yet biochemistry has already unraveled chemical pathways and processes in cells that make us who we are. Personalized medicine is becoming possible thanks to disciplines biochemistry has spawned, including genomics and metabolomics.

The earliest roots of biochemistry date from almost 2 centuries ago, when an experiment by Friedrich Wöhler accidentally created a compound now known as urea. It turned out to be identical to a crystal that appeared when he dried urine. This demonstration made it clear, for the first time, that ordinary chemistry had to be possible inside of cells.
As early investigators began to take apart the cell, they increasingly began to discover both the magic of biochemistry and its roots in traditional chemistry. Two discoveries at roughly the same time in the 1860s were inheritance and the existence of DNA. But the significance of these remained unrealized for decades.
The famous physicist Erwin Schrödinger wrote a seminal book for lay readers entitled What Is Life? based on lectures he had been giving in Dublin. This book set the theoretical framework for what we now take for granted—that everything we associate with life has its roots in molecules. Watson and Crick in 1953 pointed to Schrödinger’s book as inspiration for their search to find the structure of DNA.
Everyone knew that the chemistry of reproduction had to be distinctive, but it took a long time to realize that what enabled cells to reproduce was their ability to store information, read that information, and reproduce that information. No chemistry anyone saw before had ever done that.

Classical biochemistry had been concerned with enzymes and other molecular reactions found inside and among cells. Now a new field called molecular biology came into being, with the master instructions that cells need to carry out their activities. The 2 fields became intertwined, and the 2 names for this combined subject are basically interchangeable.

Molecules and Minerals
Biochemistry is mostly about molecules. The molecules of biochemistry
are overwhelmingly built using primarily just 6 bonding elements: carbon, oxygen, nitrogen, and hydrogen, with supporting help from sulfur and phosphorus.
What matters for joining these atoms together is electrons. Chemical bonds always involve electrons—the smallest parts of their atoms by far. Electrons are negatively charged and located outside the nucleus of the atom. The number and kind of bonds an atom can make is due to the number of electrons it can share, release, or steal. Of those, the bonds that biochemistry cares about most involve electron sharing. It is these covalent bonds that stick us together.
Cells are mostly water, which is just hydrogen covalently bonded with oxygen—hydrogen dioxide. The oxygen can make 2 bonds; each hydrogen can only make one bond. More importantly, they share electrons with each other. The other 4 elements that are of primary importance for making bonds in biochemistry also like to share.
The element whose atoms are arguably the most important for life is carbon. Carbon’s importance is directly traced to its electrons. It has 4 electrons involved in reactions, and they all participate in sharing with other atoms. Sometimes the sharing is equal, while other times it’s unequal, but carbon never gives up its electrons entirely or takes those of another atom.
Carbon’s ability to make 4 bonds also makes it central to the construction of large and complicated molecules. A carbohydrate molecule, for example, is a bunch of carbons that have been hydrated with a bunch of water. Biochemistry is all about large carbon-centered molecules and their relationships to the water of the cell.